Patent Application
20180030460
A Sequence Listing in ASCII text format, submitted under 37 C.F.R. §1.821, entitled 9737-41_ST25.txt, 127,549 bytes in size, generated Apr. 14, 2016 and filed via EFS-Web, is provided in lieu of a paper copy. This Sequence Listing is hereby incorporated herein by reference into the specification for its disclosures.
The present invention relates to the development of genetically engineered yeasts that can produce hydrocarbons in a controllable and economic fashion. More specifically the invention relates to the production of, for instance liquid alkanes and alkenes, that can be used for liquid transportation fuels, specialty chemicals, or feed stock for further chemical conversion.
Increased petroleum prices along with concerns about carbon dioxide emission and the lack of sustainability of fossil fuels have been strongly motivating the development and production of biofuels. As about 80% of mineral oils are being used for liquid transportation fuels, there is particular focus on developing alternative biotech processes to replace these.
Currently, the dominating biofuel is ethanol. This is produced in very large quantities, particularly in Brazil from sugar cane and in the USA from corn, but there are also several key initiatives on establishing so-called second-generation bioethanol production, where cellulosic biomass is used as the feedstock. The production of advanced biofuels to be used as gasoline does not solve a major problem associated with ensuring provision of jetfuels and fuels for maritime and heavy duty road transportation, both of which require high-density fuels—generally known as diesel-fuels.
Currently, biodiesel is produced from vegetable oils, but this biodiesel production is problematic since it competes against use of these oils in the food sector. Furthermore, the yield of oil per hectare is very low compared with that of sugar cane or other sugar crops. This type of biodiesel consists mainly of fatty acid alkyl esters (FAAEs). Recently, initiatives have been started to produce FAAEs in microorganisms such as the bacterium Escherichia coli and the yeast Saccharomyces cerevisiae with sugars as substrate, which would allow for higher per hectare yields resulting in a lower environmental impact. A disadvantage of FAAEs is that they contain oxygen, which leads to a lower energy density compared to pure hydrocarbon molecules.
A primary object of the present invention is to provide a genetically engineered yeast that can produce hydrocarbons, including but not limited to alkanes and alkenes, in a controllable and economic fashion.
An aspect of the embodiments relates to a yeast lacking a gene encoding hexadecanal dehydrogenase (HFD1) or comprising a disrupted gene encoding HFD1. The yeast also comprises at least one heterologous gene encoding an enzyme involved in a pathway of producing hydrocarbons.
Another aspect of the embodiments relates to a method for producing hydrocarbons. The method comprises culturing a yeast lacking a gene encoding hexadecenal dehydrogenase (HFD1) or comprising a disrupted gene encoding HFD1 in culture conditions suitable for production of the hydrocarbons from the yeast. The method also comprises collecting the hydrocarbons from the culture medium in which the yeast is cultured and/or from the yeast.
A further aspect of the embodiments relates to use of a yeast lacking a gene encoding hexadecenal dehydrogenase (HFD1) or comprising a disrupted gene encoding HFD1 for the production of hydrocarbons. In one embodiment, Saccharomyces cerevisiae was metabolically engineered to synthesize medium-chain alkanes. The inventors identified and demonstrated the importance of eliminating hexadecenal dehydrogenase Hfd1 in combination with heterologous expression of one or more enzymes, and/or biosynthetic and/or metabolic pathways, in enabling biosynthesis of the former compounds in yeast. The requirement of HFD1 deletion further illustrates a key difference between yeast and bacteria, in which the main competing enzymes are fatty aldehyde reductases and fatty alcohol dehydrogenases that convert the fatty aldehyde intermediate reversibly into a fatty alcohol.
The fatty acid derivatives (e.g., alkanes, alkenes, fatty alcohols) produced by the recombinant yeast of this invention are liquid (e.g., carbon chains with 5-17 carbon atoms). Such liquid alkanes and/or alkenes can be used, for example, as liquid transportation fuels. These and other aspects of the invention are set forth in more detail in the description of the invention below.
The present invention now will be described hereinafter with reference to the accompanying drawings and examples, in which embodiments of the invention are shown. This description is not intended to be a detailed catalog of all the different ways in which the invention may be implemented, or all the features that may be added to the instant invention. For example, features illustrated with respect to one embodiment may be incorporated into other embodiments, and features illustrated with respect to a particular embodiment may be deleted from that embodiment. Thus, the invention contemplates that in some embodiments of the invention, any feature or combination of features set forth herein can be excluded or omitted. In addition, numerous variations and additions to the various embodiments suggested herein will be apparent to those skilled in the art in light of the instant disclosure, which do not depart from the instant invention. Hence, the following descriptions are intended to illustrate some particular embodiments of the invention, and not to exhaustively specify all permutations, combinations and variations thereof.
Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. The terminology used in the description of the invention herein is for the purpose of describing particular embodiments only and is not intended to be limiting of the invention.
All publications, patent applications, patents and other references cited herein are incorporated by reference in their entireties for the teachings relevant to the sentence and/or paragraph in which the reference is presented.
Unless the context indicates otherwise, it is specifically intended that the various features of the invention described herein can be used in any combination. Moreover, the present invention also contemplates that in some embodiments of the invention, any feature or combination of features set forth herein can be excluded or omitted. To illustrate, if the specification states that a composition comprises components A, B and C, it is specifically intended that any of A, B or C, or a combination thereof, can be omitted and disclaimed singularly or in any combination.
An alternative type of diesel fuel can include terpene derived hydrocarbons. Since terpene derived diesels need chemical finishing due to the unsaturated nature of the primary fermentation products, an ideal biofuel would comprise saturated alkanes, which are also the main component of petrodiesels. Biosynthetically they are derived from fatty acids, which are constructed from the building block acetyl-CoA.
Biosynthetic pathways leading to alkane formation have however only been elucidated very recently, mainly in plants and bacteria. The“n−1 pathway” from cyanobacteria, is a two-step process, in which activated fatty acids are first reduced to fatty aldehydes and then decarbonylated to form alkanes. This pathway was transferred to E. coli and the resultant recombinant bacterium has been used in a fermentation process developed by a US-based company LS9.
The present invention provides a further industrial organism, yeast, that produces fatty acid derivatives (e.g., alkanes, alkenes, fatty alcohols and the like). Using today's methods, production of such fatty acid derivatives has not been efficient in yeast, since the yields are too low and it has not been possible to obtain short/medium chain fatty acid derivatives. However, the present inventors surprisingly discovered that deleting a hexadecenal dehydrogenase gene, HFD1, in yeast led to the blocking of the conversion of fatty aldehyde to fatty acid, thereby resulting in the production of, for example, alkanes, alkenes and fatty alcohols. Due to its adaptability to fermentation conditions, such as low pH, yeast provides an ideal industrial microorganism for the production of these fatty acid derivatives.
The HDF1 gene in yeast has so far only been studied in the context of Sjögren-Larssons disease, but has never been associated with production of fatty acid derivatives as in the present invention. Hexadecenal dehydrogenase Hfd1 (encoded by HFD1) competes for substrate with the heterologous fatty aldehyde decarbonylases leading to an ATP consuming futile cycle. By the discovery of the present inventors that a knock-out of this gene in yeast, alone or in combination with the integration of one or more heterologous nucleotide sequences and/or biosynthetic pathways, can alter the products of fatty acid biosynthesis and metabolism, the inventors have provided a solution to the utilization of different fatty acid biosynthetic machineries in the cytosol and in the mitochondria, respectively for the synthesis of medium and long chain fatty acids, and their subsequent conversion into alkanes, alkenes and/or fatty alcohols.
In the present invention, the inventors demonstrate fatty acid derived alkane biosynthesis in the yeast S. cerevisiae by expression of an alkane biosynthetic pathway consisting of a FAR, encoded by Synechoccocus elongatus orf1594, and a FADO, encoded by S. elongatus orf1593 (see
Hence, to ensure efficient functionality of the pathway the inventors chose to verify the fatty aldehyde supply by FAR. To confirm the supply of fatty aldehydes, fatty alcohol synthesis was used as an indicator. The detection of fatty alcohols as byproducts of alkane biosynthesis has been observed in E. coli, and is suspected to be a result of the activity of endogenous promiscuous aldehyde reductases and alcohol dehydrogenases. Yeast contains around 40 homologues of such reductases and dehydrogenases, and consequently fatty alcohol synthesis was expected to occur after the introduction of FAR. Nevertheless, when SeFAR was overexpressed in a wild-type yeast strain, it yielded only trace amounts of fatty alcohols (
The detection of heptadecane in the wild-type background strain KB17 carrying SeFAR, SeFADO, and EcF/FNR and the absence of the fatty alcohol octadecanol in the hfd1Δ SeFAR strain suggests that Hfd1 and the endogenous aldehyde reductases/alcohol dehydrogenases cannot use octadecanal as a substrate. This is in agreement with the detection of very long chain alkanes. The modest increase in fatty alcohol titer after FAR expression in a hfd1 strain, is most likely due to the low affinity of FAR for fatty acyl-CoA (it prefers fatty acyl-ACP). These results illustrate the importance of HFD1 deletion to enable fatty aldehyde supply.
Subsequently, the SeFADO and the EcF/FNR reducing system were introduced in the hfd1Δ strain, as deletion of HFD1 alone is sufficient to provide fatty aldehydes for the upstream part of the alkane pathway (which had been shown by the increased production of fatty alcohols). Subsequently, the alkane production increased drastically to 18.6±1.4 mg/gDW in this hfd1Δ SeFADO EcF/FNR strain (
Similarly, we also realized medium-chain alkane production after HFD1 disruption in a S288C background. Interestingly, expression of only SeFAR and SeFADO in this strain resulted in pentadecane and heptadecane biosynthesis, possibly indicating the presence of a reducing system that is absent in the CEN.PK background strain.
In some embodiments of the invention, yeasts can be modified to overproduce acyl-CoA, fatty acids or acyl-ACPs in order to further increase the production of alkanes, alkenes and/or fatty alcohols. In one embodiment, increasing the fatty acid synthesis can be accomplished by overexpressing fatty acid biosynthetic genes, including but not limited to ACC1 (encoding acetyl-CoA carboxylase), FAS1 (encoding the beta-subunit of fatty acid synthetase) and FAS2 (encoding the alpha-subunit of fatty acid synthetase). The inventors have in addition to these pathways also expressed several alternative alkane/alkene biosynthetic pathways in order to enable the biosynthesis of short, medium, and long chain alkanes, alkenes, and the like.
