Patent Application
20110207183
The present invention is directed to a method utilizing a microorganism with reduced isocitrate dehydrogenase activity for the production of fine chemicals. Said fine chemicals may be amino acids, monomers for polymer synthesis, sugars, lipids, oils, fatty acids or vitamins, and are preferably amino acids of the aspartate family, especially methionine or lysine, or derivatives of said amino acids, especially cadaverine.
Furthermore, the present invention relates to a recombinant microorganism having a reduced isocitrate dehydrogenase activity in comparison to the initial microorganism and the use of such microorganism in producing fine chemicals such as aspartate family amino acids and their derivatives.
Fine chemicals, which includes e.g. organic acids such as lactic acid, organic amines such as diaminopentane (cadaverine), proteogenic or non-proteogenic amino acids, carbohydrates, aromatic compounds, heteroaromatic compounds such as dipicolinate, vitamins and cofactors, saturated and unsaturated fatty acids, are typically used and needed in the pharmaceutical, agriculture, cosmetic as well as food and feed industry, but also as monomers for polymer synthesis. They are generally produced by chemical processes, but a growing number of fine chemicals is produced by fermentation processes as well.
As regards for example the amino acid methionine, currently worldwide annual production amounts to about 500,000 tons. The standard industrial production process is not by fermentation but a multi-step chemical process. Methionine is the first limiting amino acid in livestock of poultry feed and due to this mainly applied as a feed supplement. Various attempts have been published in the prior art to produce methionine by fermentation e.g. using microorganisms such as E. coli.
Other amino acids such as glutamate, lysine, and threonine, are produced by e.g. fermentation methods. For these purposes, certain microorganisms such as C. glutamicum have been proven to be particularly suited. The production of amino acids by fermentation has the particular advantage that only L-amino acids are produced and that environmentally problematic chemicals such as solvents as they are typically used in chemical synthesis are avoided.
As regards fine chemicals like dipicolinate, cadaverine or β-lysine, said compounds are used in diverse fields and generally produced by non-fermentative methods.
Dipicolinic acid (CAS number 499-83-2), also known as pyridine-2,6-dicarboxylic acid or DPA, is used in different technical fields, for example as monomer in the synthesis of polyester or polyamide type of copolymers, precursor for pyridine synthesis, stabilizing agent for peroxides and peracids, for example t-butyl peroxide, dimethyl-cyclohexanon peroxide, peroxyacetic acid and peroxy-monosulphuric acid, ingredient for polishing solution of metal surfaces, stabilizing agent for organic materials susceptible to be deteriorated due to the presence of traces of metal ions (sequestrating effect), stabilizing agent for epoxy resins, and stabilizing agent for photographic solutions or emulsions (preventing the precipitation of calcium salts). It is well known that DPA is biosynthesized in endospores of bacteria. An enzyme catalyzing the biosynthesis of DPA from dihydrodipicolinate is dipicolinate synthetase. Said enzyme has been isolated from Bacillus subtilis and further characterized. It is encoded by the spoVF operon (BG10781, BG10782).
In the 1950's, L-β-lysine was identified in several strongly basic peptide antibiotics produced by Streptomyces. Antibiotics that yield L-β-lysine upon hydrolysis include viomycin, streptolin A, streptothricin, roseothricin and geomycin (Stadtman, Adv. Enzymol. Relat. Areas Molec. Biol. 38:413 (1973)). β-Lysine is also a constituent of antibiotics produced by the fungi Nocardia, such as mycomycin, and β-lysine may be used to prepare other biologically active compounds. However, the chemical synthesis of β-lysine is time consuming, requires expensive starting materials, and generally results in a racemic mixture.
1,5-Diaminopentane is a relatively expensive specialty chemical which is currently produced by a chemical process (decarboxylation) of L-lysine. Diaminopentane produced by fermentation is not yet available on the market.
The fermentative production of fine chemicals is today typically carried out in microorganisms such as Corynebacterium glutamicum (C. glutamicum), Escherichia coli (E. coli), Saccharomyces cerevisiae (S. cerevisiae), Schizosaccharomyces pombe (S. pombe), Pichia pastoris (P. pastoris), Aspergillus niger, Bacillus subtilis, Ashbya gossypii or Gluconobacter oxydans. Especially Corynebacterium glutamicum is known for its ability to produce amino acids in large quantities, e.g., L-glutamate and L-lysine (Kinoshita, S. (1985) Glutamic acid bacteria; p. 115-142 in: A. L. Demain and N. A. Solomon (ed.), Biology of industrial microorganisms, Bejamin/Cummings Publishing Co., London).
Some of the attempts in the prior art to produce fine chemicals such as amino acids, lipids, vitamins or carbohydrates in microorganisms such as E. coli and C. glutamicum have tried to achieve this goal by e.g. increasing the expression of genes involved in the biosynthetic pathways of the respective fine chemicals. If e.g. a certain step in the biosynthetic pathway of an amino acid such as methionine or lysine is known to be rate-limiting, over-expression of the respective enzyme may allow obtaining a microorganism that yields more product of the catalysed reaction and therefore will ultimately lead to an enhanced production of the respective amino acid. Similarly, if a certain enzymatic step in the biosynthetic pathway of an e.g. desired amino acid is known to be non-desirable as it channels a lot of metabolic energy into formation of undesired by-products it may be contemplated to down-regulate expression of the respective enzymatic activity in order to favour only such metabolic reactions that ultimately lead to the formation of the amino acid in question.
Attempts to increase production of e.g. methionine or lysine by up- and/or downregulating the expression of genes being involved in the biosynthesis of methionine or lysine are e.g. described in WO 02/10209, WO 2006/008097, and WO 2005/059093.
Attempts to increase production of fine chemicals like e.g. cadaverine, dipicolinate or β-lysine by up- and/or downregulating the expression of genes being involved in the biosynthesis of biological precursors of said compounds are e.g. described in WO 2007/113127, WO 2007/101867, and EP 08151031.5.
Isocitrate dehydrogenase (ICD, sometimes also called IDH, EC 1.1.1.42, SEQ ID NO:3) is an enzyme which participates in the citric acid cycle (TCA) of, e.g., C. glutamicum. It catalyzes the third step of the cycle: the oxidative decarboxylation of isocitrate, producing alpha-ketoglutarate and CO2.
The gene encoding ICD in C. glutamicum was identified, cloned and characterized by Eikmanns et al. (Eikmanns, B. et al., J. Bacteriol. (1995) 177:774-782). Inactivation of the chromosomal icd gene encoding ICD by knockout in C. glutamicum leads to glutamate auxotrophy (Eikmanns, B. et al., J. Bacteriol. (1995) 177:774-782).
Overexpression of ICD in C. glutamicum and E. coli did not enhance glutamate production (Eikmanns, B. et al., J. Bacteriol. (1995) 177:774-782). However, it was reported in DE 10210967 that overexpression of ICD in E. coli leads to an increased threonine production. Contradictory results are reported for the co-expression of icd with the gene encoding glutamate dehydrogenase in C. glutamicum: whilst Eikmanns did not register any effect, an improved glutamate yield is reported in JP63214189 and JP2520895.
Even in view of the reported attempts to increase production of fine chemicals like amino acids of the aspartate family, their biochemical precursors and derivatives thereof, there is still a need for alternative methods of production.
It is one objective of the present invention to provide alternative fermentative methods and microorganisms for the use in said methods to produce fine chemicals using an industrially important microorganism such as C. glutamicum with heretoforth unknown characteristics.
These and other objectives as they will become apparent from the ensuing description of the invention are solved by the present invention as described in the independent claims. The dependent claims relate to preferred embodiments.
In one embodiment, the present invention relates to a method for the production of fine chemicals using cells with a reduced activity of isocitrate dehydrogenase. The downregulation of said enzyme was heretoforth unknown to lead to improved yields of certain biochemical products, especially of products downstream of aspartate.
The fine chemicals produced by the method according to present invention are preferably synthesized via intermediates of the biosynthetic pathways leading from aspartate to methionine and/or lysine. The fine chemicals are preferably naturally occurring amino acids such as lysine, threonine, isoleucine or methionine, or nitrogen containing derivatives thereof, such as β-lysine, dipicolinate and 1,5-diaminopentane.
The cells used in the production method may be prokaryotes, lower eukaryotes, isolated plant cells, yeast cells, isolated insect cells or isolated mammalian cells, in particular cells in cell culture systems. In the context of present invention, the term “microorganism” is used for said kinds of cells.
A preferred kind of microorganism wherein the ICD activity is reduced for performing the present invention is a Corynebacterium wherein the ICD expression is reduced and particularly preferably a C. glutamicum wherein the ICD expression is reduced.
A recombinant microorganism which has a reduced ICD activity, and preferably comprises a modified nucleotide sequence leading to said reduced expression of ICD in the host cell also forms part of the invention. Such a microorganism may be C. glutamicum.
The present invention also relates to the use of the aforementioned recombinant microorganism for producing fine chemicals, especially via intermediates of the biosynthetic pathways leading from aspartate to methionine and/or lysine. It may be particularly used for production of naturally occurring amino acids such as lysine, threonine, isoleucine or methionine. It may also be particularly used for production of nitrogen containing fine chemicals such as β-lysine, dipicolinate and 1,5-diaminopentane.
In particular, the following embodiments of the invention are provided:
C. glutamicum icd including native DNA sequence 500 nt up-
subterminale, adapted to Corynebactierum codon usage
Corynebactierum codon usage
The following abbreviations, terms and definitions are used herein:
IDH, isocitrate dehydrogenase; ICD, isocitrate dehydrogenase; the abbreviations “ICD” and “IDH” are used synonymously for isocitrate dehydrogenase; WT, wild type; PPP, pentose phosphate pathway; DAP, diaminopentane; DPA, dipicolinic acid.
As used in the context of present invention, the singular forms of “a” and “an” also include the respective plurals unless the context clearly dictates otherwise. Thus, the term “a microorganism” can include more than one microorganism, namely two, three, four, five etc. microorganisms of a kind.
The term “about” in context with a numerical value or parameter range denotes an interval of accuracy that the person skilled in the art will understand to still ensure the technical effect of the feature in question. The term typically indicates deviation from the indicated numerical value of +/−10%, preferably +/−5%.
Unless indicated otherwise, a compound or amino acid mentioned in the context of present invention may have any stereochemistry, including a mixture of different steroisomers. Preferably, the amino acids, their precursors and derivatives have L-configuration. Specifically preferred configurations are indicated where appropriate.
Unless indicated otherwise, the acids obtained by the method according to present invention may be in the form of a free acid, a partial or complete salt of said acid or in the form of mixtures of the acid and its salt. Vice versa, the amines obtained by the method according to present invention may be in the form of a free amine, a partial or complete salt of said amine or in the form of mixtures of the amine and its salt.
The term “host cell” for the purposes of the present invention refers to any isolated cell that is commonly used for expression of nucleotide sequences for production of e.g. polypeptides or fine chemicals. In particular the term “host cell” relates to prokaryotes, lower eukaryotes, plant cells, yeast cells, insect cells or mammalian cell culture systems.
The term “microorganism” relates to prokaryotes, lower eukaryotes, isolated plant cells, yeast cells, isolated insect cells or isolated mammalian cells, in particular cells in cell culture systems. The microorganisms suitable for performing the present invention comprise yeasts such as S. pombe or S. cerevisiae and Pichia pastoris. Mammalian cell culture systems may be selected from the group comprising e.g. NIH T3 cells, CHO cells, COS cells, 293 cells, Jurkat cells and HeLa cells. In the context of present invention, a microorganism is preferably a prokaryote or a yeast cell. Preferred microorganisms in the context of present invention are indicated below in the “detailed description” section. Particularly preferred are Corynebacteria.
“Native” is a synonym for “wild type” and “naturally occurring”. A “wild-type” microorganism is, unless indicated otherwise, the common naturally occurring form of the indicated microorganism. Generally, a wild-type microorganism is a non-recombinant microorganism.
“Initial” is a synonym to “starting”. An “initial” nucleotide sequence or enzyme activity is the starting point for its modification, e.g. by mutation or addition of inhibitors. Any “initial” sequence, enzyme or microorganism lacks a distinctive feature which its “final” or “modified” counterpart possesses and which is indicated in the specific context (e.g. a reduced ICD activity). The term “initial” in the context of present invention encompasses the meaning of the term “native”, and in a preferred aspect is a synonym for “native”.
Any wild-type or mutant (non-recombinant or recombinant mutant) microorganism may be further modified by non-recombinant (e.g. addition of specific enzyme inhibitors) or recombinant methods resulting in a microorganism which differs for the initial microorganism in at least one physical or chemical property, and in one particular aspect of present invention in its ICD activity. In the context of present invention, the initial, non-modified microorganism is designated as “initial microorganism” or “initial (microorganism) strain”. Any reduction of ICD activity in a microorganism in comparison to the initial strain with a given ICD expression level is determined by comparison of ICD activity in both microorganisms under comparable conditions.
Typically, microorganisms in accordance with the invention are obtained by introducing genetic alterations in an intial microorganism which does not carry said genetic alteration.
A “derivative” of a microorganism strain is a strain that is derived from its parent strain by e.g. classical mutagenesis and selection or by directed mutagenesis. E.g., the strain C. glutamicum ATCC13032lysCfbr (WO 2005/059093) is a lysine production strain derived from ATCC13032, as well as LU11424.
The term “nucleotide sequence” or “nucleic acid sequence” for the purposes of the present invention relates to any nucleic acid molecule that encodes for polypeptides such as peptides, proteins etc. These nucleic acid molecules may be made of DNA, RNA or analogues thereof. However, nucleic acid molecules made of DNA are preferred.
“Recombinant” in the context of present invention means “being prepared by or the result of genetic engineering”. Thus, a “recombinant microorganism” comprises at least one “recombinant nucleic acid” or “recombinant protein”. A recombinant microorganism preferably comprises an expression vector or cloning vector, or it has been genetically engineered to contain the cloned nucleic acid sequence(s) in the endogenous genome of the host cell.
“Heterologous” is any nucleic acid or polypeptide/protein introduced into a cell or organism by genetic engineering with respect to said cell or organism, and irrespectively of its organism of origin. Thus, a DNA isolated from a microorganism and introduced into another microorganism of the same species is a heterologous DNA with respect to the latter, genetically modified microorganism in the context of present invention, even though the term “homologous” is sometimes used in the art for this kind of genetically engineered modifications. However, the term “heterologous” is preferably addressing a non-homologous nucleic acid or polypeptide/protein in the context of present invention. “Heterologous protein/nucleic acid” is synonymous to “recombinant protein/nucleic acid”.
The terms “express”, “expressing,” “expressed” and “expression” refer to expression of a gene product (e.g., a biosynthetic enzyme of a gene of a pathway) in a host organism. The expression can be done by genetic alteration of the microorganism that is used as a starting organism. In some embodiments, a microorganism can be genetically altered (e.g., genetically engineered) to express a gene product at an increased level relative to that produced by the starting microorganism or in a comparable microorganism which has not been altered. Genetic alteration includes, but is not limited to, altering or modifying regulatory sequences or sites associated with expression of a particular gene (e.g. by adding strong promoters, inducible promoters or multiple promoters or by removing regulatory sequences such that expression is constitutive), modifying the chromosomal location of a particular gene, altering nucleic acid sequences adjacent to a particular gene such as a ribosome binding site or transcription terminator, increasing the copy number of a particular gene, modifying proteins (e.g., regulatory proteins, suppressors, enhancers, transcriptional activators and the like) involved in transcription of a particular gene and/or translation of a particular gene product, or any other conventional means of deregulating expression of a particular gene using routine in the art (including but not limited to use of antisense nucleic acid molecules, for example, to block expression of repressor proteins).
A “conservative amino acid exchange” means that one or more amino acids in an initial amino acid sequence are substituted by amino acids with similar chemical properties, e.g. Val by Ala. The ratio of substituted amino acids in comparison to the initial polypeptide sequence is preferably from 0 to 30% of the total amino acids of the initial amino acid sequence, more preferably from 0 to 15%, most preferably from 0 to 5%.
Conservative amino acid exchanges are preferably between the members of one of the following amino acid groups:
Specifically preferred conservative amino acid exchanges are as follows:
The term “isolated” means “separate or purified from its organism of origin”. More specifically, an isolated cell of a multicellular organism is separate or has been purified from its organism of origin. This encompasses biochemically purified and recombinantly produced cells.
As used herein, a “precursor” or “biochemical precursor” of an amino acid is a compound preceding (“upstream”) the amino acid in the biochemical pathway leading to the formation of said amino acid in the microorganism of present invention, especially a compound formed in the last few steps of said biochemical pathway. In the context of present invention, a “precursor” of lysine, methionine, threonine or isoleucine, i.e. of any amino acid of the aspartate family besides aspartate, is any intermediate formed during biochemical conversion of aspartate to the respective amino acid in a wild-type organism in vivo.
As used herein, the term “derivative” (with the exception of its use in the context “derivative of a microorganism”, see above) means any chemical compound derivable from (i) the amino acids of the aspartate family or (ii) their biochemical precursors in the biochemical pathways downstream of aspartate by enzymatic or non-enzymatic conversions, enzymatic conversions being preferred. Preferably, the conversion results in at least one of the following:
(i) the removal of one or two carboxyl groups;
(ii) the removal of one amino group;
(iii) the shift of one amino group; and/or
(iv) a dehydrogenation.
Particularly preferred conversions and derivatives are described below in the “detailed description” section.
An “intermediate” or “intermediate product” is understood as a compound which is transiently or continuously formed during a chemical or biochemical process, in a not necessarily analytically directly detectable concentration. Said intermediate may be removed from said biochemical process by a second, chemical or biochemical reaction, in particular by a subsequent enzymatic conversion as defined below in the detailed description section. Said subsequent enzymatic conversion preferably takes place in the microorganism with a partially or completely reduced ICD activity according to present invention. In the method according to this preferred aspect, the microorganism comprises at least one heterologous enzyme catalyzing a reaction step in the subsequent conversion of the endogenous intermediate to the final product of the method.
The “aspartate family” of amino acids encompasses aspartate, asparagin, lysine, methionine, threonine and isoleucine, particularly the L-enantiomers of said amino acids. In a narrower sense, it encompasses lysine, methionine, threonine and isoleucine.
“Carbon yield” is the carbon amount found (of the product) per carbon amount consumed (of the carbon source used in the fermentation, usually a sugar), i.e. the carbon ratio of product to source.
“ICD activity” in the context of present invention means any enzymatic activity of ICD, especially any catalytic effect exerted by ICD. Specifically, the conversion of isocitrate into alpha-ketoglutarate is meant by “ICD activity”. ICD activity may be expressed as units per milligram of enzyme (specific activity) or as molecules of substrate transformed per minute per molecule of enzyme.
The present invention pertains to the biochemical transformation of amino acids and their precursors into fine chemicals by a microorganism with reduced ICD activity.
The activity of ICD provides some of the NADPH/NADH necessary for the amino acid production in a cell. Thus, it did not seem obvious previous to the conception of present invention to reduce ICD activity in a cell in order to amplify its amino acid production, especially the production of amino acids of the aspartate family and their precursors.
Surprisingly, it was now found that a reduction of the ICD activity in a microorganism leads to an increased level of production of amino acids of the aspartate family, of their precursors in the biochemical pathways downstream of aspartate, and of certain derivatives of said amino acids and precursors in said microorganism. The derivatives are synthesized by endogenous or heterologous enzymes, preferably by heterologous enzymes, particularly by the heterologous enyzmes as outlined in
1,5-diaminopentane: polyamide monomer, polyurethane monomer, piperidine precursor
beta-lysine: caprolactam precursor, polyamide monomer
dipicolinate: polyester monomer, polyamide monomer, stabilizing agent.
