# Patent

## Title
Recombinant Escherichia coli having enhanced acetyl-coenzyme a synthetase activity for producing glyerol and glycerol-derived products

## Abstract

Recombinant Escherichia coli (E. coli) bacteria that have enhanced acetyl-CoA synthetase activity and the ability to produce glycerol and glycerol-derived products, such as 3-hydroxypropionic acid, methylglyoxal, 1,2-propanediol, and 1,3-propanediol, are described. The recombinant E. coli comprise a promoter operably linked to a nucleotide sequence encoding a polypeptide having acetyl-CoA synthetase enzyme activity, wherein the promoter and nucleotide sequence are each independently either native or non-native.

## Background
FIELD OF THE INVENTION
The invention relates to the fields of microbiology and molecular biology. More specifically, recombinant Escherichia coli (E. coli) having enhanced acetyl-coenzyme A (acetyl-CoA) synthetase activity and the ability to produce glycerol and glycerol-derived products, and methods of utilizing such recombinant bacteria are provided.
BACKGROUND OF THE INVENTION
The polyol 1,3-propanediol (PDO) is a monomer useful in the production of a variety of polymers including polyesters, polyurethanes, polyethers and cyclic compounds. The polymers are ultimately used in fibers, films, coatings, composite materials, solvents, anti-freeze, copolyesters and other value-added applications. Although 1,3-propanediol may be produced by chemical synthesis, biological production via fermentation provides several advantages over chemical synthesis, including providing a sustainable, more environmentally friendly process. Fermentation using recombinantly-engineered bacteria using inexpensive carbon sources such as glucose or other sugars to produce 1,3-propanediol are known (see for example, U.S. Pat. No. 5,686,276, U.S. Pat. No. 6,358,716, U.S. Pat. No. 6,136,576, and U.S. Pat. No. 7,524,660). However, fermentative routes to producing 1,3-propanediol generate residual materials, such as acetate, which can compromise the quality of the polymers produced from this monomer. Consequently, the residual materials need to be removed from the 1,3-propanediol product by various separation methods, including ion exchange and distillation. The presence of acetate is particularly problematic because a high ion exchange capacity is required to reduce its concentration to acceptable levels.
Therefore, there is a need to reduce the amount of acetate produced during the production of 1,3-propanediol and other glycerol-derived products by fermentation to increase the capacity of the separation process required to obtain a product having acceptable purity levels. Additionally, acetate is a by-product known to inhibit bacterial growth (Lin et al., Appl. Microbiol. Biotechnol. 71:870-874, 2006), so a decrease in acetate production may lead to increased yields of 1,3-propanediol.
SUMMARY OF THE INVENTION
In one embodiment, the invention provides a recombinant E. coli comprising a promoter operably linked to a nucleotide sequence encoding a polypeptide having acetyl-CoA synthetase enzyme activity; wherein the promoter and nucleotide sequence are each independently either native or non-native; further wherein said recombinant E. coli has enhanced acetyl-CoA synthetase enzyme activity relative to a parent E. coli from which the recombinant E. coli was derived, and said recombinant E. coli produces glycerol, 1,3-propanediol and/or 3-hydroxypropionic acid; provided that if the promoter and nucleotide sequence are both native, said recombinant E. coli comprises at least two copies of the promoter and nucleotide sequence.
In another embodiment, the invention provides a process for making glycerol, 1,3-propanediol, and/or 3-hydroxypropionic acid comprising:

    
    
        a) culturing a recombinant E. coli as described herein in a suitable growth medium; and
        b) optionally, recovering the glycerol, 1,3-propanediol, and/or 3-hydroxypropionic acid produced.
    
    


BRIEF SEQUENCE DESCRIPTIONS
The following sequences conform with 37 C.F.R. 1.821 1.825 (“Requirements for Patent Applications Containing Nucleotide Sequences and/or Amino Acid Sequence Disclosures—the Sequence Rules”) and consistent with World Intellectual Property Organization (WIPO) Standard ST.25 (2009) and the sequence listing requirements of the EPO and PCT (Rules 5.2 and 49.5(a bis), and Section 208 and Annex C of the Administrative Instructions). The symbols and format used for nucleotide and amino acid sequence data comply with the rules set forth in 37 C.F.R. §1.822.







TABLE A







Summary of Gene and Protein SEQ ID Numbers










Coding
Encoded



Sequence
Protein


Gene
SEQ ID NO:
SEQ ID NO:












GPD1 from Saccharomyces cerevisiae
1
2


GPD2 from Saccharomyces cerevisiae
3
4


GPP1 from Saccharomyces cerevisiae
5
6


GPP2 from Saccharomyces cerevisiae
7
8


dhaB1 from Klebsiella pneumoniae
9
10


dhaB2 from Klebsiella pneumoniae
11
12


dhaB3 from Klebsiella pneumoniae
13
14


aldB from Escherichia coli
15
16


aldA from Escherichia coli
17
18


aldH from Escherichia coli
19
20


galP from Escherichia coli
21
22


dhaT from Klebsiella pneumoniae
23
24


dhaX gene from Klebsiella pneumoniae
25
26


acs from Escherichia coli
27
28


acs1 from Saccharomyces cerevisiae
29
30


acs2 from Saccharomyces cerevisiae
31
32









SEQ ID NO:33 is the nucleotide sequence of the phage T5 promoter.
SEQ ID NO:34 is the nucleotide sequence of the Pcat promoter.
SEQ ID NO:35 is the nucleotide sequence of plasmid pSYCO101.
SEQ ID NO:36 is the nucleotide sequence of plasmid pSYCO103.
SEQ ID NO:37 is the nucleotide sequence of plasmid pSYCO106.
SEQ ID NO:38 is the nucleotide sequence of plasmid pSYCO109.
SEQ ID NO:39 is the nucleotide sequence of plasmid pSYCO400/AGRO.
SEQ ID NOs:40-51, 56, 57, 59, 60, 66-71, 73, and 74 are nucleotide sequences of primers used in the Examples herein.
SEQ ID NO:52 is the nucleotide sequence of plasmid pDCQ702, as described in Example 1 herein.
SEQ ID NO:53 is the nucleotide sequence of plasmid pDCQ703, as described in Example 1 herein.
SEQ ID NO:54 is the nucleotide sequence of the loxP-KanR-loxP-PT5 cassette, as described in Example 1 herein.
SEQ ID NO:55 is the nucleotide sequence of the loxP-KanR-loxP-Pcat cassette, as described in Example 1 herein.
SEQ ID NO:58 is the coding sequence of the E. coli fucP gene.
SEQ ID NO:61 is the nucleotide sequence of plasmid pMTP1.5fucP, described in Example 2 herein.
SEQ ID NO:62 is the nucleotide sequence of the synthetic linker sequence used in the construction of plasmid pMTP1.5fucPpmeI, as described in Example 2 herein.
SEQ ID NO:63 is the nucleotide sequence of plasmid pMTP1.6fucP, described in Example 2 herein.
SEQ ID NO:64 is the nucleotide sequence of plasmid pDCQ804, described in Example 2 herein.
SEQ ID NO:65 is the nucleotide sequence of plasmid pDCQ805, described in Example 2 herein.
SEQ ID NOs:72 and 75 are the nucleotide sequences of the TaqMan® probes described in Example 7 herein.
SEQ ID NO:76 is the nucleotide sequence of plasmid pDCQ806, described in Examples 8-10 herein.
SEQ ID NO:77 is the nucleotide sequence of plasmid pDCQ807, described in Examples 8-10 herein.