In some aspects of the invention, alkenes and/or alkanes with 5-17 carbon atoms are preferred. To achieve these chain lengths, the chain length of the fatty-acids used for conversion to alkanes and/or alkenes can be regulated.
For example, shorter chain molecules can be obtained by introducing a fatty acid synthase from humans, by expression of the alkane/alkene pathways in the mitochondria, or by reversed beta-oxidation in the cytosol.
A still further aspect comprises eliminating non-essential pathways in the yeast that consume (activated) fatty acids and thus compete with the production of fatty acid derivatives. Such nonessential pathways can include but are not limited to elimination of storage lipid formation and peroxisomal beta-oxidation.
In an additional embodiment, the NADPH supply can be modified (e.g., increased) in the recombinant yeast. Since NADPH is an essential cofactor of fatty acid biosynthesis, by increasing the supply of NADPH, it may be possible to further increase the production of fatty acid derivatives according to this invention.
Hence, in one embodiment, the invention provides a genetically modified/non-native strain of yeast comprising a disrupted gene encoding hexadecenal dehydrogenase (HFD1).
In some aspects of the invention, the disruption of the HFD1 gene results in a gene that is inoperative or knocked out and/or a nonfunctional gene product (e.g., a polypeptide having no activity as compared to the activity of the Hfd1 wild type polypeptide). In other embodiments, the disruption of the HFD1 gene results in a gene product that has reduced activity (e.g., 0 to 20% of the activity of the HFD1 wild type polypeptide). In still other embodiments, the disruption of the HFD1 gene results in reduced expression of a gene product as compared to the Hfd1 wild type polypeptide.
As used herein the terms a ype polypepHFD1 geneed herein the terms a ype polypepHFD1″ are used interchangeably.
A “disrupted gene” as defined herein involves any mutation or modification to a gene resulting in a partial or fully non-functional gene and gene product. Such a mutation or modification includes, but is not limited to, a missense mutation, a nonsense mutation, a deletion, a substitution, an insertion, and the like. Furthermore, a disruption of a gene can be achieved also, or alternatively, by mutation or modification of control elements controlling the transcription of the gene, such as mutation or modification in a promoter and/or enhancement elements. In such a case, such a mutation or modification results in partially or fully loss of transcription of the gene, i.e. a lower or reduced transcription as compared to native and non-modified control elements. As a result a reduced, if any, amount of the gene product will be available following transcription and translation.
The objective of gene disruption is to reduce the available amount of the gene product, including fully preventing any production of the gene product, or to express a gene product that lacks or having lower enzymatic activity as compared to the native or wild type gene product.
A yeast useful with this invention can be any yeast useful in industrial and fermentation practices. In one embodiment, the yeast can be from the genus Saccharomyces. In other embodiments, the yeast is Saccharomyces cerevisiae.
In some embodiments, the genetically modified yeast strain of this invention (e.g., comprising at least a disrupted HDF1 gene) can further comprise one or more additional genetic modifications to improve production of desired products. Such modifications can include, but are not limited to:
(1) introduction of new enzymes, and/or biosynthetic and/or metabolic pathways, including, but not limited to expression of an alkane biosynthetic pathway consisting of Synechoccous elongatus FAR and Synechoccous elongatus FADO and;
(2) optionally, ferrodoxin (F) and ferrodoxin NADP+ reductase (FNR) may be introduced to supply electrons.
In still some embodiments, the yeast strains of the invention can additionally comprise genetic modifications that eliminate or reduce non-essential pathways. Such modifications can eliminate or reduce the utilization or consumption of fatty acids by enzymes or pathways that compete with the production of fatty acid derivatives such as alkanes, alkenes and fatty alcohols in the recombinant yeast strains. Exemplary embodiments of such non-essential pathways can include but are not limited to storage lipid formation and beta-oxidation. In particular embodiments, storage lipid formation can be eliminated or reduced by disrupting the genes encoding, for example, acyl-CoA:sterol acyltransferase (ARE1, ARE2), diacylglycerol acyltransferase (DGA1, LRO1). In other embodiments, beta-oxidation and free fatty acid activation can be eliminated or reduced by disrupting the genes encoding, for example, PDX1, FAA1, FAA4.
In additional aspects of the invention, the genetically modified yeast of the invention can be further modified to express heterologous fatty acid biosynthetic polypeptides for increased production of fatty acids. Nonlimiting examples of genes encoding such heterologous polypeptides Acc1, Fas1 and Fas2 (from e.g., Rhodosporidium toruloides).
NADPH is a cofactor in the synthesis of fatty acids. To increase the availability of NADPH for fatty acid biosynthesis, the genetically modified yeast of the invention can be further modified for heterologous expression of non-phosphorylating NADP+-dependent glyceraldehydes-3-phosphate dehydrogenase (GAPN) (from e.g., Streptococcus mutans). In other aspects, the yeast can be modified to disrupt GDH1 encoding NADP-dependent glutamate dehydrogenase. In still other embodiments, the yeast of the invention can be further modified to overexpress GDH2 encoding NAD-dependent glutamate dehydrogenase.
In additional embodiments, the yeast of the invention (e.g., comprising at least a disrupted HDF1 gene) can be further modified to comprise genetic modifications to increase production of fatty acid derivatives having particular chain lengths (e.g., short, medium, long chain fatty acid derivatives). In one aspect, the yeast can be modified to express a chimeric cytosolic pathway for the production of medium chain fatty acids or an increased ratio of medium-chain to long-chain fatty acids. Thus, for example, the yeast can be modified to (over)express in the cytosol FOX2, FOX3, ERG10 and TES1 (derived from, for example, S. cerevisiae), and/or yqeF, fadA, fabB and tdTER (from bacteria).
Fatty acid chain length can also be regulated through modification of expression of thioesterases. Thus, in some embodiments, the yeast of this invention can be further modified to express a thiesterase having a desired chain length specificity (e.g., tesA, tesB, fadM, yciA from, e.g. E. coli).
In particular embodiments, the genetically modified yeast of the invention can be further modified to produce short chain fatty acid derivatives (e.g., alkanes, alkenes, fatty alcohols and the like). Non-limiting examples of genes useful for such modifications include fpr and fdx from, for example, E. coli; and/or ferredoxin (orf_1499, petF) and ferredoxin-NADPH reductase (orf_0978, petH) from Synechococcus elongatus. Accordingly, in some embodiments, a genetically modified yeast of this invention can further comprise nucleic acid constructs comprising nucleotide sequences encoding fpr and/or fdx and/or nucleotide sequences encoding petF and/or petH.
In additional embodiments, the yeast strains of this invention (e.g., comprising at least a disrupted HFD1 gene) can further comprise nucleic acid constructs comprising nucleotide sequences encoding enzymes and/or biosynthetic pathways for conversion of fatty acids to alkanes and/or alkenes. Thus in some embodiments, the genetically modified yeast of the invention can be further modified to express Mycobacterium marinum carboxylic acid reductase and Musca domestica CYP4G2 decarbonylase (decarbonylase is also referred to as deformylating oxygenase in the art). In a representative embodiment, the yeast can be further modified to express a thioesterase, or an additional thioesterase, to relieve fatty acid biosynthess repression by acyl-CoA and to increase substrate availability for alkane and alkene biosynthesis. In other embodiments, the yeast strains of the invention can be modified to comprise expression of Synechococcus elongatus orf1594 and ACS, Musca domestica CYP4GT decarbonylase and NADPH-cytochrome P450 reductase. In further embodiments, the yeast strains of the invention can be modified to express Acinetobacter baylyi Acr1, Musca domestica CYP4GT decarbonylase and NADPH-cytochrome P450 reductase.
In further aspects of the invention, the bacterial luminescence pathway and a cyanobacterial fatty aldehyde decarbonylase can be expressed in the yeast strains of the invention in order to utilize fatty acyl-CoA in the synthesis of alkanes and alkenes. Thus, in a representative embodiment, the yeast strains of the invention comprising at least a disrupted HFD1 gene further comprises LuxC, LuxD and LuxE from Photorhabdus luminescens and Nostoc punctiforme FAD.
In other embodiments, the yeast strains of the invention can be further modified to comprise a pathway for conversion of fatty acids to terminal alkenes. A nonlimiting example of such a pathway includes Jeotgalicoccus spp orf880, Escherichia coli GroEL and Escherichia coli GroES.
The genetically modified yeast strain can additionally comprise carboxylic acid reductase (from e.g., Mycobacterium marinum) and decarbonylase (from e.g., Musca domestica) for conversion of fatty acids to alkanes and alkenes.
In some embodiments, short chain alkanes and alkenes are the desired product. Accordingly, in some embodiments, the genetically modified yeast of the invention can comprise modifications to their mitochondrial fatty acid biosynthetic pathway. In a representative embodiment, the genetically modified yeast of the invention can be modified to express in their mitochondria the Mycobacterium marinum CAR fatty acid reductase, the Nostoc puntiforme fatty aldehyde decarbonylase and Aspergillus nidulans phosphopantetheinyl transferase NpgA, optionally, the yeast can be modified to additionally overexpress components of the yeast mitochondrial fatty acid biosynthetic pathway, including but not limited to Etr1 (2-enoyl thioester reductase) and Hfa1 (acetyl-CoA carboxylase). In some embodiments, the yeast mitochondrial fatty acid biosynthetic pathway components to be overexpressed can further comprise CEM1, HTD2, OAR1, and MCT1. In further embodiments, the yeast comprising modifications to their mitochondrial fatty acid biosynthetic pathway can additionally comprise fdx and fpr from E. coli, wherein the respective protein sequences comprise mitochondrial localization signal(s) to direct them to the mitochondria. In still further embodiments, the yeast comprising modifications to their mitochondrial fatty acid biosynthetic pathway can additionally comprise nucleic acids encoding thioesterase to be expressed in the mitochondria. Non-limiting examples of thiesterases with activity towards medium chain fatty acyl-ACP include Acinetobacter baylyi TesA, Cocos nucifera FatB1, or homologue thioesterases thereof.
In additional embodiments, the yeast of the invention can be further modified to express a formate dehydrogenase enzyme in the mitochondria. Non-limiting examples of formate dehydrogenase enzymes include Fdh1 and/or Fdh2, which can be introduced into the yeast with mitochondrial localization signals.
In some embodiments the genetically modified yeast of the invention can be modified to have improved fatty aldehyde decarbonylase activity (thereby improving alkane and/or alkene production) by fusing a catalase to a fatty aldehyde decarbonylase (e.g., Synechoccocus elongatus orf1593 or Nostoc punctiforme FAD).