In a preferred aspect of present invention, the production method according to embodiment (1) is a fermentative method. However, other methods of biotechnological production of chemical compounds are also considered, including in vivo production in plants and non-human animals.
The method for the fermentative production of fine chemicals according to embodiment (1) may comprise the cultivation of at least one—preferably recombinant—microorganism having a reduced ICD activity such that the carbon flux through the glyoxylate shunt is increased.
In a further preferred aspect of embodiment (1), the microorganism used in the production method is a recombinant microorganism. Inasfar as other methods of biotechnological production of chemical compounds are also considered, including in vivo production in plants and non-human animals, the organism of choice is preferably a recombinant organism.
In any embodiment of present invention, the isocitrate dehydrogenase activity in the microorganism used for the embodiment is partially or completely reduced.
A microorganism having a reduced ICD activity according to present invention has lost its initial ICD activity partially or completely when compared with an initial microorganism of the same species and genetical background. Preferably, about at least 1%, at least 2%, at least 4%, at least 6%, at least 8%, at least 10%, more preferably at least 20%, at least 40%, at least 60%, at least 80%, at least 90%, at least 95% or all of the initial activity of ICD is lost in the microorganism. The extent of reduction of activity is determined in comparison to the level of activity of the endogenous ICD activity in an initial microorganism under comparable conditions.
It is understood that it is not always desirable to reduce ICD activity as much as possible. In certain cases an incomplete reduction of any of the levels indicated above, but also of intermediate levels like, e.g., 25%, 40%, 50% etc., may be sufficient and desirable.
An incomplete loss of ICD activity is preferred, as this keeps up the TCA and allows the microorganism to further produce glutamate and other biomolecules synthesized from alpha-ketoglutarate.
In embodiments wherein a complete or near complete (i.e. 90% or greater) loss of ICD activity characterizes the microorganism, the cultivation media for the microorganism, especially the media used in the production according to embodiment (1) may be supplemented by one or more essential compounds lacking in the microorganism due to the suppression of ICD activity. Especially glutamate may be supplemented to the media as it is an inexpensive, easiliy accessable compound.
In organisms possessing more than one ICD encoding gene and/or more than one kind of ICD, the ICD activity reduction may be a reduction in activity of all, several or only one of the different kinds of ICD. A specific reduction of less than all kinds of ICD is preferred for the reasons indicated above in context with the incomplete loss of ICD.
The reduction of ICD activity necessary for present invention may be either an endogenous trait of the microorganism used in the method according to embodiment (1), e.g. a trait due to spontaneous mutations, or due to any method known in the art for suppressing or inhibiting an enzymatic activity in part or completely, especially an enzymatic activity in vivo. The reduction of enzymatic activity may occur at any stage of enzyme synthesis and enzyme reactions, at the genetic, transcription, translation or reaction level.
The decrease of ICD activity is preferably the result of genetic engineering. To reduce the amount of expression of one or more endogenous ICD gene(s) in a host cell and to thereby decrease the amount and/or activity of the ICD in the host cell in which the icd target gene is suppressed, any method known in the art may be applied. For down-regulating expression of a gene within a microorganism such as E. coli or C. glutamicum or other host cells such as P. pastoris and A. niger, a multitude of technologies such as gene knockout approaches, antisense technology, RNAi technology etc. are available. One may delete the initial copy of the respective gene and/or replace it with a mutant version showing decreased activity, particularly decreased specific activity, or express it from a weak promoter. Or one may exchange the start codon of an icd gene, the promoter of an icd gene, introduce mutations by random or target mutagenesis, disrupt or knock-out an icd gene. Furtheron, one may introduce destabilizing elements into the mRNA or introduce genetic modifications leading to deterioration of ribosomal binding sites (RBS) of the RNA. Finally, one may add specific ICD inhibitors to the reaction mixture.
In a first preferred aspect of embodiment (1), the ICD activity is reduced due to partial or complete reduction of ICD expression. “Reducing the expression of at least one ICD in a microorganism” refers to any reduction of expression in a microorganism in comparison to an initial microorganism with a given ICD expression level. This, of course, assumes that the comparison is made for comparable host cell types, comparable genetic background situations etc. Preferably, the reduction of expression is achieved as listed above or described in the following.
In a particular aspect of present invention, the microorganism has lost its initial ICD activity due to a decrease in ICD expression, preferably a decrease by at least about 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100%, with the extent of reduction of expression being determined in comparison to the level of expression of the polypeptide in an initial microorganism. The extent of reduction of expression is determined in comparison to the level of expression of the endogenous ICD that is expressed from the initial icd nucleotide sequence in an intial microorganism under comparable conditions.
In organisms possessing more than one ICD encoding gene and/or more than one kind of ICD, the reduction of ICD expression may concern one, several or all icd genes. A specific reduction of expression of less than all icd genes is preferred for the reasons indicated above in context with the incomplete loss of ICD.
In one preferred aspect, “reduction of expression” means the situation that if one replaces an endogenous nucleotide sequence coding for a polypeptide with a modified nucleotide sequence that encodes for a polypeptide of substantially the same amino acid sequence and/or function, a reduced amount of the encoded polypeptide will be expressed within the modified cells.
A specific aspect of this downregulation mode is the knock-out of the icd gene (compare example 4). It may be achieved by any known knock-out protocol suitable for the microorganism in question. Particularly preferred methods for knock-out and for production of fine chemicals using the resulting knock-out mutants are described in example 4.
The knock-out of the icd may lead to complete or near-complete loss of ICD activity. Thus, in order to avoid deficiency symptoms and to keep the microorganism alive, a supplementation of the culturing media with deficient ICD-dependent products like glutamate may be necessary for knock-out mutants.
In a further preferred aspect, “reduction of expression” means the down-regulation of expression by antisense technology or RNA interference (where applicable, e.g. in eucaryotic cell cultures) to interfere with gene expression. These techniques may affect icd mRNA levels and/or icd translational efficiency.
In yet a further preferred aspect, “reduction of expression” means the deletion or disruption of the icd gene combined with the introduction of a “weak” icd gene, i.e. a gene encoding an ICD whose enzymatic activity is lower than the initial ICD activity, or by integration of the icd site at a weakly expressed site resulting in less ICD activity inside the cell. This may be done by integrating the icd gene at a chromosomal locus from which genes are less well transcribed, or by introducing a mutant or heterologous icd gene with lower specific activity or which is less efficiently transcribed, less efficiently translated or less stable in the cell. The introduction of this mutant icd gene can be performed by using a replicating plasmid or by integration into the genome.
In yet a further preferred aspect, “reduction of expression” means that the reduced ICD activity is the result of lowering the mRNA levels by lowering transcripton from the chromosomally encoded icd gene, preferably by mutation of the initial promoter or replacement of the initial ICD promoter by a weakened version of said promoter or by a weaker heterologous promoter. Particularly preferred methods for performing this aspect and for production of fine chemicals using the resulting mutants are described in example 6.
In yet a further preferred aspect, “reduction of expression” means that the reduced ICD activity is the result of RBS mutation leading to a decreased binding of ribosomes to the translation initiation site and thus to a decreased translation of icd mRNA. The mutation can either be a simple nucleotide change and/or also affect the spacing of the RBS in relation to the start codon. To achieve these mutations, a mutant library containing a set of mutated RBSs may be generated. A suitable RBS may be selected, e.g. by selecting for lower ICD activity. The initial RBS may then be replaced by the selected RBS. Particularly preferred methods for performing this aspect and for production of fine chemicals using the resulting mutants are described in example 6.
In yet a further preferred aspect, “reduction of expression” is achieved by lowering mRNA levels by decreasing the stability of the mRNA, e.g. by changing the secondary structure.
In yet a further preferred aspect, “reduction of expression” is achieved by icd regulators, e.g. transcriptional regulators.
A specific method for dowregulating ICD expression in yet a further preferred aspect is the codon usage method described in PCT/EP2007/061151, which is hereby incorporated by reference inasfar as application of the codon usage method for downregulating ICD activity in microorganisms, especially in Corynebacterium and E. coli is concerned. PCT/EP2007/061151 describes a method of reducing the amount of at least one polypeptide in a host cell, comprising the step of expressing in said host cell a modified nucleotide sequence instead of a non-modified nucleotide sequence encoding for a polypeptide of substantially the same amino acid sequence and/or function wherein said modified nucleotide sequence is derived from the non-modified nucleotide sequence such that at least one codon of the non-modified nucleotide sequence is replaced in the modified nucleotide sequence by a less frequently used codon according to the codon usage of the host cell.
In case of modified nucleotide sequences that are to be expressed in Corynebacterium and particularly preferably in C. glutamicum for reducing the amount of the ICD, at least one, at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, preferably at least 1%, at least 2%, at least 4%, at least 6%, at least 8%, at least 10%, more preferably at least 20%, at least 40%, at least 60%, at least 80%, even more preferably at least 90% or least 95% and most preferably all of the codons of the non-modified nucleotide sequences may be replaced in the modified nucleotide sequence by less frequently used codons for the respective amino acid. In an even more preferred embodiment the afore-mentioned number of codons to be replaced refers to frequent, very frequent, extremely frequent or the most frequent codons. In another particularly preferred embodiment, the above number of codons are replaced by the least frequently used codons. In all these cases will the reference codon usage be based on the codon usage of the Corynebacterium and preferably C. glutamicum and preferably on the codon usage of abundant proteins of Corynebacterium and preferably C. glutamicum. See also PCT/EP2007/061151 for detailed explanation.
A particularly preferred aspect of the invention relates to a method wherein the decrease of the expression of isocitrate dehydrogenase in a microorganism is achieved by adapting the codon usage as described in PCT/EP2007/061151. The microorganism can be a Corynebacterium, with C. glutamicum being preferred. These methods may be used to improve synthesis of amino acids and particularly of methionine and/or lysine as well as of derivatives thereof and derivatives of the precursors of said amino acids, such as 1,5-diaminopentane, β-lysine and dipicolinate. Thus, microorganisms with a reduced ICD activity due to application of the codon usage method described in PCT/EP2007/061151 are in one preferred aspect of present invention the microorganisms of choice for performing the method according to embodiment (1). Microorganisms with a reduced ICD activity due to replacement of their start codon, e.g. of ATG, are particularly preferred, especially a microorganism wherein the start codon ATG has been replaced by GTG. PCT/EP2007/061151 does especially describe the reduction of ICD in C. glutamicum cells by replacement of the start codon with GTG in one embodiment and by change of a glycine and an isoleucine codon from GGC ATT to GGG ATA at positions 32 and 33 of native ICD (compare SEQ ID NO:3 versus SEQ ID Nos:4 to 7). These two embodiments of PCT/EP2007/061151 are the methods of choice for reduction of ICD activity in one aspect of the production method of embodiment (1) and their use in the method according to embodiment (1) of present invention is therefore specifically incorporated by reference. Their preparation and use is demostrated in examples 1 and 3. The microorganisms described in said examples are preferred embodiments of present invention, particularly the strain ICD ATG GTG.
On the other hand, in a different particularly preferred aspect of present invention, microorganisms with a reduced ICD activity due to application of the codon usage method described in PCT/EP2007/061151 are excluded from being the microorganisms of choice in the method according to embodiment (1). According to said aspect, the method of embodiment (1) is an embodiment of present invention with the proviso that the reduction of ICD expression is not due to the expression of a modified ICD encoding nucleotide sequence (icd sequence) instead of the native icd sequence of the microorganism wherein said modified icd encoding sequence is derived from the non-modified icd sequence such that at least one codon of the non-modified nucleotide sequence is replaced in the modified icd sequence by a less frequently used codon according to the codon usage of the host cell. In other words, the method of embodiment (1) is an embodiment of present invention with the proviso that the reduction of ICD expression is not due to modified codon usage as described in PCT/EP2007/061151 and that no microorganism described in PCT/EP2007/061151 is used. More preferably, the method of embodiment (1) is an embodiment of present invention with the proviso that, when the fine chemicals are selected from the group consisting of lysine, threonine and methionine, the reduction of ICD expression is not due to the expression of a modified ICD encoding nucleotide sequence (icd sequence) instead of the native icd sequence of the microorganism wherein said modified icd encoding sequence is derived from the non-modified icd sequence such that at least one codon of the non-modified nucleotide sequence is replaced in the modified icd sequence by a less frequently used codon according to the codon usage of the microorganism.
Said provisos do not apply to production of fine chemicals with a microorganism whose ICD expression is reduced due to modified codon usage as described in PCT/EP2007/061151 and which in addition comprises a heterologous enzyme catalyzing the conversion of an endogenous biosynthetic intermediate or final product of the microorganism into a non-native target compound of the fine chemical synthesis (see below). Preferably, said heterologous enzyme is selected from the group consisting of enzymes catalyzing one or more steps in the synthesis or biosynthesis of fine chemicals, particularly of fine chemicals derivable from lysine or its biochemical precursors downstream of aspartate via enzymatic conversion. More preferably, it is an enzyme catalyzing a decarboxylation, a deamination, a transamination, the shift of an amino group along an organic molecule, an oxidation and/or cyclisation reaction. Even more preferably, it is selected from the group consisting of dipicolinate synthase, lysine decarboxylase and lysine 2,3-aminomutase. Particularly preferred is a microorganism comprising a heterologous dipicolinate synthase, lysine decarboxylase or lysine 2,3-aminomutase. In other words, in this particularly preferred embodiment, the microorganism may have reduced ICD activity due to modified codon usage as described in PCT/EP2007/061151 and may even be a microorganism described in PCT/EP2007/061151, but additionally comprises a heterologous dipicolinate synthase, lysine decarboxylase or lysine 2,3-aminomutase.
The preparation of fine chemicals according to embodiment (1) of present invention may be performed with a microorganism whose ICD acitivity is reduced due to codon usage as described in PCT/EP2007/061151 if the fine chemical is none of the fine chemicals listed in PCT/EP2007/061151. Therefore, as the biochemical precursors of amino acids in the biochemical pathways downstream of aspartate (e.g. precursors of the amino acids lysine, methionine, threonine and isoleucine, like 2,3-dihydrodipicolinate, diaminopimelate, homoserine, homocysteine and 2,3-dihydroxy-3-methylvalerate), and native or non-native derivatives of said amino acids or biochemical precursors are not listed as products of the microorganisms described in PCT/EP2007/061151, a compound selected from said group of precursors and derivatives is the preferred product of the method according to embodiment (1). Even more preferred is the preparation of a derivate, preferably a non-native derivate, of said amino acids or precursors, particularly of lysine or one of its native precursors downstream of aspartate (e.g. 2,3-dihydrodipicolinate). Especially preferred is the preparation of a compound selected from the group consisting of 1,5-diaminopentane (cadaverine), β-lysine and dipicolinate.
In a second preferred aspect of embodiment (1), the ICD activity is reduced due to partial or complete inhibition of the enzyme. The inhibition may be the result of binding of any known reversible or irreversible ICD inhibitor to ICD. Such inhibitors are known in the art, e.g. oxaloacetate, 2-oxoglutarate and citrate which are known as weak inhibitors of ICD in C. glutamicum, or oxaloacetate plus glyoxylate, which are known as strong inhibitors (Eikmanns et al (1995) loc. cit.). Said inhibitor may either be added to the fermentation medium, or its synthesis inside the cell may be induced by an external stimulus.
In several preferred aspects of embodiment (1) and (2), the reduced ICD activity is the result of genetically engineering a host cell (preferably a microorganism, especially a Corynebacterium), but not the result of reduced ICD expression.
Particularly, in a third preferred aspect, deleting the initial copy of an icd gene and replacing it with a mutant version encoding an ICD that shows decreased ICD activity or with a heterologous icd gene encoding an ICD having less ICD activity than the initial ICD, leads to a decrease in ICD activity of the microorganism of present invention. Particularly preferred methods for performing this aspect and for production of fine chemicals using the resulting mutants are described in example 5.
In a fourth preferred aspect, a combination of two or more of the aforementioned features leading to ICD activity reduction is realized in the microorganism according present invention.
A preferred method in accordance with embodiment (1) of the present invention comprises the step of reducing the ICD acitivity in a microorganism, preferably in Corynebacteria and more preferably in C. glutamicum, wherein the above principles are used.
The increase in biosysnthesis of members of the aspartate family and of their precursors formed by biotransformation of aspartate in a microorganism with reduced ICD activity may be due to an increased carbon flux through PPP and glyoxylate shunt as a result of ICD inhibition. The former leads to provision of sufficient reduction equivalents, i.e. NAD(P)H, for amino acid production, the latter provides the necessary carbon precursors for biosynthesis of amino acids of the aspartate family. Thus, in one preferred aspect of present invention, in the microorganism used in embodiment (1) or the microorganism according to embodiment (2), the carbon flux through
(i) the glyoxylate shunt and/or
(ii) the pentose phosphate pathway (PPP)
is increased in comparison to a wild-type microorganism. Preferably, the carbon flux through the glyoxylate shunt is increased. Any of said increases may be the result of the ICD activity reduction, the result of genetically engineering the microorganism, a native trait of the microorganism, or a combination of any of these factors. The increased carbon flux through the glyoxylate shunt is preferably the result of the ICD activity reduction and/or of genetically engineering the microorganism. The increased carbon flux through PPP is preferably the result of genetically engineering the microorganism, more preferably the result of an active upregulation of the PPP enzyme expression level, e.g. by using a strong promoter like Psod (WO 2005/059144).
As indicated above, the present invention pertains to microorganisms and to the use of microorganisms in fine chemical production. However, the use of other organisms besides microorganisms in the production method according to embodiment (1) and instead of the microorganism according to embodiment (2) is also contemplated. The term “organism” for the purposes of the present invention refers to any non-human organism that is commonly used for expression of nucleotide sequences for production of fine chemicals, in particular microorganisms as defined above, plants including algae and mosses, yeasts, and non-human animals. Organisms besides microorganisms which are particularly suitable for fine chemical production are plants and plant parts. Such plants may be monocots or dicots such as monocotyledonous or dicotyledonous crop plants, food plants or forage plants. Examples for monocotyledonous plants are plants belonging to the genera of avena (oats), triticum (wheat), secale (rye), hordeum (barley), oryza (rice), panicum, pennisetum, setaria, sorghum (millet), zea (maize) and the like.
Dicotyledonous crop plants comprise inter alia cotton, leguminoses like pulse and in particular alfalfa, soybean, rapeseed, tomato, sugar beet, potato, ornamental plants as well as trees. Further crop plants can comprise fruits (in particular apples, pears, cherries, grapes, citrus, pineapple and bananas), oil palms, tea bushes, cacao trees and coffee trees, tobacco, sisal as well as, concerning medicinal plants, rauwolfia and digitalis. Particularly preferred are the grains wheat, rye, oats, barley, rice, maize and millet, sugar beet, rapeseed, soy, tomato, potato and tobacco. Further crop plants can be taken from U.S. Pat. No. 6,137,030.
The person skilled in the art is well aware that different organisms and cells such as microorganisms, plants and plant cells, animals and animal cells etc. will differ with respect to the number and kind of icd genes and ICD proteins in a cell. Even within the same organism, different strains may show a somewhat heterogeneous expression profile on the protein level.
