Patent Application
20230183761
This application contains an electronic sequence listing. The contents of the electronic sequence listing (36803-328_Imported_ST25.txt; Size: 489,442 bytes; and Date of Creation: Jul. 22, 2022) is herein incorporated by reference in its entirety.
Provided herein are biocatalytic methods of producing terpene degradation products useful as starting material for the production of perfumery ingredients, such as, for example, ambrox. In particular novel terpene degrading polypeptides (enal-cleaving polypeptides) and novel peptides converting terpenes compounds to oxygenated derivatives (oxygenases) and mutants and variants derived therefrom are provided which may be applied in novel types of fully enzymatic multistep degradation pathways allowing the controlled, stepwise conversion and degradation of linear or cyclic terpene substrates. Said novel biosynthetic strategies allow the fully biochemical synthesis of valuable terpene-derived compounds, like for example manooloxy or gamma ambrol. The invention also provides recombinant host organisms carrying the required set of genetic information for the functional expression of the set of enzymes necessary for catalyzing the combination of enzymatic conversion and degradation steps.
Terpenes are found in most organisms (microorganisms, animals and plants). These compounds are made up of five-carbon units, so-called isoprene units, and are classified by the number of these units present in their structure. Thus hemiterpenes, monoterpenes, sesquiterpenes and diterpenes are terpenes containing 5, 10, 15 and 20 carbon atoms (i.e. 1, 2, 3 and 4 isoprene units) respectively. Sesquiterpenes, for example, are widely found in the plant kingdom. Many sesquiterpene molecules are known for their flavor and fragrance properties and their cosmetic, medicinal and antimicrobial effects. Numerous sesquiterpene hydrocarbons and sesquiterpenoids have been identified.
Biosynthetic production of terpenes involves enzymes called terpene synthases. These enzymes convert an acyclic terpene precursor in one or more terpene products. In particular, diterpene synthases produce diterpenes by cyclization of the precursor geranylgeranyl diphosphate (GGPP). The cyclization of GGPP often requires two enzyme polypeptides, a type I and a type II diterpene synthase working in combination in two successive enzymatic reactions. The type II diterpene synthases catalyze a cyclization/rearrangement of GGPP initiated by the protonation of the terminal double bond of GGPP leading to a cyclic diterpene diphosphate intermediate. This intermediate is then further converted by a type I diterpene synthase catalyzing an ionization initiated cyclization.
Diterpene synthases are present in plants and other organisms and use substrates such as GGPP but they have different product profiles. Genes and cDNAs encoding diterpene synthases have been cloned and the corresponding recombinant enzymes characterized.
Enzymes that catalyze a specific or preferential cleavage or removal of diphosphate groups from terpene diphosphate intermediates, in particular from cyclic terpene diphosphate intermediates, like the diterpenes copalyl diphosphate (CPP) or labdendiol diphosphate (LPP) have only recently be described in an earlier European patent application. (EP application number 18182783.3). By said enzymes the number or carbon atoms of the terpene diphosphate remains unchanged.
There is, however, the need terpene-derived compounds which may be considered as degradation products of terpene precursors, such as non-cyclic or cyclic sesquiterpenes or diterpenes, which in turn may the be further converted chemically and/or enzymatically into end product, to be applied for example as perfumery ingredients.
The problem to be solved by the present invention is to provide polypeptides which show the enzymatic terpene degrading activity or polypeptides which convert such terpenes into degradable derivatives.
Another problem to be solved by the present invention is the establishing of novel fully biocatalytic degradation pathway for generating defined terpene degradation products.
The above-mentioned problem could surprisingly be solved by providing a new class of polypeptides having enal-cleaving activity which allow for the first time the specific shortening of carbonyl-functionalized terpene compounds by 2 carbon atoms and respective bio catalytic processes. For example, the novel class of enzymes allows the conversion of the labdane-type compound copalal, which comprises a diterpene carbon skeleton and carries a terminal aldehyde group to the respective dinor-labdane compound manooloxy shortened by 2 carbon atoms, i.e. retaining a carbon skeleton composed of 18 carbon atoms.
The above-mentioned problem in an alternative approach could also surprisingly be solved by providing a new class of polypeptides having Baeyer-Villiger Monooxygenase (BVMO) activity which allow the specific oxidiation of terpene compounds to esters (Baeyer-Villiger oxygenation) and respective biocatalytic processes. For example, the novel class of BVMOs allows the conversion of the labdane-type compound copalal, which comprises a diterpene carbon skeleton and carries a terminal aldehyde group to the respective norlabdane formate ester. By said Baeyer-Villiger oxygenation the labdane compound may be easily converted to the respective norlabdane through the action of a polypeptide having esterase activity. This step results consequently in a shortening by one carbon atom. In case the terminal aldehyde group is replaced by a terminal keto group a shortening in the same manner but now by more than one carbonate is possible. Repetition of the combination of BVMO-catalysed oxygenation step and esterase-catalyzed cleavage step, allows the stepwise shortening of the hydrocarbon chain of the terpene molecule.
Combinations of degradation steps catalyzed by the above enal-cleaving enzymes and BVMO enzymes allow the construction of completely new biochemical degradation pathways applicable a greater variety of carbonyl functionalized chemical compounds, in particular cyclic or non-cyclic terpenes or terpenoids.
Said biocatalytic steps may be coupled to several other preceding (upstrean) or successive (downstream) enzymatic steps and allow the provision of a biocatalytic multistep process for the fully enzymatic synthesis of numerous valuable complex terpene molecules from their respective precursors.
The subsequent scheme illustrates two particular embodiments of two alternative pathways (“Enal cleaving polypeptide pathway” and “BMVO pathway)” of the present invention allowing the degradation of the labdane aldehyde copalal to manooloxy, which pathways are explained in more detail in the subsequent sections of the present specification. The scheme also illustrates the degradation of manooloxy to gamma-ambrol by applying a further BMVO-based degradation step.
In full analogy to said exemplified reaction sequences this basic biosynthetic strategy my be applied to any other isomer of copalol or to any other labdane-type aldehyde in order to provide structurally related isomers of manooloxy, gamma-ambryl acetate or gamma-ambrol.
It also may be applied to structurally different mono-cyclic or non-cyclic carbonyl compounds as herein below specified in more detail.
For the descriptions herein and the appended claims, the use of “or” means “and/or” unless stated otherwise. Similarly, “comprise”, “comprises”, “comprising”, “include”, “includes”, and “including” are interchangeable and not intended to be limiting.
It is to be further understood that where descriptions of various embodiments use the term “comprising,” those skilled in the art would understand that in some specific instances, an embodiment can be alternatively described using language “consisting essentially of” or “consisting of”.
The terms “purified”, “substantially purified”, and “isolated” as used herein refer to the state of being free of other, dissimilar compounds with which a compound of the invention is normally associated in its natural state, so that the “purified”, “substantially purified”, and “isolated” subject comprises at least 0.5%, 1%, 5%, 10%, or 20%, or at least 50% or 75% of the mass, by weight, of a given sample. In one embodiment, these terms refer to the compound of the invention comprising at least 95, 96, 97, 98, 99 or 100%, of the mass, by weight, of a given sample. As used herein, the terms “purified,” “substantially purified,” and “isolated” when referring to a nucleic acid or protein, or nucleic acids or proteins, also refers to a state of purification or concentration different than that which occurs naturally, for example in an prokaryotic or eukaryotic environment, like, for example in a bacterial or fungal cell, or in the mammalian organism, especially human body. Any degree of purification or concentration greater than that which occurs naturally, including (1) the purification from other associated structures or compounds or (2) the association with structures or compounds to which it is not normally associated in said prokaryotic or eukaryotic environment, are within the meaning of “isolated”. The nucleic acid or protein or classes of nucleic acids or proteins, described herein, may be isolated, or otherwise associated with structures or compounds to which they are not normally associated in nature, according to a variety of methods and processes known to those of skill in the art.
The term “about” indicates a potential variation of ±25% of the stated value, in particular ±15%, ±10%, more particularly ±5%, ±2% or ±1%.
The term “substantially” describes a range of values of from about 80 to 100%, such as, for example, 85-99.9%, in particular 90 to 99.9%, more particularly 95 to 99.9%, or 98 to 99.9% and especially 99 to 99.9%.
“Predominantly” refers to a proportion in the range of above 50%, as for example in the range of 51 to 100%, particularly in the range of 75 to 99.9%, more particularly 85 to 98.5%, like 95 to 99%.
A “main product” in the context of the present invention designates a single compound or a group of at least 2 compounds, like 2, 3, 4, 5 or more, particularly 2 or 3 compounds, which single compound or group of compounds is “predominantly” prepared by a reaction as described herein, and is contained in said reaction in a predominant proportion based on the total amount of the constituents of the product formed by said reaction. Said proportion may be a molar proportion, a weight proportion or, preferably based on chromatographic analytics, an area proportion calculated from the corresponding chromatogram of the reaction products.
A “side product” in the context of the present invention designates a single compound or a group of at least 2 compounds, like 2, 3, 4, 5 or more, particularly 2 or 3 compounds, which single compound or group of compounds is not “predominantly” prepared by a reaction as described herein.
Because of the reversibility of enzymatic reactions, the present invention relates, unless otherwise stated, to the enzymatic or biocatalytic reactions described herein in both directions of reaction.
“Functional mutants” of herein described polypeptides include the “functional equivalents” of such polypeptides as defined below.
The term “stereoisomers” includes conformational isomers and in particular configuration isomers.
Included in general are, according to the invention, all “stereoisomeric forms” of the compounds described herein, such as “constitutional isomers” and “stereoisomers”.
“Stereoisomeric forms” encompass in particular, “stereoisomers” and mixtures thereof, e.g. configuration isomers (optical isomers), such as enantiomers, or geometric isomers (diastereomers), such as E- and Z-isomers, and combinations thereof. If one or more asymmetric centers are present in one molecule, the invention encompasses all combinations of different conformations of these asymmetry centers, e.g. enantiomeric pairs.
“Stereoselectivity” describes the ability to produce a particular stereoisomer of a compound in a stereoisomerically pure form or to specifically convert a particular stereoisomer in an enzyme catalyzed method as described herein out of a plurality of stereoisomers. More specifically, this means that a product of the invention is enriched with respect to a specific stereoisomer, or an educt may be depleted with respect to a particular stereoisomer. This may be quantified via the purity % ee-parameter calculated according to the formula:
% ee=[XA−XB]/[XA+XB]*100,
wherein XA and XB represent the molar ratio (Molenbruch) of the stereoisomers A and B.
The terms “selectively converting” or “increasing the selectivity” in general means that a particular stereoisomeric form, as for example the E-form, of an unsaturated hydrocarbon, is converted in a higher proportion or amount (compared on a molar basis) than the corresponding other stereoisomeric form, as for example Z-form, either during the entire course of said reaction (i.e. between initiation and termination of the reaction), at a certain point of time of said reaction, or during an “interval” of said reaction. In particular, said selectivity may be observed during an “interval” corresponding 1 to 99%, 2 to 95%, 3 to 90%, 5 to 85%, 10 to 80%, 15 to 75%, 20 to 70%, 25 to 65%, 30 to 60%, or 40 to 50% conversion of the initial amount of the substrate. Said higher proportion or amount may, for example, be expressed in terms of:
a higher maximum yield of an isomer observed during the entire course of the reaction or said interval thereof;
each of which preferably being observed relative to a reference method, said reference method being performed under otherwise identical conditions with known chemical or biochemical means.
Generally also comprised in accordance with the invention are all “isomeric forms” of the compounds described herein, such as constitutional isomers and in particular stereoisomers and mixtures of these, such as, for example, optical isomers or geometric isomers, such as E- and Z-isomers, and combinations of these. If several centers of asymmetry are present in a molecule, then the invention comprises all combinations of different conformations of these centers of asymmetry, such as, for example, pairs of enantiomers, or any mixtures of stereoisomeric forms.
“Yield” and/or the “conversion rate” of a reaction according to the invention is determined over a defined period of, for example, 4, 6, 8, 10, 12, 16, 20, 24, 36 or 48 hours, in which the reaction takes place. In particular, the reaction is carried out under precisely defined conditions, for example at “standard conditions” as herein defined.
The different yield parameters (“Yield” or YP/S; “Specific Productivity Yield”; or Space-Time-Yield (STY)) are well known in the art and are determined as described in the literature.
“Yield” and “YP/S” (each expressed in mass of product produced/mass of material consumed) are herein used as synonyms.
The specific productivity-yield describes the amount of a product that is produced per h and L fermentation broth per g of biomass. The amount of wet cell weight stated as WCW describes the quantity of biologically active microorganism in a biochemical reaction. The value is given as g product per g WCW per h (i.e. g/gWCW−1 h−1). Alternatively, the quantity of biomass can also be expressed as the amount of dry cell weight stated as DCW. Furthermore, the biomass concentration can be more easily determined by measuring the optical density at 600 nm (OD600) and by using an experimentally determined correlation factor for estimating the corresponding wet cell or dry cell weight, respectively.
If the present disclosure refers to features, parameters and ranges thereof of different degree of preference (including general, not explicitly preferred features, parameters and ranges thereof) then, unless otherwise stated, any combination of two or more of such features, parameters and ranges thereof, irrespective of their respective degree of preference, is encompassed by the disclosure of the present description.
The term “domain” refers to a set of amino acids or a partial sequence of amino acids residues conserved at specific positions along an alignment of sequences of evolutionarily related proteins. While amino acids at other positions can vary between protein homologues, amino acids that are highly conserved at specific positions of such domain indicate amino acids that are likely essential in the structure, stability or function of a protein. Identified by their high degree of conservation in aligned sequences of a family of protein homologues, they can be used as identifiers to determine if any polypeptide in question belongs to a previously identified polypeptide family.
The term “motif” or consensus sequence” or “signature” refers to a short conserved region in the sequence of evolutionarily related proteins. Motifs are frequently highly conserved parts of domains, but may also include only part of the domain.
A “protein family” is defined as a group of proteins that share a common evolutionary origin reflected by their related functions, similarities in sequence, or similar primary, secondary or tertiary structure. Proteins within protein families are usually homologous and have similar structure of conserved functional domains and motifs.
Specialist databases exist for the identification of domains, for example, SMART (Schultz et al. (1998) Proc. Natl. Acad. Sci. USA 95, 5857-5864; Letunic et al. (2002) Nucleic Acids Res 30, 242-244), InterPro (Mulder et al., (2003) Nucl. Acids. Res. 31, 315-318), Prosite (Bucher and Bairoch (1994), A generalized profile syntax for biomolecular sequences motifs and its function in automatic sequence interpretation. (In) ISMB-94; Proceedings 2nd International Conference on Intelligent Systems for Molecular Biology. Altman R., Brutlag D., Karp P., Lathrop R., Searls D., Eds., pp 53-61, AAAI Press, Menlo Park; Hulo et al., Nucl. Acids. Res. 32:D134-D137, (2004)), or Pfam (Bateman et al., Nucleic Acids Research 30(1): 276-280 (2002)). Domains or motifs may also be identified using routine techniques, such as by sequence alignment.
The term “Pfam” refers to a large collection of protein domains and protein families maintained by the Pfam Consortium and available at several sponsored world wide web sites, such as http://pfam.xfam.org// (European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL EBI). The latest release of Pfam is Pfam 32.0 (September 2018), based on the UniProt Reference Proteomes (El-Gebali S. et al, 2019, Nucleic Acids Res. 47, Database issue D427-D432). Pfam domains and families are identified using multiple sequence alignments and hidden Markov models (HMMs). Pfam-A family or domain assignments, are high quality assignments generated by a curated seed alignment using representative members of a protein family and profile hidden Markov models based on the seed alignment (Unless otherwise specified, matches of a queried protein to a Pfam domain or family are Pfam-A matches). All identified sequences belonging to the family are then used to automatically generate a full alignment for the family (Sonnhammer (1998) Nucleic Acids Research 26, 320-322; Bateman (2000) Nucleic Acids Research 26, 263-266; Bateman (2004) Nucleic Acids Research 32, Database Issue, D138-D141; Finn (2006) Nucleic Acids Research Database Issue 34, D247-251; Finn (2010) Nucleic Acids Research Database Issue 38, D211-222). By accessing the Pfam database, for example, using any of the above-reference websites, protein sequences can be queried against the HMMs using HMMER homology search software (e.g., HMMER2, HMMER3, or a higher version, hmmer.janelia.org/). Significant matches that identify a queried protein as being in a pfam family (or as having a particular Pfam domain) are those in which the bit score is greater than or equal to the gathering threshold for the Pfam domain. Expectation values (e-values) can also be used as a criterion for inclusion of a queried protein in a Pfam or for determining whether a queried protein has a particular Pfam domain, where low e-values, much less than 1.0, for example less than 0.1, or less.
The “E-value” (expectation value) is the number of hits that would be expected to have a score equal to or better than this value, by chance alone. This means that a good E-value which gives a confident prediction is much less than 1. E-values around 1 is what is expected by chance. Thus, the lower the E-value, the more specific the search for domains will be. Only positive numbers are allowed. (definition by Pfam))
A “precursor” molecule of a target compound as described herein is converted to said target compound, preferably through the enzymatic action of a suitable polypeptide performing at least one structural change on said precursor molecule. For example a “diphosphate precursor” (as for example a “terpenyl diphosphate precursor”) is converted to said target compound (as for example a terpene alcohol) via enzymatic removal of the diphosphate moiety, for example by removal of mono- or diphosphate groups by a phosphatase enzyme. For example a “non-cyclic precursor” (like a non-cyclic terpenyl precursor”) may be converted to the cyclic target molecule (like a cyclic terpene compound) through the action of a cyclase or synthase enzyme, irrespective of the particular enzymatic mechanism of such enzyme, in one or more steps.
The term “protein tyrosine phosphatase” represents a group of enzymes that are generally known to remove phosphate groups from phosphorylated tyrosine residues on proteins. A particular subgroup of said family as described herein are enzymes useful to dephosphorylate phosphorylated terpene molecules.
A “terpene synthase” designates a polypeptide which converts a terpene precursor molecule to the respective terpene target molecule, like in particular a processed target terpene alcohol or terpene hydrocarbon. Non-limiting examples of such terpene precursor molecules are for example non-cyclic compounds, selected from farnesyl pyrophosphate (FPP), geranylgeranyl-pyrophosphate (GGPP), or a mixture of isopentenyl pyrophosphate (IPP) and dimethyl allyl pyrophosphate (DMAPP). In case the obtained terpene contains a diphosphate moiety the synthase is designated “terpenyl diphosphate synthase”
The terms “terpenyl diphosphate synthase” or “polypeptide having terpenyl diphosphate synthase activity” or “terpenyl diphosphate synthase protein” or “having the ability to produce terpenyl diphosphate” relate to a polypeptide capable of catalyzing the synthesis of a terpenyl diphosphate, in the form of any of its stereoisomers or a mixture thereof, starting from an acyclic terpene pyrophosphate, particularly GPP, FPP or GGPP or IPP together with DMAPP. The terpeny diphosphate may be the only product or may be part of a mixture of terpenyl phosphates. Said mixture may comprise terpenyl monophosphate and/or a terpene alcohol. The above definition also applies to the group of “bicyclic terpenyl diphosphate synthases”, which produce a bicyclic terpenyl diphosphate, like CPP or LPP. As example of such “terpenyl diphosphate synthase” enzymes there may be mentioned copalyl diphosphate synthase (CPS). Copalyl-diphosphate may be the only product or may be part of a mixture of copalyl phosphates. Said mixture may comprise copalyl-monophosphate and/or other terpenyl diphosphate. As another example of such “terpenyl diphosphate synthase” enzymes there may be mentioned and labdendiol diphosphate synthase (LPS). Labdendiol diphosphate may be the only product or may be part of a mixture of labdendiol phosphates. Said mixture may comprise labdendiol monophosphate and/or terpenyl diphosphate.
The terms “terpenyl diphosphate phosphatase” or “polypeptide having terpenyl diphosphate phosphatase activity” or “terpenyl diphosphate phosphatase protein” or “having the ability to produce terpene alcohol” relate to a polypeptide capable of catalyzing the removal (irrespective of a particular enzymatic mechanism) of a diphosphate moiety or monophosphate moieties, to form a dephosphorylated compound, in particular the corresponding alcohol compound of said terpenyl moiety. The terpene alcohol may be present in the product in any of its stereoisomers or as a mixture thereof. The terpene alcohol may be the only product or may be part of a mixture with other terpene compounds, as for example dephosphorylated analogs of the respective (for example non-cyclic) terpenyl diphosphate precursor of said terpenyl diphosphate. The above definition also applies to the group of “bicyclic terpenyl diphosphate phosphatase”, which produce a bicyclic terpene alcohol, like copalol or labdendiol.
As example of such “terpenyl diphosphate phosphatase” enzymes there may be mentioned copalyl diphosphate phosphatase (CPP phosphatase). Copalol may be the only product or may be part of a mixture with dephosphorylated precursors, like for example farnesol and/or geranylgeraniol; and/or side products resulting from enzymatic side activities in the reaction mixture, like esters or aldehydes of such alcohols or other cyclic or non-cyclic diterpenes. As another example of such “terpenyl diphosphate phosphatase” enzymes there may be mentioned and labdendiol diphosphate phosphatase (LPP phosphatase). Labdendiol may be the only product or may be part of a mixture with dephosphorylated precursors, like for example farnesol and/or geranylgeraniol; and/or side products resulting from enzymatic side activities in the reaction mixture, like esters or aldehydes of such alcohols or other cyclic or non-cyclic diterpenes.
An “enal-cleaving enzyme” or “enal-cleaving protein” or “enal-cleaving polypeptide” in the context of the present invention designates an “α,β-unsaturated aldehyde carbon-carbon double bond-cleaving enzyme, which also may be called a “α,β-unsaturated aldehyde C≡C bond-cleaving enzyme” or “α,β-unsaturated aldehyde C═C-cleaving enzyme” or a “enal C═C-cleaving enzyme”. The enal-cleaving protein of the invention, based on protein domain organization, may also be described as a member of the ‘DUF4334 protein family” and/or as a member of the “GXWXG protein family”.
More particularly, an enal cleaving enzyme of the invention has the ability to cleave labdane-type carbonyl compounds, like labdane aldehydes, in particular copalal to the respective dinorlabdane carbonyl compound. “Baeyer-Villiger monooxygenases” (BVMOs) are flavoenzymes and belong to the class of refers to a polypeptide having oxidoreductase activity (EC 1.14.13.X). They catalyze the oxidation of linear, cyclic (aromatic or non-aromatic) aldehydes or ketones to the corresponding esters or lactones, highly similar to the chemical Baeyer-Villiger oxidation. During the enzymatic oxidation one atom of molecular oxygen is incorporated into a carbon-carbon bond of a non-activated carbonyl compound. The BVMOs require NADPH or NADH as cofactor or accept both. They also require molecular oxygen as co-substrate. More particularly, a BVMO of the invention has the ability to oxidize terpene-derived aldehydes or ketones, like for example labdane-type carbonyl compounds, like labdane aldehydes, in particular copalal and/or manooloxy to the respective carbonyl ester
An “esterase” refers to a polypeptide having hydrolase activity that splits esters into an acid and an alcohol in a chemical reaction with water (hydrolysis). Esterases in the context of the present invention are selected from the class of carboxylic ester hydrolases (EC 3.1.1.-), which splits off acyl groups, like acetyl or formyl groups, from the respective etser substrate. More particularly, an esterase of the invention has the ability to cleave labdane-type ester compounds, like gamma-ambryl-acetate, to form the respective labdane-type alcohol, like gamma-ambrol.