In other embodiments, the genetically modified yeast strains of the invention can comprise Yarrowia lipoytica Yas3 repressor and a fluorescent protein expressed from an alkane response element, ARE1 containing promoter in order to be able to screen genetically modified yeast strains, including, but not limited to, the yeast strains described in this invention, for modified alkane production (e.g., increased and/or reduced as compared to a control yeast strain not comprising said modification(s)). Thus, in some embodiments, a method of screening for modified production of alkanes comprises, introducing into a yeast strain of interest a Yarrowia lipoytica Yas3 repressor, the activators Yas1 and Yas2 and a fluorescent protein expressed from an alkane response element, ARE1, containing promoter, and detecting modified production of alkanes.
The present invention provides a further method of screening for modified production of alkanes and/or alkenes (e.g., increased and/or reduced as compared to a control yeast strain not comprising said modification(s)) based on the toxicity of fatty acid accumulation in yeast strains that are modified to have reduced or no storage lipid formation and/or beta-oxidation. Thus, the consumption of fatty acids by the introduced alkane biosynthetic pathways can be evaluated by monitoring the toxicity of the genetically modified yeast strains.
The present invention further provides methods for the production of hydrocarbons in genetically modified yeast, comprising culturing a genetically modified yeast of this invention and collecting the hydrocarbons. In some embodiments, a hydrocarbon can be a fatty acid derivative, for example, an alkane, an alkene, or a fatty alcohol.
As used in the description of the invention and the appended claims, the singular forms “a,” “an” and “the” are intended to include the plural forms as well, unless the context clearly indicates otherwise.
Also as used herein, “and/or” refers to and encompasses any and all possible combinations of one or more of the associated listed items, as well as the lack of combinations when interpreted in the alternative (“or”).
The term “about,” as used herein when referring to a measurable value such as a dosage or time period and the like, is meant to encompass variations of ±20%, ±10%, ±5%, ±1%, ±0.5%, or even ±0.1% of the specified amount.
As used herein, phrases such as “between X and Y” and “between about X and Y” should be interpreted to include X and Y. As used herein, phrases such as “between about X and Y” mean “between about X and about Y” and phrases such as “from about X to Y” mean “from about X to about Y.”
The term “comprise,” “comprises” and “comprising” as used herein, specify the presence of the stated features, integers, steps, operations, elements, and/or components, but do not preclude the presence or addition of one or more other features, integers, steps, operations, elements, components, and/or groups thereof.
As used herein, the transitional phrase “consisting essentially of” means that the scope of a claim is to be interpreted to encompass the specified materials or steps recited in the claim and those that do not materially affect the basic and novel characteristic(s) of the claimed invention. Thus, the term “consisting essentially of” when used in a claim of this invention is not intended to be interpreted to be equivalent to “comprising.”
As used herein, the terms “increase,” “increases,” “increased,” “increasing,” and similar terms indicate an elevation of at least about 25%, 50%, 75%, 100%, 150%, 200%, 300%, 400%, 500% or more.
As used herein, the terms “reduce,” “reduces,” “reduced,” “reduction,” and similar terms mean a decrease of at least about 5%, 10%, 15%, 20%, 25%, 35%, 50%, 75%, 80%, 85%, 90%, 95%, 97% or more. In particular embodiments, the reduction results in no or essentially no (i.e., an insignificant amount, e.g., less than about 10% or even 5%) detectable activity or amount.
As used herein, the terms “express,” “expresses,” “expressed” or “expression,” and the like, with respect to a nucleic acid molecule and/or a nucleotide sequence (e.g., RNA or DNA) indicates that the nucleic acid molecule and/or a nucleotide sequence is transcribed and, optionally, translated. Thus, a nucleic acid molecule and/or a nucleotide sequence may express a polypeptide of interest or a functional untranslated RNA. A “functional” RNA includes any untranslated RNA that has a biological function in a cell, e.g., regulation of gene expression. Such functional RNAs include but are not limited to RNAi (e.g., siRNA, shRNA), miRNA, antisense RNA, anti-microRNA antisense oligodeoxyribonucleotide (AMO; see e.g., Lu et al. Nucleic Acids Res. 37(3):e24: 10.1093/nar/gkn1053), ribozymes, RNA aptamers and the like.
As used herein, “overexpress,” “overexpressed,” “overexpression” and the like, in reference to a polynucleotide means that the expression level of said polynucleotide is greater than that for the same polynucleotide in its native or wild type genetic context (e.g., in the same position in the genome and/or associated with the native/endogenous regulatory sequences). A nucleotide sequence can be overexpressed by inserting it into an overexpression vector. Such vectors are known in the art.
A “heterologous” or a “recombinant” nucleotide sequence is a nucleotide sequence not naturally associated with a host cell into which it is introduced, including non-naturally occurring multiple copies of a naturally occurring nucleotide sequence. A heterologous gene may optionally be codon optimized for expression in yeast according to techniques well known in the art and as further described herein. A heterologous gene also encompasses, in some embodiments, an endogenous gene controlled by a heterologous promoter and/or control elements to achieve an expression of the gene that is different from, typically higher, i.e. so-called overexpression, than normal or baseline expression of the gene in a yeast comprising the endogenous gene under control of wild type (endogenous) promoter and control elements.
A “native” or “wild type” nucleic acid, nucleotide sequence, polypeptide or amino acid sequence refers to a naturally occurring or endogenous nucleic acid, nucleotide sequence, polypeptide or amino acid sequence. Thus, for example, a “wild type mRNA” is an mRNA that is naturally occurring in or endogenous to the organism. A “homologous” nucleic acid sequence is a nucleotide sequence naturally associated with a host cell into which it is introduced.
Also as used herein, the terms “nucleic acid,” “nucleic acid molecule,” “nucleotide sequence” and “polynucleotide” refer to RNA or DNA that is linear or branched, single or double stranded, or a hybrid thereof. The term also encompasses RNA/DNA hybrids. When dsRNA is produced synthetically, less common bases, such as inosine, 5-methylcytosine, 6-methyladenine, hypoxanthine and others can also be used for antisense, dsRNA, and ribozyme pairing. For example, polynucleotides that contain C-5 propyne analogues of uridine and cytidine have been shown to bind RNA with high affinity and to be potent antisense inhibitors of gene expression. Other modifications, such as modification to the phosphodiester backbone, or the 2′-hydroxy in the ribose sugar group of the RNA can also be made.
As used herein, the term “nucleotide sequence” refers to a heteropolymer of nucleotides or the sequence of these nucleotides from the 5′ to 3′ end of a nucleic acid molecule and includes DNA or RNA molecules, including cDNA, a DNA fragment or portion, genomic DNA, synthetic (e.g., chemically synthesized) DNA, plasmid DNA, mRNA, and anti-sense RNA, any of which can be single stranded or double stranded. The terms “nucleotide sequence” “nucleic acid,” “nucleic acid molecule,” “oligonucleotide” and “polynucleotide” are also used interchangeably herein to refer to a heteropolymer of nucleotides. Nucleic acid molecules and/or nucleotide sequences provided herein are presented herein in the 5′ to 3′ direction, from left to right and are represented using the standard code for representing the nucleotide characters as set forth in the U.S. sequence rules, 37 CFR §§1.821-1.825 and the World Intellectual Property Organization (WIPO) Standard ST.25.
As used herein, the term “gene” refers to a nucleic acid molecule capable of being used to produce mRNA, antisense RNA, miRNA, anti-microRNA antisense oligodeoxyribonucleotide (AMO) and the like. Genes may or may not be capable of being used to produce a functional protein or gene product. Genes can include both coding and non-coding regions (e.g., introns, regulatory elements, promoters, enhancers, termination sequences and/or 5′ and 3′ untranslated regions). A gene may be “isolated” by which is meant a nucleic acid that is substantially or essentially free from components normally found in association with the nucleic acid in its natural state. Such components include other cellular material, culture medium from recombinant production, and/or various chemicals used in chemically synthesizing the nucleic acid.
“Introducing” in the context of a yeast cell means contacting a nucleic acid molecule with the cell in such a manner that the nucleic acid molecule gains access to the interior of the cell. Accordingly, polynucleotides and/or nucleic acid molecules can be introduced yeast cells in a single transformation event, in separate transformation events. Thus, the term “transformation” as used herein refers to the introduction of a heterologous nucleic acid into a cell. Transformation of a yeast cell can be stable or transient.
“Transient transformation” in the context of a polynucleotide means that a polynucleotide is introduced into the cell and does not integrate into the genome of the cell.
By “stably introducing” or “stably introduced” in the context of a polynucleotide introduced into a cell, it is intended that the introduced polynucleotide is stably incorporated into the genome of the cell, and thus the cell is stably transformed with the polynucleotide.
“Stable transformation” or “stably transformed” as used herein means that a nucleic acid molecule is introduced into a cell and integrates into the genome of the cell. As such, the integrated nucleic acid molecule is capable of being inherited by the progeny thereof, more particularly, by the progeny of multiple successive generations. “Genome” as used herein includes the nuclear genome. Stable transformation as used herein can also refer to a nucleic acid molecule that is maintained extrachromasomally, for example, as a minichromosome.
Transient transformation may be detected by, for example, an enzyme-linked immunosorbent assay (ELISA) or Western blot, which can detect the presence of a peptide or polypeptide encoded by one or more nucleic acid molecules introduced into an organism. Stable transformation of a cell can be detected by, for example, a Southern blot hybridization assay of genomic DNA of the cell with nucleic acid sequences which specifically hybridize with a nucleotide sequence of a nucleic acid molecule introduced into an organism (e.g., a yeast). Stable transformation of a cell can be detected by, for example, a Northern blot hybridization assay of RNA of the cell with nucleic acid sequences which specifically hybridize with a nucleotide sequence of a nucleic acid molecule introduced into a yeast or other organism. Stable transformation of a cell can also be detected by, e.g., a polymerase chain reaction (PCR) or other amplification reaction as are well known in the art, employing specific primer sequences that hybridize with target sequence(s) of a nucleic acid molecule, resulting in amplification of the target sequence(s), which can be detected according to standard methods Transformation can also be detected by direct sequencing and/or hybridization protocols well known in the art.
The terms “complementary” or “complementarity,” as used herein, refer to the natural binding of polynucleotides under permissive salt and temperature conditions by base-pairing. For example, the sequence “A-G-T” binds to the complementary sequence “T-C-A.” Complementarity between two single-stranded molecules may be “partial,” in which only some of the nucleotides bind, or it may be complete when total complementarity exists between the single stranded molecules. The degree of complementarity between nucleic acid strands has significant effects on the efficiency and strength of hybridization between nucleic acid strands.