In case an organism different from a microorganism is used in performing the present invention, a non-fermentative production method may be applied.
In present invention according to embodiments (1), (2), (3) and (4), any microorganism as defined above may be used. Preferably, the microorganism is a prokaryote. Particularly preferred for performing the present invention are microorganisms being selected from the genus of Corynebacterium and Brevibacterium, preferably Corynebacterium, with a particular focus on Corynebacterium glutamicum, the genus of Escherichia with a particular focus on Escherichia coli, the genus of Bacillus, particularly Bacillus subtilis, the genus of Streptomyces and the genus of Aspergillus.
A preferred embodiment of the invention relates to the use of microorganisms which are selected from coryneform bacteria such as bacteria of the genus Corynebacterium. Particularly preferred are the species Corynebacterium glutamicum, Corynebacterium acetoglutamicum, Corynebacterium acetoacidophilum, Corynebacterium callunae, Corynebacterium ammoniagenes, Corynebacterium thermoaminogenes, Corynebacterium melassecola and Corynebacterium effiziens. Other preferred embodiments of the invention relate to the use of Brevibacteria and particularly the species Brevibacterium flavum, Brevibacterium lactofermentum and Brevibacterium divarecatum.
In preferred embodiments of the invention the microorganism may be selected from the group consisting of Corynebacterium glutamicum ATCC13032, C. acetoglutamicum ATCC15806, C. acetoacidophilum ATCC13870, Corynebacterium thermoaminogenes FERMBP-1539, Corynebacterium melassecola ATCC17965, Corynebacterium effiziens DSM 44547, Corynebacterium effiziens DSM 44549, Brevibacterium flavum ATCC14067, Brevibacterium lactoformentum ATCC13869, Brevibacterium divarecatum ATCC 14020, Corynebacterium glutamicum KFCC10065 and Corynebacterium glutamicum ATCC21608 as well as strains that are derived thereof by e.g. classical mutagenesis and selection or by directed mutagenesis.
Other preferred strains of C. glutamicum may be selected from the group consisting of ATCC13058, ATCC13059, ATCC13060, ATCC21492, ATCC21513, ATCC21526, ATCC21543, ATCC13287, ATCC21851, ATCC21253, ATCC21514, ATCC21516, ATCC21299, ATCC21300, ATCC39684, ATCC21488, ATCC21649, ATCC21650, ATCC19223, ATCC13869, ATCC21157, ATCC21158, ATCC21159, ATCC21355, ATCC31808, ATCC21674, ATCC21562, ATCC21563, ATCC21564, ATCC21565, ATCC21566, ATCC21567, ATCC21568, ATCC21569, ATCC21570, ATCC21571, ATCC21572, ATCC21573, ATCC21579, ATCC19049, ATCC19050, ATCC19051, ATCC 19052, ATCC19053, ATCC19054, ATCC 19055, ATCC19056, ATCC19057, ATCC 19058, ATCC19059, ATCC19060, ATCC 19185, ATCC13286, ATCC21515, ATCC21527, ATCC21544, ATCC21492, NRRL B8183, NRRL W8182, B12NRRLB12416, NRRLB12417, NRRLB12418 and NRRLB11476.
The abbreviation KFCC stands for Korean Federation of Culture Collection, ATCC stands for American-Type Strain Culture Collection and the abbreviation DSM stands for Deutsche Sammlung von Mikroorganismen and Zellkulturen. The abbreviation NRRL stands for ARS cultures collection Northern Regional Research Laboratory, Peorea, Ill., USA.
Strains of Corynebacterium glutamicum that are already capable of producing fine chemicals such as L-lysine, L-methionine, L-isoleucine and/or L-threonine are particularly preferred for performing present invention. Such a strain is e.g. Corynebacterium glutamicum ATCC13032, and especially derivatives thereof. The strains ATCC 13286, ATCC 13287, ATCC 21086, ATCC 21127, ATCC 21128, ATCC 21129, ATCC 21253, ATCC 21299, ATCC 21300, ATCC 21474, ATCC 21475, ATCC 21488, ATCC 21492, ATCC 21513, ATCC 21514, ATCC 21515, ATCC 21516, ATCC 21517, ATCC 21518, ATCC 21528, ATCC 21543, ATCC 21544, ATCC 21649, ATCC 21650, ATCC 21792, ATCC 21793, ATCC 21798, ATCC 21799, ATCC 21800, ATCC 21801, ATCC 700239, ATCC 21529, ATCC 21527, ATCC 31269 and ATCC 21526 which are known to produce lysine can also preferably be used. Particularly preferred are Corynebacterium glutamicum strains that are already capable of producing fine chemicals such as L-lysine, L-methionine and/or L-threonine. Therefore strains derived from Corynebacterium glutamicum having a feedback-resistant aspartokinase and derivatives thereof are particularly preferred. This preference encompasses strains derived from Corynebacterium glutamicum ATCC13032 having a feedback-resistant aspartokinase, and particularly concerns the strains LU11424, ATCC13032lysCfbr and ATCC13286. C. glutamicum LU11424, ATCC13032lysCfbr, ATCC13032 or ATCC13286 and derivatives thereof having a feedback-resistant aspartokinase are specifically preferred microorganisms in the context of present invention. Most preferred are LU11424, ATCC13032lysCfbr or ATCC13286 and derivatives thereof, LU11424 being especially preferred.
One may use different C. glutamicum strains for replacing the endogenous copy of icd. However, it is preferred to use a C. glutamicum lysine production strain such as for example ATCC13032 lysCfbr, LU11424 or other derivatives of ATCC13032 or ATCC13286.
ATCC13032 lysCfbr may be produced starting from ATCC13032. In order to generate such a lysine producing strain, an allelic exchange of the lysC wild type gene is performed in C. glutamicum ATCC13032. To this end a nucleotide exchange is introduced into the lysC gene such that the resulting protein carries an isoleucine at position 311 instead of threonine. The detailed construction of this strain is described in patent application WO 2005/059093. The accession no. of the lysC gene is P26512.
LU11424 may be produced as described in example 1. It is a derivative of ATCC13032 lysCfbr. The ICD activity in LU11424 is preferably reduced by replacement of ATG as start codon of the isocitrate dehydrogenase encoding nucleotide sequence, preferably by replacement of ATG with GTG. The strain described in example 1 wherein the icd start codon was changed is especially preferred in the context of present invention (i.e. the strain ICD ATG→GTG). However, any ATCC13032 derivative having one or more of the modifications listed in example 1 for LU11424 and having a reduced ICD activity is also considered to be a preferred strain for performing the present invention.
It is understood that in order to be suitable for present invention all the microorganisms listed above will display a partially or completely reduced ICD activity. Preferred microorganisms in the context of present invention are recombinant microorganisms whose reduced ICD activity is the result of genetic engineering, e.g. the strain ICD ATG→GTG described in example 1.
Embodiment (1) of present invention concerns the use of an aforementioned microorganism having a reduced ICD activity to produce fine chemicals.
The term “fine chemicals” is well known to the person skilled in the art and designates compounds which can be used in different parts of the pharmaceutical industry, agricultural industry as well as in the cosmetics, food and feed industry. The term “fine chemicals” does also include monomers for polymer synthesis.
Fine chemicals can be final products or intermediates which are needed for further synthesis steps.
In the context of present invention, the term “fine chemicals” is synonymous to “a fine chemical”, i.e. to just one kind of compound. The production of a fine chemical, i.e. just one kind of target compound, by the method and microorganism of present invention is preferred.
Fine chemicals are defined as all organic molecules which contain at least two carbon atoms and additionally at least one heteroatom which is not a carbon or hydrogen atom. Preferably the term “fine chemicals” relates to organic molecules that comprise at least two carbon atoms and additionally at least one functional group, such as an hydroxy-, amino-, thiol-, carbonyl-, carboxy-, methoxy-, ether-, ester-, amido-, phosphoester-, thioether- or thioester-group.
Fine chemicals thus preferably comprise organic acids such as lactic acid, succinic acid, tartaric acid, itaconic acid etc. Fine chemicals further comprise amino acids, purine and pyrimidine bases, nucleotides, lipids, saturated and unsaturated fatty acids such as arachidonic acid, alcohols, e.g. diols such as propandiol and butandiol, carbohydrates such as hyaluronic acid and trehalose, aromatic compounds such as vanillin, vitamins and cofactors etc. Trehalose and the fine chemicals described in the following sections are preferred.
A particularly preferred group of fine chemicals for the purposes of the present invention are biosynthetic products being selected from the group consisting of organic acids, amino acids, organic amines, and heteroaromatic compounds comprising one or two nitrogens in the aromatic ring.
More preferably, the term “fine chemicals” in the context of present invention pertains to molecules comprising at least three aromatic or aliphatic carbon atoms and additionally at least one carboxy- or amino-group, even more preferably one or two carboxy- and/or amino groups. Specifically, the fine chemicals produced by the method and/or microorganism of present invention are compounds having formula I or II or salts thereof:
wherein
R1 is —COOH or H, and R2 and R3 are independently of each other NH2 or H; and wherein the following combinations are preferred:
R1=COOH, R2=NH2, R3=H; R1=H, R2=NH2, R3=H; R1=COOH, R2=H, R3=NH2.
As outlined above, the method according to embodiment (1) is particularly suitable for producing a compound selected from the group consisting of
The production of non-native derivatives, especially non-native enzymatic derivatives, and of amino acids is preferred. Of these, the production of a non-native derivative of lysine or of a non-native derivative of one of its precursors, i.e. of an intermediate in the bioconversion of aspartate into lysine, is preferred.
Specifically preferred final products of the method according to present invention are selected from the group consisting of lysine, methionine, threonine, isoleucine, 1,5-diaminopentane, β-lysine and dipicolinate. More preferably, the final products are selected from the derivatives (iii) comprised in the group of preferred final products, i.e. from the group consisting of 1,5-diaminopentane, β-lysine and dipicolinate. The production of 1,5-diaminopentane (cadverine) is most preferred.
As outlined above, it is preferred that in the method of embodiment (1) a compound selected from the group consisting of the amino acids of the aspartate family and their biochemical precursors is produced as intermediate or final product. In one aspect, an amino acid selected from the group consisting of aspartate, lysine, methionine, isoleucine and threonine is the final product of the method according to embodiment (1), wherein lysine, methionine, isoleucine and threonine, and especially lysine are preferred as final products. The L-enantiomers are especially preferred. In a second aspect, a biochemical precursor of an amino acid selected from the group consisting of lysine, methionine, isoleucine and threonine, which lies downstream of aspartate in the biosynthesis of the respective amino acid is the final product of the method according to embodiment (1).
In a third aspect, said amino acid or amino acid precursor is an intermediate product and is subsequently converted enzymatically or nonenzymatically into an derivative thereof, preferably into an organic amine, organic acid, or amino acid, in the method according to embodiment (1). Preferably, the final product is a non-native derivative of said intermediate product. A particularly preferred intermediate product which is subsequently converted is lysine or one of its biochemical precursors downstream of aspartate. Of said precursors, dihydrodipicolinate is especially preferred.
In said third aspect, the term “derivative” means any chemical compound derivable from (i) the amino acids of the aspartate family or (ii) their biochemical precursors in the biochemical pathways downstream of aspartate by enzymatic or non-enzymatic conversions, enzymatic conversions being preferred. Preferably, the conversion results in at least one of the following:
(i) the removal of one or two carboxyl groups;
(ii) the removal of one amino group;
(iii) the shift of one amino group; and/or
(iv) a dehydrogenation.
In said third aspect, said subsequent conversion is preferably an enzymatic conversion or does at least comprise one enzymatic step. The enzyme catalyzing said conversion may be endogenous or heterologous to the microorganism with reduced ICD activity. It is preferably heterologous.
The subsequent conversion preferably happens in the reaction mixture comprising the microorganism as defined in embodiment (1). It may be catalyzed by an isolated enzyme added to the reaction mixture, by a second microorganism besides the microorganism with reduced ICD activity, or by the microorganism with reduced ICD activity itself. It preferably is catalyzed by the microorganism with reduced ICD activity itself.
A preferred aspect of the method according to embodiment (1) therefore comprises the subsequent enzymatic conversion as defined above taking place in the microorganism with a partially or completely reduced ICD activity. In the method according to this preferred aspect, the microorganism preferably comprises at least one heterologous enzyme catalyzing a reaction step in the subsequent conversion of the endogenous intermediate to the final product of the method.
Said heterologous enzyme in the microorganism with reduced ICD activity may be any enzyme which is able to convert an endogenous biosynthetic intermediate or final product of the microorganism into the target compound of the fine chemical synthesis. Preferably, it is selected from the group consisting of enzymes catalyzing one or more steps in the synthesis or biosynthesis of fine chemicals, particularly of fine chemicals derivable from lysine or its biochemical precursors downstream of aspartate via enzymatic conversion. More preferably, it is an enzyme catalyzing a decarboxylation, a deamination, a transamination, the shift of an amino group along an organic molecule, an oxidation and/or cyclisation reaction. Even more preferably, it is selected from the group consisting of dipicolinate synthase, lysine decarboxylase and lysine 2,3-aminomutase. Particularly preferred is a microorganism comprising a heterologous dipicolinate synthase, lysine decarboxylase or lysine 2,3-aminomutase.
Thus, in an especially preferred aspect of the method according to embodiment (1), the microorganism comprises at least one heterologous enzyme as defined in the previous section. Particularly preferred is the use of a microorganism optimized for the preparation of one of the products selected from the group consisting of dipicolinate, 1,5-diaminopentane and β-lysine as follows: dipicolinate: microorganism with heterologous dipicolinate synthase; 1,5-diaminopentane: microorganism with heterologous lysine decarboxylase; β-lysine: microorganism with heterologous lysine 2,3-aminomutase.
For each of the preferred final products of the method according to embodiment (1), a microorganism may be used which does not only possess reduced ICD activity, but is also specifically adapted for production of the desired final product. This adaptation may be due to a repression or reduction of enzyme activities known to be responsible for the synthesis of unwanted by-products/side products. Lowering the amount or activity of an enzyme that forms part of a biosynthetic pathway may allow increasing synthesis of the aforementioned fine chemicals by e.g. shutting off production of by-products and by channelling metabolic flux into a preferred direction.
On the other hand, this adaptation may be due to an increased activity of enzymes or metabolic pathways known to enhance fine chemical production. It is preferred that said adaption of the microorganism encompasses an increase of activity and/or expression of an enzyme which catalyzes one or more than one of the conversion steps leading up to the desired final product, in particular of an enzyme catalyzing a conversion step downstream of aspartate, more particularly of an enzyme catalysing a conversion step in the conversion of aspartate to lysine or a heterologous enzyme catalyzing the conversion of an endogenous biosynthetic intermediate or final product of the microorganism into a non-native target compound of the fine chemical synthesis. It is further preferred that said adaptation is due to genetic engineering leading to the presence of at least one heterologous enzyme in the microorganism which enhances the production of the target fine chemical or is even essential for said production as the wild-type microorganism is unable to synthesize the target compound.
Thus, in the aspect of the method according to embodiment (1) wherein the target compound of the production method (1) is 1,5-diaminopentane (cadaverine), a particularly preferred microorganism for performing said method has not only a reduced ICD activity, but in addition comprises a lysine decarboxylase. Said decarboxylase is preferably a heterologous (recombinant) lysine decarboxylase. The microorganism has the ability to produce lysine and to convert it into cadaverine.
More preferably, the lysine decarboxylase is a heterologous lysine decarboxylase as described in WO 2007/113127. Lysine decarboxylase (EC 4.1.1.18) catalyzes the decarboxylation of L-lysine into cadaverine. The enzymes from E. coli having lysine decarboxylase activity are the cadA (SEQ ID NO:10) gene product (SEQ ID NO:11; Kyoto Encyclopedia of Genes and Genomes, Entry b4131) and the ldcC (SEQ ID NO:12) gene product (SEQ ID NO:13; Kyoto Encyclopedia of Genes and Genomes, Entry JW0181).
DNA molecules encoding the E. coli lysine decarboxylase can be obtained by screening cDNA or genomic libraries with polynucleotide probes having nucleotide sequences reverse-translated from the amino acid sequence of SEQ ID NO:11 or 13.
Alternatively, the E. coli lysine decarboxylase genes can be obtained by synthesizing DNA molecules using mutually priming long oligonucleotides or PCR. See, for example, Ausubel et al., (eds.), CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, pages 8.2.8 to 8.2.13 (1990), Wosnick et al., Gene 60:115 (1987); Ausubel et al. (eds.), SHORT PROTOCOLS IN MOLECULAR BIOLOGY, 3rd Edition, pages 8-8 to 8-9, John Wiley & Sons, Inc. (1995); and the further citations provided in WO 2007/113127 in connection with DNA synthesis, which are hereby incorporated by reference.
Variants of E. coli lysine decarboxylase that contain conservative amino acid changes as defined above in comparison to the parent enzyme may also be used. See also WO 2007/113127.
Conservative amino acid changes in the E. coli lysine decarboxylase can be introduced by substituting nucleotides for the nucleotides recited in SEQ ID NO:10 or 12. Such “conservative amino acid” variants can be obtained, for example, by oligonucleotide-directed mutagenesis, linker-scanning mutagenesis, mutagenesis using the polymerase chain reaction, and the like. Ausubel et al., supra, at pages 8.0.3-8.5.9; Ausubel et al. (eds.), SHORT PROTOCOLS IN MOLECULAR BIOLOGY, 3rd Edition, pages 8-10 to 8-22 (John Wiley & Sons, Inc. 1995). Also see generally, McPherson (ed.), DIRECTED MUTAGENESIS: A PRACTICAL APPROACH, IRL Press (1991). The ability of such variants to convert L-lysine to cadaverine can be determined using a standard enzyme activity assay, such as the assay described in WO 2007/113127.
Preferred lysine decarboxylases in the context of present invention are the lysine decarboxylase from E. coli and homologues thereof which have up to 80%, preferably 90% and most preferred 95% or 98% sequence identity (based on amino acid sequence) with the corresponding “original” gene product and have still the biological activity of lysine decarboxylase. These homologous genes can be easily constructed by introducing nucleotide substitutions, deletions or insertions by methods known in the art. The lysine decarboxylase of E. coli (SEQ ID NO:11 and NO:13) may also be retranslated into DNA by applying the codon usage of Corynebacterium glutamicum. These lysine decarboxylase polynucleotide sequences are useful for expression of lysine decarboxylase in a microorganism of the genus Corynebacterium, especially C. glutamicum.
An even more particularly preferred microorganism for the production of 1,5-diaminopentane has not only a reduced ICD activity and comprises a lysine decarboxylase, but does also comprise at least one additional up- or down-regulated gene encoding an enzyme playing a key role in the biosynthesis of lysine as described in WO 2007/113127. The microorganisms specifically described in WO 2007/113127 and additionally possessing the reduced ICD activity necessary for performing the present invention are most preferred for production of cadaverine. In a specifically preferred aspect, the gene diamine acetyltransferase is down-regulated, i.e. the gene is either inactivated completely or the gene activity is reduced. The sequence of diamine acetyltransferase is described in WO 2007/113127.
In the aspect of the method according to embodiment (1) wherein the target compound is β-lysine, a particularly preferred microorganism for performing said method has not only a reduced ICD activity, but in addition comprises a lysine-2,3-aminomutase. Said aminomutase is preferably a heterologous (recombinant) lysine-2,3-aminomutase. The microorganism has the ability to produce lysine and to convert it into β-lysine.