An “alcohol dehydrogenase” (ADH) in the context of the present invention refers to a polypeptide having the ability to oxidize an alcohol to the corresponding aldehyde in the presence of NAD+ or NADP+ as cofactor. Such enzymes are members of the E.C. families 1.1.1.1 (NAD+ dependent) or 1.1.1.2 (NADP+ dependent). More particularly, an ADH of the invention has the ability to oxidize labdane-type alkohols to the respective labdane-type carbonyl compounds (aldehydes or ketones), like copalol to copalal and/or labdendiol to the respective aldehyde or other labdane-type derivatives of copalol, labdendiol, for example the respective nor- or dinor-labdane derivatives of copalol or labdendiol. ADHs a sused herein may either be endogenously present in the respective biocatalytic process or may be exogenous.
“Enal-cleaving activity” is determined under “standard conditions” as described herein below: It can be determined using recombinant enal-cleaving polypeptide expressing host cells, disrupted enal-cleaving polypeptide expressing cells, fractions of these or enriched or purified enal-cleaving polypeptide, in a culture medium or reaction medium, preferably buffered, having a pH in the range of 6 to 11, preferably 7 to 9, at a temperature in the range of about 20 to 45° C., like about 25 to 40° C., preferably 25 to 32° C. and in the presence of a reference substrate, here in particular copalal, either added at an initial concentration in the range of 1 to 100 μM mg/ml, preferably 5 to 50 μM, in particular 30 to 40 μM, or endogenously produced by the host cell. The conversion reaction to form the respective cleavage product, like manooloxy is conducted from 10 min to 5 h, preferably about 1 to 2 h. The cleavage product may then be determined in conventional matter, for example after extraction with an organic solvent, like ethyl acetate.
“BVMO activity” is determined under “standard conditions” as described herein below: It can be determined using recombinant BVMO expressing host cells, disrupted BVMO expressing cells, fractions of these or enriched or purified BVMO enzyme, in a culture medium or reaction medium, preferably buffered, having a pH in the range of 6 to 11, preferably 7 to 9, at a temperature in the range of about 20 to 45° C., like about 25 to 40° C., preferably 25 to 32° C. and in the presence of a reference substrate, here in particular copalal and/or manooloxy, either added at an initial concentration in the range of 1 to 100 μM mg/ml, preferably 5 to 50 μM, in particular 30 to 40 μM, or endogenously produced by the host cell and in the presence of molecular oxygen. For in-vitro assays a cofactor selected from NADH and NADPH has to be added in a suitable easily to be determined concentration range of The conversion reaction to form the respective cleavage product, like the formyl esters 1a and/or 1b in the case of copalal or gamma-ambryl acetate in the case of manooloxy is conducted from 10 min to 5 h, preferably about 1 to 2 h. The oxidation product may then be determined in conventional matter, for example after extraction with an organic solvent, like ethyl acetate.
“Terpenyl diphosphate synthase activity” (like CPS or LPS activity) is determined under “standard conditions” as described herein below: They can be determined using recombinant terpenyl diphosphate synthase expressing host cells, disrupted terpenyl diphosphate synthase expressing cells, fractions of these or enriched or purified terpenyl diphosphate synthase enzyme, in a culture medium or reaction medium, preferably buffered, having a pH in the range of 6 to 11, preferably 7 to 9, at a temperature in the range of about 20 to 45° C., like about 25 to 40° C., preferably 25 to 32° C. and in the presence of a reference substrate, here in particular GGPP, either added at an initial concentration in the range of 1 to 100 μM mg/ml, preferably 5 to 50 μM, in particular 30 to 40 μM, or endogenously produced by the host cell. The conversion reaction to form a terpenyl diphosphate is conducted from 10 min to 5 h, preferably about 1 to 2 h. If no endogenous phosphatase is present, one or more exogenous phosphatases, for example an alkaline phosphatase, are added to the reaction mixture to convert the terpenyl diphosphate as formed by the synthase to the respective terpene alcohol. The terpene alcohol may then be determined in conventional matter, for example after extraction with an organic solvent, like ethyl acetate.
“Terpenyl diphosphate phosphatase activity” (like CPP or LPP phosphatase activity) is determined under “standard conditions” as described herein below: They can be determined using recombinant terpenyl diphosphate phosphatase expressing host cells, disrupted terpenyl diphosphate phosphatase expressing cells, fractions of these, or enriched or purified terpenyl diphosphate phosphatase enzyme, in a culture medium or reaction medium, preferably buffered, having a pH in the range of 6 to 11, preferably 7 to 9, at a temperature in the range of about 20 to 45° C., like about 25 to 40° C., preferably 25 to 32° C. and in the presence of a reference substrate, here for example CPP or LPP, either added at an initial concentration in the range of 1 to 100 μM mg/ml, preferably 5 to 50 μM, in particular 30 to 40 μM, or endogenously produced by the host cell. The conversion reaction to form a terpenyl diphosphate is conducted from 10 min to 5 h, preferably about 1 to 2 h. The terpene alcohol may then be determined in conventional matter, for example after extraction with an organic solvent, like ethyl acetate.
Particular examples of suitable standard conditions for each of the above-described enzyme activites may be taken from the Experimental Part below.
The terms “biological function,” “function”, “biological activity” or “activity” of a terpeyl synthase refer to the ability of a terpenyl diphosphate synthase as described herein to catalyze the formation of at least one terpenyl diphosphate from the corresponding precursor terpene.
The terms “biological function,” “function”, “biological activity” or “activity” of a terpenyl diphosphate phosphatase refer to the ability of the terpenyl diphosphate phosphatase as described herein to catalyze the removal of a diphosphate group from said terpenyl compound to form the corresponding terpene alcohol.
The “mevalonate pathway” also known as the “isoprenoid pathway” or “HMG-CoA reductase pathway” is an essential metabolic pathway present in eukaryotes, archaea, and some bacteria. The mevalonate pathway begins with acetyl-CoA and produces two five-carbon building blocks called isopentenyl pyrophosphate (IPP) and dimethyl allyl pyrophosphate (DMAPP). Key enzymes are acetoacetyl-CoA thiolase (atoB), HMG-CoA synthase (mvaS), HMG-CoA reductase (mvaA), mevalonate kinase (MvaK1), phosphomevalonate kinase (MvaK2), a mevalonate diphosphate decarboxylase (MvaD), and an isopentenyl diphosphate isomerase (idi). Combining the mevalonate pathway with enzyme activity to generate the terpene precursors GPP, FPP or GGPP, like in particular FPP synthase (ERG20), allows the recombinant cellular production of terpenes.
As used herein, the term “host cell” or “transformed cell” refers to a cell (or organism) altered to harbor at least one nucleic acid molecule, for instance, a recombinant gene encoding a desired protein or nucleic acid sequence which upon transcription yields at least one functional polypeptide of the present invention, in particular a terpenyl diphosphate synthase protein or terpenyl diphosphate phosphatase enzyme as defined herein above. The host cell is particularly a bacterial cell, a fungal cell or a plant cell or plants. The host cell may contain a recombinant gene or several genes, as for example organized as an operon, which has been integrated into the nuclear or organelle genomes of the host cell. Alternatively, the host may contain the recombinant gene extra-chromosomally.
The term “organism” refers to any non-human multicellular or unicellular organism such as a plant, or a microorganism. Particularly, a micro-organism is a bacterium, a yeast, an algae or a fungus.
The term “plant” is used interchangeably to include plant cells including plant protoplasts, plant tissues, plant cell tissue cultures giving rise to regenerated plants, or parts of plants, or plant organs such as roots, stems, leaves, flowers, pollen, ovules, embryos, fruits and the like. Any plant can be used to carry out the methods of an embodiment herein.
A particular organism or cell is meant to be “capable of producing FPP” when it produces FPP naturally or when it does not produce FPP naturally but is transformed to produce FPP with a nucleic acid as described herein., Organisms or cells transformed to produce a higher amount of FPP than the naturally occurring organism or cell are also encompassed by the “organisms or cells capable of producing FPP”.
A particular organism or cell is meant to be “capable of producing GGPP” when it produces GGPP naturally or when it does not produce GGPP naturally but is transformed to produce GGPP with a nucleic acid as described herein. Organisms or cells transformed to produce a higher amount of GGPP than the naturally occurring organism or cell are also encompassed by the “organisms or cells capable of producing GGPP”.
A particular organism or cell is meant to be “capable of producing terpenyl diphosphate” when it produces a terpenyl diphosphate as defined herein naturally or when it does not produce said diphosphate naturally but is transformed to produce said diphosphate with a nucleic acid as described herein. Organisms or cells transformed to produce a higher amount of terpenyl diphosphate than the naturally occurring organism or cell are also encompassed by the “organisms or cells capable of producing a terpenyl diphosphate”.
A particular organism or cell is meant to be “capable of producing terpene alcohol” when it produces a terpene alcohol as defined herein naturally or when it does not produce said alcohol naturally but is transformed to produce said alcohol with a nucleic acid as described herein. Organisms or cells transformed to produce a higher amount of a terpene alcohol than the naturally occurring organism or cell are also encompassed by the “organisms or cells capable of producing a terpene alcohol”. The same applies to a particular organism “capable of producing labdane-type alcohol”.
A particular organism or cell is meant to be “capable of producing an ester” when it produces an ester as defined herein naturally or when it does not produce said ester naturally but is transformed to produce said ester with a nucleic acid as described herein. Organisms or cells transformed to produce a higher amount of ester than the naturally occurring organism or cell are also encompassed by the “organisms or cells capable of producing an ester”.
A particular organism or cell is meant to be “capable of producing a target product” when it produces a target product as defined herein (for example the esters, alcohol, or carbonyl compounds or more particularly the labdane type compounds) naturally or when it does not produce said target product naturally but is transformed to produce said target product with a nucleic acid as described herein. Organisms or cells transformed to produce a higher amount of target product than the naturally occurring organism or cell are also encompassed by the “organisms or cells capable of producing a target product”.
The term “fermentative production” or “fermentation” refers to the ability of a microorganism (assisted by enzyme activity contained in or generated by said microorganism) to produce a chemical compound in cell culture utilizing at least one carbon source added to the incubation.
The term “fermentation broth” is understood to mean a liquid, particularly aqueous or aqueous/organic solution which is based on a fermentative process and has not been worked up or has been worked up, for example, as described herein.
An “enzymatically catalyzed” or “biocatalytic” method means that said method is performed under the catalytic action of an enzyme, including enzyme mutants, as herein defined. Thus the method can either be performed in the presence of said enzyme in isolated (purified, enriched) or crude form or in the presence of a cellular system, in particular, natural or recombinant microbial cells containing said enzyme in active form, and having the ability to catalyze the conversion reaction as disclosed herein.
The term “alpha, beta-unsaturated carbonyl” compound describes organic molecules containing an aldehyde or keto group of the general formula RaRb C═C(Rc)—C═O, wherein the C═C bond may be of any stereoisomeric configuration and wherein residues Ra, Rb and Rc may be identical or different and may have the meanings as specified below for particular alpha, beta unsaturated carbonyl compounds.
A “labdane” compound in the context of the present invention will show the following basic structure of its carbon skeleton consisting of 20 carbon atoms. The depicted numbering of carbon atoms will be applied in order to further define certain positions within said carbon skeleton.
The term “labdane” encompasses any compounds of this basic C20-structure, in any stereoisomeric form and encompassing any variant of this structure containing one or more unsaturated C—C bonds, in particular one or more C═C bonds, at any position, within the carbocyclic ring and/or the side chains. Also encompassed are variants thereof containing one or more substituents, as for example substituents selected from the group of —OH. ═O, —O—CO_R, wherein R may be straight chain or branched alkyl, in particular lower alkyl, more particularly C1-C4 aklyl, like methyl, ethyl, n- or i-propyl, or n-, i- or t-butyl; and —COOH at any of the indicated primary, secondary or tertiary C atoms.
A “labdane derived” compound of such “labdane” encompasses chemical compounds wherein the basic C20-carbon skeleton is modified by deleting one or more carbon atoms. As examples there may be mentioned:
norlabdane (C19-sceleton), dinorlabdane (C18-sceleton), trinorlabdane (C17-sceleton), and tetranorlabdane (C16-sceleton). The position of the deleted carbon atom is indicated by stating the carbon number. For example, in a norlabdane, wherein the carbonate in position 15 is missing is designated “15-norlabdane”.
A “labdane derived” compound of such “labdane” also encompasses chemical compounds wherein the basic C20-carbon skeleton is modified by inserting a hereoatom between two C-atoms of the labdane sceleoton. For example, insertion of an ether bridge between positions 14 and 15 converts the labdane to a norlabdane and particularly to a norlabdane ester.
Non-limiting examples of substituted labdanes or substituted labdane derived structures are given below:
“Diphosphate” and “pyrophosphate” as used herein are synonyms.
“Terpenes” are a large and diverse class of organic compounds, produced by a variety of plants, particularly conifers, and by some insects. Terpenes are hydrocarbons. Although sometimes used interchangeably with “terpenes”, “terpenoids” or “isoprenoids” are modified terpenes as they contain additional functional groups, usually oxygen-containing.
“Terpenoids” (“isoprenoids”) are a large and diverse class of naturally occurring organic chemicals derived from terpenes. Although sometimes used interchangeably with the term “terpenes”, “terpenoids” contain additional functional groups, usually 0-containing groups, like for example hydroxyl, carbonyl or carboxyl groups. Most are multicyclic structures with oxygen-containing functional groups. Unless stated otherwise, in the context of the present description the term “terpene” and the term “terpenoid” may be used interchangeably.
Terpenes (and terpenoids) may be classified by the number of isoprene units in the molecule; a prefix in the name indicates the number of terpene units needed to assemble the molecule. Hemiterpenes consist of a single isoprene unit. Monoterpenes consist of two isoprene units and have the molecular formula C10H16. Sesquiterpenes consist of three isoprene units and have the molecular formula C15H24. Diterpenes are composed of four isoprene units and have the molecular formula C20H32.
“Terpenyl” designates noncyclic and cyclic chemical hydrocarbyl residues which are derived from the C5 building block isoprene and in particular contain one or more such building blocks.
“Cyclic terpene” or cyclic terpenyl” or “cyclic diterpene” or cyclic diterpenyl” relates to a terpene compound or terpenyl residue which comprises in its structure at lest on, as for example 1, 2, 3, 4 or 5 carbocyclic condensed and/or non-condensed rings, preferably two carbocyclic condensed rings.
“Bicyclic terpene” or bicyclic terpenyl” or “bicyclic diterpene” or bicyclic diterpenyl” relates to a terpene compound or terpenyl residue which comprises in its structure two carbocyclic rings, preferably two carbocyclic condensed rings.
“Derivatives of terpenes” or “derivatives of terpenoids” in the context of the present invention in particular refer to such chemical compounds which are obtained from a terpene or terpenoid by chemical and/or enzymatic modification. More particularly, such derivatives encompass “hydrocarbon chain-degraded” derivatives.
A “hydrocarbon chain-degraded” terpene or terpenoid differs from the non-degraded precursor by a reduced number of carbon items of the precursor's carbon skeleton.
A “hydrocarbyl” residue is a chemical group which essentially is composed of carbon and hydrogen atoms and may be a non-cyclic, linear or branched, saturated or unsaturated moiety, or a cyclic saturated or unsaturated moiety, aromatic or non-aromatic moiety. A hydrocarbyl residue comprises 1 to 30, 1 to 25, 1 to 20, 1 to 15 or 1 to 10 or 1 to 5 carbon atoms in the case of a non-cyclic structure. It comprises 4 to 30, 4 to 25, 4 to 20, 4 to 15, 4 to 10 or in particular 4, 5, 6 or 7 carbon atoms in the case of a cyclic structure.
Said hydrocarbyl residues may be non-substituted or may carry at least one, like 1 to 5, preferably 0, 1 or 2 substituents.
Particular examples of such hydrocarbyl residues are noncyclic linear or branched alkyl or alkenyl residues as defined below; or mono- or polycyclic, in particular mono- or bicyclic, saturated or unsaturated, nonaromatic moieties, as for example found in cyclic (for example bicyclic) or noncyclic terpene type compound, and labdane type compounds as defined herein.
An “alkyl” residue represents linear or branched, saturated hydrocarbon residues. It comprises 1 to 30, 1 to 25, 1 to 20, 1 to 15 or 1 to 10 or 1 to 7, 1 to 6, 1 to 5, or 1 to 4 carbon atoms.
An “alkenyl” residue represents linear or branched, mono- or polyunsaturated hydrocarbon residues. It comprises 2 to 30, 2 to 25, 2 to 20, 2 to 15 or 2 to 10 or 2 to 7, 2 to 6, 2 to 5, or 2 to 4 carbon atoms. I may have up to 10, like 1, 2, 3, 4 or 5 C═C double bonds.
The term “lower alkyl” or “short chain alkyl” represents saturated, straight-chain or branched hydrocarbon radicals having 1 to 4, 1 to 5, 1 to 6, or 1 to 7, in particular 1 to 4 carbon atoms. As examples there may be mentioned: methyl, ethyl, n-propyl, 1-methylethyl, n-butyl, 1-methylpropyl, 2-methylpropyl, 1,1-dimethylethyl, n-pentyl, 1-methylbutyl, 2-methylbutyl, 3-methylbutyl, 2,2-dimethylpropyl, 1-ethylpropyl, n-hexyl, 1,1-dimethylpropyl, 1,2-dimethylpropyl, 1-methylpentyl, 2-methylpentyl, 3-methylpentyl, 4-methylpentyl, 1,1-dimethylbutyl, 1,2-dimethylbutyl, 1,3-dimethylbutyl, 2,2-dimethylbutyl, 2,3-dimethylbutyl, 3,3-dimethylbutyl, 1-ethylbutyl, 2-ethylbutyl, 1,1,2-trimethylpropyl, 1,2,2-trimethylpropyl, 1-ethyl-1-methylpropyl and 1-ethyl-2-methylpropyl; and also n-heptyl, and the singly or multiply branched analogs thereof.
“Long-chain alkyl” represents, for example, saturated straight-chain or branched hydrocarbyl radicals having 8 to 30, for example 8 to 20 or 8 to 15, carbon atoms, such as octyl, nonyl, decyl, undecyl, dodecyl, tridecyl, tetradecyl, pentadecyl, hexadecyl, heptadecyl, octadecyl, nonadecyl, eicosyl, hencosyl, docosyl, tricosyl, tetracosyl, pentacosyl, hexacosyl, heptacosyl, octacosyl, nonacosyl, squalyl, constitutional isomers, especially singly or multiply branched isomers thereof.
“Long-chain alkenyl” represents the mono- or polyunsaturated analogues of the above mentioned “long-chain alkyl” groups,
“Short chain alkenyl” (or “lower alkenyl”) represents mono- or polyunsaturated, especially monounsaturated, straight-chain or branched hydrocarbon radicals having 2 to 4, 2 to 6, or 2 to 7 carbon atoms and one double bond in any position, e.g. C2-C6-alkenyl such as ethenyl, 1-propenyl, 2-propenyl, 1-methylethenyl, 1-butenyl, 2-butenyl, 3-butenyl, 1-methyl-1-propenyl, 2-methyl-1-propenyl, 1-methyl-2-propenyl, 2-methyl-2-propenyl, 1-pentenyl, 2-pentenyl, 3-pentenyl, 4-pentenyl, 1-methyl-1-butenyl, 2-methyl-1-butenyl, 3-methyl-1-butenyl, 1-methyl-2-butenyl, 2-methyl-2-butenyl, 3-methyl-2-butenyl, 1-methyl-3-butenyl, 2-methyl-3-butenyl, 3-methyl-3-butenyl, 1,1-dimethyl-2-propenyl, 1,2-dimethyl-1-propenyl, 1,2-dimethyl-2-propenyl, 1-ethyl-1-propenyl, 1-ethyl-2-propenyl, 1-hexenyl, 2-hexenyl, 3-hexenyl, 4-hexenyl, 5-hexenyl, 1-methyl-1-pentenyl, 2-methyl-1-pentenyl, 3-methyl-1-pentenyl, 4-methyl-1-pentenyl, 1-methyl-2-pentenyl, 2-methyl-2-pentenyl, 3-methyl-2-pentenyl, 4-methyl-2-pentenyl, 1-methyl-3-pentenyl, 2-methyl-3-pentenyl, 3-methyl-3-pentenyl, 4-methyl-3-pentenyl, 1-methyl-4-pentenyl, 2-methyl-4-pentenyl, 3-methyl-4-pentenyl, 4-methyl-4-pentenyl, 1,1-dimethyl-2-butenyl, 1,1-dimethyl-3-butenyl, 1,2-dimethyl-1-butenyl, 1,2-dimethyl-2-butenyl, 1,2-dimethyl-3-butenyl, 1,3-dimethyl-1-butenyl, 1,3-dimethyl-2-butenyl, 1,3-dimethyl-3-butenyl, 2,2-dimethyl-3-butenyl, 2,3-dimethyl-1-butenyl, 2,3-dimethyl-2-butenyl, 2,3-dimethyl-3-butenyl, 3,3-dimethyl-1-butenyl, 3,3-dimethyl-2-butenyl, 1-ethyl-1-butenyl, 1-ethyl-2-butenyl, 1-ethyl-3-butenyl, 2-ethyl-1-butenyl, 2-ethyl-2-butenyl, 2-ethyl-3-butenyl, 1,1,2-trimethyl-2-propenyl, 1-ethyl-1-methyl-2-propenyl, 1-ethyl-2-methyl-1-propenyl and 1-ethyl-2-methyl-2-propenyl.
“Alkylene” represents straight-chain or singly or multiply branched hydrocarbon bridging groups having 1 to 10 carbon atoms, for example C1-C7-alkylene groups selected from —CH2—, —(CH2)2—, —(CH2)3—, —(CH2)4—, —(CH2)2—CH(CH3)—, —CH2—CH(CH3)—CH2—, (CH2)4—, —(CH2)5—, —(CH2)6, —(CH2)7—, —CH(CH3)—CH2—CH2—CH(CH3)— or —CH(CH3)—CH2—CH2—CH2—CH(CH3)—, and in particular C1-C4-alkylene groups selected from —CH2—, —(CH2)2—, —(CH2)3—, —(CH2)4—, —(CH2)2—CH(CH3)—, —CH2—CH(CH3)—CH2—.
An “alkylidene” group represents a straight chain or branched hydrocarbon substituent linked via a double bond to the body of the molecule. It comprises 1 to 6 carbon atoms. As examples of such “C1-C6-alkylidenes” there may be mentioned methylidene (═CH2) ethylidene, (═CH—CH2), n-propylidene, n-butylidene, n-pentlyiden, n-hexylidene and the constitutional isomers thereof, as for example iso-propylidene.