A “portion” or “fragment” of a nucleotide sequence of the invention will be understood to mean a nucleotide sequence of reduced length relative to a reference nucleic acid or nucleotide sequence and comprising, consisting essentially of and/or consisting of a nucleotide sequence of contiguous nucleotides identical or almost identical (e.g., 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 98%, 99% identical) to the reference nucleic acid or nucleotide sequence. Such a nucleic acid fragment or portion according to the invention may be, where appropriate, included in a larger polynucleotide of which it is a constituent.
Different nucleic acids or proteins having homology are referred to herein as “homologues.” The term homologue includes homologous sequences from the same and other species and orthologous sequences from the same and other species. “Homology” refers to the level of similarity between two or more nucleic acid and/or amino acid sequences in terms of percent of positional identity (i.e., sequence similarity or identity). Homology also refers to the concept of similar functional properties among different nucleic acids or proteins. Thus, the compositions and methods of the invention further comprise homologues to the nucleotide sequences and polypeptide sequences of this invention. “Orthologous,” as used herein, refers to homologous nucleotide sequences and/or amino acid sequences in different species that arose from a common ancestral gene during speciation. A homologue of a nucleotide sequence of this invention has a substantial sequence identity (e.g., at least about 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, and/or 100%) to said nucleotide sequence.
As used herein “sequence identity” refers to the extent to which two optimally aligned polynucleotide or peptide sequences are invariant throughout a window of alignment of components, e.g., nucleotides or amino acids. “Identity” can be readily calculated by known methods including, but not limited to, those described in: Computational Molecular Biology (Lesk, A. M., ed.) Oxford University Press, New York (1988); Biocomputing: Informatics and Genome Projects (Smith, D. W., ed.) Academic Press, New York (1993); Computer Analysis of Sequence Data, Part I (Griffin, A. M., and Griffin, H. G., eds.) Humana Press, New Jersey (1994); Sequence Analysis in Molecular Biology (von Heinje, G., ed.) Academic Press (1987); and Sequence Analysis Primer (Gribskov, M. and Devereux, J., eds.) Stockton Press, New York (1991).
As used herein, the term “percent sequence identity” or “percent identity” refers to the percentage of identical nucleotides in a linear polynucleotide sequence of a reference (“query”) polynucleotide molecule (or its complementary strand) as compared to a test (“subject”) polynucleotide molecule (or its complementary strand) when the two sequences are optimally aligned. In some embodiments, “percent identity” can refer to the percentage of identical amino acids in an amino acid sequence.
As used herein, the phrase “substantially identical,” in the context of two nucleic acid molecules, nucleotide sequences or protein sequences, refers to two or more sequences or subsequences that have at least about 70%, least about 75%, at least about 80%, least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% nucleotide or amino acid residue identity, when compared and aligned for maximum correspondence, as measured using one of the following sequence comparison algorithms or by visual inspection. In some embodiments of the invention, the substantial identity exists over a region of the sequences that is at least about 50 residues to about 150 residues in length. Thus, in some embodiments of the invention, the substantial identity exists over a region of the sequences that is at least about 16, at least about 18, at least about 22, at least about 25, at least about 30, at least about 40, at least about 50, about 60, about 70, about 80, about 90, about 100, about 110, about 120, about 130, about 140, about 150, or more residues in length, and any range therein. In representative embodiments, the sequences can be substantially identical over at least about 22 nucleotides. In still other embodiments, the substantial identity exists over the full length or nearly the full length of the sequence.
For sequence comparison, typically one sequence acts as a reference sequence to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are entered into a computer, subsequence coordinates are designated if necessary, and sequence algorithm program parameters are designated. The sequence comparison algorithm then calculates the percent sequence identity for the test sequence(s) relative to the reference sequence, based on the designated program parameters.
Optimal alignment of sequences for aligning a comparison window are well known to those skilled in the art and may be conducted by tools such as the local homology algorithm of Smith and Waterman, the homology alignment algorithm of Needleman and Wunsch, the search for similarity method of Pearson and Lipman, and optionally by computerized implementations of these algorithms such as GAP, BESTFIT, FASTA, and TFASTA available as part of the GCG® Wisconsin Package® (Accelrys Inc., San Diego, Calif.). An “identity fraction” for aligned segments of a test sequence and a reference sequence is the number of identical components which are shared by the two aligned sequences divided by the total number of components in the reference sequence segment, i.e., the entire reference sequence or a smaller defined part of the reference sequence. Percent sequence identity is represented as the identity fraction multiplied by 100. The comparison of one or more polynucleotide sequences may be to a full-length polynucleotide sequence or a portion thereof, or to a longer polynucleotide sequence. For purposes of this invention “percent identity” may also be determined using BLASTX version 2.0 for translated nucleotide sequences and BLASTN version 2.0 for polynucleotide sequences.
Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information. This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold. These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always <0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when the cumulative alignment score falls off by the quantity X from its maximum achieved value, the cumulative score goes to zero or below due to the accumulation of one or more negative-scoring residue alignments, or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, a cutoff of 100, M=5, N=−4, and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff, Proc. Natl. Acad. Sci. USA 89: 10915 (1989)).
In addition to calculating percent sequence identity, the BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Altschul, Proc. Nat'l. Acad. Sci. USA 90: 5873-5787 (1993)). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a test nucleic acid sequence is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleotide sequence to the reference nucleotide sequence is less than about 0.1 to less than about 0.001. Thus, in some embodiments of the invention, the smallest sum probability in a comparison of the test nucleotide sequence to the reference nucleotide sequence is less than about 0.001.
Two nucleotide sequences can also be considered to be substantially identical when the two sequences hybridize to each other under stringent conditions. In some representative embodiments, two nucleotide sequences considered to be substantially identical hybridize to each other under highly stringent conditions.
“Stringent hybridization conditions” and “stringent hybridization wash conditions” in the context of nucleic acid hybridization experiments such as Southern and Northern hybridizations are sequence dependent, and are different under different environmental parameters. An extensive guide to the hybridization of nucleic acids is found in Tij ssen Laboratory Techniques in Biochemistry and Molecular Biology-Hybridization with Nucleic Acid Probes part I chapter 2 “Overview of principles of hybridization and the strategy of nucleic acid probe assays” Elsevier, New York (1993). Generally, highly stringent hybridization and wash conditions are selected to be about 5° C. lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH.
The Tm is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. Very stringent conditions are selected to be equal to the Tm for a particular probe. An example of stringent hybridization conditions for hybridization of complementary nucleotide sequences which have more than 100 complementary residues on a filter in a Southern or northern blot is 50% formamide with 1 mg of heparin at 42° C., with the hybridization being carried out overnight. An example of highly stringent wash conditions is 0.1 5M NaCl at 72° C. for about 15 minutes. An example of stringent wash conditions is a 0.2×SSC wash at 65° C. for 15 minutes (see, Sambrook, infra, for a description of SSC buffer). Often, a high stringency wash is preceded by a low stringency wash to remove background probe signal. An example of a medium stringency wash for a duplex of, e.g., more than 100 nucleotides, is 1×SSC at 45° C. for 15 minutes. An example of a low stringency wash for a duplex of, e.g., more than 100 nucleotides, is 4-6×SSC at 40° C. for 15 minutes. For short probes (e.g., about 10 to 50 nucleotides), stringent conditions typically involve salt concentrations of less than about 1.0 M Na ion, typically about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3, and the temperature is typically at least about 30° C. Stringent conditions can also be achieved with the addition of destabilizing agents such as formamide. In general, a signal to noise ratio of 2× (or higher) than that observed for an unrelated probe in the particular hybridization assay indicates detection of a specific hybridization. Nucleotide sequences that do not hybridize to each other under stringent conditions are still substantially identical if the proteins that they encode are substantially identical. This can occur, for example, when a copy of a nucleotide sequence is created using the maximum codon degeneracy permitted by the genetic code.
The following are examples of sets of hybridization/wash conditions that may be used to clone homologous nucleotide sequences that are substantially identical to reference nucleotide sequences of the invention. In one embodiment, a reference nucleotide sequence hybridizes to the “test” nucleotide sequence in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO4, 1 mM EDTA at 50° C. with washing in 2×SSC, 0.1% SDS at 50° C. In another embodiment, the reference nucleotide sequence hybridizes to the “test” nucleotide sequence in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO4, 1 mM EDTA at 50° C. with washing in 1×SSC, 0.1% SDS at 50° C. or in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO4, 1 mM EDTA at 50° C. with washing in 0.5×SSC, 0.1% SDS at 50° C. In still further embodiments, the reference nucleotide sequence hybridizes to the “test” nucleotide sequence in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO4, 1 mM EDTA at 50° C. with washing in 0.1×SSC, 0.1% SDS at 50° C., or in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO4, 1 mM EDTA at 50° C. with washing in 0.1×SSC, 0.1% SDS at 65° C.
In particular embodiments, a further indication that two nucleotide sequences or two polypeptide sequences are substantially identical can be that the protein encoded by the first nucleic acid is immunologically cross reactive with, or specifically binds to, the protein encoded by the second nucleic acid. Thus, in some embodiments, a polypeptide can be substantially identical to a second polypeptide, for example, where the two polypeptides differ only by conservative substitutions.
In some embodiments, the recombinant nucleic acids molecules, nucleotide sequences and polypeptides of the invention are “isolated.” An “isolated” nucleic acid molecule, an “isolated” nucleotide sequence or an “isolated” polypeptide is a nucleic acid molecule, nucleotide sequence or polypeptide that, by the hand of man, exists apart from its native environment and is therefore not a product of nature. An isolated nucleic acid molecule, nucleotide sequence or polypeptide may exist in a purified form that is at least partially separated from at least some of the other components of the naturally occurring organism or virus, for example, the cell or viral structural components or other polypeptides or nucleic acids commonly found associated with the polynucleotide. In representative embodiments, the isolated nucleic acid molecule, the isolated nucleotide sequence and/or the isolated polypeptide is at least about 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, or more pure.
In other embodiments, an isolated nucleic acid molecule, nucleotide sequence or polypeptide may exist in a non-native environment such as, for example, a recombinant host cell. Thus, for example, with respect to nucleotide sequences, the term “isolated” means that it is separated from the chromosome and/or cell in which it naturally occurs. A polynucleotide is also isolated if it is separated from the chromosome and/or cell in which it naturally occurs in and is then inserted into a genetic context, a chromosome and/or a cell in which it does not naturally occur (e.g., a different host cell, different regulatory sequences, and/or different position in the genome than as found in nature). Accordingly, the recombinant nucleic acid molecules, nucleotide sequences and their encoded polypeptides are “isolated” in that, by the hand of man, they exist apart from their native environment and therefore are not products of nature, however, in some embodiments, they can be introduced into and exist in a recombinant host cell.