More preferably, the lysine-2,3-aminomutase is a heterologous lysine-2,3-aminomutase as described in WO 2007/101867. Lysine 2,3-aminomutase catalyzes the reversible isomerization of L-lysine into β-lysine. The enzyme isolated from Clostridium subterminale strain SB4 is a hexameric protein of apparently identical subunits, which has a molecular weight of 285,000, as determined from diffusion and sedimentation coefficients (Chirpich et al., J. Biol. Chem. 245:1778 (1970); Aberhart et al., J. Am. Chem. Soc. 105:5461 (1983); Chang et al., Biochemistry 35:11081 (1996)). The clostridial enzyme contains iron-sulfur clusters, cobalt and zinc, and pyridoxal 5′-phosphate, and it is activated by S-adenosylmethionine. Unlike typical adenosylcobalamin-dependent aminomutases, the clostridial enzyme does not contain or require any species of vitamin B12 coenzyme. The nucleotide and predicted amino acid sequences of clostridial lysine 2,3-aminomutase (SEQ ID NOs:14 and 16) are disclosed in U.S. Pat. No. 6,248,874 B1.
DNA molecules encoding the clostridial lysine 2,3-aminomutase can be obtained by screening cDNA or genomic libraries with polynucleotide probes having nucleotide sequences reverse-translated from the amino acid sequence of SEQ ID NO:16 or with polynucleotide probes having nucleotide sequences based upon SEQ ID NO:14. For example, a suitable library can be prepared by obtaining genomic DNA from Clostridium subterminale strain SB4 (ATCC No. 29748) and constructing a library according to standard methods. See, for example, Ausubel et al. (eds.), SHORT PROTOCOLS IN MOLECULAR BIOLOGY, 3rd Edition, pages 2-1 to 2-13 and 5-1 to 5-6 (John Wiley & Sons, Inc. 1995).
Alternatively, the lysine 2,3-aminomutase genes can be obtained by synthesizing DNA molecules using mutually priming long oligonucleotides or PCR. See, for example, Ausubel et al., (eds.), CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, pages 8.2.8 to 8.2.13 (1990), Wosnick et al., Gene 60:115 (1987); Ausubel et al. (eds.), SHORT PROTOCOLS IN MOLECULAR BIOLOGY, 3rd Edition, pages 8-8 to 8-9, John Wiley & Sons, Inc. (1995); and the further citations provided in WO 2007/113127 and WO 2007/101867 in connection with DNA synthesis, which are hereby incorporated by reference.
Variants of lysine 2,3-aminomutase that contain conservative amino acid changes as defined above in comparison to the parent enzyme may also be used. See also WO 2007/101867.
Conservative amino acid changes in the lysine 2,3-aminomutase can be introduced by substituting nucleotides for the nucleotides recited in SEQ ID NO:14. Such “conservative amino acid” variants can be obtained, for example, by oligonucleotide-directed mutagenesis, linker-scanning mutagenesis, mutagenesis using the polymerase chain reaction, and the like. Ausubel et al., supra, at pages 8.0.3-8.5.9; Ausubel et al. (eds.), SHORT PROTOCOLS IN MOLECULAR BIOLOGY, 3rd Edition, pages 8-10 to 8-22 (John Wiley & Sons, Inc. 1995). Also see generally, McPherson (ed.), DIRECTED MUTAGENESIS: A PRACTICAL APPROACH, IRL Press (1991). The ability of such variants to convert L-lysine to β-lysine can be determined using a standard enzyme activity assay, such as the assay described in WO 2007/101867.
Lysine-2,3-aminomutases from other sources than from Clostridium subterminale, e.g. from Bacillus subtilis or from Escherichia coli have been disclosed in U.S. Pat. No. 6,248,874 B1. The parts of this US patent dealing with the isolation, SEQ ID NOs and expression of lysine-2,3-aminomutases are herewith incorporated by reference expressly.
Preferred lysine-2,3-aminomutases for use in present invention are the lysine-2,3-aminomutase from Clostridium subterminale, Bacillus subtilis and Escherichia coli and their homologues having up to 80%, preferably 90%, most preferred 95% and 98% sequence identity (based on amino acid sequence) with the corresponding native amino acid sequence and have still the biological activity of lysine 2,3-aminomutase. These homologues can be easily be constructed by introducing nucleotide substitutions, deletions or insertions by methods known in the art.
Another preferred lysine-2,3-aminomutase is the lysine-2,3-aminomutase from Clostridium subterminale (SEQ ID NO:2 of U.S. Pat. No. 6,248,874 B1) which is retranslated into DNA by applying the codon usage of Corynebacterium glutamicum (SEQ ID NO:15). This lysine-2,3-aminomutase polynucleotide sequence is useful for expression of lysine 2,3-aminomutase in a microorganism of the genus Corynebacterium, especially C. glutamicum.
An even more particularly preferred microorganism for the production of β-lysine has not only a reduced ICD activity and comprises a lysine-2,3-aminomutase, but does also comprise at least one additional up- or downregulated gene encoding an enzyme playing a key role in the lysine biosynthesis as described in WO 2007/101867. The microorganisms specifically described in WO 2007/101867 and additionally possessing the reduced ICD activity necessary for performing the present invention are most preferred for production of β-lysine.
In the aspect of the method according to embodiment (1) wherein the target compound is dipicolinate, a particularly preferred microorganism for performing said method has not only a reduced ICD activity, but in addition comprises a dipicolinate synthetase. Said dipicolinate synthetase is preferably a heterologous (recombinant) dipicolinate synthetase. The microorganism has the ability to produce 2,3-dihydropicolinate and to convert it into dipicolinate.
More preferably, the dipicolinate synthetase is a heterologous dipicolinate synthetase as described in EP 08151031.5.
The fermentative production of DPA following the method according to embodiment (1) of present application comprises the cultivation of at least one recombinant microorganism with reduced ICD activity, having the ability to produce lysine via the diaminopimelate (DAP) pathway with dihydrodipicolinate, in particular L-2,3-dihydrodipicolinate, as intermediary product, and additionally having the ability to express heterologous dipicolinate synthetase, so that dihydrodipicolinate, in particular L-2,3-dihydrodipicolinate is converted into DPA.
In particular, said parent microorganism is a lysine producing bacterium, preferably a coryneform bacterium. In particular, said parent microorganism is a bacterium of the genus Corynebacterium, as for example Corynebacterium glutamicum.
Said heterologous dipicolinate synthetase is of prokaryotic or eukaryotic origin. For example, said heterologous dipicolinate synthetase may originate from a bacterium of the genus Bacillus, in particular from Bacillus subtilis. Said Bacillus enzyme is composed of alpha and beta subunits as described in EP 08151031.5. In a further embodiment of the method of the invention the heterologous dipicolinate synthetase comprises at least one alpha subunit having an amino acid sequence according to SEQ ID NO:2 of EP 08151031.5 or a sequence having at least 80% identity thereto, as for example at least 85, 90, 92, 95, 96, 97, 98 or 99% sequence identity; and at least one beta subunit having an amino acid sequence according to SEQ ID NO:3 of EP 08151031.5 or a sequence having at least 80% identity thereto, as for example at least 85, 90, 92, 95, 96, 97, 98 or 99% sequence identity.
The enzyme having dipicolinate synthetase activity may be encoded by a nucleic acid sequence, which is adapted to the codon usage of said parent microorganism having the ability to produce lysine.
For example, the enzyme having dipicolinate synthetase activity may be encoded by a nucleic acid sequence comprising
a) the spoVF gene sequence according to SEQ ID NO:17 (SEQ ID NO:1 of EP 08151031.5), or
b) a synthetic spoVF gene sequence comprising a coding sequence essentially from residue 193 to residue 1691 according to SEQ ID NO:4 of EP 08151031.5; or
c) any nucleotide sequence encoding a dipicolinate synthetase or its alpha and/or beta subunits as defined above.
DNA molecules encoding the dipicolinate synthetase can be obtained by screening cDNA or genomic libraries with polynucleotide probes having nucleotide sequences reverse-translated from the amino acid sequence of SEQ ID NO:19 or 20 or with polynucleotide probes having nucleotide sequences based upon SEQ ID NO:17. Alternatively, the dipicolinate synthetase genes can be obtained by synthesizing DNA molecules using mutually priming long oligonucleotides or PCR. See, for example, Ausubel et al., (eds.), CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, pages 8.2.8 to 8.2.13 (1990), Wosnick et al., Gene 60:115 (1987); Ausubel et al. (eds.), SHORT PROTOCOLS IN MOLECULAR BIOLOGY, 3rd Edition, pages 8-8 to 8-9, John Wiley & Sons, Inc. (1995); and the further citations provided in WO 2007/113127 and WO 2007/101867 in connection with DNA synthesis, which are hereby incorporated by reference.
Variants of dipicolinate synthetase that contain conservative amino acid changes as defined above in comparison to the parent enzyme may also be used. See also EP 08151031.5.
Conservative amino acid changes in the dipicolinate synthetase can be introduced by substituting nucleotides for the nucleotides recited in SEQ ID NO:17. Such “conservative amino acid” variants can be obtained, for example, by oligonucleotide-directed mutagenesis, linker-scanning mutagenesis, mutagenesis using the polymerase chain reaction, and the like. Ausubel et al., supra, at pages 8.0.3-8.5.9; Ausubel et al. (eds.), SHORT PROTOCOLS IN MOLECULAR BIOLOGY, 3rd Edition, pages 8-10 to 8-22 (John Wiley & Sons, Inc. 1995). Also see generally, McPherson (ed.), DIRECTED MUTAGENESIS: A PRACTICAL APPROACH, IRL Press (1991). The ability of such variants to convert 2,3-dihydrodipicolinate into DPA can be determined using a standard enzyme activity assay.
Another preferred dipicolinate synthetase is the dipicolinate synthetase from B. subtilis which is retranslated into DNA by applying the codon usage of Corynebacterium glutamicum (SEQ ID NO:18). This dipicolinate synthetase polynucleotide sequence is useful for expression of dipicolinate synthetase in a microorganism of the genus Corynebacterium, especially C. glutamicum.
An even more particularly preferred microorganism for the production of dipicolinate has not only a reduced ICD activity and comprises a dipicolinate synthetase, but does also comprise at least one additional up- or downregulated gene encoding an enzyme playing a key role in the lysine biosynthesis as described in EP 08151031.5. Particularly, a microorganism wherein one or more of the enzymes downstream of dihydrodipicolinate are downregulated, especially the enzyme converting dihydrodipicolinate itself, is preferred, as in these microorganisms the carbon loss into the native lysine biosynthesis starting fron dihydrodipicolinate is reduced, thus enhancing the carbon yield of dipicolinate. The microorganisms specifically described in EP 08151031.5 and additionally possessing the reduced ICD activity necessary for performing the present invention are most preferred for production of dipicolinate.
The dipicolinate as produced according to the present invention may be used as monomer in the synthesis of polyester or polyamide type of copolymers; precursor for pyridine synthesis; stabilizing agent for peroxides and peracids, as for example t-butyl peroxide, dimethyl-cyclohexanon peroxide, peroxyacetic acid and peroxy-monosulphuric acid; ingredient for polishing solution of metal surfaces; stabilizing agent for organic materials susceptible to be deteriorated due to the presence of traces of metal ions (sequestrating effect); stabilizing agent for epoxy resins; and stabilizing agent for photographic solutions or emulsions (in particular, by preventing the precipitation of calcium salts).
The 1,5-diaminopentane as produced according to the present invention may be used as monomer in the synthesis of polyamide or polyurethane; or as precursor for piperidine synthesis.
Beta-lysine as produced according to the present invention may be used for the synthesis of caprolactame or as monomer in the synthesis of polyamide.
In a preferred embodiment of the method (1) and the microorganism (2) of present invention, one or more than one further enzyme activity besides the ICD activity in endogenous biosynthetic pathways of the miccroorganism is modified, leading to an increase of carbon yield for the target compound. Preferably, one or more than one of the enzymes catalyzing the biochemical transformation of aspartate to lysine, methionine or isoleucine is up- or down-regulated.
Preferably, the activity of a Corynebacterium enzyme and particularly of a C. glutamicum enzyme is up- or down-regulated.
Preferably, said modification is achieved by modification of the nucleotide sequences encoding said enzymes.
In a first preferred aspect, namely in cases wherein the lysine biosynthesis shall be modified, i.e. wherein lysine, one of its derivatives or precursors are produced as intermediate or final product in the method according to embodiment (1), said modified enzymes and/or nucleotide sequences may be selected from the group consisting of sequences encoding the following gene products which are either preferably up-regulated or preferably down-regulated. The gene products which are preferably upregulated (i.e. their activity should be increased in comparison to the wild-type microorganism) are selected from the following group: aspartate kinase, aspartate-semialdehyde-dehydrogenase, dihydrodipicolinate-synthetase, dihydridipicolinate-reductase, diaminopimelate-dehydrogenase, diaminopimelate-decarboxylase, lysine-exporter, pyruvate carboxylase, phosphoenolpyruvate (PEP) carboxylase, glucose-6-phosphate-deydrogenase, 6-phospho-gluconolactonase, 6-phosphogluconate-dehydrogenase, ribose-5-phosphat-isomerase, ribose-phosphate epimerase, transketolase, transaldolase, glucosephosphate-isomerase, transcriptional regulators LuxR, transcriptional regulators LysR1, transcriptional regulators LysR2, malate-quinone-oxidoreductase, malate dehydrogenase, fructose-1,6-bisphosphatase, triosephosphate isomease, glyceraldehyde-phosphate dehydrogenase, phosphoglycerate kinase, phosphglycerate mutase enolase, pyruvate kinase, arginyl-t-RNA-synthetase, protein OpcA, 1-phosphofructokinase, 6-phosphofructokinase, biotin-ligase, isocitrate lyase, malate synthase, tetrahydropicolinat-succinylase, succinyl-aminoketopimelate-aminotransferase, succinyl-diaminopimelate-desuccinylase, diaminopimelate-epimerase, aspartate-transaminase and malate-enzyme, components of the PTS sugar uptake system, accBC (acetyl CoA carboxylase), accDA (acetyl CoA carboxylase), aceA (isocitrat-lyase), acp (acyl carrier protein), asp (aspartase), atr61 (ABC transporter), ccsB (cytochrom c synthesis protein), cdsA (phosphatidat-cytidylyltransferase), citA (sensor kinase of a 2-component system), cls (cardiolipin synthase), cma (cyclopropane-myolic acid synthase), cobW (cobalamin synthesis-related protein), cstA (carbon starvation protein A), ctaD (Cytocrom aa3 Oxidase UE1), ctaE (cytocrom aa3 oxidase UE3), ctaF, 4 (subunit of cytochrome aa3 oxidase), cysD (sufate-adenosyltransferase), cysE (serine-acetyltransferase, cysH, cysK (cysteine synthase), cysN (sulfat-adenosyltransferase), cysQ (ransport protein), dctA (C4 dicarboxylate transport protein), dep67 (cobalamin synthesis-related protein), dps (DNA protection protein), dtsR (propionyl-CoA carboxylase), fad15 (acyl-CoA-synthase), ftsX (cell division protein), glbO (HB-like protein), glk (glukokinase), gpmB (phosphoglycerate kinase II), hemD hemB (uroporphyrinogen-II-synthase, delta-aminolevulinic acid dehydratase), lldd2 (lactate dehydrogenase), metY (O-acetylhomo serine-sulfhydrylase), msiK (sugar import protein), ndkA (nucleoside diphosphate kinase), nuoU (NADH-dehydrogenase subunit U), nuoV (NADH-dehydrogenase subunit V), nuoW (NADH-dehydrogenase subunit W), oxyR (transcriptional regulator), pgsA2 (CDP-diacylglycerol-3-P-3-phosphatidyltransferase), pknB (protein kinase B), pknD (protein kinase D), plsC (1-Acyl-SN-glycerol-3-P-acyltransferase), poxB gnd (pyruvat oxidase, 6-phosphogluconate dehydrogenase), ppgK (polyphosphate glucokinase) ppsA (PEP synthase), qcrA (Rieske Fe-S-protein), qcrA (Rieske Fe-S-protein), qcrB (cytochrom B), qcrB (cytochrom B), qcrC (cytochrom C), rodA (cell division protein), rpe (ribulose phosphate isomerase), rpi (phosphopentose isomerase), sahH (adenosyl homocysteinase), sigC (sigma factor C), sigD (activator of transcrption factor sigma D), sigE (sigma factor E), sigh (sigma factor H), sigM (sigma factor M), sod (superoxiddismutase), thyA (thymidylate synthase), truB (tRNA pseudouridine 55 synthase) and zwa1 (PS1-protein).
Of these, the following are preferred for up-regulation: aspartate kinase, aspartate-semialdehyde-dehydrogenase, dihydrodipicolinate-synthetase, dihydrodipicolinate-reductase, diaminopimelate-dehydrogenase, diaminopimelate-decarboxylase, lysine-exporter, pyruvate carboxylase, phosphoenolpyruvate (PEP) carboxylase glucose-6-phosphate-deydrogenase, 6-phospho-gluconolactonase, 6-phosphogluconate-dehydrogenase, ribose-5-phosphat-isomerase, ribose-phosphate epimerase, transketolase, transaldolase, isocitrate lyase, malate synthase, tetrahydropicolinat-succinylase, succinyl-aminoketopimelate-aminotransferase, succinyl-diaminopimelate-desuccinylase and diaminopimelate-epimerase.
The gene products which are preferably downregulated (i.e. their activity should be decreased in comparison to the wild-type microorganism) in this first preferred aspect are selected from the following group:
phosphoenolpyruvate-carboxykinase, pyruvate-oxidase, homoserine-kinase, homoserine-dehydrogenase, threonine-exporter, threonine-efflux, asparaginase, aspartate-decarboxylase, threonine-synthase, citrate synthase, aconitase, isocitrate-dehydrogenase, alpha-ketoglutarate dehydrogenase, succinyl-CoA-synthase, succinat-dehydrogenase, fumarase, malate-quinone oxidoreductase, malate dehydrogenase, pyruvate kinase, malic enzyme threonine-dehydratase, homoserine-O-acetyltransferase, O-acetylhomoserine-sulfhydrylase, alr (alanine racemase), atr43 (ABC transporter), ccpA1 (catabolite control protein a), ccpA2 (catabolite control protein), chrA (two component response regulator), chrS (histidine kinase), citB (transcriptional regulator), citE (citratlyase E), citE (citrat lyase E), clpC (protease), csp1, ctaF (4. subunit of cytochrom aa3 oxidase), dctA (C4-dicarboxylat transport protein), dctQ sodit (C4-dicarboxylat transport protein), dead (DNA/RNA helicase), def (peptide deformylase), dep33 (multi drug resistance protein B), dep34 (efflux protein), fda (fructose bisphosphate ldolase), gorA (glutathion reductase), gpi/pgi (glucose-6-P-isomerase), hisC2 (histidinol phosphate aminotransferase), hom (homoserin dehydrogenase), lipA (lipoate synthase), lipB (lipoprotein-ligase B), lrp (leucine resonse regulator), luxR (transcriptional regulator), luxS (sensory transduction protein kinase), lysR1 (transcriptional regulator), lysR2 (transcriptional regulator, lysR3 (transcriptional regulator), mdhA (malate dehydrogenase), menE (O-succinylbenzoic acid CoA ligase), mikE17 (transcription factor), mqo (malate-quinon oxodoreductase), mtrA mtrB(sensor protein cpxA, regulatory component of sensory), nadA (quinolinate synthase A), nadC (niocotinate nucleotide pyrophosphase), otsA trehalose-6-P-synthase), otsB, treY, treZ (trehalose phosphatase, maltooligosyl-trehalose synthase maltooligosyl-trehalose trehalohydrolase, pepC (aminopeptidase I), pepCK (PEP-carboxykinase), pfKA pfkB (1 and 6-phosphofructokinase), poxB (pyruvate oxidase), poxB gnd (pyruvat oxidase, 6-phosphogluconate dehydrogenase), pstC2 (membrane bound phosphate transport protein), rplK (PS1-protein), sucC sucD (succinyl CoA synthetase), sugA (sugar transport protein), tmk (thymidylate kinase), zwa2, metK metZ, glyA (serinhydroxymethyltransferase), sdhC sdhA sdhB (succinat DH), smtB (transcriptional regulator), cgl1 (transcriptional regulator), hspR (transcriptional regulator), cgl2 (transcriptional regulator), cebR (transcriptional regulator), cgl3 (transcriptional regulator), gatR (transcriptional regulator), glcR (transcriptional regulator), tcmR (transcriptional regulator), smtB2 (transcriptional regulator), dtxR (transcriptional regulator), degA (transcriptional regulator), galR (transcriptional regulator), tipA2 (transcriptional regulator), mall (transcriptional regulator), cgl4 (transcriptional regulator), arsR (transcriptional regulator), merR (transcriptional regulator), hrcA (transcriptional regulator), glpR2 (transcriptional regulator), lexA (transcriptional regulator), ccpA3 (transcriptional regulator), degA2 (transcriptional regulator), methylmalonyl-CoA-mutase.