DETAILED DESCRIPTION
The disclosure of each reference set forth herein is hereby incorporated by reference in its entirety.
As used herein and in the appended claims, the singular forms “a”, “an”, and “the” include plural reference unless the context clearly dictates otherwise. Thus, for example, reference to “a cell” includes one or more cells and equivalents thereof known to those skilled in the art, and so forth.
In the context of this disclosure, a number of terms and abbreviations are used. The following definitions are provided.
“Open reading frame” is abbreviated as “ORF”.
“Polymerase chain reaction” is abbreviated as “PCR”.
“American Type Culture Collection” is abbreviated as “ATCC”.
The term “acetyl-CoA synthetase enzyme activity” refers to a polypeptide responsible for an enzyme activity that catalyzes the conversion of acetate+Coenzyme A+ATP to acetyl-CoA+diphosphate+AMP. Typical of acetyl-CoA synthetase is EC 6.2.1.1. Acetyl-CoA synthetase is encoded by the gene acs.
The term “enhanced acetyl-CoA synthetase enzyme activity” as used herein means that the recombinant E. coli disclosed herein have a higher expression level, also referred to herein as “overexpression”, of an acs gene encoding a polypeptide having acetyl-CoA synthetase activity when compared to the expression level in the parent E. coli from which the recombinant E. coli was derived. The expression level of acs can be determined using real-time PCR to determine the acs transcript levels in the E. coli as described in detail in Example 4 herein below.
The terms “glycerol derivative” and “glycerol-derived products” are used interchangeably herein and refer to a compound that is synthesized from glycerol or in a pathway that includes glycerol. Examples of such products include 3-hydroxypropionic acid, methylglyoxal, 1,2-propanediol, and 1,3-propanediol.
The term “microbial product” refers to a product that is microbially produced, i.e., the result of a microorganism metabolizing a substance. The product may be naturally produced by the microorganism, or the microorganism may be genetically engineered to produce the product.
The terms “phosphoenolpyruvate-sugar phosphotransferase system”, “PTS system”, and “PTS” are used interchangeably herein and refer to the phosphoenolpyruvate-dependent sugar uptake system.
The terms “phosphocarrier protein HPr” and “PtsH” refer to the phosphocarrier protein encoded by ptsH in E. coli. The terms “phosphoenolpyruvate-protein phosphotransferase” and “PtsI” refer to the phosphotransferase, EC 2.7.3.9, encoded by ptsI in E. coli. The terms “glucose-specific IIA component”, and “Crr” refer to enzymes designated as EC 2.7.1.69, encoded by crr in E. coli. PtsH, PtsI, and Crr comprise the PTS system.
The term “PTS minus” refers to a microorganism that does not contain a PTS system in its native state or a microorganism in which the PTS system has been inactivated through the inactivation of a PTS gene.
The terms “glycerol-3-phosphate dehydrogenase” and “G3PDH” refer to a polypeptide responsible for an enzyme activity that catalyzes the conversion of dihydroxyacetone phosphate (DHAP) to glycerol 3-phosphate (G3P). In vivo G3PDH may be NAD- or NADP-dependent. When specifically referring to a cofactor specific glycerol-3-phosphate dehydrogenase, the terms “NAD-dependent glycerol-3-phosphate dehydrogenase” and “NADP-dependent glycerol-3-phosphate dehydrogenase” will be used. As it is generally the case that NAD-dependent and NADP-dependent glycerol-3-phosphate dehydrogenases are able to use NAD and NADP interchangeably (for example by the enzyme encoded by gpsA), the terms NAD-dependent and NADP-dependent glycerol-3-phosphate dehydrogenase will be used interchangeably. The NAD-dependent enzyme (EC 1.1.1.8) is encoded, for example, by several genes including GPD1, also referred to herein as DAR1 (coding sequence set forth in SEQ ID NO:1; encoded protein sequence set forth in SEQ ID NO:2), or GPD2 (coding sequence set forth in SEQ ID NO:3; encoded protein sequence set forth in SEQ ID NO:4), or GPD3. The NADP-dependent enzyme (EC 1.1.1.94) is encoded, for example, by gpsA.
The terms “glycerol 3-phosphatase”, “sn-glycerol 3-phosphatase”, “D,L-glycerol phosphatase”, and “G3P phosphatase” refer to a polypeptide having an enzymatic activity that is capable of catalyzing the conversion of glycerol 3-phosphate and water to glycerol and inorganic phosphate. G3P phosphatase is encoded, for example, by GPP1 (coding sequence set forth in SEQ ID NO:5; encoded protein sequence set forth in SEQ ID NO:6), or GPP2 (coding sequence set forth in SEQ ID NO:7; encoded protein sequence set forth in SEQ ID NO:8).
The term “glycerol dehydratase” or “dehydratase enzyme” refers to a polypeptide having enzyme activity that is capable of catalyzing the conversion of a glycerol molecule to the product, 3-hydroxypropionaldehyde (3-HPA).
For the purposes of the present invention the dehydratase enzymes include a glycerol dehydratase (EC 4.2.1.30) and a diol dehydratase (EC 4.2.1.28) having preferred substrates of glycerol and 1,2-propanediol, respectively. Genes for dehydratase enzymes have been identified in Klebsiella pneumoniae, Citrobacter freundii, Clostridium pasteurianum, Salmonella typhimurium, Klebsiella oxytoca, and Lactobacillus reuteri, among others. In each case, the dehydratase is composed of three subunits: the large or “α” subunit, the medium or “β” subunit, and the small or “γ” subunit. The genes are also described in, for example, Daniel et al. (FEMS Microbiol. Rev. 22, 553 (1999)) and Toraya and Mori (J. Biol. Chem. 274, 3372 (1999)). Genes encoding the large or “α” (alpha) subunit of glycerol dehydratase include dhaB1 (coding sequence set forth in SEQ ID NO:9, encoded protein sequence set forth in SEQ ID NO:10), gldA and dhaB; genes encoding the medium or “β” (beta) subunit include dhaB2 (coding sequence set forth in SEQ ID NO:11, encoded protein sequence set forth in SEQ ID NO:12), gldB, and dhaC; genes encoding the small or “γ” (gamma) subunit include dhaB3 (coding sequence set forth in SEQ ID NO:13, encoded protein sequence set forth in SEQ ID NO:14), gldC, and dhaE. Other genes encoding the large or “α” subunit of diol dehydratase include pduC and pddA; other genes encoding the medium or “β” subunit include pduD and pddB; and other genes encoding the small or “γ” subunit include pduE and pddC.