In some embodiments, the nucleotide sequences and/or recombinant nucleic acid molecules of the invention can be operatively associated with a variety of promoters for expression in yeast cells. Thus, in representative embodiments, a recombinant nucleic acid of this invention can further comprise one or more promoters operably linked to one or more nucleotide sequences.
By “operably linked” or “operably associated” as used herein, it is meant that the indicated elements are functionally related to each other, and are also generally physically related. Thus, the term “operably linked” or “operably associated” as used herein, refers to nucleotide sequences on a single nucleic acid molecule that are functionally associated. Thus, a first nucleotide sequence that is operably linked to a second nucleotide sequence, means a situation when the first nucleotide sequence is placed in a functional relationship with the second nucleotide sequence. For instance, a promoter is operably associated with a nucleotide sequence if the promoter effects the transcription or expression of said nucleotide sequence. Those skilled in the art will appreciate that the control sequences (e.g., promoter) need not be contiguous with the nucleotide sequence to which it is operably associated, as long as the control sequences function to direct the expression thereof. Thus, for example, intervening untranslated, yet transcribed, sequences can be present between a promoter and a nucleotide sequence, and the promoter can still be considered “operably linked” to the nucleotide sequence.
A “promoter” is a nucleotide sequence that controls or regulates the transcription of a nucleotide sequence (i.e., a coding sequence) that is operably associated with the promoter. The coding sequence may encode a polypeptide and/or a functional RNA. Typically, a “promoter” refers to a nucleotide sequence that contains a binding site for RNA polymerase II and directs the initiation of transcription. In general, promoters are found 5′, or upstream, relative to the start of the coding region of the corresponding coding sequence. The promoter region may comprise other elements that act as regulators of gene expression. These include a TATA box consensus sequence, and often a CAAT box consensus sequence (Breathnach and Chambon, (1981) Annu. Rev. Biochem. 50:349).
Promoters can include, for example, constitutive, inducible, temporally regulated, developmentally regulated, chemically regulated, tissue-preferred and/or tissue-specific promoters for use in the preparation of recombinant nucleic acid molecules, i.e., “chimeric genes” or “chimeric polynucleotides.” In particular aspects, a “promoter” useful with the invention is a promoter capable of initiating transcription of a nucleotide sequence in a yeast cell.
The choice of promoter will vary depending on the temporal and spatial requirements for expression, and also depending on the host cell to be transformed. Promoters useful with the invention include, but are not limited to, those that drive expression of a nucleotide sequence constitutively, those that drive expression when induced, and those that drive expression in a tissue- or developmentally-specific manner. These various types of promoters are known in the art.
As used herein the terms “fatty acid derivative” or “fatty acid derivatives” includes but are not limited to hydrocarbons, such as for example alkanes and/or alkenes as well as fatty alcohols, of any length (e.g., short, medium and long chain).
Hexadecenal dehydrogenase gene HFD1 is found in Saccharomyces cerevisiae and encodes hexadecenal dehydrogenase Hfd1. HFD1 homologues can be found in other yeasts and are also envisioned to be part of this invention even though the gene name may not be the same.
Acyl-CoA or fatty acyl-CoA is a group of molecules involved in the metabolism of fatty acids. It is a transient intermediate compound formed when coenzyme A (CoA) attaches to the end of a fatty acid inside living cells.
ACP (acyl carrier protein) is a protein that covalently binds fatty acyl intermediates via a phosphopantetheine linker during the synthesis process.
Fatty acid derivatives (e.g., alkanes, alkenes and/or fatty alcohols, and the like) may be produced in yeasts by conversion of acyl coenzyme A (acyl-CoA), fatty acids, or fatty acyl-ACP. Several pathways may be used to get the yeasts to produce acyl-CoA, fatty acids, fatty acyl-ACP. However the production of the fatty acid derivatives from acyl-CoA, fatty acids and/or fatty acyl-ACP via fatty aldehydes will only be possible to a substantial extend if HDF1 is deleted.
An aspect of the embodiments relates to a yeast lacking a gene encoding hexadecanal dehydrogenase (HFD1) or comprising a disrupted gene encoding HFD1. The yeast also comprises at least one heterologous gene encoding an enzyme involved in a pathway of producing hydrocarbons.
In an embodiment, the yeast comprises at least one heterologous gene encoding an enzyme involved in a pathway of producing hydrocarbons from fatty acyl-CoA through fatty aldehydes.
In an embodiment, the yeast comprises a heterologous gene encoding a fatty acyl-CoA reductase or a fatty acyl-Acyl Carrier Protein (ACP) reductase, preferably Synechococcus elongates orf1594 or Acinetobacter baylyi Acr1.
In an embodiment, the yeast comprises a heterologous gene encoding a fatty aldehyde-deformylating oxygenase, preferably Synechococcus elongates orf1593 or Nostoc puntiforme fatty aldehyde-deformylating oxygenase.
In a particular embodiment, the heterologous gene is a fusion gene encoding a fusion of said fatty aldehyde-deformylating oxygenase and a catalase.
In a particular embodiment the yeast further comprises a heterologous gene encoding cytosolic ferredoxin, preferably Escherichia coli fdx or Synechococcus elongates petF, and a heterologous gene encoding a cytosolic ferredoxin nicotinamide adenine dinucleotide phosphate (NADP+) reductase and/or a cytosolic ferredoxin NAD+ reductase, preferably E. coli fdr or S. elongates petH and/or an E. coli or S. elongates ferredoxin NAD+ reductase.
In an embodiment, the yeast comprises a heterologous gene encoding Acinetobacter baylyi Acr1, a heterologous gene encoding Musca domestica CYP4G2 deformylating oxygenase, and a heterologous gene encoding M. domestica NADPH-cytochrome P450 reductase.
In an embodiment, the yeast comprises a heterologous gene encoding Jeotgalicoccus spp Orf80.
In a particular embodiment, the yeast further comprises a heterologous gene encoding a chaperon selected from a group consisting of Escherichia coli GroEL and E. coli GroES.
In an embodiment, the yeast comprises Photorhabdus luminescens genes LuxC, LuxD and LuxE, and a cyanobacterial fatty aldehyde-deformylating oxygenase, preferably Synechococcus elongates orf1593 or Nostoc puntiforme fatty aldehyde-deformylating oxygenase.
In an embodiment, the yeast comprises a heterologous gene encoding Mycobacterium marinum carboxylic acid reductase, a heterologous gene encoding Musca domestica CYP4G2 deformylating oxygenase, and a heterologous gene encoding a phosphopantetheinyl transferase, preferably Aspergillus nidulans phosphopantetheinyl transferase.
In an embodiment, the yeast comprises a heterologous gene encoding a fatty acyl-Acyl Carrier Protein (ACP) synthase, preferably Synechococcus elongates fatty acyl-ACP synthase, a heterologous gene encoding a fatty acyl-ACP reductase, preferably Synechococcus elongates orf1594, a heterologous gene encoding Musca domestica CYP4G2 decarbonylase, and a heterologous gene encoding M. domestica NADPH-cytochrome P450 reductase.
In an embodiment, the yeast comprises a heterologous gene encoding a fatty acid reductase and a mitochondrial localization signal (MLS), preferably Mycobacterium marinum CAR fatty acid reductase and the MLS, a heterologous gene encoding a fatty aldehyde decarbonylase and the MLS, preferably Nostoc punctiforme fatty aldehyde-deformylating oxygenase and the MLS, and a heterologous gene encoding a phosphopantetheinyl transferase and the MLS, preferably Aspergillus nidulans phosphopantetheinyl transferase and the MLS.
In a particular embodiment, the yeast further comprises at least one gene encoding a respective enzyme involved in the yeast mitochondrial fatty acid biosynthetic pathway selected from the group consisting of a yeast mitochondrial 2-enoyl thioester reductase and a yeast mitochondrial acetyl-Coenzyme A (CoA) carboxylase, a yeast mitochondrial beta-keto-acyl synthase, a yeast mitochondrial 3-hydroxyacyl-Acyl Carrier Protein (ACP) dehydratase, a yeast mitochondrial 3-oxoacyl-ACP reductase, and a yeast mitochondrial malonyl-CoA:ACP transferase, preferably selected from the group consisting of Saccharomyces cerevisiae HFA1, ETR1, CEM1, HTD2, OAR1 and MCT1.
In a particular embodiment, the yeast further comprises a heterologous gene encoding a mitochondrial thoesterase, preferably selected from the group consisting of Acinetobacter baylyi TesA and Cocos nucifera FatB 1.
In an embodiment, the yeast comprises a gene encoding a mitochondrial formate dehydrogenase, preferably an endogenous format dehydrogenase and a mitochondrial localization signal (MLS), more preferably Saccharomyces cerevisiae FDH1 and/or FDH2 and the MLS.
In an embodiment, the yeast comprises at least one heterologous gene encoding cytosolic enzyme selected from the group consisting of acetyl-Coenzyme A (CoA)C-acetyltransferase, a 3-ketoacyl-CoA thiolase, a 3-hydroxyacyl-CoA dehydrogenase, an enoyl-CoA hydratase, a trans-enoyl-CoA reductase and a thioesterase, preferably selected from the group consisting of Saccharomyces cerevisiae FOX2, FOX3, ERG10 and TES1 and bacterial yqeF, fadA, fabB and tdTER.
In an embodiment, the yeast comprises a heterologous gene encoding a thioesterase, preferably selected from the group consisting of Escherichia coli tesA, tesB, fadM and yciA.
In an embodiment the yeast lacks or has reduced non-essential storage lipid formation, preferably by lacking one or more genes selected from the group consisting of any acyl-Coenzyme A (CoA):sterol acyltransferase and any diacylgylcerol acyltransferase, more preferably by lacking one or more of Saccharomyces cerevisiae LRO1, DGA1, ARE1 and ARE2, or comprising one or more disrupted genes selected from the group.
In an embodiment, the yeast lacks or has reduced non-essential beta oxidation, preferably by lacking one or more genes selected from the group consisting of any peroxisomal fatty acyl-Coenzyme A (CoA) oxidase and any long chain fatty acyl-CoA synthetase, more preferably by lacking one or more of Saccharomyces cerevisiae FAA1, FAA4 and PDX1, or comprising one or more disrupted genes selected from the group.
In an embodiment, the yeast comprises genes adapted for overexpression enzymes involved in the fatty acid biosynthetic pathway selected from the group consisting of acetyl-Coenzyme A (CoA) carboxylase and fatty acid synthase, preferably Saccharomyces cerevisiae ACC1, FAS1, FAS2 and ACB1.