Of these, the following are preferred for down-regulation: phosphoenolpyruvate-carboxykinase, pyruvate-oxidase, homoserine-kinase, homoserine-dehydrogenase, succinyl-CoA-synthase, malate-quinone oxidoreductase and methylmalonyl-CoA-mutase.
In case the produced lysine derivate is diaminopentane, the gene diamine acetyltransferase is preferentially downregulated, i.e. the gene is either inactivated completely or the gene activity is reduced. The sequence of diamine acetyltransferase is described in WO 2007/113127.
In a second preferred aspect, namely in cases wherein the methionine biosynthesis shall be modified, i.e. wherein methionine, one of its derivatives or precursors are produced as intermediate or final product in the method according to embodiment (1), modified enzymes and/or nucleotide sequences which are preferably down-regulated may be selected from the group consisting of sequences encoding homoserine-kinase, threonine-dehydratase, threonine-synthase, meso-diaminopimelat D-dehydrogenase, phosphoenolpyruvate-carboxykinase, pyruvat-oxidase, dihydrodipicolinate-synthase, dihydrodipicolinate-reductase, and diaminopicolinate-decarboxylase. Preferably, said enzymes are downregulated. Of these, the following are preferred for down-regulation: homoserine-kinase, phosphoenolpyruvate-carboxykinase and dihydrodipicolinate-synthase.
The gene products which are preferably upregulated in this second preferred aspect are selected from the following group: cystathionin synthase, cystathionin lyase, homoserine-O-acetyltransferase, O-acetylhomoserine-sulfhydrylase, homoserine-dehydrogenase, aspartate-kinase, aspartate-semialdehyde-dehydrogenase, glycerinaldehyde-3-phosphate-dehydrogenase, 3-phosphoglycerate-kinase, pyruvate-carboxylase, triosephosphate-isomerase, transaldolase, transketolase, glucose-6-phosphate-dehydrogenase, biotine-ligase, protein OpcA, 1-phosphofructo-kinase, 6-phospho fructo-kinase, fructose-1,6-bisphosphatase, 6-phosphogluconate-dehydrogenase, homoserine-dehydrogenase, phosphoglycerate-mutase, pyruvat-kinase, aspartate-transaminase, coenzym B12-dependent methionine-synthase, coenzym B12-independent methione-synthase and malate-enzyme.
In a third preferred aspect, namely in cases wherein the threonine biosynthesis shall be modified, i.e. wherein threonine, one of its derivatives or precursors are produced as intermediate or final product in the method according to embodiment (1), the modified enzymes and/or nucleotide sequences which are preferably down-regulated may be selected from the group consisting of sequences encoding homoserine O-acetyltransferase, serine-hydroxymethyltransferase, O-acetylhomoserine-sulfhydrylase, meso-diaminopimelate D-dehydrogenase, phosphoenolpyruvate-carboxykinase, pyruvate-oxidase, dihydrodipicolinate-synthase, dihydrodipicolinate-reductase, asparaginase, aspartate-decarboxylase, lysin-exporter, acetolactate-synthase, ketol-aid-reductoisomerase, branched chain aminotransferase, coenzym B12-dependent methionine-synthase, coenzym B12-independent methione-synthase, dihydroxy acid dehydratase and diaminopicolinate-decarboxylase. Preferably, said enzymes are down-regulated.
The gene products which are preferably upregulated in this third preferred aspect are selected from the following group: threonine-dehydratase, threonine synthase, homoserine-dehydrogenase, aspartate-kinase, aspartate-semialdehyde-dehydrogenase, glycerinaldehyde-3-phosphate-dehydrogenase, 3-phosphoglycerate-kinase, pyruvate-carboxylase, triosephosphate-isomerase, transaldolase, transketolase, glucose-6-phosphate-dehydrogenase, biotine-ligase, protein OpcA, 1-phosphofructo-kinase, 6-phospho fructo-kinase, fructose-1,6-bisphosphatase, 6-phosphogluconate-dehydrogenase, phosphoglycerate-mutase, pyruvat-kinase, aspartate-transaminase and malate-enzyme. Preferably, said enzymes are upregulated.
Embodiment (1) may further include a step of recovering the target compound (fine chemical). 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. For example the target compound can be recovered from culture media by first removing the microorganisms. The remaining broth is then passed through or over a cation exchange resin to remove unwanted cations and then through or over an anion exchange resin to remove unwanted inorganic anions and organic acids.
Embodiment (2) of present invention pertains to a recombinant microorganism. Said microorganism may be any of the microorganims listed in detail above, with the same preferences as indicated in said section. In a particular aspect, it is C. glutamicum, and preferably is a C. glutamicum ATCC13032 derivative with a feedback-resistant aspartokinase, particularly is ATCC13032lysCfbr or ATCC13286, or a derivative of said strains like LU11424 (see example 1). LU11424 is especially preferred.
The microorganism according to embodiment (2) may possess any of the features described above for a microorganism used in the production method according to embodiment (1), as long as it fulfills the criteria of the proviso included into embodiment (2) in order to exclude certain microorganisms already disclosed in PCT/EP2007/061151. A microorganism with a reduced ICD activity due to application of the codon usage method described in PCT/EP2007/061151 is excluded from being the microorganism according to embodiment (2) when said microorganism is disclosed in PCT/EP2007/061151. This proviso does not exclude microorganisms wherein reduction of ICD expression is not due to the expression of a modified ICD encoding nucleotide sequence (icd sequence) instead of the native icd sequence of the microorganism wherein said modified icd encoding sequence is derived from the non-modified icd sequence such that at least one codon of the non-modified nucleotide sequence is replaced in the modified icd sequence by a less frequently used codon according to the codon usage of the host cell. In other words, a microorganism wherein the reduction of ICD expression is not due to modified codon usage as described in PCT/EP2007/061151 and which is no microorganism described in PCT/EP2007/061151, is not excluded from embodiment (2) of present invention.
This proviso does further not exclude a microorganism whose ICD expression is reduced due to modified codon usage as described in PCT/EP2007/061151 and which in addition comprises a heterologous enzyme catalyzing the conversion of an endogenous biosynthetic intermediate or final product of the microorganism into a non-native target compound of the fine chemical synthesis (see above). Preferably, said heterologous enzyme is selected from the group consisting of enzymes catalyzing one or more steps in the synthesis or biosynthesis of fine chemicals, particularly of fine chemicals derivable from lysine or its biochemical precursors downstream of aspartate via enzymatic conversion. More preferably, it is an enzyme catalyzing a decarboxylation, a deamination, a transamination, the shift of an amino group along an organic molecule, an oxidation and/or cyclisation reaction. Even more preferably, it is selected from the group consisting of dipicolinate synthase, lysine decarboxylase and lysine 2,3-aminomutase. Particularly preferred is a microorganism comprising a heterologous dipicolinate synthase, lysine decarboxylase or lysine 2,3-aminomutase. In other words, in this particularly preferred embodiment, the microorganism may have reduced ICD activity due to modified codon usage as described in PCT/EP2007/061151 and may even be a microorganism described in PCT/EP2007/061151, but additionally comprises a heterologous dipicolinate synthase, lysine decarboxylase or lysine 2,3-aminomutase.
Said microorganism according to embodiment (2) is particularly suitable for performing the method according to embodiment (1). It preferably comprises a vector and/or nucleotide sequence which leads to a lower ICD expression in Corynebacterium and preferably in C. glutamicum. In a preferred aspect, said lower ICD expression is due to replacement of ATG as start codon of the isocitrate dehydrogenase encoding nucleotide sequence, preferably to replacement of ATG with GTG.
An especially preferred microorganism according to embodiment (2) is LU11424 whose partially or completely reduced isocitrate dehydrogenase activity is due to replacement of ATG as start codon of the isocitrate dehydrogenase encoding nucleotide sequence, preferably to replacement of ATG with GTG.
Particularly, the recombinant microorganism of embodiment (2) additionally comprises a heterologous enzyme which is able to convert an amino acid of the aspartate family or one of its biochemical precursors into further fine chemicals as described above in detail in the context of embodiment (1). Said enzyme preferably is able to convert lysine or one of its biochemical precursors downstream of aspartate into further fine chemicals.
In said particular aspect, the heterologous enzyme is preferably selected from the group consisting of lysine decarboxylase, lysine-2,3-aminomutase and dipicolinate synthetase.
The use (3) of the microorganism (2) encompasses the use in a method as described for embodiment (1).
In embodiment (4) the present invention provides a method for the production of products made from the fine chemicals prepared by the method according to embodiment (1). A method of preparing
(i) a polyamide, polyurethane or piperidine, wherein 1,5-diaminopentane is an intermediate product;
(ii) a caprolactam or polyamide, wherein β-lysine is an intermediate product; or
(iii) a polyester or polyamide or stabilizing agent, wherein dipicolinate is an intermediate product
and which comprises a step wherein the intermediate product is prepared by the method as defined above for embodiment (1) is a preferred aspect of embodiment (4).
In a particular aspect of embodiment (4), the method is a process for the production of a polyamide (e.g. Nylon®) and comprises the production of cadaverine according to embodiment (1) and the reaction of said cadaverine with a dicarboxylic acid. The cadaverine is reacted in a known manner with di-, tri- or polycarboxylic acids to get polyamides. Preferably the cadaverine is reacted with dicarboxylic acids containing 4 to 10 carbons such as succinic acid, glutaric acid, adipic acid, pimelic acid, suberic acid, azelaic acid, sebacic acid, and so forth. The dicarboxylic acid is preferably a free acid.
In a further particular aspect of embodiment (4), the method is a process for the production of β-amino-ε-caprolactam, ε-caprolactam, or ε-aminocaproic acid and comprises the production of β-lysine according to embodiment (1). In one aspect of said conversion of β-lysine, the present invention provides a process for the production of β-amino-ε-caprolactam comprising as one step the method according to embodiment (1) for the production of β-lysine. β-Lysine subsequently undergoes an intramolecular cyclization resulting in β-amino-ε-caprolactam. This cyclization reaction can be performed either directly before the isolation and/or purification of the β-lysine or using the isolated β-lysine.
In a second aspect of said conversion of β-lysine, the present invention provides a process for the production of ε-caprolactam comprising as one step the method according to embodiment (1) for the production of β-lysine. As described above β-lysine further undergoes an intramolecular cyclization resulting in β-amino-ε-caprolactam, which can be deaminated selectively in order to get ε-caprolactam. This deamination process is known in the art.
In a third aspect of said conversion of β-lysine, the present invention provides a process for the production of an aminocaproic acid comprising as one step the method according to embodiment (1) for the production of β-lysine and subsequent removal of the β-amino function of β-lysine by deamination. The resulting ε-aminocaproic acid can be transformed either to ε-caprolactam or directly—without cyclization to the lactam—to a polyamide by known polymerization techniques. ε-Caprolactam is a very important monomer for the production of polyamides, especially PA6.
In a further particular aspect of embodiment (4), the method is a process for the production of a polyester or polyamide (e.g. Nylon®) copolymer and comprises the production of dipicolinate according to embodiment (1), the isolation of said dipicolinate, and the subsequent polymerization of said dipicolinate with at least one further polyvalent comonomer selected from polyols and polyamines. The dipicolinate is reacted in a known manner with di-, tri- or polyamines to obtain polyamides, or with di-, tri- or polyols to obtain polyesters. Preferably the dipicolinate is reacted with a polyamine or polyol containing 4 to 10 carbon atoms.
A person skilled in the art is familiar with how to replace e.g. a gene or endogenous nucleotide sequence that encodes for a certain polypeptide with a modified nucleotide sequence. This may e.g. be achieved by introduction of a suitable construct (plasmid without origin of replication, linear DNA fragment without origin of replication) by electroporation, chemical transformation, conjugation or other suitable transformation methods. This is followed by e.g. homologous recombination using selectable markers which ensure that only such cells are identified that carry the modified nucleotide sequence instead of the endogenous naturally occurring sequence. Other methods include gene disruption of the endogenous chromosomal locus and expression of the modified sequences from e.g. plasmids. Yet other methods include e.g. transposition. Further information as to vectors and host cells that may be used will be given below.
In general, the person skilled in the art is familiar with designing constructs such as vectors for driving expression of a polypeptide in microorganisms such as E. coli and C. glutamicum. The person skilled in the art is also well acquainted with culture conditions of microorganisms such as C. glutamicum and E. coli as well as with procedures for harvesting and purifying fine chemicals such as amino acids and particularly lysine, methionine and threonine from the aforementioned microorganisms. Some of these aspects will be set out in further detail below.
The person skilled in the art is also well familiar with techniques that allow to change the original non-modified nucleotide sequence into a modified nucleotide sequence encoding for polypeptides of identical amino acid but with different nucleic acid sequence. This may e.g. be achieved by polymerase chain reaction based mutagenesis techniques, by commonly known cloning procedures, by chemical synthesis etc. Standard techniques of recombinant DNA technology and molecular biology are described in various publications, e.g. Sambrook et al. (2001), Molecular Cloning: A Laboratory Manual, 3rd edition, Cold Spring Harbor Laboratory Press, or Ausubel et al. (eds) Current protocols in molecular biology (John Wiley & Sons, Inc. 2007). Ausubel et al., Current Protocols in Protein Science, (John Wiley & Sons, Inc. 2002). Ausubel et al. (eds.), SHORT PROTOCOLS IN MOLECULAR BIOLOGY, 3rd Edition (John Wiley & Sons, Inc. 1995). Methods specifically for C. glutamicum are described in Eggeling and Bott (eds.) Handbook of Corynebacterium (Taylor and Francis Group, 2005). Some of these procedures are set out below and in the “examples” section.
In the following, it will be described and set out in detail how genetic manipulations in microorgansims such as E. coli and particularly Corynebacterium glutamicum can be performed.
Vectors and Host Cells
As used herein, the term “vector” refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked.
One type of vector is a “plasmid”, which refers to a circular double stranded DNA loop into which additional DNA segments can be ligated. Another type of vector is a viral vector, wherein additional DNA segments can be ligated into the viral genome.
Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g., bacterial vectors having a bacterial origin of replication and episomal mammalian vectors). Other vectors (e.g., non-episomal mammalian vectors) are integrated into the genome of a host cell upon introduction into the host cell, and thereby are replicated along with the host genome. Moreover, certain vectors are capable of directing the expression of genes to which they are operatively linked.
Such vectors are referred to herein as “expression vectors”.
In general, expression vectors of utility in recombinant DNA techniques are often in the form of plasmids. In the present specification, “plasmid” and “vector” can be used interchangeably as the plasmid is the most commonly used form of vector.
However, the invention is intended to include such other forms of expression vectors, such as viral vectors (e.g., replication defective retroviruses, adenoviruses and adeno-associated viruses), which serve equivalent functions.
A recombinant expression vector suitable for preparation of the recombinant microorganism of the invention may comprise a heterologous nucleic acid as defined above in a form suitable for expression of the respective nucleic acid in a host cell, which means that the recombinant expression vectors include one or more regulatory sequences, selected on the basis of the host cells to be used for expression, which is operatively linked to the nucleic acid sequence to be expressed.
Within a recombinant expression vector, “operably linked” is intended to mean that the nucleotide sequence of interest is linked to the regulatory sequence(s) in a manner which allows for expression of the nucleotide sequence (e.g., in an in vitro transcription/translation system or in a host cell when the vector is introduced into the host cell). The term “regulatory sequence” is intended to include promoters, repressor binding sites, activator binding sites, enhancers and other expression control elements (e.g., terminators, polyadenylation signals, or other elements of mRNA secondary structure). Such regulatory sequences are described, for example, in Goeddel; Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. (1990). Regulatory sequences include those which direct constitutive expression of a nucleotide sequence in many types of host cell and those which direct expression of the nucleotide sequence only in certain host cells. Preferred regulatory sequences are, for example, promoters such as cos-, tac-, trp-, tet-, trp-, tet-, lpp-, lac-, lpp-lac-, lacIq-, T7-, T5-, T3-, gal-, trc-, ara-, SP6-, arny, SP02, e-Pp-ore PL, SOD, EFTu, EFTs, GroEL, MetZ (last five from C. glutamicum), which are used preferably in bacteria. Additional regulatory sequences are, for example, promoters from yeasts and fungi, such as ADC1, MFa, AC, P-60, CYC1, GAPDH, TEF, rp28, ADH, promoters from plants such as CaMV/35S, SSU, OCS, lib4, usp, STLS1, B33, nos or ubiquitin- or phaseolin-promoters. It is also possible to use artificial promoters. It will be appreciated by one of ordinary skill in the art that the design of the expression vector can depend on such factors as the choice of the host cell to be transformed, the level of expression of protein desired, etc. The expression vectors can be introduced into host cells to thereby produce proteins or peptides, including fusion proteins or peptides.
Any vector that is suitable to drive expression of a modified nucleotide sequence in a host cell, preferably in Corynebacterium and particularly preferably in C. glutamicum may be used for decreasing the amount of ICD in these host cells. Such vector may e.g. be a plasmid vector which is autonomously replicable in coryneform bacteria. Examples are pZ1 (Merkel et al. (1989), Applied and Environmental Microbiology 64:549-554), pEKEx1 (Eikmanns et al. (1991), Gene 102:93-98), pHS2-1 (Sonnen et al. (1991), Gene 107:69-74). These vectors are based on the cryptic plasmids pHM1519, pBL1 oder pGA1. Other suitable vectors are pClik5MCS (WO 2005/059093), or vectors based on pCG4 (U.S. Pat. No. 4,489,160) or pNG2 (Serwold-Davis et al. (1990), FEMS Microbiology Letters 66:119-124) or pAG1 (U.S. Pat. No. 5,158,891). Examples for other suitable vectors can be found in the Handbook of Corynebacterium, Chapter 23 (edited by Eggeling and Bott, ISBN 0-8493-1821-1, 2005).