Glycerol and diol dehydratases are subject to mechanism-based suicide inactivation by glycerol and some other substrates (Daniel et al., FEMS Microbiol. Rev. 22, 553 (1999)). The term “dehydratase reactivation factor” refers to those proteins responsible for reactivating the dehydratase activity. The terms “dehydratase reactivating activity”, “reactivating the dehydratase activity” and “regenerating the dehydratase activity” are used interchangeably and refer to the phenomenon of converting a dehydratase not capable of catalysis of a reaction to one capable of catalysis of a reaction or to the phenomenon of inhibiting the inactivation of a dehydratase or the phenomenon of extending the useful half-life of the dehydratase enzyme in vivo. Two proteins have been identified as being involved as the dehydratase reactivation factor (see, e.g., U.S. Pat. No. 6,013,494 and references therein; Daniel et al., supra; Toraya and Mori, J. Biol. Chem. 274, 3372 (1999); and Tobimatsu et al., J. Bacteriol. 181, 4110 (1999)). Genes encoding one of the proteins include, for example, orfZ, dhaB4, gdrA, pduG and ddrA. Genes encoding the second of the two proteins include, for example, orfX, orf2b, gdrB, pduH and ddrB.
The terms “1,3-propanediol oxidoreductase”, “1,3-propanediol dehydrogenase” and “DhaT” are used interchangeably herein and refer to the polypeptide(s) having an enzymatic activity that is capable of catalyzing the interconversion of 3-HPA and 1,3-propanediol provided the gene(s) encoding such activity is found to be physically or transcriptionally linked to a dehydratase enzyme in its natural (i.e., wild type) setting; for example, the gene is found within a dha regulon as is the case with dhaT from Klebsiella pneumoniae. Genes encoding a 1,3-propanediol oxidoreductase include, but are not limited to, dhaT from Klebsiella pneumoniae, Citrobacter freundii, and Clostridium pasteurianum. Each of these genes encode a polypeptide belonging to the family of type III alcohol dehydrogenases, which exhibits a conserved iron-binding motif, and has a preference for the NAD+/NADH linked interconversion of 3-HPA and 1,3-propanediol (Johnson and Lin, J. Bacteriol. 169, 2050 (1987); Daniel et al., J. Bacteriol. 177, 2151 (1995); and Leurs et al., FEMS Microbiol. Lett. 154, 337 (1997)). Enzymes with similar physical properties have been isolated from Lactobacillus brevis and Lactobacillus buchneri (Veiga da Dunha and Foster, Appl. Environ. Microbiol. 58, 2005 (1992)).
The term “dha regulon” refers to a set of associated polynucleotides or open reading frames encoding polypeptides having various biological activities, including but not limited to a dehydratase activity, a reactivation activity, and a 1,3-propanediol oxidoreductase. Typically a dha regulon comprises the open reading frames dhaR, orfY, dhaT, orfX, orfW, dhaB1, dhaB2, dhaB3, and orfZ as described in U.S. Pat. No. 7,371,558.
The terms “aldehyde dehydrogenase” and “Ald” refer to a polypeptide that catalyzes the conversion of an aldehyde to a carboxylic acid. Aldehyde dehydrogenases may use a redox cofactor such as NAD, NADP, FAD, or PQQ. Typical of aldehyde dehydrogenases is EC 1.2.1.3 (NAD-dependent); EC 1.2.1.4 (NADP-dependent); EC 1.2.99.3 (PQQ-dependent); or EC 1.2.99.7 (FAD-dependent). An example of an NADP-dependent aldehyde dehydrogenase is AldB (SEQ ID NO:16), encoded by the E. coli gene aldB (coding sequence set forth in SEQ ID NO:15). Examples of NAD-dependent aldehyde dehydrogenases include AldA (SEQ ID NO:18), encoded by the E. coli gene aldA (coding sequence set forth in SEQ ID NO:17); and AldH (SEQ ID NO:20), encoded by the E. coli gene aldH (coding sequence set forth in SEQ ID NO:19).
The terms “glucokinase” and “Glk” are used interchangeably herein and refer to a protein that catalyzes the conversion of D-glucose+ATP to glucose 6-phosphate+ADP. Typical of glucokinase is EC 2.7.1.2. Glucokinase is encoded by glk in E. coli. 
The terms “phosphoenolpyruvate carboxylase” and “Ppc” are used interchangeably herein and refer to a protein that catalyzes the conversion of phosphoenolpyruvate+H2O+CO2 to phosphate+oxaloacetic acid. Typical of phosphoenolpyruvate carboxylase is EC 4.1.1.31. Phosphoenolpyruvate carboxylase is encoded by ppc in E. coli. 
The terms “glyceraldehyde-3-phosphate dehydrogenase” and “GapA” are used interchangeably herein and refer to a protein having an enzymatic activity capable of catalyzing the conversion of glyceraldehyde 3-phosphate+phosphate+NAD+ to 3-phospho-D-glyceroyl-phosphate+NADH+H+. Typical of glyceraldehyde-3-phosphate dehydrogenase is EC 1.2.1.12. Glyceraldehyde-3-phosphate dehydrogenase is encoded by gapA in E. coli. 
The terms “aerobic respiration control protein” and “ArcA” are used interchangeably herein and refer to a global regulatory protein. The aerobic respiration control protein is encoded by arcA in E. coli. 
The terms “methylglyoxal synthase” and “MgsA” are used interchangeably herein and refer to a protein having an enzymatic activity capable of catalyzing the conversion of dihydroxyacetone phosphate to methylglyoxal+phosphate. Typical of methylglyoxal synthase is EC 4.2.3.3. Methylglyoxal synthase is encoded by mgsA in E. coli. 
The terms “phosphogluconate dehydratase” and “Edd” are used interchangeably herein and refer to a protein having an enzymatic activity capable of catalyzing the conversion of 6-phospho-gluconate to 2-keto-3-deoxy-6-phospho-gluconate+H2O. Typical of phosphogluconate dehydratase is EC 4.2.1.12. Phosphogluconate dehydratase is encoded by edd in E. coli. 
The term “YciK” refers to a putative enzyme encoded by yciK which is translationally coupled to btuR, the gene encoding Cob(I)alamin adenosyltransferase in E. coli. 
The term “cob(I)alamin adenosyltransferase” refers to an enzyme capable of transferring a deoxyadenosyl moiety from ATP to the reduced corrinoid. Typical of cob(I)alamin adenosyltransferase is EC 2.5.1.17. Cob(I)alamin adenosyltransferase is encoded by the gene “btuR” in E. coli, “cobA” in Salmonella typhimurium, and “cobO” in Pseudomonas denitrificans. 
The terms “galactose-proton symporter” and “GalP” are used interchangeably herein and refer to a protein having an enzymatic activity capable of transporting a sugar and a proton from the periplasm to the cytoplasm. D-glucose is a preferred substrate for GalP. Galactose-proton symporter is encoded by galP in Escherichia coli (coding sequence set forth in SEQ ID NO:21, encoded protein sequence set forth in SEQ ID NO:22).
The term “non-specific catalytic activity” refers to the polypeptide(s) having an enzymatic activity capable of catalyzing the interconversion of 3-HPA and 1,3-propanediol and specifically excludes 1,3-propanediol oxidoreductase(s). Typically these enzymes are alcohol dehydrogenases. Such enzymes may utilize cofactors other than NAD+/NADH, including but not limited to flavins such as FAD or FMN. A gene for a non-specific alcohol dehydrogenase (yqhD) is found, for example, to be endogenously encoded and functionally expressed within E. coli K-12 strains.