In an embodiment, the yeast comprises heterologous genes adapted for overexpression enzymes involved in the fatty acid biosynthetic pathway selected from the group consisting of acetyl-Coenzyme A (CoA) carboxylase and fatty acid synthase, preferably Rhodosporidium toruloides RtACC1, RtFAS1 and RtFAS2.
In an embodiment, the yeast is characterized by supply of nicotinamide adenine dinucleotide phosphate (NADPH) by:
comprising a heterologous gene encoding a non-phosphorylating NADP+-dependent glyceraldehyde-3-phosphate dehydrogenase, preferably Streptococcus mutans GAPN;
lacking an endogenous GDH1 gene encoding NAD-dependent glutamate dehydrogenase, or comprising a disrupted GDH1 gene; and/or
comprising a GDH2 gene adapted for overexpression of NAD-dependent glutamate dehydrogenase.
In an embodiment, the yeast is selected from the group consisting of a Saccharomyces yeast, Hansenula polymorpha, a Kluyveromyces yeast, a Pichia yeast, a Candida yeast, a Trichoderma yeast and Yarrowia lipolytica, preferably Saccharomyces cerevisiae.
Another aspect of the embodiments relates to a method for producing hydrocarbons. The method comprises culturing a yeast lacking a gene encoding hexadecenal dehydrogenase (HFD1) or comprising a disrupted gene encoding HFD1 in culture conditions suitable for production of the hydrocarbons from the yeast. The method also comprises collecting the hydrocarbons from the culture medium in which the yeast is cultured and/or from the yeast.
In an embodiment, culturing the yeast comprises culturing a yeast according to any of the embodiments in the culture conditions suitable for production of the hydrocarbons from the yeast.
In an embodiment, the hydrocarbons are a fatty acid derivative selected from a group consisting of an alkane, an alkene and a fatty alcohol, preferably selected from the group consisting of an alkane and an alkene.
A further aspect of the embodiments relates to use of a yeast lacking a gene encoding hexadecenal dehydrogenase (HFD1) or comprising a disrupted gene encoding HFD1 for the production of hydrocarbons.
In an embodiment, the yeast is according to any of the embodiments.
In an embodiment, the hydrocarbons are a fatty acid derivative selected from a group consisting of an alkane, an alkene and a fatty alcohol, preferably selected from the group consisting of an alkane and an alkene.
The invention will now be described with reference to the following examples. It should be appreciated that these examples are not intended to limit the scope of the claims to the invention, but are rather intended to be exemplary of certain embodiments. Any variations in the exemplified methods that occur to the skilled artisan are intended to fall within the scope of the invention.
Expression of an Alkane Biosynthetic Pathway in Saccharomyces cerevisiae hfd1Δ
The purpose of this example is to illustrate the importance of HFD1 deletion in yeast to enable, for example, alkane, alkene and fatty alcohol biosynthesis via a two-step pathway involving a fatty aldehyde as intermediate. As a proof of principal, a commercially available knock-out strain Saccharomyces cerevisiae BY4741 6550 (MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 hf1Δ) was transformed with the plasmids pAlkane0 and pKB02 carrying the Synechococcus elongatus fatty acyl-CoA/ACP reductase gene orf1594 and fatty aldehyde decarbonylase gene orf1593, and Escherichia coli DH5 ferredoxin gene fdx and ferredoxin reductase gene fpr. A control strain harboring two empty plasmids and a wild-type BY4741 (MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0) strain (harboring the same plasmids as the producer strain) were constructed simultaneously.
The genes orf1594 (NT ID 1, codon-optimized for yeast) and orf1593 (NT ID 2, idem) coding for the two-step cyanobacterial alkane biosynthetic pathway described by Schirmer et al (2010) were ordered codon-optimized for yeast from GenScript (Piscataway, N.J., USA). Orf1594 was flanked by the restriction sites BamHI/HindIII, and orf1593 by NotI/SacI. The genes were cloned into pSPGM1 (Chen et al, 2012) by restriction, ligation, and amplification in Escherichia coli DH5α resulting in plasmid pAlkane0. The Escherichia coli DH5α fdx (NT ID 8) was cloned from a single colony by PCR using the primers PR ID 158 and PR ID 159. These primers contained the restriction site NotI/SacI. The gene fpr (NT ID 9), flanked by the restriction sites BamHI/XhoI, was cut from the plasmid pISP08 (Partow et al, 2012). Both genes were cloned into pIYC04 (Chen et al, 2013) by restriction, ligation, and amplification in Escherichia coli DH5α resulting in plasmid KB02. Both plasmids were verified by restriction analysis and sequencing of each gene (PR ID 187-190). After verification, both plasmids were co-transformed into chemical competent yeast cells (Gietz et al, 2002).
Four independent clones were isolated for both the producer and control strain by streak purification onto fresh SD-His-Ura 2% glucose plates. Successful transformation of the producer was verified by colony PCR (using primers PR ID 150-151, 154-155, and 158-161). Each clone was grown overnight in a 5 ml YPD (yeast peptone dextrose) pre-culture and inoculated the next day at 0.2 OD in 25 ml 2% glucose synthetic medium (dropout uracil and histidine) in 250 ml shake flasks. The cultures were incubated at 30° C. and 200 rpm. After 48 h, cell pellets were collected by centrifugation 5 minutes at 1000 rcf, washed twice with 5 ml phosphate buffer (10 mM KH2PO4, pH 7.5). Extraction of lipids and alkanes was carried out as described by Khoomrung et al (2013), with the exception that the final sample was dissolved in hexane (instead of chloroform/methanol). Subsequently, 2 μl injections were analyzed using a gas chromatograph (Focus GC, ThermoScientific) mass spectrometer (DSQII ThermoScientific) equipped with a ZB-5MS Guardian (L=30 m, ID 0.25 mm, df=0.25 Phenomenex) column. The inlet temperature was set to 250° C., the helium (carrier) gas flow to 1 ml/min splitless. The initial oven temperature was set to 50° C. and held for 5 minutes, then the temperature was ramped to 310° C. by 10° C./min and held for 6 minutes. The mass transfer line temperature was set to 300° C., the ion source temperature was set to 230° C. and a full scan for m/z of 50 to 650 was performed.
A gas chromatogram spectrum of one independent clone of the producing strain, one control, and a standard run is shown in
Deletion of Hexadecenal Dehydrogenase HFD1 in Saccharomyces cerevisiae CEN.PK113-11C
The purpose of this example is to show how HFD1 was deleted in Saccharomyces cerevisiae CEN.PK113-11C which is a commercially available strain. The yeast Saccharomyces cerevisiae possesses hexadecenal dehydrogenase Hfd1, an enzyme which will compete for substrate with the heterologous fatty aldehyde decarbonylases and leads to an ATP consuming futile cycle. In cyanobacteria, it has been shown that deletion of a similar gene led to fatty aldehyde accumulation. Saccharomyces cerevisiae HFD1 was deleted using the strategy depicted in
Expression of Escherichia coli Ferredoxin and Escherichia coli Ferredoxin:NADPH Reductase in Saccharomyces cerevisiae
It has been shown that cyanobacterial fatty aldehyde decarbonylases require an electron transfer system and that Escherichia coli ferredoxin and ferredoxin:NADPH reductase can be used as such. The yeast Saccharomyces cerevisiae contains ferredoxin and ferredoxin:NADPH reductase homologues (Yah1 and Arh1, respectively), but they are localized to the mitochondria and can therefore most likely not be used by the cytosolic expressed fatty aldehyde decarbonylase. The Escherichia coli DH5α fdx (NT ID 8) was cloned from a single colony by PCR using the primers PR ID 212 and PR ID 213. The gene fpr (NT ID 9), was cloned from the plasmid pISP08 (Partow et al, 2012) by PCR using the primers PR ID 214 and PR ID 215.To enable alka/ene biosynthesis, this plasmid carries a fatty acid reductase and fatty aldehyde decarbonylase homologous (as described in Example 1; cloned using primers PR ID 208-211). Combinations of these genes were introduced into pYX212 by using a modular pathway engineering strategy as described before (Zhou et al., 2012), resulting in the plasmids pAlkane1, pAlkane 7, pAlkane 8, and pFAR see
Shake flask batch fermentations were carried out in minimal medium containing 30 g/l glucose (Verduyn et al., 1992). Cultures were inoculated, from overnight precultures, at 0.1 OD in 25 ml minimal medium supplemented with histidine (40 mg/1; Sigma Aldrich) in 250 ml shake flasks. The shake flasks were incubated at 30° C. and 200 rpm orbital shaking. After 48 hours the cells were harvested by centrifugation (5 minutes; 1000 g) and washed once with 5 ml phosphate buffer (10 mM KH2PO4, pH 7.5). The supernatant was removed, the pellet frozen in liquid nitrogen and freeze dried (Christ Alpha 2-4 LSC, Martin Christ Gefriertrocknungsanlagen GmbH, Osterode am Harz, Germany) for 48 hours. Alkanes were extracted from the freeze dried cell pellets as described before (Khoomrung et al., 2013), with the exceptions that the extracted fraction was dissolved in hexane (alkanes) and that hexadecane (alkanes) was used as an internal standard. Samples were analyzed by gas chromatography (FocusGC, ThermoFisher Scientific) coupled to mass spectrometry (DSQII, ThermoFisher Scientific) using a Zebron ZB-5MS Guardian capillary GC column (30 m×0.25 mm×0.25 Phenomenex, Væløse, Denmark). The GC-MS conditions are described in Example 1. Analytical standards for alkanes (Sigma Aldrich) were analyzed during the same run for peak identification and quantification. The alkane production levels as observed for the wild-type and hfd1Δ strains carrying the plasmid pAlkane1 (KB17 and KB19), pAlkane 7 (KB18), or pAlkane 8 (KB16) is shown in
Expression of Synechococcus Elongatus PCC7942 Ferredoxin and Synechococcus elongatus Ferredoxin: NADPH Reductase in Saccharomyces cerevisiae
Recently the endogenous Synechococcus elongatus electron transfer system was identified and shown to be more efficient in vitro than the heterologous system. The Synechococcus elongatus PCC7942 ferredoxin (orf_1499, petF, P ID 6) and ferredoxin-NADPH reductase (orf_0978, petH, P ID 7) genes are codon optimized for expression in yeast. Subsequently they are cloned similar to the E coli homologues, as described in example 3, and cotransformed with fatty aldehyde decarbonylase homologue carrying plasmid as described in example 1.