An “alkenylidene” represents the mono-unsaturated analogue of the above mentioned alkylidenes with more than 2 carbon atoms and may be called “C3-C6-alkenylidenes”. n-propenylidene, n-butenylidene, n-pentenlyiden, and n-hexenylidene may be mentioned as examples.
The “substituent” of the above mentioned residues contains one hetero atom, like O or N. Preferably the substituents are independently selected from —OH, C═O, or —COOH. Most preferably said substituent is —OH.
A “mono- or polycyclic hydrocarbyl residue” comprise 1, 2 or 3 condensed (anellated) or non-condensed, optionally substituted, saturated or unsaturated hydrocarbon ring groups (or “carbocyclic” groups). Each cycle may comprise independently of each other 3 to 8, in particular 5 to 7, more particularly 6 ring carbon atoms. As examples of monocyclic residues there may be mentioned “cycloalkyl” groups which are carbocyclic radicals having 3 to 7 ring carbon atoms, such as cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, and cyclooctyl; and the corresponding “cycloalkenyl” groups. Cycloalkenyl” (or “mono- or polyunsaturated cycloalkyl”) represents, in particular, monocyclic, mono- or polyunsaturated carbocyclic groups having 5 to 8, preferably up to 6, carbon ring members, for example monounsaturated cyclopentenyl, cyclohexenyl, cycloheptenyl and cyclooctenyl radicals.
As examples of polycyclic residues there may be mentioned groups wherein 1, 2 or 3 of such cycloalkyl and/or cycloalkenyl are linked together, as for example anellated, in order to form a polycyclic cycloalkyl or cycloalkenyl ring. As non-limiting example the bicyclic decalinyl residue composed of two anellated 6-membered carbon rings may be mentioned.
The number of substituents in such mono- or polycyclic hydrocarbyl residues may vary from 1 to 10, in particular 1 to 5 substituents. Suitable substituents of such cyclic residues are selected from lower alkyl, lower alkenyl, alkylidene, alkenylidene, or residues containing one hetero atom, like O or N as for example —OH or —COOH. In particular the substituents are independently selected from —OH, — COOH, methyl and methylidene.
Unsaturated cyclic groups may contain 1 or more, as for example 1, 2 or 3 C═C bonds and are aromatic, or in particular nonaromatic.
The above-mentioned mono- or polycyclic saturated or unsaturated groups may also contain at least one, like 1, 2, 3 or 4 ring heteroatoms, such as 0, N or S.
Overview of Particular Compound Names and their Structural Formulae
The numbering of amino acid residues refers to the residue number in the respective SEQ ID NO of the respective protein sequence in the attached sequence listing
The numbering of amino acid residues refers to the residue number in the respective SEQ ID NO of the respective protein sequence in the attached sequence listing
In this context the following definitions apply:
The generic terms “polypeptide” or “peptide”, which may be used interchangeably, refer to a natural or synthetic linear chain or sequence of consecutive, peptidically linked amino acid residues, comprising about 10 to up to more than 1.000 residues. Short chain polypeptides with up to 30 residues are also designated as “oligopeptides”.
The term “protein” refers to a macromolecular structure consisting of one or more polypeptides. The amino acid sequence of its polypeptide(s) represents the “primary structure” of the protein. The amino acid sequence also predetermines the “secondary structure” of the protein by the formation of special structural elements, such as alpha-helical and beta-sheet structures formed within a polypeptide chain. The arrangement of a plurality of such secondary structural elements defines the “tertiary structure” or spatial arrangement of the protein. If a protein comprises more than one polypeptide chains said chains are spatially arranged forming the “quaternary structure” of the protein. A correct spacial arrangement or “folding” of the protein is prerequisite of protein function. Denaturation or unfolding destroys protein function. If such destruction is reversible, protein function may be restored by refolding.
A typical protein function referred to herein is an “enzyme function”, i.e. the protein acts as biocatalyst on a substrate, for example a chemical compound, and catalyzes the conversion of said substrate to a product. An enzyme may show a high or low degree of substrate and/or product specificity.
A “polypeptide” referred to herein as having a particular “activity” thus implicitly refers to a correctly folded protein showing the indicated activity, as for example a specific enzyme activity.
Thus, unless otherwise indicated the term “polypeptide” also encompasses the terms “protein” and “enzyme”.
Similarly, the term “polypeptide fragment” encompasses the terms “protein fragment” and “enzyme fragment”.
The term “isolated polypeptide” refers to an amino acid sequence that is removed from its natural environment by any method or combination of methods known in the art and includes recombinant, biochemical and synthetic methods.
“Target peptide” refers to an amino acid sequence which targets a protein, or polypeptide to intracellular organelles, i.e., mitochondria, or plastids, or to the extracellular space (secretion signal peptide). A nucleic acid sequence encoding a target peptide may be fused to the nucleic acid sequence encoding the amino terminal end, e.g., N-terminal end, of the protein or polypeptide, or may be used to replace a native targeting polypeptide.
The present invention also relates to “functional equivalents” (also designated as “analogs” or “functional mutations”) of the polypeptides specifically described herein.
For example, “functional equivalents” refer to polypeptides which, in a test used for determining enzymatic terpenyl diphosphate synthase activity, or terpenyl diphosphate phosphatase activity display at least a 1 to 10%, or at least 20%, or at least 50%, or at least 75%, or at least 90% higher or lower activity, as that of the polypeptides specifically described herein.
“Functional equivalents”, according to the invention, also cover particular mutants, which, in at least one sequence position of an amino acid sequences stated herein, have an amino acid that is different from that concretely stated one, but nevertheless possess one of the aforementioned biological activities, as for example enzyme activity. “Functional equivalents” thus comprise mutants obtainable by one or more, like 1 to 20, in particular 1 to 15 or 5 to 10 amino acid additions, substitutions, in particular conservative substitutions, deletions and/or inversions, where the stated changes can occur in any sequence position, provided they lead to a mutant with the profile of properties according to the invention. Functional equivalence is in particular also provided if the activity patterns coincide qualitatively between the mutant and the unchanged polypeptide, i.e. if, for example, interaction with the same agonist or antagonist or substrate, however at a different rate, (i.e. expressed by a EC50 or IC50 value or any other parameter suitable in the present technical field) is observed. Examples of suitable (conservative) amino acid substitutions are shown in the following table:
“Functional equivalents” in the above sense are also “precursors” of the polypeptides described herein, as well as “functional derivatives” and “salts” of the polypeptides.
“Precursors” are in that case natural or synthetic precursors of the polypeptides with or without the desired biological activity.
The expression “salts” means salts of carboxyl groups as well as salts of acid addition of amino groups of the protein molecules according to the invention. Salts of carboxyl groups can be produced in a known way and comprise inorganic salts, for example sodium, calcium, ammonium, iron and zinc salts, and salts with organic bases, for example amines, such as triethanolamine, arginine, lysine, piperidine and the like. Salts of acid addition, for example salts with inorganic acids, such as hydrochloric acid or sulfuric acid and salts with organic acids, such as acetic acid and oxalic acid, are also covered by the invention.
“Functional derivatives” of polypeptides according to the invention can also be produced on functional amino acid side groups or at their N-terminal or C-terminal end using known techniques. Such derivatives comprise for example aliphatic esters of carboxylic acid groups, amides of carboxylic acid groups, obtainable by reaction with ammonia or with a primary or secondary amine; N-acyl derivatives of free amino groups, produced by reaction with acyl groups; or O-acyl derivatives of free hydroxyl groups, produced by reaction with acyl groups.
“Functional equivalents” naturally also comprise polypeptides that can be obtained from other organisms, as well as naturally occurring variants. For example, areas of homologous sequence regions can be established by sequence comparison, and equivalent polypeptides can be determined on the basis of the concrete parameters of the invention.
“Functional equivalents” also comprise “fragments”, like individual domains or sequence motifs, of the polypeptides according to the invention, or N- and or C-terminally truncated forms, which may or may not display the desired biological function. Preferably such “fragments” retain the desired biological function at least qualitatively.
“Functional equivalents” are, moreover, fusion proteins, which have one of the polypeptide sequences stated herein or functional equivalents derived there from and at least one further, functionally different, heterologous sequence in functional N-terminal or C-terminal association (i.e. without substantial mutual functional impairment of the fusion protein parts). Non-limiting examples of these heterologous sequences are e.g. signal peptides, histidine anchors or enzymes.
“Functional equivalents” which are also comprised in accordance with the invention are homologs to the specifically disclosed polypeptides. These have at least 60%, preferably at least 75%, in particular at least 80 or 85%, such as, for example, 90, 91, 92, 93, 94, 95, 96, 97, 98 or 99%, homology (or identity) to one of the specifically disclosed amino acid sequences, calculated by the algorithm of Pearson and Lipman, Proc. Natl. Acad, Sci. (USA) 85(8), 1988, 2444-2448. A homology or identity, expressed as a percentage, of a homologous polypeptide according to the invention means in particular an identity, expressed as a percentage, of the amino acid residues based on the total length of one of the amino acid sequences described specifically herein.
The identity data, expressed as a percentage, may also be determined with the aid of BLAST alignments, algorithm blastp (protein-protein BLAST), or by applying the Clustal settings specified herein below.
In the case of a possible protein glycosylation, “functional equivalents” according to the invention comprise polypeptides as described herein in deglycosylated or glycosylated form as well as modified forms that can be obtained by altering the glycosylation pattern.
Functional equivalents or homologues of the polypeptides according to the invention can be produced by mutagenesis, e.g. by point mutation, lengthening or shortening of the protein or as described in more detail below.
Functional equivalents or homologs of the polypeptides according to the invention can be identified by screening combinatorial databases of mutants, for example shortening mutants. For example, a variegated database of protein variants can be produced by combinatorial mutagenesis at the nucleic acid level, e.g. by enzymatic ligation of a mixture of synthetic oligonucleotides. There are a great many methods that can be used for the production of databases of potential homologues from a degenerated oligonucleotide sequence. Chemical synthesis of a degenerated gene sequence can be carried out in an automatic DNA synthesizer, and the synthetic gene can then be ligated in a suitable expression vector. The use of a degenerated genome makes it possible to supply all sequences in a mixture, which code for the desired set of potential protein sequences. Methods of synthesis of degenerated oligonucleotides are known to a person skilled in the art.
In the prior art, several techniques are known for the screening of gene products of combinatorial databases, which were produced by point mutations or shortening, and for the screening of cDNA libraries for gene products with a selected property. These techniques can be adapted for the rapid screening of the gene banks that were produced by combinatorial mutagenesis of homologues according to the invention. The techniques most frequently used for the screening of large gene banks, which are based on a high-throughput analysis, comprise cloning of the gene bank in expression vectors that can be replicated, transformation of the suitable cells with the resultant vector database and expression of the combinatorial genes in conditions in which detection of the desired activity facilitates isolation of the vector that codes for the gene whose product was detected. Recursive Ensemble Mutagenesis (REM), a technique that increases the frequency of functional mutants in the databases, can be used in combination with the screening tests, in order to identify homologues.
An embodiment provided herein provides orthologs and paralogs of polypeptides disclosed herein as well as methods for identifying and isolating such orthologs and paralogs. A definition of the terms “ortholog” and “paralog” is given below and applies to amino acid and nucleic acid sequences.
The polypeptides of the invention include all active forms, including active subsequences, e.g., catalytic domains or active sites, of an enzyme of the invention. In one aspect, the invention provides catalytic domains or active sites as set forth below. In one aspect, the invention provides a peptide or polypeptide comprising or consisting of an active site domain as predicted through use of a database such as Pfam (http://pfam.wustl.edu/hmmsearch.shtml) (which is a large collection of multiple sequence alignments and hidden Markov models covering many common protein families, The Pfam protein families database, A. Bateman, E. Birney, L. Cerruti, R. Durbin, L. Etwiller, S. R. Eddy, S. Griffiths-Jones, K. L. Howe, M. Marshall, and E. L. L. Sonnhammer, Nucleic Acids Research, 30(1):276-280, 2002) or equivalent, as for example InterPro and SMART databases (http://www.ebi.ac.uk/interpro/scan.html, http://smart.embl-heidelberg.de/).
The invention also encompasses “polypeptide variant” having the desired activity, wherein the variant polypeptide is selected from an amino acid sequence having at least 40%, 45%, 50%. 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99%, sequence identity to a specific, in particular natural, amino acid sequence as referred to by a specific SEQ ID NO and contains at least one substitution modification relative said SEQ ID NO.
In this context the following definitions apply:
The terms “nucleic acid sequence,” “nucleic acid,” “nucleic acid molecule” and “polynucleotide” are used interchangeably meaning a sequence of nucleotides. A nucleic acid sequence may be a single-stranded or double-stranded deoxyribonucleotide, or ribonucleotide of any length, and include coding and non-coding sequences of a gene, exons, introns, sense and anti-sense complimentary sequences, genomic DNA, cDNA, miRNA, siRNA, mRNA, rRNA, tRNA, recombinant nucleic acid sequences, isolated and purified naturally occurring DNA and/or RNA sequences, synthetic DNA and RNA sequences, fragments, primers and nucleic acid probes. The skilled artisan is aware that the nucleic acid sequences of RNA are identical to the DNA sequences with the difference of thymine (T) being replaced by uracil (U). The term “nucleotide sequence” should also be understood as comprising a polynucleotide molecule or an oligonucleotide molecule in the form of a separate fragment or as a component of a larger nucleic acid.
An “isolated nucleic acid” or “isolated nucleic acid sequence” relates to a nucleic acid or nucleic acid sequence that is in an environment different from that in which the nucleic acid or nucleic acid sequence naturally occurs and can include those that are substantially free from contaminating endogenous material.
The term “naturally-occurring” as used herein as applied to a nucleic acid refers to a nucleic acid that is found in a cell of an organism in nature and which has not been intentionally modified by a human in the laboratory.
A “fragment” of a polynucleotide or nucleic acid sequence refers to contiguous nucleotides that is particularly at least 15 bp, at least 30 bp, at least 40 bp, at least 50 bp and/or at least 60 bp in length of the polynucleotide of an embodiment herein. Particularly the fragment of a polynucleotide comprises at least 25, more particularly at least 50, more particularly at least 75, more particularly at least 100, more particularly at least 150, more particularly at least 200, more particularly at least 300, more particularly at least 400, more particularly at least 500, more particularly at least 600, more particularly at least 700, more particularly at least 800, more particularly at least 900, more particularly at least 1000 contiguous nucleotides of the polynucleotide of an embodiment herein. Without being limited, the fragment of the polynucleotides herein may be used as a PCR primer, and/or as a probe, or for anti-sense gene silencing or RNAi.
As used herein, the term “hybridization” or hybridizes under certain conditions is intended to describe conditions for hybridization and washes under which nucleotide sequences that are significantly identical or homologous to each other remain bound to each other. The conditions may be such that sequences, which are at least about 70%, such as at least about 80%, and such as at least about 85%, 90%, or 95% identical, remain bound to each other. Definitions of low stringency, moderate, and high stringency hybridization conditions are provided herein below. Appropriate hybridization conditions can also be selected by those skilled in the art with minimal experimentation as exemplified in Ausubel et al. (1995, Current Protocols in Molecular Biology, John Wiley & Sons, sections 2, 4, and 6). Additionally, stringency conditions are described in Sambrook et al. (1989, Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring Harbor Press, chapters 7, 9, and 11).
“Recombinant nucleic acid sequences” are nucleic acid sequences that result from the use of laboratory methods (for example, molecular cloning) to bring together genetic material from more than on source, creating or modifying a nucleic acid sequence that does not occur naturally and would not be otherwise found in biological organisms.
“Recombinant DNA technology” refers to molecular biology procedures to prepare a recombinant nucleic acid sequence as described, for instance, in Laboratory Manuals edited by Weigel and Glazebrook, 2002, Cold Spring Harbor Lab Press; and Sambrook et al., 1989, Cold Spring Harbor, N.Y., Cold Spring Harbor Laboratory Press.
The term “gene” means a DNA sequence comprising a region, which is transcribed into a RNA molecule, e.g., an mRNA in a cell, operably linked to suitable regulatory regions, e.g., a promoter. A gene may thus comprise several operably linked sequences, such as a promoter, a 5′ leader sequence comprising, e.g., sequences involved in translation initiation, a coding region of cDNA or genomic DNA, introns, exons, and/or a 3′non-translated sequence comprising, e.g., transcription termination sites.
“Polycistronic” refers to nucleic acid molecules, in particular mRNAs, that can encode more than one polypeptide separately within the same nucleic acid molecule
A “chimeric gene” refers to any gene which is not normally found in nature in a species, in particular, a gene in which one or more parts of the nucleic acid sequence are present that are not associated with each other in nature. For example the promoter is not associated in nature with part or all of the transcribed region or with another regulatory region. The term “chimeric gene” is understood to include expression constructs in which a promoter or transcription regulatory sequence is operably linked to one or more coding sequences or to an antisense, i.e., reverse complement of the sense strand, or inverted repeat sequence (sense and antisense, whereby the RNA transcript forms double stranded RNA upon transcription). The term “chimeric gene” also includes genes obtained through the combination of portions of one or more coding sequences to produce a new gene.
A “3′ UTR” or “3′ non-translated sequence” (also referred to as “3′ untranslated region,” or “3′end”) refers to the nucleic acid sequence found downstream of the coding sequence of a gene, which comprises, for example, a transcription termination site and (in most, but not all eukaryotic mRNAs) a polyadenylation signal such as AAUAAA or variants thereof. After termination of transcription, the mRNA transcript may be cleaved downstream of the polyadenylation signal and a poly(A) tail may be added, which is involved in the transport of the mRNA to the site of translation, e.g., cytoplasm.
The term “primer” refers to a short nucleic acid sequence that is hybridized to a template nucleic acid sequence and is used for polymerization of a nucleic acid sequence complementary to the template.
The term “selectable marker” refers to any gene which upon expression may be used to select a cell or cells that include the selectable marker. Examples of selectable markers are described below. The skilled artisan will know that different antibiotic, fungicide, auxotrophic or herbicide selectable markers are applicable to different target species.
The invention also relates to nucleic acid sequences that code for polypeptides as defined herein.
In particular, the invention also relates to nucleic acid sequences (single-stranded and double-stranded DNA and RNA sequences, e.g. cDNA, genomic DNA and mRNA), coding for one of the above polypeptides and their functional equivalents, which can be obtained for example using artificial nucleotide analogs.
The invention relates both to isolated nucleic acid molecules, which code for polypeptides according to the invention or biologically active segments thereof, and to nucleic acid fragments, which can be used for example as hybridization probes or primers for identifying or amplifying coding nucleic acids according to the invention.
The present invention also relates to nucleic acids with a certain degree of “identity” to the sequences specifically disclosed herein. “Identity” between two nucleic acids means identity of the nucleotides, in each case over the entire length of the nucleic acid.
The “identity” between two nucleotide sequences (the same applies to peptide or amino acid sequences) is a function of the number of nucleotide residues (or amino acid residues) or that are identical in the two sequences when an alignment of these two sequences has been generated. Identical residues are defined as residues that are the same in the two sequences in a given position of the alignment. The percentage of sequence identity, as used herein, is calculated from the optimal alignment by taking the number of residues identical between two sequences dividing it by the total number of residues in the shortest sequence and multiplying by 100. The optimal alignment is the alignment in which the percentage of identity is the highest possible. Gaps may be introduced into one or both sequences in one or more positions of the alignment to obtain the optimal alignment. These gaps are then taken into account as non-identical residues for the calculation of the percentage of sequence identity. Alignment for the purpose of determining the percentage of amino acid or nucleic acid sequence identity can be achieved in various ways using computer programs and for instance publicly available computer programs available on the world wide web.
Particularly, the BLAST program (Tatiana et al, FEMS Microbiol Lett., 1999, 174:247-250, 1999) set to the default parameters, available from the National Center for Biotechnology Information (NCBI) website at ncbi.nlm.nih.gov/BLAST/bl2seq/wblast2.cgi, can be used to obtain an optimal alignment of protein or nucleic acid sequences and to calculate the percentage of sequence identity.
In another example the identity may be calculated by means of the Vector NTI Suite 7.1 program of the company Informax (USA) employing the Clustal Method (Higgins D G, Sharp P M. ((1989))) with the following settings:
Multiple alignment parameters:
Alternatively the identity may be determined according to Chenna, et al. (2003), the web page: http://www.ebi.ac.uk/Tools/clustalw/index.html# and the following settings
All the nucleic acid sequences mentioned herein (single-stranded and double-stranded DNA and RNA sequences, for example cDNA and mRNA) can be produced in a known way by chemical synthesis from the nucleotide building blocks, e.g. by fragment condensation of individual overlapping, complementary nucleic acid building blocks of the double helix. Chemical synthesis of oligonucleotides can, for example, be performed in a known way, by the phosphoamidite method (Voet, Voet, 2nd edition, Wiley Press, New York, pages 896-897). The accumulation of synthetic oligonucleotides and filling of gaps by means of the Klenow fragment of DNA polymerase and ligation reactions as well as general cloning techniques are described in Sambrook et al. (1989), see below.
The nucleic acid molecules according to the invention can in addition contain non-translated sequences from the 3′ and/or 5′ end of the coding genetic region.
The invention further relates to the nucleic acid molecules that are complementary to the concretely described nucleotide sequences or a segment thereof.
The nucleotide sequences according to the invention make possible the production of probes and primers that can be used for the identification and/or cloning of homologous sequences in other cellular types and organisms. Such probes or primers generally comprise a nucleotide sequence region which hybridizes under “stringent” conditions (as defined herein elsewhere) on at least about 12, preferably at least about 25, for example about 40, 50 or 75 successive nucleotides of a sense strand of a nucleic acid sequence according to the invention or of a corresponding antisense strand.
“Homologous” sequences include orthologous or paralogous sequences. Methods of identifying orthologs or paralogs including phylogenetic methods, sequence similarity and hybridization methods are known in the art and are described herein.
“Paralogs” result from gene duplication that gives rise to two or more genes with similar sequences and similar functions. Paralogs typically cluster together and are formed by duplications of genes within related plant species. Paralogs are found in groups of similar genes using pair-wise Blast analysis or during phylogenetic analysis of gene families using programs such as CLUSTAL. In paralogs, consensus sequences can be identified characteristic to sequences within related genes and having similar functions of the genes.
“Orthologs”, or orthologous sequences, are sequences similar to each other because they are found in species that descended from a common ancestor. For instance, plant species that have common ancestors are known to contain many enzymes that have similar sequences and functions. The skilled artisan can identify orthologous sequences and predict the functions of the orthologs, for example, by constructing a polygenic tree for a gene family of one species using CLUSTAL or BLAST programs. A method for identifying or confirming similar functions among homologous sequences is by comparing of the transcript profiles in host cells or organisms, such as plants or microorganisms, overexpressing or lacking (in knockouts/knockdowns) related polypeptides. The skilled person will understand that genes having similar transcript profiles, with greater than 50% regulated transcripts in common, or with greater than 70% regulated transcripts in common, or greater than 90% regulated transcripts in common will have similar functions. Homologs, paralogs, orthologs and any other variants of the sequences herein are expected to function in a similar manner by making the host cells, organism such as plants or microorganisms producing terpene synthase proteins.