Recombinant expression vectors can be designed for expression of specific nucleotide sequences in prokaryotic or eukaryotic cells. For example, the nucleotide sequences can be expressed in bacterial cells such as C. glutamicum and E. coli, insect cells (using baculovirus expression vectors), yeast and other fungal cells (see Romanos, M. A. et al. (1992), Yeast 8:423-488; van den Hondel, C. A. M. J. J. et al. (1991) in: More Gene Manipulations in Fungi, J. W. Bennet & L. L. Lasure, eds., p. 396-428, Academic Press: San Diego; and van den Hondel, C. A. M. J. J. & Punt, P. J. (1991) in: Applied Molecular Genetics of Fungi, Peberdy, J. F. et al., eds., p. 1-28, Cambridge University Press: Cambridge), algae and multicellular plant cells (see Schmidt, R. and Willmitzer, L. (1988) Plant Cell Rep.: 583-586). Suitable host cells are discussed further in Goeddel, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. (1990). Alternatively, the recombinant expression vector can be transcribed and translated in vitro, for example using T7 promoter regulatory sequences and T7 polymerase.
Expression of proteins in prokaryotes is most often carried out with vectors containing constitutive or inducible promoters directing the expression of either fusion or non-fusion proteins.
Fusion vectors add a number of amino acids to a protein encoded therein, usually to the amino terminus of the recombinant protein but also to the C-terminus or fused within suitable regions in the proteins. Such fusion vectors typically serve four purposes: 1) to increase expression of recombinant protein; 2) to increase the solubility of the recombinant protein; 3) to aid in the purification of the recombinant protein by acting as a ligand in affinity purification; and 4) to provide a “tag” for later detection of the protein. Often, in fusion expression vectors, a proteolytic cleavage site is introduced at the junction of the fusion moiety and the recombinant protein to enable separation of the recombinant protein from the fusion moiety subsequent to purification of the fusion protein. Such enzymes, and their cognate recognition sequences, include Factor Xa, thrombin and enterokinase.
Typical fusion expression vectors include pGEX (Pharmacia Biotech Inc; Smith, D. B. and Johnson, K. S. (1988) Gene 67:31-40), pMAL (New England Biolabs, Beverly, Mass.) and pRIT5 (Pharmacia, Piscataway, N.J.) which fuse glutathione S-transferase (GST), maltose E binding protein, or protein A, respectively.
Examples of suitable inducible non-fusion E. coli expression vectors include pTrc (Amann et al., (1988) Gene 69: 301-315), pLG338, pACYC184, pBR322, pUC18, pUC19, pKC30, pRep4, pHS1, pHS2, pPLc236, pMBL24, pLG200, pUR290, pIN-III113-B1, egt11, pBdC1, and pET 11d (Studier et al., Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. (1990) 60-89; and Pouwels et al., eds. (1985) Cloning Vectors. Elsevier: New York, ISBN 0 444 904018). Target gene expression from the pTrc vector relies on host RNA polymerase transcription from a hybrid trp-lac fusion promoter. Target gene expression from the pET 11d vector relies on transcription from a T7 gnlO-lac fusion promoter mediated by a coexpressed viral RNA polymerase (T7gnl). This viral polymerase is supplied by host strains BL21 (DE3) or HMS174 (DE3) from a resident X prophage harboring a T7gnl gene under the transcriptional control of the lacUV 5 promoter. For transformation of other varieties of bacteria, appropriate vectors may be selected. For example, the plasmids pIJ101, pIJ364, pIJ702 and pIJ361 are known to be useful in transforming Streptomyces, while plasmids pUB110, pC194 or pBD214 are suited for transformation of Bacillus species. Several plasmids of use in the transfer of genetic information into Corynebacterium include pHM1519, pBL1, pSA77 or pAJ667 (Pouwels et al., eds. (1985) Cloning Vectors. Elsevier: New York ISBN 0 444 904018).
Examples of suitable C. glutamicum and E. coli shuttle vectors are e.g. pClik5aMCS (WO 2005/059093) or can be found in Eikmanns et al. ((1991) Gene 102:93-8).
Examples for suitable vectors to manipulate Corynebacteria can be found in the Handbook of Corynebacterium (edited by Eggeling and Bott, ISBN 0-8493-1821-1, 2005). One can find a list of E. coli-C. glutamicum shuttle vectors (table 23.1), a list of E. coli-C. glutamicum shuttle expression vectors (table 23.2), a list of vectors which can be used for the integration of DNA into the C. glutamicum chromosome (table 23.3), a list of expression vectors for integration into the C. glutamicum chromosome (table 23.4.), as well as a list of vectors for site-specific integration into the C. glutamicum chromosome (table 23.6).
In another embodiment, the expression vector is a yeast expression vector. Examples of vectors for expression in yeast S. cerevisiae include pYepSecl (Baldari, et al., (1987) Embo J. 6:229-234), 21, pAG-1, Yep6, Yep13, pEMBLYe23, pMFa (Kurjan and Herskowitz, (1982) Cell 30:933-943), pJRY88 (Schultz et al., (1987) Gene 54:113-123), and pYES2 (Invitrogen Corporation, San Diego, Calif.). Vectors and methods for the construction of vectors appropriate for use in other fungi, such as the filamentous fungi, include those detailed in: van den Hondel, C. A. M. J. J. & Punt, P. J. (1991) in: Applied Molecular Genetics of Fungi, J. F. Peberdy et al., eds., p. 1-28, Cambridge University Press: Cambridge, and Pouwels et al., eds. (1985) Cloning Vectors. Elsevier: New York (ISBN 0 444 904018).
For the purposes of the present invention, an operative link is understood to be the sequential arrangement of promoter (including the ribosomal binding site (RBS)), coding sequence, terminator and, optionally, further regulatory elements in such a way that each of the regulatory elements can fulfill its function, according to its determination, when expressing the coding sequence.
In another embodiment, heterologous nucleotide sequences may be expressed in unicellular plant cells (such as algae) or in plant cells from higher plants (e.g., the spermatophytes, such as crop plants). Examples of plant expression vectors include those detailed in: Becker, D., Kemper, E., Schell, J. and Masterson, R. (1992) Plant Mol. Biol. 20:1195-1197; and Bevan, M. W. (1984) Nucl. Acid. Res. 12:8711-8721, and include pLGV23, pGHlac+, pBIN19, pAK2004, and pDH51 (Pouwels et al., eds. (1985) Cloning Vectors. Elsevier: New York ISBN 0 444 904018).
For other suitable expression systems for both prokaryotic and eukaryotic cells see chapters 16 and 17 of Sambrook, J. et al. Molecular Cloning: A Laboratory Manual. 3rd ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 2003.
In another embodiment, a recombinant expression vector is capable of directing expression of a nucleic acid preferentially in a particular cell type, e.g. in plant cells (e.g., tissue-specific regulatory elements are used to express the nucleic acid). Tissue-specific regulatory elements are known in the art.
Another aspect of the invention pertains to organisms or host cells into which a recombinant expression vector or nucleic acid has been introduced. The resulting cell or organism is a recombinant cell or organism, respectively. It is understood that such terms refer not only to the particular subject cell but also to the progeny or potential progeny of such a cell when the progeny is comprising the recombinant nucleic acid. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term as used herein, inasfar as the progeny still expresses or is able to express the recombinant protein.
Vector DNA can be introduced into prokaryotic or eukaryotic cells via conventional transformation or transfection techniques. As used herein, the terms “transformation” and “transfection”, “conjugation” and “transduction” are intended to refer to a variety of art-recognized techniques for introducing foreign nucleic acid (e.g., linear DNA or RNA (e.g., a linearized vector or a gene construct alone without a vector) or nucleic acid in the form of a vector (e.g., a plasmid, phage, phasmid, phagemid, transposon or other DNA)) into a host cell, including calcium phosphate or calcium chloride co-precipitation, DEAE-dextran-mediated transfection, lipofection, natural competence, conjugation chemical-mediated transfer, or electroporation. Suitable methods for transforming or transfecting host cells can be found in Sambrook, et al. (Molecular Cloning: A Laboratory Manual. 3rd ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 2003), and other laboratory manuals.
In order to identify and select these integrants, a gene that encodes a selectable marker (e.g., resistance to antibiotics) is generally introduced into the host cells along with the gene of interest. Preferred selectable markers include those which confer resistance to drugs, such as G418, hygromycin, kanamycine, tetracycline, ampicillin and methotrexate. Nucleic acid encoding a selectable marker can be introduced into a host cell on the same vector as that encoding the above-mentioned modified nucleotide sequences or can be introduced on a separate vector. Cells stably transfected with the introduced nucleic acid can be identified by drug selection (e.g., cells that have incorporated the selectable marker gene will survive, while the other cells die).
When plasmids without an origin of replication and two different marker genes are used (e.g. pClik int sacB), it is also possible to generate marker-free strains which have part of the insert inserted into the genome. This is achieved by two consecutive events of homologous recombination (see also Becker et al., APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 71 (12), p. 8587-8596; Eggeling and Bott (eds) Handbook of Corynebacterium (Taylor and Francis Group, 2005)). The sequence of plasmid pClik int sacB can be found in WO 2005/059093 as SEQ ID NO:24; therein, the plasmid is called pCIS.
In another embodiment, recombinant microorganisms can be produced which contain selected systems which allow for regulated expression of the introduced gene. For example, inclusion of a nucleotide sequence on a vector placing it under control of the lac operon permits expression of the gene only in the presence of IPTG. Such regulatory systems are well known in the art.
Growth of Escherichia coli and Corynebacterium glutamicum-Media and Culture Conditions
In one embodiment, the method comprises culturing the microorganism in a suitable medium for fine chemical production. In another embodiment, the method further comprises isolating the fine chemical from the medium or the host cell.
The person skilled in the art is familiar with the cultivation of common microorganisms such as C. glutamicum and E. coli. Thus, a general teaching will be given below as to the cultivation of E. coli and C. glutamicum. Additional information may be retrieved from standard textbooks for cultivation of E. coli and C. glutamicum.
E. coli strains are routinely grown in MB and LB broth, respectively (Follettie et al. (1993) J. Bacteriol. 175:4096-4103). Minimal media for E. coli is M9 and modified MCGC (Yoshihama et al. (1985) J. Bacteriol. 162:591-597), respectively. Glucose may be added at a final concentration of 1%. Antibiotics may be added in the following amounts (micrograms per millilitre): ampicillin, 50; kanamycin, 25; nalidixic acid, 25. Amino acids, vitamins, and other supplements may be added in the following amounts: methionine, 9.3 mM; arginine, 9.3 mM; histidine, 9.3 mM; thiamine, 0.05 mM. E. coli cells are routinely grown at 37° C., respectively.
Genetically modified Corynebacteria are typically cultured in synthetic or natural growth media. A number of different growth media for Corynebacteria are both well-known and readily available (Liebl et al. (1989) Appl. Microbiol. Biotechnol., 32:205-210; von der Osten et al. (1998) Biotechnology Letters, 11:11-16; Pat. DE 4,120,867; Liebl (1992) “The Genus Corynebacterium”, in: The Procaryotes, Volume II, Balows, A. et al., eds. Springer-Verlag). Instructions can also be found in the Handbook of Corynebacterium (edited by Eggeling and Bott, ISBN 0-8493-1821-1, 2005).
These media consist of one or more carbon sources, nitrogen sources, inorganic salts, vitamins and trace elements. Preferred carbon sources are sugars, such as mono-, di-, or polysaccharides. For example, glucose, fructose, mannose, galactose, ribose, sorbose, lactose, maltose, sucrose, glycerol, raffinose, starch or cellulose serve as very good carbon sources.
It is also possible to supply sugar to the media via complex compounds such as molasses or other by-products from sugar refinement. It can also be advantageous to supply mixtures of different carbon sources. Other possible carbon sources are alcohols and organic acids, such as methanol, ethanol, acetic acid or lactic acid. Nitrogen sources are usually organic or inorganic nitrogen compounds, or materials which contain these compounds. Exemplary nitrogen sources include ammonia gas or ammonia salts, such as NH4Cl or (NH4)2SO4, NH4OH, nitrates, urea, amino acids or complex nitrogen sources like corn steep liquor, soy bean flour, soy bean protein, yeast extract, meat extract and others.
The overproduction of methionine is possible using different sulfur sources. Sulfates, thiosulfates, sulfites and also more reduced sulfur sources like H2S and sulfides and derivatives can be used. Also organic sulfur sources like methyl mercaptan, thioglycolates, thiocyanates, and thiourea, sulfur containing amino acids like cysteine and other sulfur containing compounds can be used to achieve efficient methionine production. Formate may also be possible as a supplement as are other C1 sources such as methanol or formaldehyde.
Inorganic salt compounds which may be included in the media include the chloride-, phosphorous- or sulfate-salts of calcium, magnesium, sodium, cobalt, molybdenum, potassium, manganese, zinc, copper and iron. Chelating compounds can be added to the medium to keep the metal ions in solution. Particularly useful chelating compounds include dihydroxyphenols, like catechol or protocatechuate, or organic acids, such as citric acid. It is typical for the media to also contain other growth factors, such as vitamins or growth promoters, examples of which include biotin, riboflavin, thiamine, folic acid, nicotinic acid, pantothenate and pyridoxine. Growth factors and salts frequently originate from complex media components such as yeast extract, molasses, corn steep liquor and others. The exact composition of the media compounds depends strongly on the immediate experiment and is individually decided for each specific case. Information about media optimization is available in the textbook “Applied Microbiol. Physiology, A Practical Approach” (Eds. P. M. Rhodes, P. F. Stanbury, IRL Press (1997) pp. 53-73, ISBN 0 19 963577 3). It is also possible to select growth media from commercial suppliers, like standard 1 (Merck) or BHI (grain heart infusion, DIFCO) or others.
Examples for preferred media in the context of present invention are described in the Examples section below.
All medium components should be 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, if necessary, separately.
All media components may be present at the beginning of growth, or they can optionally be added continuously or batchwise. Culture conditions are defined separately for each experiment.
The temperature depends on the microorganism used and usually should be in a range between 15° C. and 45° C. The temperature can be kept constant or can be altered during the experiment. The pH of the medium may be in the range of 5 to 8.5, preferably around 7.0, and can be maintained by the addition of buffers to the media. An exemplary buffer for this purpose is a potassium phosphate buffer. Synthetic buffers such as MOPS, HEPES, ACES and others can alternatively or simultaneously be used. It is also possible to maintain a constant culture pH through the addition of NaOH or NH4OH during growth. If complex medium components such as yeast extract are utilized, the necessity for additional buffers may be reduced, due to the fact that many complex compounds have high buffer capacities. If a fermentor is utilized for culturing the microorganisms, the pH can also be controlled using gaseous ammonia.
The incubation time is usually in a range from several hours to several days. This time is selected in order to permit the maximal amount of product to accumulate in the broth. The disclosed growth experiments can be carried out in a variety of vessels, such as microtiter plates, glass tubes, glass flasks or glass or metal fermentors of different sizes. For screening a large number of clones, the microorganisms should be cultured in microtiter plates, glass tubes or shake flasks, either with or without baffles. Preferably 100 ml shake flasks are used, filled with 10% (by volume) of the required growth medium. The flasks should be shaken on a rotary shaker (amplitude 25 mm) using a speed-range of 100-300 rpm. Evaporation losses can be diminished by the maintenance of a humid atmosphere; alternatively, a mathematical correction for evaporation losses should be performed.
Examples for preferred culture conditions are described in the Examples section below.
If genetically modified clones are tested, an unmodified control clone (e.g. the parent strain) or a control clone containing the basic plasmid without any insert should also be tested. The medium is inoculated to an OD600 of 0.5-1.5 using cells grown on agar plates, such as CM plates (10 g/l glucose, 2.5 g/l NaCl, 2 g/l urea, 10 g/l polypeptone, 5 g/l yeast extract, 5 g/l meat extract, 22 g/l NaCl, 2 g/l urea, 10 g/l polypeptone, 5 g/l yeast extract, 5 g/l meat extract, 22 g/l agar, pH 6.8 with 2M NaOH) that had been incubated at 30° C.
Inoculation of the media is accomplished by either introduction of a saline suspension of C. glutamicum cells from CM plates or addition of a liquid preculture of this bacterium.
Quantification of Amino Acids and their Intermediates
Quantification of amino acids and their intermediates may be performed by any textbook method known to a person skilled in the art. In the following, said quantification is exemplified by the quantification of methionine. Further exemplifications of quantification are presented in the Examples section. The latter are preferred in the context of present invention.
The analysis is done by HPLC (Agilent 1100, Agilent, Waldbronn, Germany) with a guard cartridge and a Synergi 4 μm column (MAX-RP 80 Å, 150*4.6 mm) (Phenomenex, Aschaffenburg, Germany). Prior to injection the analytes are derivatized using o-phthaldialdehyde (OPA) and mercaptoethanol as reducing agent (2-MCE). Additionally sulfhydryl groups are blocked with iodoacetic acid. Separation is carried out at a flow rate of 1 ml/min using 40 mM NaH2PO4 (eluent A, pH=7.8, adjusted with NaOH) as polar and a methanol water mixture (100/1) as non-polar phase (eluent B). The following gradient is applied: Start 0% B; 39 min 39% B; 70 min 64% B; 100% B for 3.5 min; 2 min 0% B for equilibration. Derivatization at room temperature is automated as described below. Initially 0.5 μl of 0.5% 2-MCE in bicine (0.5M, pH 8.5) are mixed with 0.5 μl cell extract. Subsequently 1.5 μl of 50 mg/ml iodoacetic acid in bicine (0.5M, pH 8.5) are added, followed by addition of 2.5 μl bicine buffer (0.5M, pH 8.5). Derivatization is done by adding 0.5 μl of 10 mg/ml OPA reagent dissolved in 1/45/54 v/v/v of 2-MCE/MeOH/bicine (0.5M, pH 8.5). Finally the mixture is diluted with 32 μl H2O. Between each of the above pipetting steps there is a waiting time of 1 min. A total volume of 37.5 μl is then injected onto the column. The analytical results can be significantly improved, if the auto sampler needle is periodically cleaned during (e.g. within waiting time) and after sample preparation. Detection is performed by a fluorescence detector (340 nm excitation, emission 450 nm, Agilent, Waldbronn, Germany). For quantification α-amino butyric acid (ABA) is used as internal standard.
Recombination Protocol for C. glutamicum
In the following it will be described how a strain of C. glutamicum with increased efficiency of fine chemical production can be constructed using a specific recombination protocol.
“Campbell in,” as used herein, refers to a transformant of an original host cell in which an entire circular double stranded DNA molecule (for example a plasmid being based on pClik int sacB) has integrated into a chromosome by a single homologous recombination event (a cross-in event), which effectively results in the insertion of a linearized version of said circular DNA molecule into a first DNA sequence of the chromosome that is homologous to a first DNA sequence of the said circular DNA molecule. “Campbelled in” refers to the linearized DNA sequence that has been integrated into the chromosome of a “Campbell in” transformant. A “Campbell in” contains a duplication of the first homologous DNA sequence, each copy of which includes and surrounds a copy of the homologous recombination crossover point. The name comes from Professor Alan Campbell, who first proposed this kind of recombination.