Conversion of Fatty Acyl-CoA to alka/enes by Expression of Acinetobacter baylyi Acr1 and Musca domestica CYP4G2 Decarbonylase in Saccharomyces cerevisiae hfd1Δ
The purpose of this example is to illustrate the possibility of expression of a fatty acyl-CoA preferring fatty acid reductase in combination with a P450 type decarbonylase. Thus this pathway will convert fatty acyl-CoA to alkanes and alkenes via the intermediates fatty acyl-CoA and fatty aldehydes.
The plasmid pAlkane3 was constructed similar to the method described in example 8. For expression in yeast codon optimized genes encoding Acinetobacter baylyi Acr1 (NT ID 22), Musca domestica CYP4G2 (NT ID 14), and Musca domestica NADPH-cytochrome P450 reductase (NT ID 15) were cloned using primers with to the gene homologous regions (PR ID 201-202, 196-197, 192-193). The pathway was subsequently assembled as described in Shao et al, 2009 and Zhou et al, 2012.
Cells were cultivated and analyzed as described in example 1.
Conversion of Fatty Acids to Terminal Alkenes by Expression of Jeotgalicoccus Spp orf880, Escherichia coli GroEL and Escherichia coli GroES in Saccharomyces cerevisiae
The purpose of this example is to illustrate the improvement of conversion efficiency of the decarboxylation pathway by expression of chaperones. This will improve the folding of Jeotgalicoccus spp Orf880p. Overexpression of GroEL and GroES is done e.g. according to Guadelupe-Medina et al, 2013 on a HIS marker plasmid (e.g. pIYC04).
The gene Jeotgalicoccus spp Orf880 (NT ID 4, codon-optimized for yeast) coding for the one-step cyanobacterial alkane biosynthetic pathway was ordered codon-optimized for yeast from GenScript (Piscataway, N.J., USA). The gene was flanked by the restriction sites NotI/SacI and it was cloned into pSP-GM1 (Chen et al, 2012) by restriction, ligation, and amplification in Escherichia coli DH5α. The resulting plasmid OleT was verified by restriction analysis and sequencing (PR ID 188-189). After verification, the plasmids were cotransformed into chemical competent yeast cells (Gietz et al, 2002).
Cells are cultivated and analyzed as described in example 1.
Conversion of Acyl-CoA to Alka/Enes by Expression of Escherichia coli TesA, Photorhabdus luminescens LuxC, LuxD, and LuxE, and Nostoc punctiforme FAD in Saccharomyces cerevisiae hfd1Δ
This invention demonstrates the utilization of fatty acyl-CoA for the synthesis of alkanes and alkenes (see
The Photorhabdus luminescens genes encoding LuxC (P ID 3), LuxD (P ID 4), and LuxE (P ID 5) were codon-optimized for expression in yeast, and cloned using primers PR ID 212-217. A pathway consisting of these three genes, a Synechoccous elongatus (NT ID 2, cloned using primers PR ID 220-221) or a Nostoc punctiforme FAD gene (NT ID 3, cloned using primers PR ID 218-219), and Escherichia coli truncated thioesterase TesA (NT ID 56, cloned using primers PR ID) is assembled on a plasmid pAlkane8 and pAlkane5 similar to the method described in examples 3. The transformation of the plasmids into CEN.PK113-11C hfd1Δ was carried out according to Gietz et al, 2002. Cells were cultivated and analyzed as described in example 1.
The gas chromatogram spectra as observed for the hfd1Δ strain carrying the plasmid pAlkane5 (carrying the Nostoc punctiforme FAD) or pAlkane9 (carrying the Synechoccous elongatus FAD) are shown in
Conversion of Fatty Acids to alka/enes by Expression of Mycobacterium marinum Carboxylic Acid Reductase and Musca domestica CYP4G2 Decarbonylase in Saccharomyces cerevisiae hfd1Δ
In this invention the Mycobacterium marinum carboxylic acid reductase (NT ID 7) was expressed in Saccharomyces cerevisiae CEN.PK113-11C hfd1Δ to convert fatty acids to fatty aldehydes. The Musca domestica CYP4G2 P450 decarbonylase (NT ID 14) enzyme was also expressed to subsequently convert these fatty aldehydes into alka/enes. The plasmid pAlkane4 was constructed by cloning the for yeast codon optimized genes encoding Mycobacterium marinum CAR (NT ID 14), Musca domestica CYP4G2 (NT ID 14), Musca domestica NADPH-cytochrome P450 reductase (NT ID 15), and the Aspergillus nidulans phosphopantetheinyl transferase NpgA (NT ID 5) with overlap primers (PR ID114-115, 112-113, 192-193 and 108-109, respectively). The pathway was subsequently assembled as described in Shao et al, 2009 and Zhou et al, 2012. Cells were cultivated and analyzed as described in example 1. In addition to these four enzymes, an additional thioesterase is expressed to relieve fatty acid biosynthesis repression by acyl-CoA and to increase substrate availability for this pathway.
Conversion of Fatty Acids to alka/enes by Expression of Synechococcus elongatus PCC7942 ACS, Synechococcus elongatus PCC7942 Orf1594 and Musca domestica CYP4G2 Decarbonylase in Saccharomyces cerevisiae hfd1Δ
The purpose of this example is to illustrate the possibility of expression of a fatty acyl-ACP synthase to provide more of the preferred substrate acyl-ACP for the fatty acyl-ACP reductase, and the combination of a P450 type decarbonylase and cyanobacterial reductase. Thus this pathway will convert fatty acids to alkanes and alkenes via the intermediates fatty acyl-ACP and fatty aldehydes.
The plasmid pAlkane2 was constructed similar to the method described in example 8. For expression in yeast codon optimized genes encoding Synechococcus elongatus PCC7942 orf1594 (NT ID 1), Musca domestica CYP4G2 (NT ID 14), Musca domestica NADPH-cytochrome P450 reductase (NT ID 15), and Synechococcus elongatus ACS (NT ID 6?) were cloned using primers with to the gene homologous regions (PR ID 194-195, 196-197, 192-193, 110-111, respectively). The pathway was subsequently assembled as described in Shao et al, 2009 and Zhou et al, 2012.
Cells were cultivated and analyzed as described in example 1. In addition to these four genes, an additional thioesterase with preference for acyl-CoA over acyl-ACP is expressed to increase the levels of free fatty acids.
Fusing of Nostoc punctiforme Fatty Aldehyde Decarbonylase to Catalase and Expression in Saccharomyces cerevisiae hfd1Δ for Improved Fatty Aldehyde to alka/ene Conversion
The purpose of this invention is to improve the catalytic activity of the fatty aldehyde decarbonylase, which can be the Synechoccocus elongatus PCC7942 orf1593 (NT ID 2) or the Nostoc punctiforme FAD (NT ID 3), or a homologue.
The fatty aldehyde decarbonylase can be fused to a catalase as has been shown by Andre et al (2013). This will improve the activity of this enzyme and thus the alka/ene formation. The proposed mechanism is that the toxic byproduct hydrogen peroxide is broken down by the catalase, thereby avoiding that it can inhibit the decarbonylase. The novelty would be to express such a fusion enzyme in yeast together with HFD1 deletion. A heterologously expressed fatty acid reductase, as described in, for example, example 8, and the endogenous fatty acid synthesis via the breakdown of spingholipids, can supply the fatty aldehydes for the decarbonylase-catalase fusion enzyme.
Expression of Alkane or Alkene Biosynthetic Pathway in the Mitochondria of Saccharomyces cerevisiae
The purpose of this example is to illustrate the utilization of the mitochondrial fatty acid biosynthetic machinery for the synthesis of short chain fatty acids, and its subsequent conversion into short chain alkanes and alkenes.
In this experiment the Mycobacterium marinum CAR (NT ID 7) fatty acid reductase and the Nostoc puntiforme (NT ID 3) fatty aldehyde decarbonylase encoding genes were expressed in the mitochondria of Saccharomyces cerevisiae CEN.PK113-11C. All enzymes not localized by default into the mitochondria were directed there by attaching a mitochondrial localization signal (Hurt et al, 1985) to the front of each gene. In addition to the alkane biosynthetic pathway, the genes encoding key components of the mitochondrial fatty acid machinery Etr1 (2-enoyl thioester reductase) and Hfa1 (acetyl-CoA carboxylase) were overexpressed to ensure sufficient precursor supply for the alkane pathway.
The plasmid pAlkane6 was constructed similar to the method described in example 5, 8 and 9. For expression in yeast codon optimized genes encoding Mycobacterium marinum CAR (NT ID 14, attached MLS), Nostoc punctiforme FAD (NT ID 3, attached MLS), Aspergillus nidulans phosphopantetheinyl transferase NpgA (NT ID 5, attached MLS), Saccharomyces cerevisiae Hfa1 (NT ID 61), and Saccharomyces cerevisiae Etr1 (NT ID 60) were cloned using primers with to the gene homologous regions (PR ID 165-178, respectively, HFA1 was split up in three parts due to its length). The pathway was subsequently assembled as described in Shao et al, 2009 and Zhou et al, 2012.
Escherichia coli fdx (NT ID 8) and fpr (NT ID 9) were cloned from Escherichia coli DH5α genomic DNA, a mitochondrial localization signal (Hurt et al, 1985) was included in the forward primers in front of each gene, and the resulting gene fragments were ligated into the plasmid pIYC04 (Chen et al, 2012). The resulting plasmid, KB03, was verified by sequencing using primers PR ID 187-190. Subsequently the pAlkane6 and pKB03 plasmids were transformed into Saccharomyces cerevisiae CEN.PK113-11C by chemical transformation (Gietz et al, 2002) and successful transformants were selected on HIS dropout plates. To enable alka/ene biosynthesis, this plasmid can be co-transformed with a plasmid carrying fatty acid reductase and fatty aldehyde decarbonylase homologous and auxiliary enzymes.
Precursor supply can possibly be enhanced by removing post translational modification sites in Etr1 (K301) and Hfa1 (1157S), and by further overexpression of the remaining fatty acid biosynthetic enzymes (e.g. Cem1, Htd2, Oar1, and Mct1).
Expression of a thioesterase is required to provide sufficient precursors to the mitochondrial alkane pathway since there is no known yeast mitochondrial thioesterase with activity towards medium chain fatty acyl-ACP. Acinetobacter baylyi TesA (P ID 2), Cocos nucifera FatB1 (P ID 1), or homologue thioesterases have been shown to have preference for C8-C14 fatty acyl-ACPs. A thioesterase gene will be codon-optimized for expression in yeast, and subsequently expressed and directed to the mitochondria in a similar fashion as described above.