The terms “1.6 long GI promoter”, “1.20 short/long GI Promoter”, and “1.5 long GI promoter” refer to polynucleotides or fragments containing a promoter from the Streptomyces lividans glucose isomerase gene as described in U.S. Pat. No. 7,132,527. These promoter fragments include a mutation which decreases their activities as compared to the wild type Streptomyces lividans glucose isomerase gene promoter.
The terms “function” and “enzyme function” are used interchangeably herein and refer to the catalytic activity of an enzyme in altering the rate at which a specific chemical reaction occurs without itself being consumed by the reaction. It is understood that such an activity may apply to a reaction in equilibrium where the production of either product or substrate may be accomplished under suitable conditions.
The terms “polypeptide” and “protein” are used interchangeably herein.
The terms “carbon substrate” and “carbon source” are used interchangeably herein and refer to a carbon source capable of being metabolized by the recombinant E. coli disclosed herein. The carbon source may comprise monosaccharides such as glucose and fructose, oligosaccharides such as lactose or sucrose, and polysaccharides.
The terms “host cell” and “host bacterium” are used interchangeably herein and refer to a bacterium capable of receiving foreign or heterologous genes and capable of expressing those genes to produce an active gene product.
As used herein, “nucleic acid” means a polynucleotide and includes a single or double-stranded polymer of deoxyribonucleotide or ribonucleotide bases. Nucleic acids may also include fragments and modified nucleotides. Thus, the terms “polynucleotide”, “nucleic acid sequence”, “nucleotide sequence” or “nucleic acid fragment” are used interchangeably herein and refer to a polymer of RNA or DNA that is single- or double-stranded, optionally containing synthetic, non-natural or altered nucleotide bases. Nucleotides (usually found in their 5′-monophosphate form) are referred to by their single letter designation as follows: “A” for adenylate or deoxyadenylate (for RNA or DNA, respectively), “C” for cytidylate or deoxycytidylate, “G” for guanylate or deoxyguanylate, “U” for uridylate, “T” for deoxythymidylate, “R” for purines (A or G), “Y” for pyrimidines (C or T), “K” for G or T, “H” for A or C or T, “I” for inosine, and “N” for any nucleotide.
A polynucleotide may be a polymer of RNA or DNA that is single- or double-stranded, that optionally contains synthetic, non-natural or altered nucleotide bases. A polynucleotide in the form of a polymer of DNA may be comprised of one or more segments of cDNA, genomic DNA, synthetic DNA, or mixtures thereof.
“Gene” refers to a nucleic acid fragment that expresses a specific protein, and which may refer to the coding region alone or may include regulatory sequences preceding (5′ non-coding sequences) and following (3′ non-coding sequences) the coding sequence. “Native gene” refers to a gene as found in nature with its own regulatory sequences. “Chimeric gene” refers to any gene that is not a native gene, comprising regulatory and coding sequences that are not found together in nature. Accordingly, a chimeric gene may comprise regulatory sequences and coding sequences that are derived from different sources, or regulatory sequences and coding sequences derived from the same source, but arranged in a manner different than that found in nature. “Endogenous gene” refers to a native gene in its natural location in the genome of an organism. A “foreign” gene refers to a gene that is introduced into the host organism by gene transfer. Foreign genes can comprise genes inserted into a non-native organism, genes introduced into a new location within the native host, or chimeric genes.
The term “native nucleotide sequence” refers to a nucleotide sequence that is normally found in the host microorganism.
The term “non-native nucleotide sequence” refers to a nucleotide sequence that is not normally found in the host microorganism.
The term “native promoter” refers to a promoter linked to a gene in the same manner in which it is normally found in a host microorganism.
The term “non-native promoter” refers to a promoter linked to a gene to which it is not normally linked.
The term “native polypeptide” refers to a polypeptide that is normally found in the host microorganism.
The term “non-native polypeptide” refers to a polypeptide that is not normally found in the host microorganism.
The terms “encoding” and “coding” are used interchangeably herein and refer to the process by which a gene, through the mechanisms of transcription and translation, produces an amino acid sequence.
The term “coding sequence” refers to a nucleotide sequence that codes for a specific amino acid sequence.
“Suitable regulatory sequences” refer to nucleotide sequences located upstream (5′ non-coding sequences), within, or downstream (3′ non-coding sequences) of a coding sequence, and which influence the transcription, RNA processing or stability, or translation of the associated coding sequence. Regulatory sequences may include promoters, enhancers, silencers, 5′ untranslated leader sequence (e.g., between the transcription start site and the translation initiation codon), introns, polyadenylation recognition sequences, RNA processing sites, effector binding sites and stem-loop structures.
The term “expression cassette” refers to a fragment of DNA comprising the coding sequence of a selected gene and regulatory sequences preceding (5′ non-coding sequences) and following (3′ non-coding sequences) the coding sequence that are required for expression of the selected gene product. Thus, an expression cassette is typically composed of: 1) a promoter sequence; 2) a coding sequence (i.e., ORF) and, 3) a 3′ untranslated region (e.g., a terminator) that, in eukaryotes, usually contains a polyadenylation site. The expression cassette(s) is usually included within a vector, to facilitate cloning and transformation. Different organisms, including bacteria, yeast, and fungi, can be transformed with different expression cassettes as long as the correct regulatory sequences are used for each host.