The term “selectable marker” refers to any gene which upon expression may be used to select a cell or cells that include the selectable marker. Examples of selectable markers are described below. The skilled artisan will know that different antibiotic, fungicide, auxotrophic or herbicide selectable markers are applicable to different target species.
A nucleic acid molecule according to the invention can be recovered by means of standard techniques of molecular biology and the sequence information supplied according to the invention. For example, cDNA can be isolated from a suitable cDNA library, using one of the concretely disclosed complete sequences or a segment thereof as hybridization probe and standard hybridization techniques (as described for example in Sambrook, (1989)).
In addition, a nucleic acid molecule comprising one of the disclosed sequences or a segment thereof, can be isolated by the polymerase chain reaction, using the oligonucleotide primers that were constructed on the basis of this sequence. The nucleic acid amplified in this way can be cloned in a suitable vector and can be characterized by DNA sequencing. The oligonucleotides according to the invention can also be produced by standard methods of synthesis, e.g. using an automatic DNA synthesizer.
Nucleic acid sequences according to the invention or derivatives thereof, homologues or parts of these sequences, can for example be isolated by usual hybridization techniques or the PCR technique from other bacteria, e.g. via genomic or cDNA libraries. These DNA sequences hybridize in standard conditions with the sequences according to the invention.
“Hybridize” means the ability of a polynucleotide or oligonucleotide to bind to an almost complementary sequence in standard conditions, whereas nonspecific binding does not occur between non-complementary partners in these conditions. For this, the sequences can be 90-100% complementary. The property of complementary sequences of being able to bind specifically to one another is utilized for example in Northern Blotting or Southern Blotting or in primer binding in PCR or RT-PCR.
Short oligonucleotides of the conserved regions are used advantageously for hybridization. However, it is also possible to use longer fragments of the nucleic acids according to the invention or the complete sequences for the hybridization. These “standard conditions” vary depending on the nucleic acid used (oligonucleotide, longer fragment or complete sequence) or depending on which type of nucleic acid—DNA or RNA—is used for hybridization. For example, the melting temperatures for DNA:DNA hybrids are approx. 10° C. lower than those of DNA:RNA hybrids of the same length.
For example, depending on the particular nucleic acid, standard conditions mean temperatures between 42 and 58° C. in an aqueous buffer solution with a concentration between 0.1 to 5×SSC (1×SSC=0.15 M NaCl, 15 mM sodium citrate, pH 7.2) or additionally in the presence of 50% formamide, for example 42° C. in 5×SSC, 50% formamide. Advantageously, the hybridization conditions for DNA:DNA hybrids are 0.1×SSC and temperatures between about 20° C. to 45° C., preferably between about 30° C. to 45° C. For DNA:RNA hybrids the hybridization conditions are advantageously 0.1×SSC and temperatures between about 30° C. to 55° C., preferably between about 45° C. to 55° C. These stated temperatures for hybridization are examples of calculated melting temperature values for a nucleic acid with a length of approx. 100 nucleotides and a G+C content of 50% in the absence of formamide. The experimental conditions for DNA hybridization are described in relevant genetics textbooks, for example Sambrook et al., 1989, and can be calculated using formulae that are known by a person skilled in the art, for example depending on the length of the nucleic acids, the type of hybrids or the G+C content. A person skilled in the art can obtain further information on hybridization from the following textbooks: Ausubel et al. (eds), (1985), Brown (ed) (1991).
“Hybridization” can in particular be carried out under stringent conditions. Such hybridization conditions are for example described in Sambrook (1989), or in Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6.
As used herein, the term hybridization or hybridizes under certain conditions is intended to describe conditions for hybridization and washes under which nucleotide sequences that are significantly identical or homologous to each other remain bound to each other. The conditions may be such that sequences, which are at least about 70%, such as at least about 80%, and such as at least about 85%, 90%, or 95% identical, remain bound to each other. Definitions of low stringency, moderate, and high stringency hybridization conditions are provided herein.
Appropriate hybridization conditions can be selected by those skilled in the art with minimal experimentation as exemplified in Ausubel et al. (1995, Current Protocols in Molecular Biology, John Wiley & Sons, sections 2, 4, and 6). Additionally, stringency conditions are described in Sambrook et al. (1989, Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring Harbor Press, chapters 7, 9, and 11).
As used herein, defined conditions of low stringency are as follows. Filters containing DNA are pretreated for 6 h at 40° C. in a solution containing 35% formamide, 5×SSC, 50 mM Tris-HCl (pH 7.5), 5 mM EDTA, 0.1% PVP, 0.1% Ficoll, 1% BSA, and 500 μg/ml denatured salmon sperm DNA. Hybridizations are carried out in the same solution with the following modifications: 0.02% PVP, 0.02% Ficoll, 0.2% BSA, 100 μg/ml salmon sperm DNA, 10% (wt/vol) dextran sulfate, and 5-20×106 32P-labeled probe is used. Filters are incubated in hybridization mixture for 18-20 h at 40° C., and then washed for 1.5 h at 55° C. In a solution containing 2×SSC, 25 mM Tris-HCl (pH 7.4), 5 mM EDTA, and 0.1% SDS. The wash solution is replaced with fresh solution and incubated an additional 1.5 h at 60° C. Filters are blotted dry and exposed for autoradiography.
As used herein, defined conditions of moderate stringency are as follows. Filters containing DNA are pretreated for 7 h at 50° C. in a solution containing 35% formamide, 5×SSC, 50 mM Tris-HCl (pH 7.5), 5 mM EDTA, 0.1% PVP, 0.1% Ficoll, 1% BSA, and 500 μg/ml denatured salmon sperm DNA. Hybridizations are carried out in the same solution with the following modifications: 0.02% PVP, 0.02% Ficoll, 0.2% BSA, 100 μg/ml salmon sperm DNA, 10% (wt/vol) dextran sulfate, and 5-20×106 32P-labeled probe is used. Filters are incubated in hybridization mixture for 30 h at 50° C., and then washed for 1.5 h at 55° C. In a solution containing 2×SSC, 25 mM Tris-HCl (pH 7.4), 5 mM EDTA, and 0.1% SDS. The wash solution is replaced with fresh solution and incubated an additional 1.5 h at 60° C. Filters are blotted dry and exposed for autoradiography.
As used herein, defined conditions of high stringency are as follows. Prehybridization of filters containing DNA is carried out for 8 h to overnight at 65° C. in buffer composed of 6×SSC, 50 mM Tris-HCl (pH 7.5), 1 mM EDTA, 0.02% PVP, 0.02% Ficoll, 0.02% BSA, and 500 μg/ml denatured salmon sperm DNA. Filters are hybridized for 48 h at 65° C. in the prehybridization mixture containing 100 μg/ml denatured salmon sperm DNA and 5-20×106 cpm of 32P-labeled probe. Washing of filters is done at 37° C. for 1 h in a solution containing 2×SSC, 0.01% PVP, 0.01% Ficoll, and 0.01% BSA. This is followed by a wash in 0.1×SSC at 50° C. for 45 minutes.
Other conditions of low, moderate, and high stringency well known in the art (e.g., as employed for cross-species hybridizations) may be used if the above conditions are inappropriate (e.g., as employed for cross-species hybridizations).
A detection kit for nucleic acid sequences encoding a polypeptide of the invention may include primers and/or probes specific for nucleic acid sequences encoding the polypeptide, and an associated protocol to use the primers and/or probes to detect nucleic acid sequences encoding the polypeptide in a sample. Such detection kits may be used to determine whether a plant, organism, microorganism or cell has been modified, i.e., transformed with a sequence encoding the polypeptide.
To test a function of variant DNA sequences according to an embodiment herein, the sequence of interest is operably linked to a selectable or screenable marker gene and expression of said reporter gene is tested in transient expression assays, for example, with microorganisms or with protoplasts or in stably transformed plants.
The invention also relates to derivatives of the concretely disclosed or derivable nucleic acid sequences.
Thus, further nucleic acid sequences according to the invention can be derived from the sequences specifically disclosed herein and can differ from it by one or more, like 1 to 20, in particular 1 to 15 or 5 to 10 additions, substitutions, insertions or deletions of one or several (like for example 1 to 10) nucleotides, and furthermore code for polypeptides with the desired profile of properties.
The invention also encompasses nucleic acid sequences that comprise so-called silent mutations or have been altered, in comparison with a concretely stated sequence, according to the codon usage of a special original or host organism.
According to a particular embodiment of the invention variant nucleic acids may be prepared in order to adapt its nucleotide sequence to a specific expression system. For example, bacterial expression systems are known to more efficiently express polypeptides if amino acids are encoded by particular codons. Due to the degeneracy of the genetic code, more than one codon may encode the same amino acid sequence, multiple nucleic acid sequences can code for the same protein or polypeptide, all these DNA sequences being encompassed by an embodiment herein. Where appropriate, the nucleic acid sequences encoding the polypeptides described herein may be optimized for increased expression in the host cell. For example, nucleic acids of an embodiment herein may be synthesized using codons particular to a host for improved expression.
The invention also encompasses naturally occurring variants, e.g. splicing variants or allelic variants, of the sequences described therein.
Allelic variants may have at least 60% homology at the level of the derived amino acid, preferably at least 80% homology, quite especially preferably at least 90% homology over the entire sequence range (regarding homology at the amino acid level, reference should be made to the details given above for the polypeptides). Advantageously, the homologies can be higher over partial regions of the sequences.
The invention also relates to sequences that can be obtained by conservative nucleotide substitutions (i.e. as a result thereof the amino acid in question is replaced by an amino acid of the same charge, size, polarity and/or solubility).
The invention also relates to the molecules derived from the concretely disclosed nucleic acids by sequence polymorphisms. Such genetic polymorphisms may exist in cells from different populations or within a population due to natural allelic variation. Allelic variants may also include functional equivalents. These natural variations usually produce a variance of 1 to 5% in the nucleotide sequence of a gene. Said polymorphisms may lead to changes in the amino acid sequence of the polypeptides disclosed herein. Allelic variants may also include functional equivalents.
Furthermore, derivatives are also to be understood to be homologs of the nucleic acid sequences according to the invention, for example animal, plant, fungal or bacterial homologs, shortened sequences, single-stranded DNA or RNA of the coding and noncoding DNA sequence. For example, homologs have, at the DNA level, a homology of at least 40%, preferably of at least 60%, especially preferably of at least 70%, quite especially preferably of at least 80% over the entire DNA region given in a sequence specifically disclosed herein.
Moreover, derivatives are to be understood to be, for example, fusions with promoters. The promoters that are added to the stated nucleotide sequences can be modified by at least one nucleotide exchange, at least one insertion, inversion and/or deletion, though without impairing the functionality or efficacy of the promoters. Moreover, the efficacy of the promoters can be increased by altering their sequence or can be exchanged completely with more effective promoters even of organisms of a different genus.
Moreover, a person skilled in the art is familiar with methods for generating functional mutants, that is to say nucleotide sequences which code for a polypeptide with at least 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity to anyone of amino acid related SEQ ID NOs as disclosed herein and/or encoded by a nucleic acid molecule comprising a nucleotide sequence having at least 70% sequence identity to anyone of the nucleotide related SEQ ID NOs as disclosed herein.
Depending on the technique used, a person skilled in the art can introduce entirely random or else more directed mutations into genes or else noncoding nucleic acid regions (which are for example important for regulating expression) and subsequently generate genetic libraries. The methods of molecular biology required for this purpose are known to the skilled worker and for example described in Sambrook and Russell, Molecular Cloning. 3rd Edition, Cold Spring Harbor Laboratory Press 2001.
Methods for modifying genes and thus for modifying the polypeptide encoded by them have been known to the skilled worker for a long time, such as, for example
Using so-called directed evolution (described, inter alia, in Reetz M T and Jaeger K-E (1999), Topics Curr Chem 200:31; Zhao H, Moore J C, Volkov A A, Arnold F H (1999), Methods for optimizing industrial polypeptides by directed evolution, In: Demain A L, Davies J E (Ed.) Manual of industrial microbiology and biotechnology. American Society for Microbiology), a skilled worker can produce functional mutants in a directed manner and on a large scale. To this end, in a first step, gene libraries of the respective polypeptides are first produced, for example using the methods given above. The gene libraries are expressed in a suitable way, for example by bacteria or by phage display systems.
The relevant genes of host organisms which express functional mutants with properties that largely correspond to the desired properties can be submitted to another mutation cycle. The steps of the mutation and selection or screening can be repeated iteratively until the present functional mutants have the desired properties to a sufficient extent. Using this iterative procedure, a limited number of mutations, for example 1, 2, 3, 4 or 5 mutations, can be performed in stages and assessed and selected for their influence on the activity in question. The selected mutant can then be submitted to a further mutation step in the same way. In this way, the number of individual mutants to be investigated can be reduced significantly.
The results according to the invention also provide important information relating to structure and sequence of the relevant polypeptides, which is required for generating, in a targeted fashion, further polypeptides with desired modified properties. In particular, it is possible to define so-called “hot spots”, i.e. sequence segments that are potentially suitable for modifying a property by introducing targeted mutations.
Information can also be deduced regarding amino acid sequence positions, in the region of which mutations can be effected that should probably have little effect on the activity, and can be designated as potential “silent mutations”.
In this context the following definitions apply:
“Expression of a gene” encompasses “heterologous expression” and “over-expression” and involves transcription of the gene and translation of the mRNA into a protein. Overexpression refers to the production of the gene product as measured by levels of mRNA, polypeptide and/or enzyme activity in transgenic cells or organisms that exceeds levels of production in non-transformed cells or organisms of a similar genetic background.
“Expression vector” as used herein means a nucleic acid molecule engineered using molecular biology methods and recombinant DNA technology for delivery of foreign or exogenous DNA into a host cell. The expression vector typically includes sequences required for proper transcription of the nucleotide sequence. The coding region usually codes for a protein of interest but may also code for an RNA, e.g., an antisense RNA, siRNA and the like.
An “expression vector” as used herein includes any linear or circular recombinant vector including but not limited to viral vectors, bacteriophages and plasmids. The skilled person is capable of selecting a suitable vector according to the expression system. In one embodiment, the expression vector includes the nucleic acid of an embodiment herein operably linked to at least one “regulatory sequence”, which controls transcription, translation, initiation and termination, such as a transcriptional promoter, operator or enhancer, or an mRNA ribosomal binding site and, optionally, including at least one selection marker. Nucleotide sequences are “operably linked” when the regulatory sequence functionally relates to the nucleic acid of an embodiment herein.
An “expression system” as used herein encompasses any combination of nucleic acid molecules required for the expression of one, or the co-expression of two or more polypeptides either in vivo of a given expression host, or in vitro. The respective coding sequences may either be located on a single nucleic acid molecule or vector, as for example a vector containing multiple cloning sites, or on a polycistronic nucleic acid, or may be distributed over two or more physically distinct vectors. As a particular example there may be mentioned an operon comprising a promotor sequence, one or more operator sequences and one or more structural genes each encoding an enzyme as described herein
As used herein, the terms “amplifying” and “amplification” refer to the use of any suitable amplification methodology for generating or detecting recombinant of naturally expressed nucleic acid, as described in detail, below. For example, the invention provides methods and reagents (e.g., specific degenerate oligonucleotide primer pairs, oligo dT primer) for amplifying (e.g., by polymerase chain reaction, PCR) naturally expressed (e.g., genomic DNA or mRNA) or recombinant (e.g., cDNA) nucleic acids of the invention in vivo, ex vivo or in vitro.
“Regulatory sequence” refers to a nucleic acid sequence that determines expression level of the nucleic acid sequences of an embodiment herein and is capable of regulating the rate of transcription of the nucleic acid sequence operably linked to the regulatory sequence. Regulatory sequences comprise promoters, enhancers, transcription factors, promoter elements and the like.
A “promoter”, a “nucleic acid with promoter activity” or a “promoter sequence” is understood as meaning, in accordance with the invention, a nucleic acid which, when functionally linked to a nucleic acid to be transcribed, regulates the transcription of said nucleic acid. “Promoter” in particular refers to a nucleic acid sequence that controls the expression of a coding sequence by providing a binding site for RNA polymerase and other factors required for proper transcription including without limitation transcription factor binding sites, repressor and activator protein binding sites. The meaning of the term promoter also includes the term “promoter regulatory sequence”. Promoter regulatory sequences may include upstream and downstream elements that may influences transcription, RNA processing or stability of the associated coding nucleic acid sequence. Promoters include naturally-derived and synthetic sequences. The coding nucleic acid sequences is usually located downstream of the promoter with respect to the direction of the transcription starting at the transcription initiation site.
In this context, a “functional” or “operative” linkage is understood as meaning for example the sequential arrangement of one of the nucleic acids with a regulatory sequence. For example the sequence with promoter activity and of a nucleic acid sequence to be transcribed and optionally further regulatory elements, for example nucleic acid sequences which ensure the transcription of nucleic acids, and for example a terminator, are linked in such a way that each of the regulatory elements can perform its function upon transcription of the nucleic acid sequence. This does not necessarily require a direct linkage in the chemical sense. Genetic control sequences, for example enhancer sequences, can even exert their function on the target sequence from more remote positions or even from other DNA molecules. Preferred arrangements are those in which the nucleic acid sequence to be transcribed is positioned behind (i.e. at the 3′-end of) the promoter sequence so that the two sequences are joined together covalently. The distance between the promoter sequence and the nucleic acid sequence to be expressed recombinantly can be smaller than 200 base pairs, or smaller than 100 base pairs or smaller than 50 base pairs.
In addition to promoters and terminator, the following may be mentioned as examples of other regulatory elements: targeting sequences, enhancers, polyadenylation signals, selectable markers, amplification signals, replication origins and the like. Suitable regulatory sequences are described, for example, in Goeddel, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. (1990).
The term “constitutive promoter” refers to an unregulated promoter that allows for continual transcription of the nucleic acid sequence it is operably linked to.
As used herein, the term “operably linked” refers to a linkage of polynucleotide elements in a functional relationship. A nucleic acid is “operably linked” when it is placed into a functional relationship with another nucleic acid sequence. For instance, a promoter, or rather a transcription regulatory sequence, is operably linked to a coding sequence if it affects the transcription of the coding sequence. Operably linked means that the DNA sequences being linked are typically contiguous. The nucleotide sequence associated with the promoter sequence may be of homologous or heterologous origin with respect to the plant to be transformed. The sequence also may be entirely or partially synthetic. Regardless of the origin, the nucleic acid sequence associated with the promoter sequence will be expressed or silenced in accordance with promoter properties to which it is linked after binding to the polypeptide of an embodiment herein. The associated nucleic acid may code for a protein that is desired to be expressed or suppressed throughout the organism at all times or, alternatively, at a specific time or in specific tissues, cells, or cell compartment. Such nucleotide sequences particularly encode proteins conferring desirable phenotypic traits to the host cells or organism altered or transformed therewith. More particularly, the associated nucleotide sequence leads to the production of the product or products of interest as herein defined in the cell or organism. Particularly, the nucleotide sequence encodes a polypeptide having an enzyme activity as herein defined.
The nucleotide sequence as described herein above may be part of an “expression cassette”. The terms “expression cassette” and “expression construct” are used synonymously. The (preferably recombinant) expression construct contains a nucleotide sequence which encodes a polypeptide according to the invention and which is under genetic control of regulatory nucleic acid sequences.
In a process applied according to the invention, the expression cassette may be part of an “expression vector”, in particular of a recombinant expression vector.
An “expression unit” is understood as meaning, in accordance with the invention, a nucleic acid with expression activity which comprises a promoter as defined herein and, after functional linkage with a nucleic acid to be expressed or a gene, regulates the expression, i.e. the transcription and the translation of said nucleic acid or said gene. It is therefore in this connection also referred to as a “regulatory nucleic acid sequence”. In addition to the promoter, other regulatory elements, for example enhancers, can also be present.
An “expression cassette” or “expression construct” is understood as meaning, in accordance with the invention, an expression unit which is functionally linked to the nucleic acid to be expressed or the gene to be expressed. In contrast to an expression unit, an expression cassette therefore comprises not only nucleic acid sequences which regulate transcription and translation, but also the nucleic acid sequences that are to be expressed as protein as a result of transcription and translation.
The terms “expression” or “overexpression” describe, in the context of the invention, the production or increase in intracellular activity of one or more polypeptides in a microorganism, which are encoded by the corresponding DNA. To this end, it is possible for example to introduce a gene into an organism, replace an existing gene with another gene, increase the copy number of the gene(s), use a strong promoter or use a gene which encodes for a corresponding polypeptide with a high activity; optionally, these measures can be combined.
Preferably such constructs according to the invention comprise a promoter 5′-upstream of the respective coding sequence and a terminator sequence 3′-downstream and optionally other usual regulatory elements, in each case in operative linkage with the coding sequence.
Nucleic acid constructs according to the invention comprise in particular a sequence coding for a polypeptide for example derived from the amino acid related SEQ ID NOs as described therein or the reverse complement thereof, or derivatives and homologs thereof and which have been linked operatively or functionally with one or more regulatory signals, advantageously for controlling, for example increasing, gene expression.
In addition to these regulatory sequences, the natural regulation of these sequences may still be present before the actual structural genes and optionally may have been genetically modified so that the natural regulation has been switched off and expression of the genes has been enhanced. The nucleic acid construct may, however, also be of simpler construction, i.e. no additional regulatory signals have been inserted before the coding sequence and the natural promoter, with its regulation, has not been removed. Instead, the natural regulatory sequence is mutated such that regulation no longer takes place and the gene expression is increased.
A preferred nucleic acid construct advantageously also comprises one or more of the already mentioned “enhancer” sequences in functional linkage with the promoter, which sequences make possible an enhanced expression of the nucleic acid sequence. Additional advantageous sequences may also be inserted at the 3′-end of the DNA sequences, such as further regulatory elements or terminators. One or more copies of the nucleic acids according to the invention may be present in a construct. In the construct, other markers, such as genes which complement auxotrophisms or antibiotic resistances, may also optionally be present so as to select for the construct.
Examples of suitable regulatory sequences are present in promoters such as cos, tac, trp, tet, trp-tet, lpp, lac, lpp-lac, lacIq, T7, T5, T3, gal, trc, ara, rhaP (rhaPBAD)SP6, lambda-PR or in the lambda-PL promoter, and these are advantageously employed in Gram-negative bacteria. Further advantageous regulatory sequences are present for example in the Gram-positive promoters amy and SPO2, in the yeast or fungal promoters ADC1, MFalpha, AC, P-60, CYC1, GAPDH, TEF, rp28, ADH. Artificial promoters may also be used for regulation.
For expression in a host organism, the nucleic acid construct is inserted advantageously into a vector such as, for example, a plasmid or a phage, which makes possible optimal expression of the genes in the host. Vectors are also understood as meaning, in addition to plasmids and phages, all the other vectors which are known to the skilled worker, that is to say for example viruses such as SV40, CMV, baculovirus and adenovirus, transposons, IS elements, phasmids, cosmids and linear or circular DNA or artificial chromosomes. These vectors are capable of replicating autonomously in the host organism or else chromosomally. These vectors are a further development of the invention. Binary or cpo-integration vectors are also applicable.