“Campbell out,” as used herein, refers to a cell descending from a “Campbell in” transformant, in which a second homologous recombination event (a cross out event) has occurred between a second DNA sequence that is contained on the linearized inserted DNA of the “Campbelled in” DNA, and a second DNA sequence of chromosomal origin, which is homologous to the second DNA sequence of said linearized insert, the second recombination event resulting in the deletion (jettisoning) of a portion of the integrated DNA sequence, but, importantly, also resulting in a portion (this can be as little as a single base) of the integrated Campbelled in DNA remaining in the chromosome, such that compared to the original host cell, the “Campbell out” cell contains one or more intentional changes in the chromosome (for example, a single base substitution, multiple base substitutions, insertion of a heterologous gene or DNA sequence, insertion of an additional copy or copies of a homologous gene or a modified homologous gene, or insertion of a DNA sequence comprising more than one of these aforementioned examples listed above).
A “Campbell out” cell or strain is usually, but not necessarily, obtained by a counter-selection against a gene that is contained in a portion (the portion that is desired to be jettisoned) of the “Campbelled in” DNA sequence, for example the Bacillus subtilis sacB gene, which is lethal when expressed in a cell that is grown in the presence of about 5% to 10% sucrose. Either with or without a counter-selection, a desired “Campbell out” cell can be obtained or identified by screening for the desired cell, using any screenable phenotype, such as, but not limited to, colony morphology, colony color, presence or absence of antibiotic resistance, presence or absence of a given DNA sequence by polymerase chain reaction, presence or absence of an auxotrophy, presence or absence of an enzyme, colony nucleic acid hybridization, antibody screening, etc. The term “Campbell in” and “Campbell out” can also be used as verbs in various tenses to refer to the method or process described above.
It is understood that the homologous recombination events that lead to a “Campbell in” or “Campbell out” can occur over a range of DNA bases within the homologous DNA sequence, and since the homologous sequences will be identical to each other for at least part of this range, it is not usually possible to specify exactly where the crossover event occurred. In other words, it is not possible to specify precisely which sequence was originally from the inserted DNA, and which was originally from the chromosomal DNA. Moreover, the first homologous DNA sequence and the second homologous DNA sequence are usually separated by a region of partial non-homology, and it is this region of non-homology that remains deposited in a chromosome of the “Campbell out” cell.
For practicality, in C. glutamicum, typical first and second homologous DNA sequences are at least about 200 base pairs in length, and can be up to several thousand base pairs in length, however, the procedure can be made to work with shorter or longer sequences. For example, a length for the first and second homologous sequences can range from about 500 to 2000 bases, and the obtaining of a “Campbell out” from a “Campbell in” is facilitated by arranging the first and second homologous sequences to be approximately the same length, preferably with a difference of less than 200 base pairs and most preferably with the shorter of the two being at least 70% of the length of the longer in base pairs. The “Campbell In and -Out-method” is described in WO 2007/012078 and Eggeling and Bott (eds) Handbook of Corynebacterium (Taylor and Francis Group, 2005), Chapter 23.
Preferred recombination protocols for C. glutamicum are described in the Examples section.
The present invention is described in more detail by reference to the following examples. It should be understood that these examples are for illustrative purposes only and are not to be construed as limiting the invention.
In the following examples, standard techniques of recombinant DNA technology and molecular biology were used that were described in various publications, e.g. Sambrook et al. (2001), Molecular Cloning: A Laboratory Manual, 3rd edition, Cold Spring Harbor Laboratory Press, or Ausubel et al. (2007), Current Protocols in Molecular Biology, Current Protocols in Protein Science, edition as of 2002, Wiley Interscience. Unless otherwise indicated, all cells, reagents, devices and kits were used according to the manufacturer's instructions.
The examples of PCT/EP2007/061151 inasfar as they pertain to ICD reduction via codon usage and to its effects on production of methionine are herewith incorporated by reference.
1.1 Construction of a Corynebacterium glutamicum Strain with Reduced ICD Activity
To reduce the activity of isocitrate dehydrogenase (Genbank Accession code X71489), a change in codon usage was made. The original start codon ATG was replaced by a GTG. The manipulation was made on the only chromosomal copy of the icd gene of Corynebacterium glutamicum. The subsequent measurement of ICD activity directly allows a readout of the effect.
The sequence of ICD ATG-GTG is depicted in
To this end the sequence of ICD ATG-GTG was cloned into the vector pClik int sacB (Becker et al (2005), Applied and Environmental Microbiology, 71 (12), p. 8587-8596) being a plasmid containing the following elements:
This plasmid allows the integration of sequences at the genomic locus of C. glutamicum.
Construction of the Plasmid pClik int sacB ICD ATG-GTG
The insert was amplified by PCR using genomic DNA of ATCC 13032 as a template. The modification of the coding region was achieved by fusion PCR using the following oligonucleotides. The table shows the primers used as well as the template DNA:
The product of the fusion PCR was purified, digested with XhoI and MluI, purified again and ligated into pClik int sacB which had been linearized with the same restriction enzymes. The integrity of the insert was confirmed by sequencing.
The coding sequence of the optimised sequence ICD ATG→GTG is shown in FIG. 2 of PCT/EP2007/061151 (SEQ ID NO:2 of PCT/EP2007/061151; SEQ ID NO:4 of present sequence listing).
The resulting plasmid is called pClik int sacB ICD ATG-GTG.
Construction of Strains with Modified ICD Expression Levels
The plasmid pClik int sacB ICD ATG-GTG was then used to replace the native coding region of the icd gene by the coding region with the modified start codon. The strain used was LU11424.
Two consecutive recombination events, one in each of the up- and the downstream region respectively, are necessary to change the coding sequence. The method of replacing the endogenous genes with the optimized genes is in principle described in the publication by Becker et al. (vide supra). The most important steps are:
One may use different C. glutamicum strains for replacing the endogenous copy of icd. However, it is preferred to use a C. glutamicum lysine production strain such as for example LU11424 or other derivatives of ATCC13032, ATCC12032lysCfbr or ATCC13286. LU11424 is especially preferred.
LU11424 had been constructed by several consecutive steps of genetic engineering starting from ATCC13032.
LU11424 contains the following modifications:
The expression unit Psod (promoter including ribosomal binding site) is described in WO 2005/059144. The Psod sequence is (5′ to 3′):
The above modifications were all introduced using a similar strategy as for the manipulation of the icd gene (i.e. by the “Campbell in/Campbell out” method described above). The plasmids used for the manipulations were all based on pClik int sacB (see above) or pK19mobsacB (SEQ ID NO:21).
The lysine production strain LU11424 in which ICD activity was lowered by changing the icd start codon from ATG to GTG was called ICD ATG-GTG (synonym ICD ATG→GTG).
1.2 Effects on ICD Activity, Lysine Production, and Production of Trehalose
The effects of the manipulation of the icd gene were confirmed in two independent test series. In the first of these series, the ICD activity and the lysine production were determined. The second test series did additionally contain determination of trehalose production.
1.2.1 First Test Series: ICD Activity and Lysine Production
Effect on ICD Activity
The successful manipulation of the icd gene was confirmed by determination of the ICD enzyme activity of strain ICD ATG-GTG as compared to the initial strain LU11424. For determination of the activity of isocitrate dehydrogenase, cell free extracts were prepared from overnight cultures. Cells were grown in complex medium containing 37 g/L BHI (Bacto™ Brain Heart Infusion) inoculated with single cells from agar plates. Cells were harvested by centrifugation (13.000×g, 5 min, Centrifuge 5415 R, Eppendorf, Hamburg, Germany), washed with reaction buffer (100 mM Tris-HCl, pH 7.8) and cells were disrupted with glasbeads in a ribolyser (Schwingmühle, Retsch, Haan, Germany). Cell debris was removed by centrifugation (13.000×g, 15 min, Centrifuge 5415 R, Eppendorf, Hamburg, Germany) and cell free extracts were used to determine protein content and enzyme activity. Protein concentration was measured by the method of Bradford using a Bradford reagent from Bio-Rad (Quick Start™ Bradford Due Reagent, Bio-Rad Laboratories, Hercules, Calif., United States). Enzyme activity was determined by following the increase in absorbance at 340 nm. The reaction was carried out in a total volume of 1 ml at pH 7.8 containing 100 mM Tris/HCl, 10 mM MgCl2, 0.5 mM NADP, 1 mM isocitrate and 50 μl of the crude cell extract. Negative controls were carried out without isocitrate or without cell extract, respectively. The specific activity of the enzyme is given in mU/mg protein (1 U=1 μmol/min at 30° C.).
The data show that ICD activity in strain ICD ATG→GTG is significantly lower than in the initial strain, LU11424.
Effect on Lysine Productivity
To analyze the effect of the lowered ICD activity on lysine production, the generated strain was compared to the parent strain.
Conditions for growth of the strains were as follows:
Media: First pre-cultures were grown in complex medium containing 5 g L−1 glucose, 5 g L−1 yeast extract, 10 g L−1 tryptone and 5 g L−1 NaCl. Agar plates were prepared by adding 18 g L−1 agar. Second pre-cultivations and main cultivations were performed in minimal medium containing 55 mM glucose. The minimal medium additionally contained per liter: 0.055 g CaCl2.2H2O, 0.2 g MgSO4.7H2O, 1 g NaCl, 25 g K2HPO4, 7.7 g KH2PO4, 15 g (NH4)2SO4, 0.5 mg biotin, 1 mg Ca-panthothenic acid, 1 mg thiamine.HCl, 20 mg FeSO4, 30 mg 3,4-dihydroxybenzoic acid and 10 ml of a 100× trace element solution. The trace element solution contained per liter: 200 mg FeCl3.6H2O, 200 mg MnSO4.H2O, 50 mg ZnSO4.7H2O, 20 mg CuCl2.2H2O, 20 mg NaB4O7.10H2O and 10 mg (NH4)6Mo7O24.4H2O and was adjusted to pH 1.
Cultivation: Single colonies from agar plates were used to inoculate the first pre-culture which incubated for 8 h in 50 mL complex medium in 500 mL baffled flasks. Subsequently, cells were harvested by centrifugation (8,800×g, 2 min, 4° C.), washed with sterile 0.9% NaCl, and used as inoculum for the second pre-culture (25 ml minimal medium in 250 ml baffled flasks). Main cultures were performed in 50 ml medium in 500 ml baffled flasks and inoculated with exponentially growing cells from the second pre-culture. All cultivation experiments were carried out at 30° C. and 230 rpm on a rotary shaker (shaking diameter 5 cm, Multitron, Infors AG, Bottmingen, Switzerland). The pH was in a range of 7.1±0.2 over the cultivation time. After 18 hours, a sample was taken from the exponentially growing culture to analyze cell concentration, substrate consumption and product formation. Cell concentration was determined by measurement of the optical density at 660 nm (Spectrophotometer, Libra S11, Biochrom, Cambridge, UK). If necessary, samples were diluted on an analytical balance (CP255D, Sartorius, Göttingen, Germany) to obtain absorbance values between 0.05 and 0.3.
Concentration of glucose was determined with a glucose kit from Boehringer Mannheim. Lysine concentration was determined with an optical enzymatic test using a lysine calibration curve. The reaction was performed in a volume of 1 ml and contained 0.9 ml 100 mM Tris-HCl (pH 8.0), 1 mg ABTS, 80 mU lysine oxidase, 400 mU peroxidase and the reaction was started by adding 100 μl culture supernatant. After 6 minutes, the absorbance at 436 nm was measured. If necessary, the culture supernatant was diluted to obtain absorbance values that are within the range of the calibration curve.
It can be easily seen that strains with lowered ICD activity have a higher lysine yield (more than 1.3 fold higher than in initial strain).
1.2.2 Second Test Series: ICD Activity, Production of Lysine and Trehalose
The successful manipulation of the icd gene was confirmed again by determination of the ICD enzyme activity of strain ICD ATG→GTG as compared to the initial strain LU11424 and by determination of the lysine production. Additionally, production of trehalose was measured.
Medium composition: Complex medium, used for agar plates and first pre-cultures, contained 10 g L−1 peptone, 5 g L−1 beef extract, 5 g L−1 yeast extract, 2.5 g L−1 NaCl, 10 g L−1 glucose and 2 g L−1 urea with or without 18 g L−1 agar, respectively. Second pre-culture and main culture were performed in minimal medium containing: (A) 500 mL salt solution (1 g NaCl, 55 mg MgCl2.7H2O and 200 mg CaCl), (B) 100 mL substrate solution (100 g L−1 glucose or fructose, respectively), (C) 100 mL buffer solution (2 M potassium phosphate, pH 7.8), (D) 100 mL solution B (150 g L−1 (NH4)2SO4, pH 7.0), (E) 20 mL vitamin solution (25 mg L−1 biotin, 50 mg L−1 thiamine.HCl and 50 mg L−1 panthothenic acid), (F) 10 mL FeSO4-solution (2 g L−1 FeSO4, pH 1.0), (G) 10 ml 100× trace elements (Vallino, J. J., and G. Stephanopoulos, reprinted from Biotechnol Bioeng 41:633-646 (1993) in Biotechnol Bioeng 67:872-85 (1993)) and (H) 1 mL DHB-solution (30 mg mL−1 3,4-dihydroxybenzoic acid in 0.3 M NaOH) adjusted to 1 L with milliQ purified water. Solutions were separately sterilized by autoclaving (A-D) or by filtration (E-H). The different medium compounds were combined at room temperature freshly before use.
Cultivation and growth conditions: Cells from glycerol stocks (10% glycerol, 50 mg L−1 lactose) stored at −80° C. were spread on agar plates and incubated for 48 h at 30° C. First pre-cultures were grown in 25 ml complex medium (250 ml baffled shake flasks) for 10 h at 30° C. and 230 rpm on a rotary shaker (Multitron, Infors AG, Bottmingen, Switzerland). After centrifugation (3 min, 7000×g, Biofuge stratos, Heraeus, Hanau, Germany) cells were washed with sterile 0.9% NaCl and used as inoculum for the second preculture (50 ml in 500 ml baffled shake flasks). In the mid-exponential growth phase, cells were harvested and washed as described above and used to inoculate the main culture. This was performed in triplicate using 2 L baffled shake flasks with 200 ml medium. During the cultivation the pH remained constant within a range of 7.1±0.1 and sufficient oxygen supply was ensured.
Substrate and Product Analysis
Concentration of glucose, lysine and further products was determined in 1:10-diluted cultivation supernatant. Glucose was quantified with a biochemical analyzer (YSI 2700 Select, Kreienbaum, Langenfeld, Germany). Concentration of organic acids and trehalose was determined by a LaChrome HPLC system consisting of an autosampler L-2200, pump L-2130, UV detector L-2400, RI detector L-24900 and column oven L-2350 (Hitachi, VWR, Darmstadt, Germany) on an Aminex HPX-87H column (300×7.8; Bio-Rad, Hercules, Calif.) at 45° C., with 10 mM H2SO4 as mobile phase and a flow rate of 0.5 ml/min and detection via refraction index (sugars) or UV absorbance (organic acids) at 210 nm. The protocol for quantification of amino acids included pre-column derivatisation with o-phthaldehyde (OPA) and separation on a C18 column (Gemini5u, Phenomenex, Aschaffenburg, Germany) as described (Krömer, J. O. et al., Anal Biochem 340:171-3 (2005)). To reduce measurement time the gradient profile was changed and eluent B was added with 4% min−1. Cell concentration was determined in a photometer (Libra S11, Biochrome, Cambridge, UK) at 660 nm or gravimetrically as cell dry mass (CDM) (CP225D, Sartorius, Göttingen, Germany). For the latter, cells from 15 mL culture broth were harvested by centrifugation (10 min, 9800×g, Biofuge stratos, Heraeus, Hanau, Germany), washed 3 times with water and subsequently dried at 80° C. for 3 days. The correlation factor between OD660 (Libra S11, Biochrome, Cambridge, UK) and CDM was determined to 1 OD=0.258 (g CDM) L−1.
Cell Disruption
Cells were grown as described above with a main culture volume of 50 ml (500 ml baffled shake flasks). Cells were harvested in the exponential growth phase by centrifugation (5 min, 9800×g, 4° C., Biofuge stratos, Heraeus, Hanau, Germany), washed with disruption buffer (100 mM TrisHCl, pH 7.8) and subsequently resuspended in 10 ml of the same buffer. Cell suspension was aliquoted in 750 μl amounts in 2 ml Eppendorf tubes containing glass beads. Disruption was performed in a ribolyzer (MM301, Retsch, Haan, Germany) at 30 Hz (2×5 min; 5 minutes break in between). Crude cell extracts were obtained by centrifugation for 10 minutes at 13000×g (Centrifuge 5415R, Eppendorf, Hamburg, Germany) and used for determination of enzyme activity and protein content. The latter was quantified by the method of Bradford (Anal Biochem 72:248-54 (1976)) with a reagent solution from BioRad (Quick Start Bradford Dye, BioRad, Hercules, USA).
Isocitrate Dehydrogenase Activity
Analysis of in vitro activity of ICD was based on the protocol of Chen et al. (Chen, R., and H. Yang, Arch Biochem Biophys 383:238-45 (2000)). The reaction was carried out in a volume of 1 ml at pH 7.8 and 30° C. in 1.5-ml polystyrene cuvettes. The assay mixture contained 100 mM Tris/HCl (pH 7.8), 10 mM MgCl2, 1 mM isocitrate, 0.5 mM NADP and 25 μl of crude cell extract. The change in absorbance at 340 nm due to NADPH formation was monitored online (Specord 40, Analytik Jena, Jena, Germany). Negative control was carried out without isocitrate or without cell extract, respectively. Specific activity of ICD in crude cell extracts of C. glutamicum LU11424 and ICD ATG→GTG grown in minimal medium containing glucose as carbon source is given in table 5. 1 U=1 μmol/min at 30° C.; molar extinction coefficient of NADPH=6.22 L mmol−1cm−1.
The data show that ICD activity in strain ICD ATG GTG is significantly lower than in the initial strain, LU11424.
Lysine and Trehalose Production
The production characteristics of lysine producing C. glutamicum LU11424 and ICD ATG→GTG on glucose are provided in table 6. The yields given in table 6 are biomass yield (YX/S), lysine yield (YLys/S), and trehalose yield (YTre/S), all per consumed glucose (S), and represent mean values from three parallel cultivation experiments and corresponding deviations. The yields were determined as slope of the linear best fit when plotting product formation and substrate consumption.
It can be easily seen that the strain with lowered ICD activity has a higher lysine and trehalose yield (more than 1.3 fold higher than in initial strain).
In a further experiment described in PCT/EP2007/061151, isocitrate dehydrogenase carrying the above mentioned ATG-GTG mutation in the start codon (compare example 1.1) was cloned into pClik as described above leading to pClik int sacB ICD (ATG-GTG) (SEQ ID NO:15 of PCT/EP2007/061151, SEQ ID NO:5 of present sequence listing shows the vector insert). Subsequently, strain M2620 was constructed by campbelling in and campbelling out the plasmid pClik int sacB ICD (ATG-GTG) (SEQ ID NO:15 of PCT/EP2007/061151) into the genome of the strain 0M469. The strain 0M469 has been described in WO 2007/012078.
The strain was grown as described in WO 2007/020295. After 48 h incubation at 30° C. the samples were analyzed for sugar consumption. It was found that the strains had used up all added sugar, meaning that all strains had used the same amount of carbon source. Synthesized methionine was determined by HPLC as described above and in WO 2007/020295.
From the data in table 7 it can be seen that the strain M2620 with an altered start codon of the ICD gene and therefore altered ICD activity has higher methionine productivity. Since all carbon source is used up after 48 h, one can also directly see, that the carbon yield (amount of formed product per sugar consumed) for the produced methionine is higher in this strain.