“Transformation” refers to the transfer of a nucleic acid molecule into a host organism, resulting in genetically stable inheritance. The nucleic acid molecule may be a plasmid that replicates autonomously, for example, or it may integrate into the genome of the host organism. Host organisms transformed with the nucleic acid fragments are referred to as “recombinant” or “transformed” organisms or “transformants”. “Stable transformation” refers to the transfer of a nucleic acid fragment into a genome of a host organism, including both nuclear and organellar genomes, resulting in genetically stable inheritance. In contrast, “transient transformation” refers to the transfer of a nucleic acid fragment into the nucleus, or DNA-containing organelle, of a host organism resulting in gene expression without integration or stable inheritance.
“Codon degeneracy” refers to the nature in the genetic code permitting variation of the nucleotide sequence without affecting the amino acid sequence of an encoded polypeptide. The skilled artisan is well aware of the “codon-bias” exhibited by a specific host cell in usage of nucleotide codons to specify a given amino acid. Therefore, when synthesizing a gene for improved expression in a host cell, it is desirable to design the gene such that its frequency of codon usage approaches the frequency of preferred codon usage of the host cell.
The terms “subfragment that is functionally equivalent” and “functionally equivalent subfragment” are used interchangeably herein. These terms refer to a portion or subsequence of an isolated nucleic acid fragment in which the ability to alter gene expression or produce a certain phenotype is retained whether or not the fragment or subfragment encodes an active enzyme. Chimeric genes can be designed for use in suppression by linking a nucleic acid fragment or subfragment thereof, whether or not it encodes an active enzyme, in the sense or antisense orientation relative to a promoter sequence.
The term “conserved domain” or “motif” means a set of amino acids conserved at specific positions along an aligned sequence of evolutionarily related proteins. While amino acids at other positions can vary between homologous proteins, amino acids that are highly conserved at specific positions indicate amino acids that are essential in the structure, the stability, or the activity of a protein.
The terms “substantially similar” and “corresponds substantially” are used interchangeably herein. They refer to nucleic acid fragments wherein changes in one or more nucleotide bases do not affect the ability of the nucleic acid fragment to mediate gene expression or produce a certain phenotype. These terms also refer to modifications of the nucleic acid fragments of the instant invention such as deletion or insertion of one or more nucleotides that do not substantially alter the functional properties of the resulting nucleic acid fragment relative to the initial, unmodified fragment. It is therefore understood, as those skilled in the art will appreciate, that the invention encompasses more than the specific exemplary sequences. Moreover, the skilled artisan recognizes that substantially similar nucleic acid sequences encompassed by this invention are also defined by their ability to hybridize (under moderately stringent conditions, e.g., 0.5×SSC (standard sodium citrate), 0.1% SDS (sodium dodecyl sulfate), 60° C.) with the sequences exemplified herein, or to any portion of the nucleotide sequences disclosed herein and which are functionally equivalent to any of the nucleic acid sequences disclosed herein. Stringency conditions can be adjusted to screen for moderately similar fragments, such as homologous sequences from distantly related organisms, to highly similar fragments, such as genes that duplicate functional enzymes from closely related organisms. Post-hybridization washes determine stringency conditions.
The term “selectively hybridizes” includes reference to hybridization, under stringent hybridization conditions, of a nucleic acid sequence to a specified nucleic acid target sequence to a detectably greater degree (e.g., at least 2-fold over background) than its hybridization to non-target nucleic acid sequences and to the substantial exclusion of non-target nucleic acids. Selectively hybridizing sequences are two nucleotide sequences wherein the complement of one of the nucleotide sequences typically has about at least 80% sequence identity, or 90% sequence identity, up to and including 100% sequence identity (i.e., fully complementary) to the other nucleotide sequence.
The term “stringent conditions” or “stringent hybridization conditions” includes reference to conditions under which a probe will selectively hybridize to its target sequence. Probes are typically single stranded nucleic acid sequences which are complementary to the nucleic acid sequences to be detected. Probes are “hybridizable” to the nucleic acid sequence to be detected. Generally, a probe is less than about 1000 nucleotides in length, optionally less than 500 nucleotides in length.
Hybridization methods are well defined. Typically the probe and sample are mixed under conditions which will permit nucleic acid hybridization. This involves contacting the probe and sample in the presence of an inorganic or organic salt under the proper concentration and temperature conditions. Optionally a chaotropic agent may be added. Nucleic acid hybridization is adaptable to a variety of assay formats. One of the most suitable is the sandwich assay format. A primary component of a sandwich-type assay is a solid support. The solid support has adsorbed to it or covalently coupled to it an immobilized nucleic acid probe that is unlabeled and complementary to one portion of the sequence.
Stringent conditions are sequence-dependent and will be different in different circumstances. By controlling the stringency of the hybridization and/or washing conditions, target sequences can be identified which are 100% complementary to the probe (homologous probing). Alternatively, stringency conditions can be adjusted to allow some mismatching in sequences so that lower degrees of similarity are detected (heterologous probing).
Typically, stringent conditions will be those in which the salt concentration is less than about 1.5 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 at least about 30° C. for short probes (e.g., 10 to 50 nucleotides) and at least about 60° C. for long probes (e.g., greater than 50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. Exemplary low stringency conditions include hybridization with a buffer solution of 30 to 35% formamide, 1 M NaCl, 1% SDS (sodium dodecyl sulfate) at 37° C., and a wash in 1× to 2×SSC (20×SSC=3.0 M NaCl/0.3 M trisodium citrate) at 50 to 55° C. Exemplary moderate stringency conditions include hybridization in 40 to 45% formamide, 1 M NaCl, 1% SDS at 37° C., and a wash in 0.5× to 1×SSC at 55 to 60° C. Exemplary high stringency conditions include hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37° C., and a wash in 0.1×SSC at 60 to 65° C.