Suitable plasmids are, for example, in E. coli pLG338, pACYC184, pBR322, pUC18, pUC19, pKC30, pRep4, pHS1, pKK223-3, pDHE19.2, pHS2, pPLc236, pMBL24, pLG200, pUR290, pIN-III113-B1, λgt11 or pBdCI, in Streptomyces pIJ101, pIJ364, pIJ702 or pIJ361, in Bacillus pUB110, pC194 or pBD214, in Corynebacterium pSA77 or pAJ667, in fungi pALS1, pIL2 or pBB116, in yeasts 2alphaM, pAG-1, YEp6, YEp13 or pEMBLYe23 or in plants pLGV23, pGHlac+, pBIN19, pAK2004 or pDH51. The abovementioned plasmids are a small selection of the plasmids which are possible. Further plasmids are well known to the skilled worker and can be found for example in the book Cloning Vectors (Eds. Pouwels P. H. et al. Elsevier, Amsterdam-New York-Oxford, 1985, ISBN 0 444 904018).
In a further development of the vector, the vector which comprises the nucleic acid construct according to the invention or the nucleic acid according to the invention can advantageously also be introduced into the microorganisms in the form of a linear DNA and integrated into the host organism's genome via heterologous or homologous recombination. This linear DNA can consist of a linearized vector such as a plasmid or only of the nucleic acid construct or the nucleic acid according to the invention.
For optimal expression of heterologous genes in organisms, it is advantageous to modify the nucleic acid sequences to match the specific “codon usage” used in the organism. The “codon usage” can be determined readily by computer evaluations of other, known genes of the organism in question.
An expression cassette according to the invention is generated by fusing a suitable promoter to a suitable coding nucleotide sequence and a terminator or polyadenylation signal. Customary recombination and cloning techniques are used for this purpose, as are described, for example, in T. Maniatis, E. F. Fritsch and J. Sambrook, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1989) and in T. J. Silhavy, M. L. Berman and L. W. Enquist, Experiments with Gene Fusions, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1984) and in Ausubel, F. M. et al., Current Protocols in Molecular Biology, Greene Publishing Assoc. and Wiley Interscience (1987).
For expression in a suitable host organism, the recombinant nucleic acid construct or gene construct is advantageously inserted into a host-specific vector which makes possible optimal expression of the genes in the host. Vectors are well known to the skilled worker and can be found for example in “cloning vectors” (Pouwels P. H. et al., Ed., Elsevier, Amsterdam-New York-Oxford, 1985).
An alternative embodiment of an embodiment herein provides a method to “alter gene expression” in a host cell. For instance, the polynucleotide of an embodiment herein may be enhanced or overexpressed or induced in certain contexts (e.g. upon exposure to certain temperatures or culture conditions) in a host cell or host organism.
Alteration of expression of a polynucleotide provided herein may also result in ectopic expression which is a different expression pattern in an altered and in a control or wild-type organism. Alteration of expression occurs from interactions of polypeptide of an embodiment herein with exogenous or endogenous modulators, or as a result of chemical modification of the polypeptide. The term also refers to an altered expression pattern of the polynucleotide of an embodiment herein which is altered below the detection level or completely suppressed activity.
In one embodiment, provided herein is also an isolated, recombinant or synthetic polynucleotide encoding a polypeptide or variant polypeptide provided herein.
In one embodiment, several polypeptide encoding nucleic acid sequences are co-expressed in a single host, particularly under control of different promoters. In another embodiment, several polypeptide encoding nucleic acid sequences can be present on a single transformation vector or be co-transformed at the same time using separate vectors and selecting transformants comprising both chimeric genes. Similarly, one or polypeptide encoding genes may be expressed in a single plant, cell, microorganism or organism together with other chimeric genes.
Depending on the context, the term “host” can mean the wild-type host or a genetically altered, recombinant host or both.
In principle, all prokaryotic or eukaryotic organisms may be considered as host or recombinant host organisms for the nucleic acids or the nucleic acid constructs according to the invention.
Using the vectors according to the invention, recombinant hosts can be produced, which are for example transformed with at least one vector according to the invention and can be used for producing the polypeptides according to the invention. Advantageously, the recombinant constructs according to the invention, described above, are introduced into a suitable host system and expressed. Preferably common cloning and transfection methods, known by a person skilled in the art, are used, for example co-precipitation, protoplast fusion, electroporation, retroviral transfection and the like, for expressing the stated nucleic acids in the respective expression system. Suitable systems are described for example in Current Protocols in Molecular Biology, F. Ausubel et al., Ed., Wiley Interscience, New York 1997, or Sambrook et al. Molecular Cloning: A Laboratory Manual. 2nd edition, Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989.
Advantageously, microorganisms such as bacteria, fungi or yeasts are used as host organisms. Advantageously, gram-positive or gram-negative bacteria are used, preferably bacteria of the families Enterobacteriaceae, Pseudomonadaceae, Rhizobiaceae, Streptomycetaceae, Streptococcaceae or Nocardiaceae, especially preferably bacteria of the genera Escherichia, Pseudomonas, Streptomyces, Lactococcus, Nocardia, Burkholderia, Salmonella, Agrobacterium, Clostridium or Rhodococcus. The genus and species Escherichia coli is quite especially preferred. Furthermore, other advantageous bacteria are to be found in the group of alpha-Proteobacteria, beta-Proteobacteria or gamma-Proteobacteria. Advantageously also yeasts of families like Saccharomyces or Pichia are suitable hosts.
Alternatively, entire plants or plant cells may serve as natural or recombinant host. As non-limiting examples the following plants or cells derived therefrom may be mentioned the genera Nicotiana, in particular Nicotiana benthamiana and Nicotiana tabacum (tobacco); as well as Arabidopsis, in particular Arabidopsis thaliana.
Depending on the host organism, the organisms used in the method according to the invention are grown or cultured in a manner known by a person skilled in the art. Culture can be batchwise, semi-batchwise or continuous. Nutrients can be present at the beginning of fermentation or can be supplied later, semicontinuously or continuously. This is also described in more detail below.
The invention further relates to methods for recombinant production of polypeptides according to the invention or functional, biologically active fragments thereof, wherein a polypeptide-producing microorganism is cultured, optionally the expression of the polypeptides is induced by applying at least one inducer inducing gene expression and the expressed polypeptides are isolated from the culture. The polypeptides can also be produced in this way on an industrial scale, if desired.
The microorganisms produced according to the invention can be cultured continuously or discontinuously in the batch method or in the fed-batch method or repeated fed-batch method. A summary of known cultivation methods can be found in the textbook by Chmiel (Bioprozesstechnik 1. Einfithrung in die Bioverfahrenstechnik [Bioprocess technology 1. Introduction to bioprocess technology] (Gustav Fischer Verlag, Stuttgart, 1991)) or in the textbook by Storhas (Bioreaktoren and periphere Einrichtungen [Bioreactors and peripheral equipment] (Vieweg Verlag, Braunschweig/Wiesbaden, 1994)).
The culture medium to be used must suitably meet the requirements of the respective strains. Descriptions of culture media for various microorganisms are given in the manual “Manual of Methods for General Bacteriology” of the American Society for Bacteriology (Washington D. C., USA, 1981).
These media usable according to the invention usually comprise one or more carbon sources, nitrogen sources, inorganic salts, vitamins and/or trace elements.
Preferred carbon sources are sugars, such as mono-, di- or polysaccharides. Very good carbon sources are for example glucose, fructose, mannose, galactose, ribose, sorbose, ribulose, lactose, maltose, sucrose, raffinose, starch or cellulose. Sugars can also be added to the media via complex compounds, such as molasses, or other by-products of sugar refining. It can also be advantageous to add mixtures of different carbon sources. Other possible carbon sources are oils and fats, for example soybean oil, sunflower oil, peanut oil and coconut oil, fatty acids, for example palmitic acid, stearic acid or linoleic acid, alcohols, for example glycerol, methanol or ethanol and organic acids, for example acetic acid or lactic acid.
Nitrogen sources are usually organic or inorganic nitrogen compounds or materials that contain these compounds. Examples of nitrogen sources comprise ammonia gas or ammonium salts, such as ammonium sulfate, ammonium chloride, ammonium phosphate, ammonium carbonate or ammonium nitrate, nitrates, urea, amino acids or complex nitrogen sources, such as corn-steep liquor, soya flour, soya protein, yeast extract, meat extract and others. The nitrogen sources can be used alone or as a mixture.
Inorganic salt compounds that can be present in the media comprise the chloride, phosphorus or sulfate salts of calcium, magnesium, sodium, cobalt, molybdenum, potassium, manganese, zinc, copper and iron.
Inorganic sulfur-containing compounds, for example sulfates, sulfites, dithionites, tetrathionates, thiosulfates, sulfides, as well as organic sulfur compounds, such as mercaptans and thiols, can be used as the sulfur source.
Phosphoric acid, potassium dihydrogen phosphate or dipotassium hydrogen phosphate or the corresponding sodium-containing salts can be used as the phosphorus source.
Chelating agents can be added to the medium, in order to keep the metal ions in solution. Especially suitable chelating agents comprise dihydroxyphenols, such as catechol or protocatechuate, or organic acids, such as citric acid.
The fermentation media used according to the invention usually also contain other growth factors, such as vitamins or growth promoters, which include for example biotin, riboflavin, thiamine, folic acid, nicotinic acid, pantothenate and pyridoxine. Growth factors and salts often originate from the components of complex media, such as yeast extract, molasses, corn-steep liquor and the like. Moreover, suitable precursors can be added to the culture medium. The exact composition of the compounds in the medium is strongly dependent on the respective experiment and is decided for each specific case individually. Information on media optimization can be found in the textbook “Applied Microbiol. Physiology, A Practical Approach” (Ed. P. M. Rhodes, P. F. Stanbury, IRL Press (1997) p. 53-73, ISBN 0 19 963577 3). Growth media can also be obtained from commercial suppliers, such as Standard 1 (Merck) or BHI (brain heart infusion, DIFCO) and the like.
All components of the medium are sterilized, either by heat (20 min at 1.5 bar and 121° C.) or by sterile filtration. The components can either be sterilized together, or separately if necessary. All components of the medium can be present at the start of culture or can be added either continuously or batchwise.
The culture temperature is normally between 15° C. and 45° C., preferably 25° C. to 40° C. and can be varied or kept constant during the experiment. The pH of the medium should be in the range from 5 to 8.5, preferably around 7.0. The pH for growing can be controlled during growing by adding basic compounds such as sodium hydroxide, potassium hydroxide, ammonia or ammonia water or acid compounds such as phosphoric acid or sulfuric acid. Antifoaming agents, for example fatty acid polyglycol esters, can be used for controlling foaming. To maintain the stability of plasmids, suitable selective substances, for example antibiotics, can be added to the medium. To maintain aerobic conditions, oxygen or oxygen-containing gas mixtures, for example ambient air, are fed into the culture. The temperature of the culture is normally in the range from 20° C. to 45° C. The culture is continued until a maximum of the desired product has formed. This target is normally reached within 10 hours to 160 hours.
The fermentation broth is then processed further. Depending on requirements, the biomass can be removed from the fermentation broth completely or partially by separation techniques, for example centrifugation, filtration, decanting or a combination of these methods or can be left in it completely.
If the polypeptides are not secreted in the culture medium, the cells can also be lysed and the product can be obtained from the lysate by known methods for isolation of proteins. The cells can optionally be disrupted with high-frequency ultrasound, high pressure, for example in a French press, by osmolysis, by the action of detergents, lytic enzymes or organic solvents, by means of homogenizers or by a combination of several of the aforementioned methods.
The polypeptides can be purified by known chromatographic techniques, such as molecular sieve chromatography (gel filtration), such as Q-sepharose chromatography, ion exchange chromatography and hydrophobic chromatography, and with other usual techniques such as ultrafiltration, crystallization, salting-out, dialysis and native gel electrophoresis. Suitable methods are described for example in Cooper, T. G., Biochemische Arbeitsmethoden [Biochemical processes], Verlag Walter de Gruyter, Berlin, New York or in Scopes, R., Protein Purification, Springer Verlag, New York, Heidelberg, Berlin.
For isolating the recombinant protein, it can be advantageous to use vector systems or oligonucleotides, which lengthen the cDNA by defined nucleotide sequences and therefore code for altered polypeptides or fusion proteins, which for example serve for easier purification. Suitable modifications of this type are for example so-called “tags” functioning as anchors, for example the modification known as hexa-histidine anchor or epitopes that can be recognized as antigens of antibodies (described for example in Harlow, E. and Lane, D., 1988, Antibodies: A Laboratory Manual. Cold Spring Harbor (N.Y.) Press). These anchors can serve for attaching the proteins to a solid carrier, for example a polymer matrix, which can for example be used as packing in a chromatography column, or can be used on a microtiter plate or on some other carrier.
At the same time these anchors can also be used for recognition of the proteins. For recognition of the proteins, it is moreover also possible to use usual markers, such as fluorescent dyes, enzyme markers, which form a detectable reaction product after reaction with a substrate, or radioactive markers, alone or in combination with the anchors for derivatization of the proteins.
The enzymes or polypeptides according to the invention can be used free or immobilized in the method described herein. An immobilized enzyme is an enzyme that is fixed to an inert carrier. Suitable carrier materials and the enzymes immobilized thereon are known from EP-A-1149849, EP-A-1 069 183 and DE-OS 100193773 and from the references cited therein. Reference is made in this respect to the disclosure of these documents in their entirety. Suitable carrier materials include for example clays, clay minerals, such as kaolinite, diatomaceous earth, perlite, silica, aluminum oxide, sodium carbonate, calcium carbonate, cellulose powder, anion exchanger materials, synthetic polymers, such as polystyrene, acrylic resins, phenol formaldehyde resins, polyurethanes and polyolefins, such as polyethylene and polypropylene. For making the supported enzymes, the carrier materials are usually employed in a finely-divided, particulate form, porous forms being preferred. The particle size of the carrier material is usually not more than 5 mm, in particular not more than 2 mm (particle-size distribution curve). Similarly, when using dehydrogenase as whole-cell catalyst, a free or immobilized form can be selected. Carrier materials are e.g. Ca-alginate, and carrageenan. Enzymes as well as cells can also be crosslinked directly with glutaraldehyde (cross-linking to CLEAs). Corresponding and other immobilization techniques are described for example in J. Lalonde and A. Margolin “Immobilization of Enzymes” in K. Drauz and H. Waldmann, Enzyme Catalysis in Organic Synthesis 2002, Vol. III, 991-1032, Wiley-VCH, Weinheim. Further information on biotransformations and bioreactors for carrying out methods according to the invention are also given for example in Rehm et al. (Ed.) Biotechnology, 2nd Edn, Vol 3, Chapter 17, VCH, Weinheim.
The reaction of the present invention may be performed under in vivo or in vitro conditions.
The at least one polypeptide/enzyme which is present during a method of the invention or an individual step of a multistep-method as defined herein above, can be present in living cells naturally or recombinantly producing the enzyme or enzymes, in harvested cells. i.e. under in vivo conditions, or, in dead cells, in permeabilized cells, in crude cell extracts, in purified extracts, or in essentially pure or completely pure form, i.e. under in vitro conditions. The at least one enzyme may be present in solution or as an enzyme immobilized on a carrier. One or several enzymes may simultaneously be present in soluble and/or immobilised form.
The methods according to the invention can be performed in common reactors, which are known to those skilled in the art, and in different ranges of scale, e.g. from a laboratory scale (few millilitres to dozens of litres of reaction volume) to an industrial scale (several litres to thousands of cubic meters of reaction volume). If the polypeptide is used in a form encapsulated by non-living, optionally permeabilized cells, in the form of a more or less purified cell extract or in purified form, a chemical reactor can be used. The chemical reactor usually allows controlling the amount of the at least one enzyme, the amount of the at least one substrate, the pH, the temperature and the circulation of the reaction medium. When the at least one polypeptide/enzyme is present in living cells, the process will be a fermentation. In this case the biocatalytic production will take place in a bioreactor (fermenter), where parameters necessary for suitable living conditions for the living cells (e.g. culture medium with nutrients, temperature, aeration, presence or absence of oxygen or other gases, antibiotics, and the like) can be controlled. Those skilled in the art are familiar with chemical reactors or bioreactors, e.g. with procedures for up-scaling chemical or biotechnological methods from laboratory scale to industrial scale, or for optimizing process parameters, which are also extensively described in the literature (for biotechnological methods see e.g. Crueger and Crueger, Biotechnologie—Lehrbuch der angewandten Mikrobiologie, 2. Ed., R. Oldenbourg Verlag, Munchen, Wien, 1984).
Cells containing the at least one enzyme can be permeabilized by physical or mechanical means, such as ultrasound or radiofrequency pulses, French presses, or chemical means, such as hypotonic media, lytic enzymes and detergents present in the medium, or combination of such methods. Examples for detergents are digitonin, n-dodecylmaltoside, octylglycoside, Triton® X-100, Tween® 20, deoxycholate, CHAPS (3-[(3-Cholamidopropyl)dimethylammonio]-1-propansulfonate), Nonidet® P40 (Ethylphenolpoly(ethyleneglycolether), and the like.
Instead of living cells biomass of non-living cells containing the required biocatalyst(s) may be applied of the biotransformation reactions of the invention as well.
If the at least one enzyme is immobilised, it is attached to an inert carrier as described above.
The conversion reaction can be carried out batch wise, semi-batch wise or continuously. Reactants (and optionally nutrients) can be supplied at the start of reaction or can be supplied subsequently, either semi-continuously or continuously.
The reaction of the invention, depending on the particular reaction type, may be performed in an aqueous, aqueous-organic or non-aqueous reaction medium.
An aqueous or aqueous-organic medium may contain a suitable buffer in order to adjust the pH to a value in the range of 5 to 11, like 6 to 10.
In an aqueous-organic medium an organic solvent miscible, partly miscible or immiscible with water may be applied. Non-limiting examples of suitable organic solvents are listed below. Further examples are mono- or polyhydric, aromatic or aliphatic alcohols, in particular polyhydric aliphatic alcohols like glycerol.
The non-aqueous medium may contain is substantially free of water, i.e. will contain less that about 1 wt.-% or 0.5 wt.-% of water.
Biocatalytic methods may also be performed in an organic non-aqueous medium. As suitable organic solvents there may be mentioned aliphatic hydrocarbons having for example 5 to 8 carbon atoms, like pentane, cyclopentane, hexane, cyclohexane, heptane, octane or cyclooctane; aromatic carbohydrates, like benzene, toluene, xylenes, chlorobenzene or dichlorobenzene, aliphatic acyclic and ethers, like diethylether, methyl-tert.-butylether, ethyl-tert.-butylether, dipropylether, diisopropylether, dibutylether; or mixtures thereof.
The concentration of the reactants/substrates may be adapted to the optimum reaction conditions, which may depend on the specific enzyme applied. For example, the initial substrate concentration may be in the 0.1 to 0.5 M, as for example 10 to 100 mM.
The reaction temperature may be adapted to the optimum reaction conditions, which may depend on the specific enzyme applied. For example, the reaction may be performed at a temperature in a range of from 0 to 70° C., as for example 20 to 50 or 25 to 40° C. Examples for reaction temperatures are about 30° C., about 35° C., about 37° C., about 40° C., about 45° C., about 50° C., about 55° C. and about 60° C.
The process may proceed until equilibrium between the substrate and then product(s) is achieved, but may be stopped earlier. Usual process times are in the range from 1 minute to 25 hours, in particular 10 min to 6 hours, as for example in the range from 1 hour to 4 hours, in particular 1.5 hours to 3.5 hours. These parameters are non-limiting examples of suitable process conditions.
If the host is a transgenic plant, optimal growth conditions can be provided, such as optimal light, water and nutrient conditions, for example.
The methodology of the present invention can further include a step of recovering an end or intermediate product, optionally in stereoisomerically or enantiomerically substantially pure form. The term “recovering” includes extracting, harvesting, isolating or purifying the compound from culture or reaction media. Recovering the compound can be performed according to any conventional isolation or purification methodology known in the art including, but not limited to, treatment with a conventional resin (e.g., anion or cation exchange resin, non-ionic adsorption resin, etc.), treatment with a conventional adsorbent (e.g., activated charcoal, silicic acid, silica gel, cellulose, alumina, etc.), alteration of pH, solvent extraction (e.g., with a conventional solvent such as an alcohol, ethyl acetate, hexane and the like), distillation, dialysis, filtration, concentration, crystallization, recrystallization, pH adjustment, lyophilization and the like.
Identity and purity of the isolated product may be determined by known techniques, like High Performance Liquid Chromatography (HPLC), gas chromatography (GC), Spektroskopy (like IR, UV, NMR), Colouring methods, TLC, NIRS, enzymatic or microbial assays. (see for example: Patek et al. (1994) Appl. Environ. Microbiol. 60:133-140; Malakhova et al. (1996) Biotekhnologiya 11 27-32; and Schmidt et al. (1998) Bioprocess Engineer. 19:67-70. Ullmann's Encyclopedia of Industrial Chemistry (1996) Bd. A27, VCH: Weinheim, S. 89-90, S. 521-540, S. 540-547, S. 559-566, 575-581 and S. 581-587; Michal, G (1999) Biochemical Pathways: An Atlas of Biochemistry and Molecular Biology, John Wiley and Sons; Fallon, A. et al. (1987) Applications of HPLC in Biochemistry in: Laboratory Techniques in Biochemistry and Molecular Biology, Bd. 17.)
The cyclic terpene compound produced in any of the method described herein can be converted to derivatives such as, but not limited to hydrocarbons, esters, amides, glycosides, ethers, epoxides, aldehydes, ketons, alcohols, diols, acetals or ketals. The terpene compound derivatives can be obtained by a chemical method such as, but not limited to oxidation, reduction, alkylation, acylation and/or rearrangement. Alternatively, the terpene compound derivatives can be obtained using a biochemical method by contacting the terpene compound with an enzyme such as, but not limited to an oxidoreductase, a monooxygenase, a dioxygenase, a transferase. The biochemical conversion can be performed in-vitro using isolated enzymes, enzymes from lysed cells or in-vivo using whole cells.
The invention also relates to methods for the fermentative production of terpene/terpenoid compounds like labdane type compounds.
A fermentation as used according to the present invention can, for example, be performed in stirred fermenters, bubble columns and loop reactors. A comprehensive overview of the possible method types including stirrer types and geometric designs can be found in “Chmiel: Bioprozesstechnik: Einführung in die Bioverfahrenstechnik, Band 1”. In the process of the invention, typical variants available are the following variants known to those skilled in the art or explained, for example, in “Chmiel, Hammes and Bailey: Biochemical Engineering”, such as batch, fed-batch, repeated fed-batch or else continuous fermentation with and without recycling of the biomass. Depending on the production strain, sparging with air, oxygen, carbon dioxide, hydrogen, nitrogen or appropriate gas mixtures may be effected in order to achieve good yield (YP/S).