Expression of Mitochondrial Formate Dehydrogenase in Saccharomyces cerevisiae
Yeast contains a formate dehydrogenase enzyme which is localized to the cytosol. Expression of formate dehydrogenase in the mitochondria might be required to breakdown the toxic byproduct formate of the decarbonylation reaction. Overexpression of endogenous formate dehydrogenase Fdh1 and/or Fdh2 and localization of these proteins to the mitochondria can be achieved by introducing a 5′ mitochondrial localization signal into each gene (as has been described for others genes in example 11).
Construction of a Cytosolic Pathway for Medium-Chain Saturated Fatty Acid Production in Saccharomyces cerevisiae
This chimeric cytosolic pathway, composed of an acetyl-CoA C-acetyltransferase (YqeF or Erg10p), a 3-ketoacyl-CoA thiolase (FadA or Fox3p), a 3-hydroxyacyl-CoA dehydrogenase and enoyl-CoA hydratase multifunctional enzyme (FadB or Fox2p), a trans-enoyl-CoA reductase (tdTER) and a thioesterase (Tes1p) (
Rbee (pox1Δ faa1Δ faa4Δ yqeF fadA fadB tdTER TES1c)
Rbye (pox1Δ faa1Δ faa4Δ ERG10 fadA fadB tdTER TES1c)
Rbey (pox1Δ faa1Δ faa4Δ yqeF FOX3c FOX2c tdTER TES1c)
Rbyy (pox1Δ faa1Δ faa4Δ ERG10 FOX3c FOX2c tdTER TES1c)
Regulation of produced fatty-acid chain length by expression of different thioesterase genes
Different thioesterase homologues have different chain-length specificities. Therefore, coupling of any of the homologues with a fatty-acyl-CoA producing pathway results in production of fatty acids with different chain lengths depending on the thioesterase gene being expressed. Integration of this regulation on an alkane/alkene producing pathway from acetyl-CoA allows production of hydrocarbons with a desired specific chain-length. Thioesterase genes tesA, tesB, fadM or yciA from E. coli were used for construction of Rbyy strain (EXAMPLE 13) instead of the TES1c thioesterase gene. The genes tesA (NT ID 56), tesB (NT ID 57), fadM (NT ID 58) and yciA (NT ID 59) were optimized for expression in yeast and synthesized by GenScript (Piscataway, N.J., USA). These genes were amplified using primers PR ID 88 to 95. All the primers used allow the cloning of any of the selected amplified genes with the pPGK1 promoter in the pX-2-loxP-KlURA3 (Mikkelsen et al, 2012) integration vector following the USER cloning method (Nour-Eldin et al, 2006). As explained in EXAMPLE 13, FOX3-pPGK1-pTEF1-FOX2 was cloned into pXI-3-loxP-URA3 vector and tdTER-pPGK1-pTEF1-ERG10 was cloned into pXI-5-loxp-Sphis5 vector. All the integration constructs were linearized by restriction using NotI restriction enzyme and transformed into strain poxb 1 faa1 faa4 strain (EXAMPLE 16). After integration of the pXI-3-loxP-URA3- and the pXI-5-loxp-Sphis5-derived constructs, the cells were transformed with a Cre recombinase expression plasmid to delete auxotrophy markers by recombination of loxP sites flanking the marker. The originated strain was then transformed with the pX-2-loxP-KlURA3 plasmid containing either pPGK1-tesA, pPGK1-tesB, pPGK1-fadM or pPGK1-yciA.
Expression of a heterologous fatty acid synthase and alternative thioesterase modules as described by Leber and DaSilva (2013) will enable the synthesis of medium chain fatty acids and products derived thereof
This example describes the elimination of non-essential pathways that consume (activated) fatty acids and thus compete with alkane/alkene production, i.e. storage lipid formation and beta-oxidation. “Activated fatty acid” as used herein means fatty acids coupled to CoA or ACP.
For the deletion of ARE1, the 5′ and 3′ ends of the ARE1 open reading frame were individually amplified from genomic DNA of CEN.PK 113-5D (MATa ura3-52) by PCR using primers PR ID 1/2 and PR ID 3/4, respectively. The kanMX expression cassette was amplified in two overlapping parts from plasmid pUG6 (Güldener et al, 1996) using primers PR ID 5/6 and 7/8, respectively. KanMX was looped out as described previously with help of the Cre recombinase expression plasmid pSH47 (Güldener et al, 1996).
The same approach was used for deletion of ARE2, DGA1, LRO1, and PDX1. Primers PR ID 9-12 were used for deletion of ARE2, primers PR ID 13-16 were used for deletion of DGA1, primers PR ID 17-20 were used for deletion of LRO1, and primers PR ID 21-24 were used for deletion of PDX1.
Deletion of FAA1 and FAA4 is e.g. described in Runguphan and Keasling (2013).
This example describes the overexpression of genes leading to increased production of (activated) fatty acids.
Overexpression of ACC1, FAS1 and FAS2 is e.g. described in Runguphan and Keasling (2013).
Mutations S659A and S1157A were introduced into the ACC1 gene by PCR to prevent enzyme regulation by phosphorylation, i.e. to increase enzyme activity.
ACB1 (NT ID 47) was amplified by PCR from genomic DNA of S. cerevisiae with the oligonucleotide primers PR ID 25/26 and restricted with BamHI/KpnI. The BamHI/KpnI digested DNA fragment was ligated into the BamHI/KpnI sites of vector pSP-GM2 (Partow et al, 2010; Chen et al, 2012) to construct pSP-A. Yeast strains were transformed with the resulting plasmid.
Expression of Rhodosporidium toruloides fatty acid biosynthetic genes ACC1, FAS1, and FAS2 in Saccharomyces cerevisiae
As Rhodosporidium toruloides has higher efficiency in lipid production, fatty acid biosynthetic genes RtACC1 (NT ID 19), RtFAS1 (NT ID 20), and RtFAS2 (NT ID 21) from R. toruloides can be used for improving the production of fatty acids as well as fatty acid derivatives. The genes were cloned from a cDNA library as described previously (Zhu et al, 2012) with primers pairs RtACC-F (PR ID 120)/RtACC-R (PR ID 121), RtFAS1-F (PR ID 116)/RtFAS1-R (PR ID 117) and RtFAS2-F (PR ID 118)/RtFAS2-R (PR ID 119) and assembled as has been described in Shao et al (2009) and Zhou et al (2012). The expression of RtACC1 and RtFAS1/2, as well their combined expression, increased fatty acid biosynthesis in JV03 (Saccharomyces cerevisiae MATaMAL2-8c SUC2 ura3-52 HIS3 are1Δ dga1Δ are2Δ lro1Δ pox1Δ, Valle-Rodriguez et al 2014) (
This example describes different ways to increase the supply of NADPH, an essential cofactor in fatty acid biosynthesis.
Heterologous expression of a non-phosphorylating NADP+-dependent glyceraldehyde-3-phosphate dehydrogenase (GAPN) from Streptococcus mutans is e.g. described in Kocharin et al (2013).
Deletion of GDH1 encoding NADP-dependent glutamate dehydrogenase and overexpression of GDH2 encoding NAD-dependent glutamate dehydrogenase is e.g. described in Asadollahi et al (2009).
Conversion of Fatty Acyl-CoA to Fatty Alcohols by Expression of Marinobacter aquaeolei VT8 Maqu_2507 Fatty Acyl-CoA Reductase in Saccharomyces cerevisiae
This invention relates to the direct conversion of fatty acyl-CoA into fatty alcohols by a fatty acyl-CoA reductase.
The plasmid pAlcohol1 was constructed similar to the method described in example 5, 7, 8, 9. For expression in yeast codon optimized genes Marinobacter aquaeolei VT8 Maqu_2507 (NT ID 16) was cloned using primers with to the gene homologous regions (PR ID 206-207). The pathway was subsequently assembled in PYX212 as described in Shao et al, 2009 and Zhou et al, 2012. pAlcohol1 enabled the production of 3.4 mg/L fatty alcohol in S. cerevisiae CEN.PK 113-11C in shake flask fermentation.
Cells are cultivated and analyzed as described in example 1.
Construction of an Intracellular Alkane Sensor by the Expression of Yarrowia lipolytica Yas3 Repressor and Yas1, Yas2 Activator and a Fluorescent Protein Expressed from an ARE1 Containing Promoter in Saccharomyces cerevisiae.
The purpose of this example is to describe the design of an alkane biosensor that can be used to screen for better alkane producer. This can be a strain in which the fatty acid substrate is overproduced (e.g. as described in example 16), or classical mutagenesis experiments to optimize the enzymes of the pathway, or screening of homologue and/or libraries to improve the alkane production. It is based on the negative regulator (Yas3) and two activators (Yas1, Yas2) of alkane metabolism enzymes in the alkane consuming yeast Yarrowia lipolytica. The repressor Yas3 is released from the alkane response elements (ARE1) in a promoter in the presence of medium chain alkanes.
The Yarrowia alkane-reponsive promoter of the ALK1 gene was cloned in front of a reporter gene such as GFP to screen for alkane production. Alternatively, the alkane response element was integrated as one or several copies into a S. cerevisiae promoter (here the TEF1 promoter) and cloned in front of the reporter gene. For this, a truncated version of the TEF1 promoter was used and combined with three ARE1 binding sites in front of it (NT ID 64). For another strategy three ARE1 binding sites were integrated at specific positions in the complete TEF promoter (NT ID 65).
In addition, the Yarrowia lypolytica transcriptional activators Yas1 and Yas2 as well as the repressor Yas3 necessary for alkane-mediated transcription regulation will be introduced into S. cerevisiae together with the reporter construct.
Expressing the repressor gene Yas3 in presence of the two activators Yas1 and Yas2 leads to a 100-fold repression of the green fluorescence reporter signal, indicating the functionality of the system and the sensor range. Exposing the system to alkanes gave a clear response and increased green fluorescence signal, as demonstrated in
This application is a continuation of U.S. patent application Ser. No. 15/029,818, filed on Apr. 15, 2016, which is a 35 U.S.C. §371 national phase application of International Application Serial No. PCT/SE2014/051229, filed Oct. 17, 2014, which claims the benefit, under 35 U.S.C. §119 (a) of U.S. Application Ser. No. 61/893,125, filed Oct. 18, 2013, the entire contents of each of which are incorporated by reference herein.
| Number | Date | Country | |
|---|---|---|---|
| 61893125 | Oct 2013 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 15029818 | Apr 2016 | US |
| Child | 15682002 | US |