Construction of Strains with Modified ICD Expression Level
The plasmid pClik int sacB ICD ATG→GTG (see example 1.1, synonyms: pClik int sacB ICD (ATG-GTG), pClik int sacB ICD ATG-GTG, vector insert see SEQ ID NO:5) is used for construction of diaminopentane producing strains with modified ICD expression level in comparison to the host strain.
The parent strain used is a 1,5-diaminopentane (1,5-DAP) producer derived from C. glutamicum wild type strain ATCC 13032 by incorporation of a point mutation T311I into the aspartokinase gene (NCgl 0247) and subsequent amplification of the gene dosage by addition of a strong promoter Psod, duplication of the diaminopimelate dehydrogenase gene (NCgl 2528), disruption of the phosphoenolpyruvate carboxykinase gene (NGgl 2765) and chromosomal integration of the E. coli lysine decarboxylase gene (Kyoto Encyclopedia of Genes and Genomes, Entry JW0181). Each of said modifications to ATCC 13032 is performed by applying generally known methods of recombinant DNA technology. The sequences of the plasmids used for establishing the 1,5-DAP producer parent strain are shown in SEQ ID NOs: 21 to 24. SEQ ID NO:21 may be used for deletion of the pepCK gene (delta pepCK). SEQ ID NO:22 may be used for duplication of the ddh gene (2×ddh). SEQ ID NO:23 may be used for the amplification of ask gene dosage by integration of Psod promoter upstream of the ask gene (Psodk ask). SEQ ID NO:24 may be used for the construction of the diaminopentane production strain by intengration of E. coli ldcC in the bioD region of a C. glutamicum lysine producer. Then, pClick int sacB ICD ATG->GTG or any other plasmid whose integration would lead to a decrease in ICD activity in the host cell may be introduced into the parent strain by the methods described under “Construction of strains with modified ICD expression levels” in example 1 for a lysine producer.
To analyze the effect of the codon usage amended IDH ATG-GTG, the optimized strains are compared to 1,5-DAP productivity of the parent strain as described under “Determination of ICD activity” in example 1 for a lysine producer.
Effect on 1,5-DAP Productivity
To analyze the effect of the modified expression of ICD on 1,5-DAP productivity, the optimized strains are compared to 1,5-DAP productivity of the parent strains.
To this end the strains are grown on CM-plates (10% sucrose, 10 g/l glucose, 2.5 g/l NaCl, 2 g/l urea, 10 g/l Bacto Pepton, 10 g/l yeast extract, 22 g/l agar) for 2 days at 30° C. Subsequently cells are scraped from the plates and re-suspended in saline. For the main culture 10 ml of production medium (40 g/l sucrose, 60 g/l molasses (calculated with respect to 100% sugar content), 50 g/l (NH4)2SO4, 0.6 g/l KH2PO4, 0.4 g/l MgSO4.7H2O, 2 mg/l FeSO4.7H2O, 2 mg/l MnSO4.H2O, 0.3 mg/l thiamine.HCl, 1 mg/l biotin) and 0.5 g autoclaved CaCO3 in a 100 ml Erlenmeyer flask are incubated together with the cell suspension up to an OD600 of 1.5. The cells are then grown for 72 hours on a shaker of the type Infors AJ118 (Infors, Bottmingen, Switzerland) at 220 rpm.
Subsequently, the concentration of 1,5-DAP that is segregated into the medium is determined. This is done using HPLC on an Agilent 1100 Series LC system HPLC. A precolumn derivatisation with ortho-phthalaldehyde allows to quantify the formed 1,5-DAP. The separation of the mixture can be done on a Gemini C18 column (Phenomenex). EluentA is 40 mM NaH2PO4.H2O, pH7.8 and eluent B Acetonitril:Methanol:H2O 45:45:10. Detection is done by a fluorescence detector.
As strains with lowered ICD activity have higher lysine productivity, it seems reasonable that strains with lowered ICD activity will have higher 1,5-DAP productivities.
To delete the icd coding region, a deletion cassette containing ˜300-600 consecutive nucleotides upstream of the icd coding sequence directly fused to 300-600 consecutive nucleotides downstream of the icd coding region is inserted into pClik int sacB. The resulting plasmid is called pClik int sacB delta icd (SEQ ID NO:8).
The plasmid is then transformed into C. glutamicum by standard methods, e.g. electroporation. Methods for transformation are found in e.g. Thierbach et al. (Applied Microbiology and Biotechnology 29:356-362 (1988)), Dunican and Shivnan (Biotechnology 7:1067-1070 (1989)), Tauch et al. (FEMS Microbiological Letters 123, 343-347 (1994)), and DE 10046870.
Two consecutive recombination events, one in each of the up- and the downstream region respectively, are necessary to delete the complete coding sequence. The method of replacing the endogenous gene with the deletion cassette using the plasmid pClik int sacB is in principle described in the publication by Becker et al. (vide supra). The most important steps are:
Suitable primers are (5′ to 3′):
A strain in which the complete coding region of ICD was removed should result in a PCR product of about 440 base pairs (more precisely: 442 bp), while the parent strain with the wild type icd gene should show a band of about 2660 base pairs.
Successful deletion can furthermore be confirmed by Southern blotting or measuring ICD activity.
The resulting strain which contains a complete deletion of the icd coding region is called delta icd.
As this strain will lack ICD activity and therefore be unable to synthesise glutamate, it is useful to let this strain grow on rich medium or supply glutamate if grown on minimal medium.
More detailed methods on how to delete genes in C. glutamicum are also described in Eggeling and Bott (eds) “Handbook of Corynebacterium” (Taylor and Francis Group, 2005) Chapter 23.8.
The effect of icd deletion on the productivity of lysine, methionine, beta-lysine, diaminopentane, dipicolinate can be monitored as described above and in WO 2007/101867, WO 2007/113127.
In general, for production of any target fine chemical, the same culture medium and conditions as for lysine production as described in WO 2005/059139 can be employed. The strains are precultured on CM agar overnight at 30° C. Cultured cells are harvested in a microtube containing 1.5 ml of 0.9% NaCl and cell density is determined by the absorbance at 610 nm following vortex. For the main culture, suspended cells are inoculated to reach 1.5 of initial OD into 10 ml of the production medium (called medium I in WO 2005/059139) contained in an autoclaved 100 ml of Erlenmeyer flask having 0.5 g of CaCO3. Main culture is performed on a rotary shaker (Infors AJ118, Bottmingen, Switzerland) with 200 rpm for 48-78 hours at 30° C. For cell growth measurement, 0.1 ml of culture broth is mixed with 0.9 ml of 1 N HCl to eliminate CaCO3, and the absorbance at 610 nm is measured following appropriate dilution. The concentration of the product and residual sugar including glucose, fructose and sucrose are measured by HPLC method (Agilent 1100 Series LC system).
More experimental details are now described for one possible strategy to replace the original icd sequence by a mutant sequence with lower ICD activity.
1. Generation and Selection of icd Mutants with Lower Activity
In a first step, the icd coding sequence is cloned into a replicating plasmid which contains all regulatory sequences, such as promoter, RBS and a terminator sequence functioning in the host cell, which may be C. glutamicum. Ideally, a shuttle plasmid is used which can replicate in E. coli and in C. glutamicum. An example for such a shuttle vector is pClik5aMCS (WO 2005/059093). More suitable shuttle vectors can be found in Eikmanns et al. (Gene (1991) 102:93-8) or in the “Handbook of Corynebacterium” (edited by Eggeling and Bott, ISBN 0-8493-1821-1, 2005). One can find there a list of E. coli-C. glutamicum shuttle vectors (table 23.1) and a list of E. coli-C. glutamicum shuttle expression vectors (table 23.2). The latter are preferred as they already contain suitable promoters driving the expression of the cloned gene.
Standard methods of molecular biology, such as cloning including the amplicifation by PCR, digestion with restriction enzymes, ligation, transformation are known to the expert and can be found in standard protocol books such as Ausubel et al. (eds) Current protocols in molecular biology. (John Wiley & Sons, Inc. 2007), Sambrook et al., MOLECULAR CLONING: A LABORATORY MANUAL, Second Edition, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1989), and Ausubel et al. (eds.), SHORT PROTOCOLS IN MOLECULAR BIOLOGY, 3rd Edition (John Wiley & Sons, Inc. 1995).
A set of mutant variants of the icd coding sequence is generated by site-directed mutagenenis. Methods for mutagenesis can be found in Glick and Pasternak MOLECULAR BIOTECHNOLOGY. PRINCIPLES AND APPLICATIONS OF RECOMBINANT DNA; 2nd edition (American Sicienty for Microbiology, 1998), Chapter 8: Directed Mutagenensis and Protein Engineering, and Ausubel et al. (eds) Current protocols in molecular biology. (John Wiley & Sons, Inc. 2007). Chapter 8.
The resulting set of plasmids encoding a library of icd variants is usually generated in E. coli.
Subsequently, the library may be transformed into C. glutamicum by standard methods, such as electroporation. Methods for transformation are found in e.g. Thierbach et al. (Applied Microbiology and Biotechnology 29:356-362 (1988)), Dunican and Shivnan (Biotechnology 7:1067-1070 (1989)), Tauch et al. (FEMS Microbiological Letters 123:343-347 (1994)) or Eggeling and Bott (eds) Handbook of Corynebacterium” (Taylor and Francis Group, 2005) ISBN 0-8493-1821-1.
The resulting clones should then be tested on ICD activity. The method to measure ICD enzyme activity from crude cell extract is described in example 1.
As a control, the wild type icd gene cloned in the same plasmid as the icd variant library is determined in parallel.
Based on these results, ICD variants with lower activity compared to the wild type icd gene can be selected.
The mutants resulting in lower ICD activity can either have lower specific activity (e.g. each protein molecule is less active), be transcribed or translated less efficiently, or be less stable.
2. Replacement of the Wild Type icd Gene with a Mutant with Lower ICD Activity
To replace the wild type icd coding region by a variant with lower ICD activity, one can apply a two step strategy. In a first step, the coding region of the wild type icd gene is completely deleted from the genome. There is literature describing that cells with disrupted icd are viable. (Eikmanns et al (1995) J Bacteriol (1995) 177(3):774-782).
a) Deletion of Wild Type icd
The method of deletion of icd is described in example 4. The resulting strain is called delta icd.
b) Insertion of the Mutant icd Sequence
In a second step, the variant icd coding sequence is inserted into the delta icd strain. To do so, the mutant icd sequence is cloned into a suitable integration plasmid, e.g. pClik int sacB (see above) flanked by the same ˜300-600 upstream and downstream nucleotides used for the deletion construct in example 4.
Once this plasmid containing mutant icd is transformed into C. glutamicum, clones which have—after two consecutive steps of homologous recombination—inserted the mutant icd coding region into the icd locus can be identified by a similar strategy as above. PCR primers specific for the mutant ICD coding region may be used to distinguish between the delta icd strain and the positive clone.
Clones which have successfully replaced the wild type icd coding region by the mutant icd coding region will be called “icd (mut)” in the following.
3. Determination of ICD activity
The ICD activity of strain “icd (mut)” should be compared to the activity of the parent strain containing the wild type icd gene. The method for this is described in example 1.
4. Analysis of Effects for the Production of Fine Chemicals
The above replacement of wild type icd by mutant icd may be done in strains producing different chemicals by fermentation.
Suitable strains include C. glutamicum engineered to produce the following chemicals (references for strains which can be used as production strains in brackets):
The cultivation and detection for lysine, methionine and diaminopentane production is described in the other examples. In general, for any of the target fine chemicals, the same culture medium and conditions as for lysine production can be employed as described in WO 2005/059139. The strains are precultured on CM agar overnight at 30° C. Cultured cells are harvested in a microtube containing 1.5 ml of 0.9% NaCl and cell density is determined by the absorbance at 610 nm following vortex. For the main culture, suspended cells are inoculated to reach 1.5 of initial OD into 10 ml of the production medium (called medium I in WO 2005/059139) contained in an autoclaved 100 ml of Erlenmeyer flask having 0.5 g of CaCO3. Main culture is performed on a rotary shaker (Infors AJ118, Bottmingen, Switzerland) with 200 rpm for 48-78 hours at 30° C. For cell growth measurement, 0.1 ml of culture broth is mixed with 0.9 ml of 1 N HCl to eliminate CaCO3, and the absorbance at 610 nm is measured following appropriate dilution. The concentration of the product and residual sugar including glucose, fructose and sucrose are measured by HPLC method (Agilent 1100 Series LC system).
The accumulation of the target product is expected to be higher in the strains in which ICD activity was reduced.
a) Identification of a Suitable Upstream Sequence (Promoter Plus RBS)
First, an upstream sequence which is weaker than the native icd promoter has to be identified. The new upstream sequence can be derived from Corynebacterium or from other organisms. Several promoters (incl RBS) which function in bacteria, more specifically in coryneform bacteria, have been identified. Examples of such promoters are described in: DE-A-44 40 118, Reinscheid et al., Microbiology 145:503 (1999), Patek et al., Microbiology 142:1297 (1996), WO 02/40679, DE-A-103 59 594, DE-A-103 59 595, DE-A-103 59 660 and DE-A-10 2004 035 065.
In addition, other upstream regions which are weaker than the native icd promoter may be used for the replacement of the icd promoter.
The strength of upstream regions can be measured using a reporter system, such as described in Patek et al (1996) Promoters from corynebacterium glutamicum: cloning, molecular analysis and search for a consensus motif. Microbiology 142:1297-1309.
Alternatively, one may introduce mutations in the native upstream sequence and subsequently analyze its transcriptional activity. Preferably, the 83 nt upstream sequence of the icd start codon is used, as in this regions there is no coding region of other genes. The sequence of the upstream region is shown below (bold letters).
Methods on how to mutagenize DNA sequences including promoter sequences are well known to the expert and also described in e.g. Bernard R. Glick, Jack J. Pasternak: Molecular Biotechnology: Principles and Applications of Recombinant DNA. 2nd edition. 1998. ISBN 1-55581-136-1; Chapter 8: Directed Mutagenesis and Protein engineering. A suitable promoter sequence may then be selected.
An upstream region with lower transcriptional or translational activity should be used to replace the original promoter driving ICD expression. Technically, the replacement can be done by two consecutive homologous recombination events, by the same methodology as the replacement of the icd coding region described in the previous examples.
The resulting strain will have lowered ICD activity. The effect on the productivity can be analyzed as described in Example 5.
Sequence of the ICD Gene Including 500 nt Up- and Downstream Region (SEQ ID NO:2)
Presumed promoter region (Upstream region): bold letters
Coding region: italic
Downstream region: normal
gcgcgcatcctcgaagacctcgcagattccgatattccaggaaccgccatgatcgaaatcccctcagatgacgat
gcacttgccatcgagggaccttcctccatcgatgtgaaatggctgccccgcaacggccgcaagcacggtgaattgt
tgatggaaaccctggccctccaccatgaagaaacagaagctgcagccacctccgaaggcgaacttgtgtgggag
actcctgtgttctccgccactggcgaacagatcacagaatccaacccacgttcaggcgactactactggattgctg
gcgaaagtggtgtcgtgaccagcattcgtcgatctctagtgaaagagaaaggcctcgaccgttcccaagtggcatt
catggggtattggaaacacggcgtttccatgcggggctga
aactgccaccataggcgccagcaattagtagaaca
ctgtattctaggtagctgaacaaaagagcccatcaaccaaggagactc
atggctaagatcatctggacccgcaccg
acgaagcaccgctgctcgcgacctactcgctgaagccggtcgtcgaggcatttgctgctaccgcgggcattgaggtc
gagacccgggacatttcactcgctggacgcatcctcgcccagttcccagagcgcctcaccgaagatcagaaggtag
gcaacgcactcgcagaactcggcgagcttgctaagactcctgaagcaaacatcattaagcttccaaacatctccgctt
ctgttccacagctcaaggctgctattaaggaactgcaggaccagggctacgacatcccagaactgcctgataacgcc
accaccgacgaggaaaaagacatcctcgcacgctacaacgctgttaagggttccgctgtgaacccagtgctgcgtg
aaggcaactctgaccgccgcgcaccaatcgctgtcaagaactttgttaagaagttcccacaccgcatgggcgagtgg
tctgcagattccaagaccaacgttgcaaccatggatgcaaacgacttccgccacaacgagaagtccatcatcctcga
cgctgctgatgaagttcagatcaagcacatcgcagctgacggcaccgagaccatcctcaaggacagcctcaagcttc
ttgaaggcgaagttctagacggaaccgttctgtccgcaaaggcactggacgcattccttctcgagcaggtcgctcgcg
caaaggcagaaggtatcctcttctccgcacacctgaaggccaccatgatgaaggtctccgacccaatcatcttcggcc
acgttgtgcgcgcttacttcgcagacgttttcgcacagtacggtgagcagctgctcgcagctggcctcaacggcgaaa
acggcctcgctgcaatcctctccggcttggagtccctggacaacggcgaagaaatcaaggctgcattcgagaaggg
cttggaagacggcccagacctggccatggttaactccgctcgcggcatcaccaacctgcatgtcccttccgatgtcatc
gtggacgcttccatgccagcaatgattcgtacctccggccacatgtggaacaaagacgaccaggagcaggacaccc
tggcaatcatcccagactcctcctacgctggcgtctaccagaccgttatcgaagactgccgcaagaacggcgcattcg
atccaaccaccatgggtaccgtccctaacgttggtctgatggctcagaaggctgaagagtacggctcccatgacaag
accttccgcatcgaagcagacggtgtggttcaggttgtttcctccaacggcgacgttctcatcgagcacgacgttgagg
caaatgacatctggcgtgcatgccaggtcaaggatgccccaatccaggattgggtaaagcttgctgtcacccgctccc
gtctctccggaatgcctgcagtgttctggttggatccagagcgcgcacacgaccgcaacctggcttccctcgttgagaa
gtacctggctgaccacgacaccgagggcctggacatccagatcctctcccctgttgaggcaacccagctctccatcga
ccgcatccgccgtggcgaggacaccatctctgtcaccggtaacgttctgcgtgactacaacaccgacctcttcccaatc
ctggagctgggcacctctgcaaagatgctgtctgtcgttcctttgatggctggcggcggactgttcgagaccggtgctgg
tggatctgctcctaagcacgtccagcaggttcaggaagaaaaccacctgcgttgggattccctcggtgagttcctcgca
ctggctgagtccttccgccacgagctcaacaacaacggcaacaccaaggccggcgttctggctgacgctctggaca
aggcaactgagaagctgctgaacgaagagaagtccccatcccgcaaggttggcgagatcgacaaccgtggctccc
acttctggctgaccaagttctgggctgacgagctcgctgctcagaccgaggacgcagatctggctgctaccttcgcac
cagtcgcagaagcactgaacacaggcgctgcagacatcgatgctgcactgctcgcagttcagggtggagcaactga
ccttggtggctactactcccctaacgaggagaagctcaccaacatcatgcgcccagtcgcacagttcaacgagatcgt
tgacgcactgaagaagtaaagtctcttcacaaaaagcgctgtgcttcctcacatggaagcacagcgctttttcatatttttat
| Number | Date | Country | Kind |
|---|---|---|---|
| 08155436.2 | Apr 2008 | EP | regional |
| Filing Document | Filing Date | Country | Kind | 371c Date |
|---|---|---|---|---|
| PCT/EP2009/055146 | 4/28/2009 | WO | 00 | 3/19/2011 |