The culture medium that is to be used must satisfy the requirements of the particular strains in an appropriate manner. Descriptions of culture media for various microorganisms are given in the handbook “Manual of Methods for General Bacteriology” of the American Society for Bacteriology (Washington D. C., USA, 1981).
These media that can be used according to the invention may comprise one or more sources of carbon, sources of nitrogen, inorganic salts, vitamins and/or trace elements.
Preferred sources of carbon are sugars, such as mono-, di- or polysaccharides. Very good sources of carbon are for example glucose, fructose, mannose, galactose, ribose, sorbose, ribulose, lactose, maltose, sucrose, raffinose, starch or cellulose. Sugars can also be added to the media via complex compounds, such as molasses, or other by-products from sugar refining. It may also be advantageous to add mixtures of various sources of carbon. Other possible sources of carbon are oils and fats such as soybean oil, sunflower oil, peanut oil and coconut oil, fatty acids such as palmitic acid, stearic acid or linoleic acid, alcohols such as glycerol, methanol or ethanol and organic acids such as acetic acid or lactic acid.
Sources of nitrogen are usually organic or inorganic nitrogen compounds or materials containing these compounds. Examples of sources of nitrogen include ammonia gas or ammonium salts, such as ammonium sulfate, ammonium chloride, ammonium phosphate, ammonium carbonate or ammonium nitrate, nitrates, urea, amino acids or complex sources of nitrogen, such as corn-steep liquor, soybean flour, soy-bean protein, yeast extract, meat extract and others. The sources of nitrogen can be used separately or as a mixture.
Inorganic salt compounds that may be present in the media comprise the chloride, phosphate or sulfate salts of calcium, magnesium, sodium, cobalt, molybdenum, potassium, manganese, zinc, copper and iron.
Inorganic sulfur-containing compounds, for example sulfates, sulfites, di-thionites, tetrathionates, thiosulfates, sulfides, but also organic sulfur compounds, such as mercaptans and thiols, can be used as sources of sulfur.
Phosphoric acid, potassium dihydrogenphosphate or dipotassium hydrogenphosphate or the corresponding sodium-containing salts can be used as sources of phosphorus.
Chelating agents can be added to the medium, in order to keep the metal ions in solution. Especially suitable chelating agents comprise dihydroxyphenols, such as catechol or protocatechuate, or organic acids, such as citric acid.
The fermentation media used according to the invention may also contain other growth factors, such as vitamins or growth promoters, which include for example biotin, riboflavin, thiamine, folic acid, nicotinic acid, pantothenate and pyridoxine. Growth factors and salts often come from complex components of the media, such as yeast extract, molasses, corn-steep liquor and the like. In addition, suitable precursors can be added to the culture medium. The precise composition of the compounds in the medium is strongly dependent on the particular experiment and must be decided individually for each specific case. Information on media optimization can be found in the textbook “Applied Microbiol. Physiology, A Practical Approach” (1997) Growing media can also be obtained from commercial suppliers, such as Standard 1 (Merck) or BHI (Brain heart infusion, DIFCO) etc.
All components of the medium are sterilized, either by heating (20 min at 1.5 bar and 121° C.) or by sterile filtration. The components can be sterilized either together, or if necessary separately. All the components of the medium can be present at the start of growing, or optionally can be added continuously or by batch feed.
The temperature of the culture is normally between 15° C. and 45° C., preferably 25° C. to 40° C. and can be kept constant or can be varied during the experiment. The pH value of the medium should be in the range from 5 to 8.5, preferably around 7.0. The pH value for growing can be controlled during growing by adding basic compounds such as sodium hydroxide, potassium hydroxide, ammonia or ammonia water or acid compounds such as phosphoric acid or sulfuric acid. Antifoaming agents, e.g. fatty acid polyglycol esters, can be used for controlling foaming. To maintain the stability of plasmids, suitable substances with selective action, e.g. antibiotics, can be added to the medium. Oxygen or oxygen-containing gas mixtures, e.g. the ambient air, are fed into the culture in order to maintain aerobic conditions. The temperature of the culture is normally from 20° C. to 45° C. Culture is continued until a maximum of the desired product has formed. This is normally achieved within 1 hour to 160 hours.
The methodology of the present invention can further include a step of recovering said terpene alcohol.
The term “recovering” includes extracting, harvesting, isolating or purifying the compound from culture media. Recovering the compound can be performed according to any conventional isolation or purification methodology known in the art including, but not limited to, treatment with a conventional resin (e.g., anion or cation exchange resin, non-ionic adsorption resin, etc.), treatment with a conventional adsorbent (e.g., activated charcoal, silicic acid, silica gel, cellulose, alumina, etc.), alteration of pH, solvent extraction (e.g., with a conventional solvent such as an alcohol, ethyl acetate, hexane and the like), distillation, dialysis, filtration, concentration, crystallization, recrystallization, pH adjustment, lyophilization and the like.
Before the intended isolation the biomass of the broth can be removed. Processes for removing the biomass are known to those skilled in the art, for example filtration, sedimentation and flotation. Consequently, the biomass can be removed, for example, with centrifuges, separators, decanters, filters or in flotation apparatus. For maximum recovery of the product of value, washing of the biomass is often advisable, for example in the form of a diafiltration. The selection of the method is dependent upon the biomass content in the fermenter broth and the properties of the biomass, and also the interaction of the biomass with the product of value.
In one embodiment, the fermentation broth can be sterilized or pasteurized. In a further embodiment, the fermentation broth is concentrated. Depending on the requirement, this concentration can be done batch wise or continuously. The pressure and temperature range should be selected such that firstly no product damage occurs, and secondly minimal use of apparatus and energy is necessary. The skillful selection of pressure and temperature levels for a multistage evaporation in particular enables saving of energy.
The following examples are illustrative only and are not intended to limit the scope of the embodiments an embodiments described herein.
The numerous possible variations that will become immediately evident to a person skilled in the art after heaving considered the disclosure provided herein also fall within the scope of the invention.
The invention will now be described in further detail by way of the following Examples.
Unless otherwise stated, all chemical and biochemical materials and microorganisms or cells employed herein are commercially available products.
Unless otherwise specified, recombinant proteins are cloned and expressed by standard methods, such as, for example, as described by Sambrook, J., Fritsch, E. F. and Maniatis, T., Molecular cloning: A Laboratory Manual, 2nd Edition, Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989.
The expression vectors were transformed into E. coli KRX cells (Promega Corporation, Madison, Wis., USA) and the transformed cells were selected on LB medium plates supplemented with the appropriate antibiotic. The cells were then grown in 25 mL liquid LB medium supplemented with the appropriate antibiotic at 37° C. to an OD of 1. The expression of the recombinant proteins was induced with 1 mM isopropyl-1-thio-β-D-galactopyranoside and 0.1% (w/v) L-rhamnose monohydrate, and the cells were incubated 24 hours at 25° C. with moderate shaking.
The bacterial cells were harvested by centrifugation (5000 g, 12 min) and disrupted by sonication (Sonics, Vibra cell X 130 sonicator equipped with a 6 mm diameter tip microprobe; 3 times 20 second 20 kHz pulses at 80% of maximum power) on ice, in 1.8 mL of 50 mM MOPSO buffer pH 7.4 containing 15% glycerol. The lysates were cleared by centrifugation (3500 g, 8 min, 4° C.) and the resulting supernatants were stored frozen and used as the enzyme source for in vitro assays.
The protein fractions containing one of the recombinant proteins was incubated 4 hours at 24° C. with shaking at 230 rpm in assays consisting of 20 μl of cell-free extract, 160 to 320 mg/L of substrate (using a 40 g/L substrate stock solution in DMSO), 1 mM of cofactor whenever relevant, and 50 mM MOPSO pH 7.4 in a final volume of 0.5 to 1 mL in borosilicate glass and PTFE sealed screw-capped tubes (11 mL capacity) (Wheaton, Millville, N.J. 08332 USA). Assays were extracted with 1 volume of methyl-tert-butyl-ether (MTBE) and analyzed by GC-MS as described below.
Bioconversions of compounds were performed using E. coli cells expressing recombinant enzymes. The expression vectors are transformed into E. coli KRX cells (Promega Corporation, Madison, Wis., USA) and the transformed cells were selected on LB medium plates supplemented with the appropriate antibiotic. The cells were first cultivated overnight at 30° C. in 5 mL LB medium supplemented 1% glucose and with the appropriate antibiotic. The next day, 20 mL of TB medium (Terrific Broth) supplemented with the appropriate antibiotic were inoculated with an initial optical density of 0.2 to 0.75. The culture were incubated in shake flasks at 37° C. until an optical density of 1 to 4 was reached and the expression of the recombinant proteins was induced by the addition of 0.1 mM isopropyl-1-thio-β-D-galactopyranoside IPTG and 0.1% rhamnose. The cultures were then distributed in 0.5 to 1 mL aliquotes in 12 mL glass tubes and incubated at 20° C. with moderate shaking.
The substrate was added to each tube 90 minutes after induction of the expression of the recombinant protein. The substrate was either added to a final concentration of 0.25 to 1 g/L using a 40 g/L stock solution in DMSO. Alternatively, an emulsion was prepared containing 150 mg/mL of Tween® 80 (Sigma-Aldrich) and 300 mg/mL of substrate in water and added to the assays to reach a final concentration of 12 mg/mL of substrate.
After 8 to 48 hours of incubation, the cultures were extracted with one volume of MTBE and analyzed by GC-MS as described below.
The DP1205 E. coli cells were transformed with one or two expression plasmids carrying terpene biosynthesis genes and/or terpene modification enzymes and the transformed cells were cultured with the appropriate antibiotics (kanamycin (50 μg/mL) and/or chloramphenicol (34 μg/mL)) on LB-agarose plates. Single colonies were used to inoculate 5 mL liquid LB medium supplemented with the same antibiotics, 4 g/L glucose and 10% (v/v) dodecane. The next day 2 mL of TB medium supplemented with the same antibiotics and 10% (v/v) dodecane were inoculated with 0.2 mL of the overnight culture. The cultures were incubated at 37° C. until an optical density of 3 was reached. The expression of the recombinant proteins was then induced by addition of 1 mM IPTG and the cultures were incubated for 72 h at 20° C.
The cultures were then extracted with one volume of (MTBE) and the composition of the organic phase was analyzed by GC-MS as described below. For quantification an internal standard (α-longipinene (Aldrich)) was added to the extract prior to GC-MS analysis and concentrations of the components were estimated based on comparison of the peak areas.
Samples of whole cell bioconversion assays were analyzed using an Agilent 7890A GC system coupled with a 5975C series Mass Selective Detector (MSD) and equipped with a split/splitless injector (Agilent Technologies, CA).
The GC inlet temperature was set to 230° C. and 1.0 μL of sample was injected in split mode (split ratio 20:1) and analyzed on a DB-5 ms capillary column (30 m×0.25 mm inner diameter×0.25 μm film thickness; Agilent J&W) using helium as a carrier gas at a constant flow of 1 mL/min. The initial temperature of the oven was set at 80° C. and was programmed to 240° C. (10° C./min; hold 1 min) and then to 300° C. (20° C./min; hold 1 min).
Samples of in vitro assays were analyzed using an Agilent 6890N GC system coupled with a 5975 series Mass Selective Detector (MSD) and equipped with a split/splitless injector (Agilent Technologies, CA) and a CombiPAL autosampler (CTC Analytics, Zwingen, Switzerland) injection system. The GC inlet temperature was set to 250° C. and 1.0 μL of sample was injected in pulsed-splitless mode (pulse pressure 1.56 bar, pulse time 0.6 min) and analyzed on a DB-1 ms capillary column (30 m×0.25 mm inner diameter×0.25 μm film thickness; Agilent J&W) using helium as a carrier gas at a constant flow of 1.2 mL/min. The initial temperature of the oven was set at 100° C. (hold 1 min) and was programmed to 260° C. (10 to 20° C./min) and then to 300° C. (30° C./min; hold 1 min). For smaller molecular mass compounds, the same conditions were used for analysis except that the oven initial temperature was lowered down to 80° C.
Recombinant strains capable of producing or converting compounds were engineered by introducing nucleotide sequences encoding for one or more of the following proteins:
Bacterial host cells for in vitro enzyme assays or whole cell bioconversion assays were selected from E. coli KRX cells (Promega Corporation, Madison, Wis., USA) and E. coli BL21 Star™ (DE3) cells (ThermoFisher).
For the biochemical production of terpene compounds using one or more enzyme(s) selected from the enzymes listed above, the host cell was engineered to produce increased amounts of farnesyl-pyrophosphate (FPP) using a mevalonate enzyme pathway and was further transformed to express sesquiterpene or diterpene biosynthesis enzymes.
Engineering of a Recombinant E. coli Strain for Production of FPP by Chromosomal Integration of the Genes Encoding Mevalonate Pathway Enzymes.
An E. coli strain was engineered to produce farnesyl-pyrophosphate (FPP) by chromosomal integration of recombinant genes encoding mevalonate pathway enzymes. See also construction scheme and recombination events depicted in
An upper pathway operon (operon 1 from acetyl-CoA to mevalonate) was designed consisting of the atoB gene from E. coli encoding an acetoacetyl-CoA thiolase, and the mvaA and mvaS genes from Staphylococcus aureus encoding a HMG-CoA synthase and a HMG-CoA reductase, respectively.
As a lower mevalonate pathway operon (operon 2 from mevalonate to farnesyl pyrophosphate), a natural operon from the gram-negative bacteria Streptococcus pneumoniae was selected, encoding a mevalonate kinase (mvaK1), a phosphomevalonate kinase (mvaK2), a phosphomevalonate decarboxylase (mvaD), and an isopentenyl diphosphate isomerase (fni).
A codon optimized Saccharomyces cerevisiae FPP synthase encoding gene (ERG20) was introduced at the 3′-end of the upper pathway operon to convert isopentenyl-diphosphate (IPP) and dimethylallyl-diphosphate (DMAPP) into FPP.
The above described operons were synthesized by DNA 2.0 and integrated into the araA gene of the Escherichia coli strain BL21(DE3). The heterologous pathway was introduced in two separate recombination steps using the CRISPR/Cas9 genome engineering system. The first operon (lower pathway; operon 2) to be integrated carries a spectinomycin (Spec) marker which was used to screen for Spec resistant candidate integrants. The second operon was designed to displace the Spec marker of the previously integrated operon and was accordingly screened for Spec candidate integrants following the second recombination event (see
Engineering of recombinant bacterial cells for the production of copalol.
An operon was constructed containing two cDNAs encoding for:
The cDNAs encoding for AspWeTPP and PvCPS were codon optimized (SEQ ID NOs: 171 and 174). An operon was designed containing the two cDNAs and an RBS sequence (AAGGAGGTAAAAAA) (SEQ ID NO: 196) placed upstream of the cDNAs. The operon was synthesized and cloned into the pJ401 expression plasmid (ATUM, Newark, Calif.) providing the plasmid pJ401-CPOL-4.
Transformation of E. coli cells such as the DP1205 E. coli cells with the plasmid pJ401-CPOL-4 provides recombinant cells capable of producing copalol when cultivated under conditions enabling production of terpene compounds.
An operon was constructed containing 3 cDNAs encoding for:
The cDNAs encoding for AspWeTPP, AzTolADH1 and PvCPS were codon optimized (SEQ ID NOs: 171, 168 and 174). An operon was designed containing successively the three cDNAs and an RBS sequence (AAGGAGGTAAAAAA) (SEQ ID NO: 196) placed upstream of each cDNA. The operon was synthesized and cloned into the pJ401 expression plasmid (ATUM, Newark, Calif.) providing the plasmid pJ401-CPAL-1.
Transformation of E. coli cells such as the DP1205 E. coli cells with the plasmid pJ401-CPAL-1 provides recombinant cells capable of producing copalal when cultivated under conditions enabling production of terpene compounds.
An operon was constructed containing two cDNAs encoding for:
The cDNAs encoding for TalCeTPP and CdGeoA were codon optimized (SEQ ID NOs: 177 and 180). An operon was designed containing successively the two cDNAs and an RBS sequence (AAGGAGGTAAAAAA) (SEQ ID NO: 196) placed upstream of each cDNA. The operon was synthesized and cloned into the pJ401 expression plasmid (ATUM, Newark, Calif.) providing the plasmid pJ401-FAL-1.
Transformation of E. coli cells such as the DP1205 E. coli cells with the plasmid pJ401-FAL-1 provides recombinant cells capable of producing farnesal when cultivated under conditions enabling production of terpene compounds.
An operon was constructed containing three cDNAs encoding for:
The cDNAs encoding for TalVeTPP, SsLPS and CrtE were codon optimized (SEQ ID NOs: 195, 189 and 192). An operon was designed containing successively the three cDNAs and an RBS sequence (AAGGAGGTAAAAAA) (SEQ ID NO: 196) placed upstream of each cDNA. The operon was synthesized and cloned in the pJ401 expression plasmid (ATUM, Newark, Calif.) providing the plasmid pJ401-LOH-2.
Transformation of E. coli cells such as the DP1205 E. coli cells with the plasmid pJ401-LOH-2 provides recombinant cells capable of producing labdendiol when cultivated under conditions enabling production of terpene compounds.
All yeast cell transformations were performed with the lithium acetate protocol as described in Gietz and Woods, Methods Enzymol., 2002, 350:87-96. Transformation mixtures were plated on SmUra- or SmLeu-media plates containing 6.7 g/L of Yeast Nitrogen Base without amino acids (BD Difco, New Jersey, USA), 1.92 g/L Dropout supplement without uracil (Sigma Aldrich, Missouri, USA) or 1.6 g/L Dropout supplement without leucine (Sigma Aldrich, Missouri, USA), 20 g/L glucose and 20 g/L agar. Plates were incubated for 3-4 days at 30° C.
To increase the level of endogenous farnesyl-diphosphate (FPP) pool in S. cerevisiae cells, an extra copy of all yeast endogenous genes involved in the mevalonate pathway, from ERG10 coding for acetyl-CoA C-acetyltransferase to ERG20 coding for FPP synthetase, were integrated into the genome of the S. cerevisiae strain CEN.PK2-1C (Euroscarf, Frankfurt, Germany) under the control of galactose-inducible promoters, similarly as described in Paddon et al., Nature, 2013, 496:528-532. Briefly, three cassettes were integrated in the LEU2, TRP1 and URA3 loci respectively. A first cassette contained the genes ERG20 and a truncated HMG1 (tHMG1 as described in Donald et al., Proc Natl Acad Sci USA, 1997, 109:E111-8) under the control of the bidirectional promoter of GAL10/GAL1 and the genes ERG19 and ERG13 also under the control of the GAL10/GAL1 promoter. The cassette was flanked by two 100 nucleotides regions corresponding to the up- and down-stream sections of LEU2. A second cassette contained the genes IDI1 and tHMG1 which were under the control of the GAL10/GAL1 promoter and the gene ERG13 under the control of the promoter region of GAL7. The cassette was flanked by two 100 nucleotides regions corresponding to the up- and down-stream sections of TRP1. A third cassette contained the genes ERG10, ERG12, tHMG1 and ERG8, all under the control of GAL10/GAL1 promoters. The cassette was flanked by two 100 nucleotides regions corresponding to the up- and down-stream sections of URA3. All genes in the three cassettes included 200 nucleotides of their own terminator regions. Also, an extra copy of GAL4 under the control of a mutated version of its own promoter, as described in Griggs and Johnston, Proc Natl Acad Sci USA, 1991, 88:8597-8601, was integrated upstream of the ERG9 promoter region. In addition, the expression of ERG9 was modified by promoter exchange. The GAL7, GAL10 and GAL1 genes were deleted using a cassette containing the HIS3 gene with its own promoter and terminator. The resulting strain was mated with the strain CEN.PK2-1D (Euroscarf, Frankfurt, Germany) obtaining a diploid strain termed YST045 which was induced for sporulation according to Solis-Escalante et al., FEMS Yeast Res, 2015, 15:2. Spore separation was achieved by resuspension of asci in 200 μL 0.5M sorbitol with 2 μL zymolyase (1000 U mL−1, Zymo research, Irvine, Calif.) and incubation at 37° C. for 20 minutes. The mixture was then plated on media containing 20 g/L peptone, 10 g/L yeast extract and 20 g/L agar, and one germinated spore was isolated and termed YST075.
For copalol production, expression of the GGPP synthase carG (from Blakeslea trispora, NCBI accession JQ289995.1) (SEQ ID NO: 182), the copalyl-pyrophosphate synthase SmCPS2 (from Salvia miltiorrhiza, NCBI accession ABV57835.1) (SEQ ID NO: 185) and the copalyl-pyrophosphate phosphatase TalVeTPP (from Talaromyces verruculosus, NCBI accession KUL89334.1) (SEQ ID NO: 194) in the different engineered yeast cells was achieved with a plasmid system constructed in vivo using yeast endogenous homologous recombination as previously described in Kuijpers et al., Microb Cell Fact, 2013, 12:47. The plasmid is composed of six DNA fragments which were used for S. cerevisiae co-transformation. The fragments were:
For degradation of copalol to manooloxy using different alcohol dehydrogenases (ADHs), Baeyer-Villiger monooxygenases (BVMOs) and esterases (ESTs), genome integrations in the strain YST075 were performed. Each integration cassette was formed by four fragments:
For degradation of copalol to manooloxy, using an alcohol dehydrogenase and different enal-cleaving polypeptides, genome integrations in the strain YST075 were performed, each integration cassette was formed by three fragments:
1) A fragment containing 658 bp corresponding to the upstream section of the NDT80 gene and the sequence 5′-GCAGGCAGCTCCATTTCATGTAGGTGATTTATCCCTCCGGGCGGTATTTGAGACT CTCGG-3′ (SEQ ID NO: 121), this fragment was obtained by PCR with genomic DNA from the strain YST075 as template;
2) a fragment containing the sequence 5′-GCAGGCAGCTCCATTTCATGTAGGTGATTTATCCCTCCGGGCGGTATTTGAGACT CTCGG-3′ (SEQ ID NO: 121), the intergenic region between GAL1 and GAL10 genes, one of the genes encoding for an enal-cleaving polypeptide, the terminator region of the ADH1 gene and the sequence 5′-ACTGCTGGGTACTGTTCAGGCACGATAGGAAATGCGTCCAGCGCATACACCAGT CTTAGC-3′ (SEQ ID NO: 122), this fragment was obtained by DNA synthesis (ATUM, Menlo Park, Calif. 94025); and
3) a fragment containing the sequence 5′-ACTGCTGGGTACTGTTCAGGCACGATAGGAAATGCGTCCAGCGCATACACCAGT CTTAGC-3′ (SEQ ID NO: 122), the PGK1 terminator region, the gene coding for an alcohol dehydrogenase, the promoter region of the genes GAL1 and GAL10, the sequence 5′-AGTCGACCTTACAGCGCCTGGGACTCTACATAAACATGCAGCGAACATGCTTTCC AACGC-3′ (SEQ ID NO: 123) and 405 bp corresponding to the NDT80 gene. This fragment was obtained by DNA synthesis (ATUM, Menlo Park, Calif. 94025).
In all cases, copalol production was achieved by expressing the biosynthetic pathway in a plasmid system as described above.
For degradation of copalol to gamma-ambryl acetate using an alcohol dehydrogenase, an enal-cleaving polypeptide and different Baeyer-Villiger monooxygenases (BVMOs), genome integrations in the strain YST075 were performed; each integration cassette was formed by three fragments:
(1) A fragment containing 658 bp corresponding to the upstream section of the NDT80 gene and the sequence 5′-GCAGGCAGCTCCATTTCATGTAGGTGATTTATCCCTCCGGGCGGTATTTGAGACT CTCGG-3′ (SEQ ID NO: 121), this fragment was obtained by PCR with genomic DNA from the strain YST075 as template;
(2) a fragment containing the sequence 5′-GCAGGCAGCTCCATTTCATGTAGGTGATTTATCCCTCCGGGCGGTATTTGAGACT CTCGG-3′ (SEQ ID NO: 121), the terminator region of the CYC1 gene, one of the genes coding for the tested BVMOs, the intergenic region between GAL1 and GAL10 genes, the gene encoding for an enal-cleaving polypeptide, the terminator region of the ADH1 gene and the sequence 5′-ACTGCTGGGTACTGTTCAGGCACGATAGGAAATGCGTCCAGCGCATACACCAGT CTTAGC-3′ (SEQ ID NO: 122), this fragment was obtained by DNA synthesis (ATUM, Menlo Park, Calif. 94025); and
(3) a fragment containing the sequence 5′-ACTGCTGGGTACTGTTCAGGCACGATAGGAAATGCGTCCAGCGCATACACCAGT CTTAGC-3′ (SEQ ID NO: 122), the PGK1 terminator region, the gene coding for an alcohol dehydrogenase, the promoter region of the genes GAL1 and GAL10, the sequence 5′-AGTCGACCTTACAGCGCCTGGGACTCTACATAAACATGCAGCGAACATGCTTTCC AACGC-3′ (SEQ ID NO: 123) and 405 bp corresponding to the NDT80 gene. This fragment was obtained by DNA synthesis (ATUM, Menlo Park, Calif. 94025).
In all cases, copalol production was achieved by expressing the biosynthetic pathway in a plasmid system as described above.
For degradation of copalol to gamma-ambrol using an alcohol dehydrogenase, an enal-cleaving polypeptide, a Baeyer-Villiger monooxygenases (BVMOs) and different esterases (EST), genome integrations in the strain YST075 were performed; each integration cassette was formed by four overlapping fragments:
Evaluation of the production of terpenes and derivatives from engineered yeast cells was achieved by culturing cells under conditions similarly as described in Westfall et al., Proc Natl Acad Sci USA, 2012, 109:E111-118 with 10% dodecane or 10% isopropyl myristate (IPM) as organic overlay. The cultures were then extracted with two volumes of MTBE and the composition of the organic phase was analyzed by GC-MS using an Agilent 7890A GC system coupled with a 5975C series Mass Selective Detector (MSD) and equipped with a split/splitless injector and a GC Injector 80 injection system (Agilent Technologies, CA). The GC inlet temperature was set to 260° C. and 1.0 μl of sample was injected in splitless mode and analyzed on a HP-5 GC column (30 m×0.25 mm×0.25 μm; Agilent J&W) using helium as a carrier gas at a constant flow of 1.2 mL/min. The initial temperature of the oven was set at 100° C. and was programmed to 300° C. (10° C./min).
Codon optimized cDNAs encoding for SCH23-BVMO1 from Hyphozyma roseonigra (SEQ ID NO: 2), SCH24-BVMO1 from Filobasidium magnum (SEQ ID NO: 6) and SCH46-BVMO1 from Bensingtonia ciliata (SEQ ID NO: 13) were synthesized and cloned in the pJ414 expression plasmid (ATUM, Newark, Calif.) providing the plasmids pJ414-SCH23-BVMO1, pJ414-SCH24-BVMO1 and pJ414-SCH46-BVMO1. KRX E. coli cells (Promega Corporation, Madison, Wis., USA) were transformed with these expression plasmids. The transformed cells were grown and used in whole cell bioconversion assay as described above using manooloxy as substrate. A negative control was included consisting of the cells transformed with an empty plasmid. In the presence of the SCH23-BVMO1, SCH24-BVMO1 or SCH46-BVMO1 recombinant proteins, conversion of manooloxy to gamma-ambryl acetate was observed (
These results show that SCH23-BVMO1, SCH24-BVMO1 and SCH46-BVMO1 catalyse a Baeyer-Villiger type oxidation of manooloxy.
Codon optimized cDNAs encoding for SCH23-BVMO1 from Hyphozyma roseonigra (SEQ ID NO: 3), SCH24-BVMO1 from Filobasidium magnum (SEQ ID NO: 7) and SCH46-BVMO1 from Bensingtonia ciliata (SEQ ID NO: 14) were synthesized and cloned in the pJ414 expression plasmid (ATUM, Newark, Calif.) providing the plasmids pJ414-SCH23-pJ414-SCH24-BVMO1 and pJ414-SCH46-BVMO1. KRX E. coli cells (Promega Corporation, Madison, Wis., USA) were transformed with these expression plasmids. The cells were grown and used in whole cell bioconversion assay as described above using a mixture of cis-copalal and trans-copalal as substrate. A negative control was included consisting of the cells transformed with an empty plasmid. In the presence of the SCH23-BVMO1, SCH24-BVMO1 or SCH46-BVMO1 recombinant proteins, conversion of cis-copalal and trans-copalal was observed. The GC-MS analysis of the products (
Time point measurements of the bioconversion show the formation of compounds 1a and 1b as intermediate products.
In this scheme, the recombinant enzymes catalyse two Baeyer-Villiger type oxidations on two different aldehydes. First, the α,β-unsaturated aldehyde group of trans-copalal is oxidized to form compound 1a in the first Baeyer-Villiger oxidations by the recombinant enzyme. The enol formate functional group of compounds 1a is unstable under the experimental conditions and is patially hydrolysed to form compound 2a. This latter compound is rapidly converted via a keto-enol tautomerization to compound 3 (3a and 3b) and is therefore not detected in the GC-MS analysis. Compound 3 (3a and 3b) is the substrate of the same enzyme which catalyses a second Baeyer-Villiger oxidations to form compound 4 (4a and 4b). The reaction scheme bellow depicts the similar reactions in the transformation of cis-copalal by SCH23-BVMO1, SCH24-BVMO1 or SCH46-BVMO1.
These results show that SCH23-BVMO1, SCH24-BVMO1 and SCH46-BVMO1 catalyse a Baeyer-Villiger type oxidation on labdane aldehyde compounds.
For this experiment the following recombinant proteins were used: SCH23-BVMO1 from Hyphozyma roseonigra (SEQ ID NO: 2) SCH24-BVMO1 from Filobasidium magnum (SEQ ID NO: 6), SCH23-EST from Hyphozyma roseonigra (SEQ ID NO: 20) and SCH24-EST from Filobasidium magnum (SEQ ID NO: 24). Codon optimized cDNAs encoding for SCH23-BVMO1 (SEQ ID NO: 3) and SCH24-BVMO1 (SEQ ID NO: 7) were synthesized and cloned in the pJ414 expression plasmid (ATUM, Newark, Calif.) providing the plasmids pJ414-SCH23-BVMO1 and pJ414-SCH24-BVMO1. Codon optimized cDNAs encoding for SCH23-EST (SEQ ID NO: 21) and SCH24-EST (SEQ ID NO: 25) were synthesized and cloned in the pJ431 expression plasmid (ATUM, Newark, Calif.) providing the plasmids pJ414-SCH23-EST, pJ414-SCH24-EST.
KRX E. coli cells (Promega Corporation, Madison, Wis., USA) were transformed with each of these expression plasmids. The transformed cells were grown and cell free lysates were prepared as described. In vitro enzymatic assays were performed with either of these protein fractions or with a combination of two of these protein fractions. The in vitro assays conditions were as described above with addition of 160 mg/L of manooloxy, 60 μM flavine adenine dinucleotide (FAD) and 500 μM reduced β-Nicotinamide adenine dinucleotide phosphate (NADPH).
Using crude fractions containing the recombinant SCH23-BVMO1 and SCH24-BVMO1 proteins, conversion of manooloxy to gamma-ambrol acetate was observed. No conversion was detected when using a control lysate obtained from E. coli cells transformed with an empty plasmid (
In vitro enzymatic assays were also performed using protein fractions containing a recombinant esterase enzyme and using a combination of protein fractions containing a recombinant BVMO and a recombinant esterase enzyme. These assays were performed as described above using manooloxy as substrate. The GC-MS analysis of the products formed (
This experiment shows that in the presence of a BVMO and esterase, manooloxy can be converted to gamma-ambrol following the reaction scheme depicted bellow:
Codon optimized cDNAs encoding for SCH23-EST from Hyphozyma roseonigra (SEQ ID NO: 21), SCH24-EST from Filobasidium magnum (SEQ ID NO: 25) and SCH46-EST from Bensingtonia ciliata (SEQ ID NO: 32) were synthesized and cloned in the pJ414 expression plasmid (ATUM, Newark, Calif.) providing the plasmids pJ414-SCH23-EST1, pJ414- and pJ414-SCH46-EST1. KRX E. coli cells (Promega Corporation, Madison, Wis., USA) were transformed with these expression plasmids. The transformed cells were grown and cell free lysates were prepared as described. In vitro enzymatic assays were performed with these protein fractions following the conditions described above.
As shown in
From these experiments, the following enzymatic reaction can be drawn:
For this experiment the following recombinant proteins were used: SCH23-BVMO1 from Hyphozyma roseonigra (SEQ ID NO: 2), SCH24-BVMO1 from Filobasidium magnum (SEQ ID NO: 6), SCH25-BVMO1 from Papiliotrema laurentii (SEQ ID NO: 10), SCH23-EST from Hyphozyma roseonigra (SEQ ID NO: 20), SCH24-EST from Filobasidium magnum (SEQ ID NO: 24), SCH25-EST from Papiliotrema laurentii (SEQ ID NO: 28).
Codon optimized cDNAs encoding for SCH23-BVMO1 (SEQ ID NO: 3), SCH24-BVMO1 (SEQ ID NO: 7) and SCH25-BVMO1 (SEQ ID NO: 11) were synthesized and cloned in the pJ414 expression plasmid (ATUM, Newark, Calif.) providing the plasmids pJ414-SCH23-BVMO1, pJ414-SCH24-BVMO1 and pJ414-SCH25-BVMO1. Codon optimized cDNAs encoding for SCH23-EST (SEQ ID NO: 21), SCH24-EST (SEQ ID NO: 25) and SCH25-EST (SEQ ID NO: 29) were synthesized and cloned in the pJ431 expression plasmid (ATUM, Newark, Calif.) providing the plasmids pJ414-SCH23-EST, pJ414-SCH25-EST.
KRX E. coli cells (Promega Corporation, Madison, Wis., USA) were transformed with these expression plasmids. The transformed cells were grown and cell free lysates were prepared as described. In vitro enzymatic assays were performed with protein fractions containing a recombinant BVMO enzyme or a recombinant esterase enzyme or by combining of protein fractions containing recombinant BVMO and esterase enzymes. The assays were performed as described above with addition of 320 mg/L of a mixture of cis-copalal and trans-copalal as substrate, 60 μM flavine adenine dinucleotide (FAD) and 500 μM reduced (3-Nicotinamide adenine dinucleotide phosphate (NADPH).
Similar conversion of cis- and trans-copalal was observed when SCH24-BVMO1 was combined with esterase SCH23-EST or SCH24-EST (
From these experiments the following enzyme pathway can be deduced.
In this experiment, the plasmid pJ401-CPAL-1 (described above) was used to transform E. coli cells to produce copalal as described in the experimental section. When DP1205 E. coli cells were transformed and cultivated unter the conditions described in the experimental section, formation of trans-copalal and cis-copalal was observed (
The bacteria cells were then transformed with a second expression plasmid carrying a codon optimized cDNA encoding for SCH24-BVMO1 from Filobasidium magnum (ATCC® 20918™) (SEQ ID NO: 7) or SCH46-BVMO1 from Bensingtonia ciliata (SEQ ID NO: 14). These plasmid was prepared by cloning the optimized cDNAs in the pJ423 expression plasmid (ATUM, Newark, Calif.) providing the plasmids pJ423-SCH23-BVMO and pJ423-SCH46-BVMO, respectively. The cells transformed with two plasmids were cultivated and the production of terpene compounds and terpene derivatives was analysed using the conditions described in the experimental section. Under these conditions the compounds 1a and 1b, 3a and 3b, and 4a and 4b were detected in the solvent extract of the culture broth (
Similarly, bacteria cells were co-transformed with the plasmid pJ401-CPAL-1 and with a second plasmid carrying a gene encoding for a BVMO and a gene encoding for an esterase. :pJ423-SCH24-BVMO-SCH24-EST, prepared by inserting a synthetic operon composed of a codon optimized cDNA encoding SCH24-BVMO1 (SEQ ID NO: 7) and a codon optimized cDNA encoding SCH24-EST (SEQ ID NO: 25) into the pJ423 expression plasmid (ATUM, Newark, Calif.), or pJ423-SCH46-BVMO-SCH46-EST, a plasmid prepared by inserting a synthetic operon composed of a codon optimized cDNA encoding SCH46-BVMO (SEQ ID NO: 14) and a codon optimized cDNA encoding SCH46-EST (SEQ ID NO: 32) into the pJ423 expression plasmid (ATUM, Newark, Calif.). The cells were cultivated and the production of terpene compounds and terpene derivatives was analysed using the conditions described in the experimental section. Under these conditions, the compounds 5a and 5b were detected and decreased amounts of the pathway intermediates (compounds 1a, 1b, 3a, 3b, 4a and 4b) were observed.
This experiment series shows that the following biosynthetic pathway can be introduced in a host cells transformed to express diterpene biosynthesis enzymes in combination with a BVMO and an esterase.
For this experiment, the following alcohol dehydrogenases were evaluated for the oxidation of compounds 5a and 5b to manooloxy:
RrhSecADH from Rhodococcus rhodochrous (SEQ ID NO: 146),
SCH80-00043 from Rhodococcus rhodochrous (SEQ ID NO: 149),
SCH80-04254 from Rhodococcus rhodochrous (SEQ ID NO: 152),
SCH80-06135 from Rhodococcus rhodochrous (SEQ ID NO: 155),
SCH80-06582 from Rhodococcus rhodochrous (SEQ ID NO: 158),
(see also WO2005/026338); the above ADHs are merely non-limiting examples and may be replaced by other known ADHs may
Codon optimized cDNAs encoding for each of these proteins were synthesized and cloned in the vector pJ401 providing plasmids pJ401-RrhSecADH, pJ401-SCH80-00043, pJ401-SCH80-04254, pJ401-SCH80-06135 and pJ401-SCH80-06582 (ATUM, Newark, Calif.).
KRX E. coli cells (Promega Corporation, Madison, Wis., USA) were transformed with these expression plasmids. The transformed cells were grown and used in a whole cell bioconversion assay as described above using a mixture of compounds 5a and 5b as substrate. Five hours after the induction of the expression of the recombinant proteins, the substrate was added to a final concentration of 0.55 mg/mL using an emulsion containing 50 mg/mL of tween 80 and 25 mg/mL of substrate in water. A negative control was included consisting of the cells transformed with an empty plasmid. The oxidation reaction was observed only in the presence of the SCH80-06135 and RrhSecADH recombinant proteins (
In this experiment, the plasmid pJ401-CPAL-1 (described above) was used to transform the DP1205 E. coli cells creating a background strain producing copalal (cis- and trans-isomer) as described in the previous section.
This strain was then co-transformed with the plasmid pJ423-SCH24-BVMO-SCH24-EST (described above) allowing a further expression of a BVMO and an esterase in the same cells. In accordance with the observation made in the previous section, this recombinant organism produces 14,15-dinor-labdane compounds.
To allow the side-chain degradation to continue to the formation of tetranor-labdane derivatives, the secondary alcohol group of compounds 5a and 5b must be oxidized to the corresponding ketone. A plasmid was thus constructed containing nucleotide sequences encoding for a BVMO, an esterase and an appropriate alcohol dehydrogenase (identified in Example 7). For the alcohol dehydrogenase, a codon optimized cDNA encoding for RrhSecADH from a Rhodococcus species (Accession number WP_043801412.1) (SEQ ID NO: 147) was synthesised and a synthetic operon was designed combining the RrhSecADH cDNA and the cDNAs encoding for SCH24-BVMO and SCH24-EST. The operon was cloned into the pJ423 expression plasmid providing the pJ423-secADH-23BVMO-EST plasmid. When DP1205 E. coli cells co-transformed with the vector pJ401-CPAL-1 and the vector pJ423-secADH-23BVMO-EST were cultivated under the conditions described above, gamma-ambrol was detected in the GC-MS analysis of the cultivation broth (
This experiment series shows that the following biosynthetic pathway can be introduced in a recombinant host cells.
For the production of manooloxy, the genes encoding for the GGPP synthase carG (from Blakeslea trispora, NCBI accession JQ289995.1) (SEQ ID NOs: 182), the copalyl-pyrophosphate synthase SmCPS2 (from Salvia miltiorrhiza, NCBI accession ABV57835.1) (SEQ ID NOs: 185), the copalyl-pyrophosphate phosphatase TalVeTPP (from Talaromyces verruculosus, NCBI accession KUL89334.1) (SEQ ID NOs: 194) and either the alcohol dehydrogenase SCH23-ADH1 (SEQ ID NOs: 134), the Baeyer-Villiger monooxygenase SCH23-BVMO1 (SEQ ID NOs: 2), the esterase SCH23-EST (SEQ ID NOs: 20) and the alcohol dehydrogenase SCH23-ADH2 (from Hyphozyma roseonigra) (SEQ ID NOs: 137) or the alcohol dehydrogenase SCH24-ADH1 (SEQ ID NOs: 140), the Baeyer-Villiger monooxygenase SCH24-BVMO1 (SEQ ID NOs: 6), the esterase SCH24-EST1 (SEQ ID NOs: 24) and the alcohol dehydrogenase SCH24-ADH2 (from Filobasidium magnum) (SEQ ID NOs: 143) were expressed in the engineered Saccharomyces cerevisiae strain YST075 as described in the general methods section above. All genes were codon optimized for their expression in S. cerevisiae (SCH23-ADH1, SEQ ID NO: 135; SCH23-BVMO1, SEQ ID NO: 4; SCH23-EST, SEQ ID NO: 22; SCH23-ADH2, SEQ ID NO: 138; SCH24-ADH1, SEQ ID NO: 141; SCH24-BVMO1, SEQ ID NO: 8; SCH24-EST, SEQ ID NO: 26; SCH24-ADH2, SEQ ID NO: 144; carG, SEQ ID NO: 183; SmCPS2, SEQ ID NO: 186; and TalVeTPP, SEQ ID NO: 195).
The strains YST120 (with SCH23-ADH1, SCH23-BVMO1, SCH23-EST and SCH23-ADH2) and YST121 (with SCH24-ADH1a, SCH24-BVMO1, SCH24-EST and SCH24-ADH2) harboring also the plasmid system for copalol biosynthesis were obtained and cultivated under the conditions described in the general methods section above.
Under these conditions, copalol was identified in all cultures. Only strains containing SCH23-ADH1 or SCH24-ADH1 were able to convert copalol into copalal (
In addition, manooloxy was identified in the cultures containing the strains YST120 and YST121 harboring the plasmid with copalol biosynthetic genes (
alcohol dehydrogenases (ADHs), Baeyer-Villiger monooxygenases (BVMOs) and esterases (ESTs) from Hyphozyma roseonigra or Cryptococcus albidus.
For the production of manooloxy, the genes encoding for the GGPP synthase carG (from Blakeslea trispora, NCBI accession JQ289995.1), the copalyl-pyrophosphate synthase SmCPS2 (from Salvia miltiorrhiza, NCBI accession ABV57835.1), the copalyl-pyrophosphate phosphatase TalVeTPP (from Talaromyces verruculosus, NCBI accession KUL89334.1), the alcohol dehydrogenase SCH23-ADH1 and either the Baeyer-Villiger monooxygenase SCH23-BVMO1 and the esterase SCH23-EST (from Hyphozyma roseonigra) or the Baeyer-Villiger monooxygenase SCH24-BVMO1 and the esterase SCH24-EST (from Cryptococcus albidus) were expressed in the engineered Saccharomyces cerevisiae strain YST075 as described in the general methods section.
The obtained strains were termed YST177 (with carG, SmCPS2, TalVeTPP, SCH23-ADH1, SCH23-BVMO1 and SCH23-EST) and YST178 (with carG, SmCPS2, TalVeTPP, SCH23-ADH1, SCH24-BVMO1 and SCH24-EST) and were cultivated as described in the general methods section above. Cultures were analyzed by GC-MS as described above.
Copalol, copalal, nerolidol, farnesol and farnesal were identified in the cultures after extraction. The engineered cells not containing the alcohol dehydrogenases SCH23-ADH2 or SCH24-ADH2 were expected to accumulate the intermediate 5a (or 5b) and to be incapable to produce manooloxy. Interestingly, manooloxy was identified (
In this experiment, the plasmid pJ401-CPOL-4 (described above) was used to transform the DP1205 E. coli cells creating a background strain producing copalol. The transformed strain produced copalol as major product with a concentration of up to 500 mg/L in the culture media in the tube assay (
This strain was then further transformed with a second plasmid carrying one or more E. coli codon optimized cDNAs derived from R. erytheropolis. Two cDNAs were selected:
Expression vectors were prepared using pJ423 as background and containing either a codon optimized cDNA encoding for SCH94-3945 (pJ423-SCH94-3945) or SCH94-3944 (pJ423-SCH94-3944) or a bicistronic operon comprised of the optimized cDNAs encoding for SCH94-3945 and SCH94-3944 (pJ423-SCH94-3944-3945).
When cells were transformed with the vector pJ401-CPOL-4 and the vector pJ423-SCH94-3944, no difference was observed in comparison with cells transformed with pJ401-CPOL-4 only, showing that the SCH94-3944 recombinant protein does not transform copalol. When cells were transformed with the vector pJ401-CPOL-4 and the vector pJ423-SCH94-3945, formation of cis-copalal and trans-copalal was observed showing that the SCH94-3945 is an alcohol dehydrogenase able to oxidase copalol to copalal (
When cells were transformed with the vector pJ401-CPOL-4 and the vector pJ423-SCH94-3944-3945, formation of manooloxy was observed as major product with a concentration of up to 1 g/L in the culture media in the tube assay. Under this assay condition, the conversion of cis- and trans-copalal was nearly complete (
This experiment shows that the SCH94-3944 enzyme can cleave the alpha-beta carbon-carbon double-bound of copalal and catalyse the direct conversion of cis-copalal and trans-copalal to the 14,15-dinor-labdane compound manooloxy, as shown in the scheme below.
In this experiment, the plasmid pJ401-FAL-1 (described above) was used to transform the DP1205 E. coli cells creating a background strain producing cis-farnesal and trans-farnesal as major products with a concentration up to 500 mg/L in the culture media in tube assay conditions (
This strain was then further transformed with the plasmid pJ423-SCH94-3944 carrying a cDNA encoding for SCH94-3944 from R. erytheropolis. The GC-MS analysis of the compounds produced by the cells showed formation of geranylacetone (
No conversion with farnesol was observed un ed the applied test conditions.
Biochemical conversion of compounds was performed using E. coli KRX (Promega) cells transformed with the plasmid pJ423-SCH94-3944, thus, overexpressing the SCH94-3944 recombinant protein. The substrate was added to the cell culture to a final concentration of 12 g/L using an 2:1 substrate:Tween 80 emulsion. The bioconversion was performed as described in the experimental section. Negative controls were performed using cells transformed with a pJ423 expression plasmid without insert. Several substrates were tested: citral (a mixture composed of geranial and neral), citronelal (2,3-dihydrocitral) and (E)-2-dodecanal. The cells were incubated for 24 hours in the presence of the various compounds and the products of the conversion were analysed as described in the experimental section.
In the presence of the SCH94-3944 recombinant protein, geranial and neral were both converted to methylheptenone (
No conversion was obtained with citronelal of the formula
in the presence of the SCH94-3944 recombinant protein (
With (E)-2-dodecanal,
conversion to decanal was observed. However, compared to citral, the conversion yield was significantly lower (
The SCH94-3944 protein sequence contains a GXWXG protein family domain and a DUF4334 protein family domain. Proteins with similar domain architectures were searched in other organisms and tested to determine if the enzymatic activity associated with SCH94-3944 can also be associated with these homologous enzymes.
In this experiment, the plasmid pJ401-CPAL-1 (described above) was used to transform the DP1205 E. coli cells creating a background strain producing copalal (cis- and trans-isomer) as described in the previous section. In this strains a FPP synthase is expressed from the genomic integrated operons. Because the terpenyl phosphatase AspWeTPP can dephosphorylate FPP in addition to GGPP, and because AzeTolADH1 can also oxidize farnesol, a significant amount of trans farnesal was detected in addition to copalal when the pJ401-CPAL-1 was used to transforme the DP1205 cells (
This strain was then co-transformed with a second plasmid carrying a gene encoding for a protein containing a GXWXG protein family domain and a DUF4334 protein family domain. Several proteins were selected:
Codon optimized cDNAs encoding for each of these proteins were designed and cloned in the pJ423 expression plasmids (ATUM, Newark, Calif.). The DP1205 E. coli cells were co-transformed with one of these plasmids and with the pasmid pJ401-CPAL-1.
This experiment shows that proteins containing a GXWXG protein family domain in the N-terminal region and a DUF4334 protein family domain in the C-terminal region can catalyse enal-cleaving activity on copalal and farnesal as shown in the schemes below.
The alignment of the amino acid sequences of the GXWXG and DUF4334 domain containing proteins having enal-cleaving activities, showed conserved amino acids along the amino acid sequence and within said two protein domains (
To evaluate the participation of the conserved residues in the GXWXG and DUF4334 domain containing enzymes to the enzymatic activity, artificial mutants of the SCH94-3944 protein were design in which the conserved residues were individually replaced by an alanine residue. The following residue were mutated: W44, T51, H53, L59, W64, K67, S71, R106, Y115, D116, D122, M136, K139, F152, L154 and R156. The modified proteins were designated SCH94-3944-W44A, SCH94-3944-T51A, SCH94-3944-H53A, SCH94-3944-L59A, SCH94-3944-W64A, SCH94-3944-K67A, SCH94-3944-S71A, SCH94-3944-R106A, SCH94-3944-Y115A, SCH94-3944-D116A, SCH94-3944-D122A, SCH94-3944-M136A, SCH94-3944-K139A, SCH94-3944-F152A, SCH94-3944-L154A and SCH94-3944-R156A.
Codon optimized cDNAs encoding for each of these proteins were designed and cloned in the pJ423 expression plasmids (ATUM, Newark, Calif.). The DP1205 E. coli cells were co-transformed with one of these plasmids and with pasmid pJ401-CPAL-1. In the presence of the SCH94-3944-W44A, SCH94-3944-K67A, SCH94-3944-D122A, SCH94-3944-F152A or SCH94-3944-L154A recombinant proteins, no conversion of copalal and farnesal was observed. In the presence of the SCH94-3944-T51A, SCH94-3944-H53A, SCH94-3944-L59A, SCH94-3944-W64A, SCH94-3944-571, SCH94-3944-R106A, SCH94-3944-Y115A, SCH94-3944-D116A, SCH94-3944-M136A, SCH94-3944-K139A and SCH94-3944-R156A enzymes, conversion of copalal and farnesal was observed but with an efficiency lower than the wild type SCH94-3944 protein.
In this experiment, the plasmid pJ401-CPAL-1 (described above) was used to transform the DP1205 E. coli cells creating a background strain producing copalal (cis- and trans-isomer) as described above.
This strain was then co-transformed with a second plasmid carrying a codon optimized nucleotide sequence encoding for either an enzyme with enal-cleaving activity or an enzyme with BVMO activity, or with a second vector carrying an operon composed of a codon optimize cDNA encoding for an enal-cleaving polypeptide and codon optimized cDNA encoding for a BVMO:
The transformed cells were cultivated and the formation of terpene derivatives was analysed by GC-MS as described above.
When cells were transformed with the vector pJ401-CPAL-1 and with an empty pJ423 vector or pJ423-AspWeBVMO, formation of only cis-copalal and trans-copalal was observed. (
When cells were transformed with the vector pJ401-CPAL-1 and with pJ423-SCH94-3944, formation of manooloxy was observed with complete conversion of copalal (
This experiment shows that the following pathway can be introduced in a host cell to produce gamma-ambryl acetate.
For the production of manooloxy, the genes encoding for the GGPP synthase carG (from Blakeslea trispora, NCBI accession JQ289995.1), the copalyl-pyrophosphate synthase SmCPS2 (from Salvia miltiorrhiza, NCBI accession ABV57835.1), the copalyl-pyrophosphate phosphatase TalVeTPP (from Talaromyces verruculosus, NCBI accession KUL89334.1), the alcohol dehydrogenase SCH23-ADH1 (from Hyphozyma roseonigra) and one of the tested enal-cleaving polypeptides were expressed in the engineered Saccharomyces cerevisiae strain YST075 as described in the general methods section.
Five enal-cleaving polypeptides were evaluated:
The constructed strains were termed YST184 (with AspWeDUF4334), YST185 (with CnecaDUF4334), YST186 (with Pdigit7033), YST187 (with SCH94-03944) and YST188 (with SCH80-05241). These strains were cultivated as described in the general methods section above; the production of manooloxy and other compounds was identified using GC-MS analysis.
Under the tested conditions, copalal, nerolidol, farnesal, geranyl acetone and manooloxy were identified in all cultures where the enal-cleaving polypeptides were expressed (
Interestingly, the total amount of identified terpenes in cultures from strains containing the alcohol dehydrogenase and the different enal-cleaving polypeptides were two- to four-folds higher than that of the control culture (
For the production of gamma-ambryl acetate, the genes encoding for the GGPP synthase carG (from Blakeslea trispora, NCBI accession JQ289995.1), the copalyl-pyrophosphate synthase SmCPS2 (from Salvia miltiorrhiza, NCBI accession ABV57835.1), the copalyl-pyrophosphate phosphatase TalVeTPP (from Talaromyces verruculosus, NCBI accession KUL89334.1), the alcohol dehydrogenase SCH23-ADH1 (from Hyphozyma roseonigra), the enal-cleaving polypeptide AspWeDUF4334 (from Aspergillus wentii; GenBank accession OJJ34591.1) and one of the tested Baeyer-Villiger monooxygenases (BVMOs) were expressed in the engineered Saccharomyces cerevisiae strain YST075 as described in general methods.
Three BVMOs were evaluated:
All genes were codon optimized for their expression in S cerevisiae (SCH23-BVMO1, SEQ ID NO: 4; SCH24-BVMO1, SEQ ID NO: 8; and AspWeBVMO, SEQ ID NO: 18).
The obtained strains were termed YST190 (with SCH23-BVMO1), YST191 (with SCH24-BVMO1) and YST192 (with AspWeBVMO). These strains were cultivated as described in the general methods section above; the production of manooloxy and other compounds was identified using GC-MS analysis.
Under the tested conditions, copalol, copalal, nerolidol, farnesol, geranyl acetone, manooloxy and gamma-ambryl acetate were identified in all cultures (
In this experiment, the plasmid pJ401-LOH-2 (described above) was used to transform the DP1205 E. coli cells creating a background strain producing labdendiol ((13E)-13-Labdene-8,15-diol) as described above.
This strain was then co-transformed with a second plasmid carrying a codon optimized nucleotide sequence encoding for an alcohol dehydrogenase and an enzyme with enal-cleaving polypeptideenal-cleaving polypeptide activity:
The transformed cells were cultivated and the formation of terpene derivatives was analysed by GC-MS as described above.
When cells were transformed with the vector pJ401-LOH-2 and with an empty pJ423 vector formation of labdendiol was observed (
When cells were transformed with the vector pJ401-LOH-2 and with pJ423-AzetolADH1 to co-express an alcohol dehydrogenase, formation of two new products were observed (
When cells were transformed with the vector pJ401-LOH-2 and with pJ423-SCH94-3944-3945 to co-express an alcohol dehydrogenase and a enal-cleaving polypeptide, formation of sclareol oxide was observed in addition to compounds 7a and 7b. The formation of sclareol oxide in the presence of a enal-cleaving polypeptide can be explained by the transformation steps shown in the scheme below. The SCH94-3944 enal-cleaving polypeptide catalyses the C—C double bond cleavage of compound 6 to the 8-Hydroxy-14,15-bisnorlabdan-13-one (8). Compound 8 is unstable and is converted under mild conditions to sclareol oxide (Barrero et al., Tetrahedron 49, (45) 1993, 10405-10412; Hua et al., Tetrahedron 67 (6) 2011, 1142-1144). The relative small final amounts of sclareol oxide relative to compounds 7a and 7b is due to the competition between the enzymatic activity of the SCH94-3944 and the chemical dehydration of compound 6.
For the production of gamma-ambrol, the genes encoding for the bifunctional enzyme PvCPS (from Talaromyces verruculosus), the copalyl-pyrophosphate phosphatase TalVeTPP (from Talaromyces veruculosum), the alcohol dehydrogenase SCH23-ADH1 (from Hyphozyma roseonigra), the enal-cleaving AspWeDUF4334 (from Aspergillus wentii), the BVMO SCH23-BVMO1 (from Hyphozyma roseonigra) and one of the tested esterases (EST) were expressed in the engineered Saccharomyces cerevisiae strain YST075 as described in general methods.
Two esterases were evaluated:
A first vector was designed containing two operons each under the control of a T5 promoter. The first operon contains two cDNAs encoding for:
The cDNAs encoding for AspWeTPP and PvCPS were codon optimized (SEQ ID NOs: 171 and 174) and the operon was designed containing the two cDNAs and an RBS sequence (AAGGAGGTAAAAAA) (SEQ ID NO: 196) placed upstream of each the cDNAs.
The second operon contains two cDNAs encoding for:
The cDNAs encoding for SCH94-3945 and SCH94-3944 were codon optimized (SEQ ID NOs: 162 and 35) and the operon was designed containing the two cDNAs and an RBS sequence (AAGGAGGTAAAAAA) (SEQ ID NO: 196) placed upstream of each the cDNAs.
The two operons were assembled in a single vector, providing pJ401-Mnoxy allowing to express all gene of the biosynthetic pathway from FPP to manooloxy.
Bacteria cells (DP1205) were co-transformed with the plasmid pJ401-Manoxy and with a second plasmid:
The transformed cells were cultivated and the production terpenes was analysed as described above under the conditions described in the experimental section.
When cells were transformed with the vector pJ401-Mnoxy and with an empty pJ423 vector, formation of only manooloxy was observed. (
When cells were transformed with the vector pJ401-Mnoxy and with pJ423-SCH24-BVMO, formation of γ-ambryl acetate was observed (
When cells were transformed with the vector pJ401-Mnoxy and with pJ423-SCH24-BVMO-SCH24-EST, formation of γ-ambrol was observed (
This experiment shows that the following pathway can be introduced in a host cell to produce gamma-ambrol.
The content of any document cross-referenced herein is incorporated by reference.
Hyphozyma
roseonigra
Hyphozyma
roseonigra
Hyphozyma
roseonigra
E.
coli optimized
Hyphozyma
roseonigra
Filobasidium
magnum
Filobasidium
magnum
Filobasidium
magnum
E.
coli optimized
Filobasidium
magnum
Papiliotrema
laurentii
Papiliotrema
laurentii
Papiliotrema
laurentii
E.
coli optimized
Bensingtonia
ciliata
Bensingtonia
ciliata
Bensingtonia
ciliata
E.
coli optimized
Aspergillus
wentii
Aspergillus
wentii
Aspergillus
wentii
E.
coli optimized
Aspergillus
wentii
Hyphozyma
roseonigra
Hyphozyma
roseonigra
Hyphozyma
roseonigra
E.
coli optimized
Hyphozyma
roseonigra
Filobasidium
magnum
Filobasidium
magnum
Filobasidium
magnum
E.
coli optimized
Filobasidium
magnum
Papiliotrema
laurentii
Papiliotrema
laurentii
Papiliotrema
laurentii
E.
coli optimized
Bensingtonia
ciliata
Bensingtonia
ciliata
Bensingtonia
ciliata
E.
coli optimized
Rhodococcus
erythropolis
Rhodococcus
erythropolis
Rhodococcus
erythropolis
E.
coli optimized
Rhodococcus
erythropolis
Rhodococcus
rhodochrous
Rhodococcus
rhodochrous
Rhodococcus
rhodochrous
E.
coli optimized
Rhodococcus
rhodochrous
Penicillium
digitatum
Penicillium
digitatum
Penicillium
digitatum
E.
coli optimized
Penicillium
digitatum
Penicillium
italicum
Penicillium
italicum
Penicillium
italicum
E.
coli optimized
Aspergillus
wentii
Aspergillus
wentii
Aspergillus
wentii
E.
coli optimized
Aspergillus
wentii
Rhodococcus
hoagii strain
Rhodococcus
hoagii strain
Rhodococcus
hoagii strain
E.
coli optimized
Rhodococcus
hoagii strain
Rhodococcus
hoagii strain
Rhodococcus
hoagii strain
E.
coli optimized
Rhodococcus
hoagii
Rhodococcus
hoagii
E.
coli optimized
Cupriavidus
necator
Cupriavidus
necator
Cupriavidus
necator
E.
coli optimized
Cupriavidus
necator
Penicillium
italicum
Penicillium
italicum
Penicillium
italicum
E.
coli optimized
Ralstonia
insidiosa
Ralstonia
insidiosa
Ralstonia
insidiosa
E.
coli optimized
Cryptococcus
gattii
Cryptococcus
gattii
Cryptococcus
gattii
E.
coli optimized
Grosmannia
clavigera
Grosmannia
clavigera
Grosmannia
clavigera
E.
coli optimized
Oidiodendron
maius Zn
Oidiodendron
maius Zn
Oidiodendron
maius Zn
E.
coli optimized
Thermomonospora
curvata
Thermomonospora
curvata
Thermomonospora
E.
coli optimized
curvata
Pseudomonas
litoralis
Pseudomonas
litoralis
Pseudomonas
litoralis
E.
coli optimized
Pseudomonas
protegens
Pseudomonas
protegens
Pseudomonas
protegens
E.
coli optimized
E.
coli optimized
E.
coli optimized
E.
coli optimized
E.
coli optimized
E.
coli optimized
E.
coli optimized
E.
coli optimized
E.
coli optimized
E.
coli optimized
E.
coli optimized
E.
coli optimized
E.
coli optimized
E.
coli optimized
E.
coli optimized
E.
coli replication origin_
E.
coli replication origin_
Hyphozyma
roseonigra
Hyphozyma
roseonigra
Hyphozyma
roseonigra
Hyphozyma
roseonigra
Hyphozyma
roseonigra
Hyphozyma
roseonigra
Filobasidium
magnum
Filobasidium
magnum
Filobasidium
magnum
Filobasidium
magnum
Filobasidium
magnum
Filobasidium
magnum
Rhodococcus sp.
Rhodococcus sp.
Rhodococcus sp.
Rhodococcus
rhodochrous
Rhodococcus
rhodochrous
Rhodococcus
rhodochrous
Rhodococcus
rhodochrous
Rhodococcus
rhodochrous
Rhodococcus
rhodochrous
Rhodococcus
rhodochrous
Rhodococcus
rhodochrous
Rhodococcus
rhodochrous
Rhodococcus
rhodochrous
Rhodococcus
rhodochrous
Rhodococcus
rhodochrous
Rhodococcus
erythropolis
Rhodococcus
erythropolis
Rhodococcus
erythropolis
Rhodococcus
rhodochrous
Rhodococcus
rhodochrous
Rhodococcus
rhodochrous
E.
coli optimized
Azoarcus
toluclasticus
Azoarcus
toluclasticus
Azoarcus
toluclasticus
Aspergillus
wentii
Aspergillus
wentii
Aspergillus
wentii
Talaromyces
verruculosus
Talaromyces
verruculosus
Talaromyces
verruculosus
Talaromyces
cellulolyticus
Talaromyces
cellulolyticus
Talaromyces
cellulolyticus
Castellaniella
defragrans
Castellaniella
defragrans
Castellaniella
defragrans
Blakeslea
trispora
Blakeslea
trispora
Blakeslea
trispora
Salvia
miltiorrhiza
Salvia
miltiorrhiza
Salvia
miltiorrhiza
Salvia
sciarea
Salvia
sciarea
Salvia
sciarea
Pantoea
agglomerans
Pantoea
agglomerans
Pantoea
agglomerans
Talaromyces
verruculosus
Talaromyces
verruculosus
Talaromyces
verruculosus
X4 can be any naturally occurring amino acid, particularly A or I
The numbering of X corresponds to its position in the sequence.
X4 can be any naturally occurring amino acid, particularly H or P.
X5 can be any naturally occurring amino acid, particularly A, D, or E.
X6 can be any naturally occurring amino acid, particularly L or V.
X7 can be any naturally occurring amino acid, particularly G or S.
X11 can be any naturally occurring amino acid, particularly F, L, or Y.
X24 can be any naturally occurring amino acid, particularly A or S.
X26 can be any naturally occurring amino acid, particularly A, C, or N.
X28 can be any naturally occurring amino acid, particularly A or T.
X29 can be any naturally occurring amino acid, particularly W or Y.
The numbering of X corresponds to its position in the sequence.
X2 can be any naturally occurring amino acid, particularly I, L, or V.
X5 can be any naturally occurring amino acid, particularly G, S, or T.
X10 can be any naturally occurring amino acid, particularly A or Q.
X12 can be any naturally occurring amino acid, particularly K or R.
X13 can be any naturally occurring amino acid, particularly W or Y.
X15 can be any naturally occurring amino acid, particularly G, P, or S.
The numbering of X corresponds to its position in the sequence.
X2 can be any naturally occurring amino acid, particularly E, K, or N.
X3 can be any naturally occurring amino acid, particularly D or G.
X5 can be any naturally occurring amino acid, particularly K, T, or V.
X7 can be any naturally occurring amino acid, particularly A or G.
X8 can be any naturally occurring amino acid, particularly L or V.
X11 can be any naturally occurring amino acid, particularly N or S.
X19 can be any naturally occurring amino acid, particularly L or V.
X21 can be any naturally occurring amino acid, particularly A or N.
The numbering of X corresponds to its position in the sequence.
X5 can be any naturally occurring amino acid, particularly L or P.
X9 can be any naturally occurring amino acid, particularly P or T.
X10 can be any naturally occurring amino acid, particularly G, H, or N.
X14 can be any naturally occurring amino acid, particularly A or S.
The numbering of X corresponds to its position in the sequence.
X7 can be any naturally occurring amino acid, particularly T or V.
X8 can be any naturally occurring amino acid, particularly S or T.
X9 can be any naturally occurring amino acid, particularly F or Y.
X10 can be any naturally occurring amino acid, particularly K or R.
X14 can be any naturally occurring amino acid, particularly K or P.
X15 can be any naturally occurring amino acid, particularly F or L.
X16 can be any naturally occurring amino acid, particularly I or V.
The numbering of X corresponds to its position in the sequence.
X3 can be any naturally occurring amino acid, particularly S or Y.
X5 can be any naturally occurring amino acid, particularly F, I, or S.
X6 can be any naturally occurring amino acid, particularly F, I, or T.
X7 can be any naturally occurring amino acid, particularly L or M.
X11 can be any naturally occurring amino acid, particularly C or G.
X13 can be any naturally occurring amino acid, particularly I or V.
X14 can be any naturally occurring amino acid, particularly A or G.
X17 can be any naturally occurring amino acid, particularly P or S.
The numbering of X corresponds to its position in the sequence.
X2 can be any naturally occurring amino acid, particularly L or V.
X7 can be any naturally occurring amino acid, particularly A or T.
X11 can be any naturally occurring amino acid, particularly L or M.
X14 can be any naturally occurring amino acid, particularly I or L.
X15 can be any naturally occurring amino acid, particularly A, K, or Q.
X16 can be any naturally occurring amino acid, particularly D, H, or S.
X19 can be any naturally occurring amino acid, particularly W or Y.
The numbering of X corresponds to its position in the sequence.
X2 can be Y or can be deleted.
X3 can be any naturally occurring amino acid.
X5 can be any naturally occurring amino acid.
X7 can be any naturally occurring amino acid.
X8 can be any naturally occurring amino acid.
X10 can be any naturally occurring amino acid.
The numbering of X corresponds to its position in the sequence.
X5 can be any naturally occurring amino acid.
X7 can be any naturally occurring amino acid.
The numbering of X corresponds to its position in the sequence.
X2 can be any naturally occurring amino acid.
X4 can be any naturally occurring amino acid.
X6 can be any naturally occurring amino acid.
X7 can be any naturally occurring amino acid.
X8 can be any naturally occurring amino acid.
X9 can be any naturally occurring amino acid.
X13 can be any naturally occurring amino acid.
The numbering of X corresponds to its position in the sequence.
X5 can be any naturally occurring amino acid.
X6 can be any naturally occurring amino acid.
X9 can be any naturally occurring amino acid.
The numbering of X corresponds to its position in the sequence.
| Number | Date | Country | Kind |
|---|---|---|---|
| 19000332.7 | Jul 2019 | EP | regional |
| 19208951.4 | Nov 2019 | EP | regional |
This application is a U.S. National Phase Application of International Patent Application No. PCT/EP2020/069217, filed Jul. 8, 2020, which claims priority to European Patent Application No. 19000332.7, filed Jul. 10, 2019, and which claims priority to European Patent Application No. 19208951.4, filed Nov. 13, 2019, the entire contents of which are hereby incorporated by reference herein.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/EP2020/069217 | 7/8/2020 | WO |