Specificity is typically the function of post-hybridization washes, the critical factors being the ionic strength and temperature of the final wash solution. For DNA-DNA hybrids, the thermal melting point (Tm) can be approximated from the equation of Meinkoth et al., Anal. Biochem. 138:267-284 (1984): Tm=81.5° C.+16.6 (log M)+0.41 (% GC)−0.61 (% form)−500/L; where M is the molarity of monovalent cations, % GC is the percentage of guanosine and cytosine nucleotides in the DNA, % form is the percentage of formamide in the hybridization solution, and L is the length of the hybrid in base pairs. The Tm is the temperature (under defined ionic strength and pH) at which 50% of a complementary target sequence hybridizes to a perfectly matched probe. Tm is reduced by about 1° C. for each 1% of mismatching; thus, Tm, hybridization and/or wash conditions can be adjusted to hybridize to sequences of the desired identity. For example, if sequences with ≧90% identity are sought, the Tm can be decreased 10° C. Generally, stringent conditions are selected to be about 5° C. lower than Tm for the specific sequence and its complement at a defined ionic strength and pH. However, severely stringent conditions can utilize a hybridization and/or wash at 1, 2, 3, or 4° C. lower than the Tm; moderately stringent conditions can utilize a hybridization and/or wash at 6, 7, 8, 9, or 10° C. lower than the Tm; low stringency conditions can utilize a hybridization and/or wash at 11, 12, 13, 14, 15, or 20° C. lower than the Tm. Using the equation, hybridization and wash compositions, and desired Tm, those of ordinary skill will understand that variations in the stringency of hybridization and/or wash solutions are inherently described. If the desired degree of mismatching results in a Tm of less than 45° C. (aqueous solution) or 32° C. (formamide solution) it is preferred to increase the SSC concentration so that a higher temperature can be used. An extensive guide to the hybridization of nucleic acids is found in Tijssen, 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); and Current Protocols in Molecular Biology, Chapter 2, Ausubel et al., Eds., Greene Publishing and Wiley-Interscience, New York (1995). Hybridization and/or wash conditions can be applied for at least 10, 30, 60, 90, 120, or 240 minutes.
“Sequence identity” or “identity” in the context of nucleic acid or polypeptide sequences refers to the nucleic acid bases or amino acid residues in two sequences that are the same when aligned for maximum correspondence over a specified comparison window.
Thus, “percentage of sequence identity” refers to the value determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide or polypeptide sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the results by 100 to yield the percentage of sequence identity. Useful examples of percent sequence identities include, but are not limited to, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95%, or any integer percentage from 50% to 100%. These identities can be determined using any of the programs described herein.
Sequence alignments and percent identity or similarity calculations may be determined using a variety of comparison methods designed to detect homologous sequences including, but not limited to, the MegAlignTM program of the LASERGENE bioinformatics computing suite (DNASTAR Inc., Madison, Wis.). Within the context of this application it will be understood that where sequence analysis software is used for analysis, that the results of the analysis will be based on the “default values” of the program referenced, unless otherwise specified. As used herein “default values” will mean any set of values or parameters that originally load with the software when first initialized.
The “Clustal V method of alignment” corresponds to the alignment method labeled Clustal V (described by Higgins and Sharp, CABIOS. 5:151-153 (1989); Higgins, D. G. et al., Comput. Appl. Biosci. 8:189-191 (1992)) and found in the MegAlignTM program of the LASERGENE bioinformatics computing suite (DNASTAR Inc., Madison, Wis.). For multiple alignments, the default values correspond to GAP PENALTY=10 and GAP LENGTH PENALTY=10. Default parameters for pairwise alignments and calculation of percent identity of protein sequences using the Clustal V method are KTUPLE=1, GAP PENALTY=3, WINDOW=5 and DIAGONALS SAVED=5. For nucleic acids these parameters are KTUPLE=2, GAP PENALTY=5, WINDOW=4 and DIAGONALS SAVED=4. After alignment of the sequences using the Clustal V program, it is possible to obtain a “percent identity” by viewing the “sequence distances” table in the same program.
The “Clustal W method of alignment” corresponds to the alignment method labeled Clustal W (described by Higgins and Sharp, supra; Higgins, D. G. et al., supra) and found in the MegAlignTM v6.1 program of the LASERGENE bioinformatics computing suite (DNASTAR Inc., Madison, Wis.). Default parameters for multiple alignment correspond to GAP PENALTY=10, GAP LENGTH PENALTY=0.2, Delay Divergen Seqs(%)=30, DNA Transition Weight=0.5, Protein Weight Matrix=Gonnet Series, DNA Weight Matrix=IUB. After alignment of the sequences using the Clustal W program, it is possible to obtain a “percent identity” by viewing the “sequence distances” table in the same program.
“BLASTN method of alignment” is an algorithm provided by the National Center for Biotechnology Information (NCBI) to compare nucleotide sequences using default parameters.
It is well understood by one skilled in the art that many levels of sequence identity are useful in identifying polypeptides, from other species, wherein such polypeptides have the same or similar function or activity. Useful examples of percent identities include, but are not limited to, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95%, or any integer percentage from 50% to 100%. Indeed, any integer amino acid identity from 50% to 100% may be useful in describing the present invention, such as 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99%. Also, of interest is any full-length or partial complement of this isolated nucleotide fragment.
Thus, the invention encompasses more than the specific exemplary nucleotide sequences disclosed herein. For example, alterations in the gene sequence which reflect the degeneracy of the genetic code are contemplated. Also, it is well known in the art that alterations in a gene which result in the production of a chemically equivalent amino acid at a given site, but do not affect the functional properties of the encoded protein are common. Substitutions are defined for the discussion herein as exchanges within one of the following five groups:

    
    
        1. Small aliphatic, nonpolar or slightly polar residues: Ala, Ser, Thr (Pro, Gly);
        2. Polar, negatively charged residues and their amides: Asp, Asn, Glu, Gln;
        3. Polar, positively charged residues: His, Arg, Lys;
        4. Large aliphatic, nonpolar residues: Met, Leu, Ile, Val (Cys); and
        5. Large aromatic residues: Phe, Tyr, Trp.

Thus, a codon for the amino acid alanine, a hydrophobic amino acid, may be substituted by a codon encoding another less hydrophobic residue (such as glycine) or a more hydrophobic residue (such as valine, leucine, or isoleucine). Similarly, changes which result in substitution of one negatively charged residue for another (such as aspartic acid for glutamic acid) or one positively charged residue for another (such as lysine for arginine) can also be expected to produce a functionally equivalent product. In many cases, nucleotide changes which result in alteration of the N-terminal and C-terminal portions of the protein molecule would also not be expected to alter the activity of the protein.

    
    


Each of the proposed modifications is well within the routine skill in the art, as is determination of retention of biological activity of the encoded products. Moreover, the skilled artisan recognizes that substantially similar sequences encompassed by this invention are also defined by their ability to hybridize under stringent conditions, as defined above.
Preferred substantially similar nucleic acid fragments of the instant invention are those nucleic acid fragments whose nucleotide sequences are at least 70% identical to the nucleotide sequence of the nucleic acid fragments reported herein. More preferred nucleic acid fragments are at least 90% identical to the nucleotide sequence of the nucleic acid fragments reported herein. Most preferred are nucleic acid fragments that are at least 95% identical to the nucleotide sequence of the nucleic acid fragments reported herein.
A “substantial portion” of an amino acid or nucleotide sequence is that portion comprising enough of the amino acid sequence of a polypeptide or the nucleotide sequence of a gene to putatively identify that polypeptide or gene, either by manual evaluation of the sequence by one skilled in the art, or by computer-automated sequence comparison and identification using algorithms such as BLAST (Basic Local Alignment Search Tool; Altschul, S. F., et al., J. Mol. Biol., 215:403-410 (1993)). In general, a sequence of ten or more contiguous amino acids or thirty or more nucleotides is necessary in order to putatively identify a polypeptide or nucleic acid sequence as homologous to a known protein or gene. Moreover, with respect to nucleotide sequences, gene-specific oligonucleotide probes comprising 20-30 contiguous nucleotides may be used in sequence-dependent methods of gene identification (e.g., Southern hybridization) and isolation (e.g., in situ hybridization of bacterial colonies or bacteriophage plaques). In addition, short oligonucleotides of 12-15 bases may be used as amplification primers in PCR in order to obtain a particular nucleic acid fragment comprising the primers. Accordingly, a “substantial portion” of a nucleotide sequence comprises enough of the sequence to specifically identify and/or isolate a nucleic acid fragment comprising the sequence. The instant specification teaches the complete amino acid and nucleotide sequence encoding particular proteins. The skilled artisan, having the benefit of the sequences as reported herein, may now use all or a substantial portion of the disclosed sequences for purposes known to those skilled in this art.
The term “complementary” describes the relationship between two sequences of nucleotide bases that are capable of Watson-Crick base-pairing when aligned in an anti-parallel orientation. For example, with respect to DNA, adenosine is capable of base-pairing with thymine and cytosine is capable of base-pairing with guanine. Accordingly, the instant invention may make use of isolated nucleic acid molecules that are complementary to the complete sequences as reported in the accompanying Sequence Listing and the specification as well as those substantially similar nucleic acid sequences.
The term “isolated” refers to a polypeptide or nucleotide sequence that is removed from at least one component with which it is naturally associated.
“Promoter” refers to a DNA sequence capable of controlling the expression of a coding sequence or functional RNA. The promoter sequence consists of proximal and more distal upstream elements, the latter elements often referred to as enhancers. Accordingly, an “enhancer” is a DNA sequence that can stimulate promoter activity, and may be an innate element of the promoter or a heterologous element inserted to enhance the level or tissue-specificity of a promoter. Promoters may be derived in their entirety from a native gene, or be composed of different elements derived from different promoters found in nature, or even comprise synthetic DNA segments. It is understood by those skilled in the art that different promoters may direct the expression of a gene in different tissues or cell types, or at different stages of development, or in response to different environmental conditions. It is further recognized that since in most cases the exact boundaries of regulatory sequences have not been completely defined, DNA fragments of some variation may have identical promoter activity. Promoters that cause a gene to be expressed in most cell types at most times are commonly referred to as “constitutive promoters”.
“3′ non-coding sequences”, “transcription terminator” and “termination sequences” are used interchangeably herein and refer to DNA sequences located downstream of a coding sequence, including polyadenylation recognition sequences and other sequences encoding regulatory signals capable of affecting mRNA processing or gene expression. The polyadenylation signal is usually characterized by affecting the addition of polyadenylic acid tracts to the 3′ end of the mRNA precursor.
The term “operably linked” refers to the association of nucleic acid sequences on a single nucleic acid fragment so that the function of one is affected by the other. For example, a promoter is operably linked with a coding sequence when it is capable of affecting the expression of that coding sequence (i.e., the coding sequence is under the transcriptional control of the promoter). Coding sequences can be operably linked to regulatory sequences in a sense or antisense orientation. In another example, the complementary RNA regions of the invention can be operably linked, either directly or indirectly, 5′ to the target mRNA, or 3′ to the target mRNA, or within the target mRNA, or a first complementary region is 5′ and its complement is 3′ to the target mRNA.
Standard recombinant DNA and molecular cloning techniques used herein are well known in the art and are described more fully in Sambrook, J., Fritsch, E. F. and Maniatis, T., Molecular Cloning: A Laboratory Manual; Cold Spring Harbor Laboratory: Cold Spring Harbor, N.Y. (1989). Transformation methods are well known to those skilled in the art and are described infra.
“PCR” or “polymerase chain reaction” is a technique for the synthesis of large quantities of specific DNA segments and consists of a series of repetitive cycles (Perkin Elmer Cetus Instruments, Norwalk, Conn.). Typically, the double-stranded DNA is heat denatured, the two primers complementary to the 3′ boundaries of the target segment are annealed at low temperature and then extended at an intermediate temperature. One set of these three consecutive steps is referred to as a “cycle”.
A “plasmid” or “vector” is an extra chromosomal element often carrying genes that are not part of the central metabolism of the cell, and usually in the form of circular double-stranded DNA fragments. Such elements may be autonomously replicating sequences, genome integrating sequences, phage or nucleotide sequences, linear or circular, of a single- or double-stranded DNA or RNA, derived from any source, in which a number of nucleotide sequences have been joined or recombined into a unique construction which is capable of introducing an expression cassette(s) into a cell.
The term “genetically altered” refers to the process of changing hereditary material by genetic engineering, transformation and/or mutation.
The term “recombinant” refers to an artificial combination of two otherwise separated segments of sequence, e.g., by chemical synthesis or by the manipulation of isolated segments of nucleic acids by genetic engineering techniques. “Recombinant” also includes reference to a cell or vector, that has been modified by the introduction of a heterologous nucleic acid or a cell derived from a cell so modified, but does not encompass the alteration of the cell or vector by naturally occurring events (e.g., spontaneous mutation, natural transformation, natural transduction, natural transposition) such as those occurring without deliberate human intervention.
The terms “recombinant construct”, “expression construct”, “chimeric construct”, “construct”, and “recombinant DNA construct”, are used interchangeably herein. A recombinant construct comprises an artificial combination of nucleic acid fragments, e.g., regulatory and coding sequences that are not found together in nature. For example, a recombinant construct may comprise regulatory sequences and coding sequences that are derived from different sources, or regulatory sequences and coding sequences derived from the same source, but arranged in a manner different than that found in nature. Such a construct may be used by itself or may be used in conjunction with a vector. If a vector is used, then the choice of vector is dependent upon the method that will be used to transform host cells as is well known to those skilled in the art. For example, a plasmid vector can be used. The skilled artisan is well aware of the genetic elements that must be present on the vector in order to successfully transform, select and propagate host cells comprising any of the isolated nucleic acid fragments of the invention. The skilled artisan will also recognize that different independent transformation events may result in different levels and patterns of expression (Jones et al., EMBO J. 4:2411-2418 (1985); De Almeida et al., Mol. Gen. Genetics 218:78-86 (1989)), and thus that multiple events may need be screened in order to obtain lines displaying the desired expression level and pattern. Such screening may be accomplished by Southern analysis of DNA, Northern analysis of mRNA expression, immunoblotting analysis of protein expression, or phenotypic analysis, among others.
The term “expression”, as used herein, refers to the production of a functional end-product (e.g., an mRNA or a protein [either precursor or mature]).
The term “introduced” means providing a nucleic acid (e.g., expression construct) or protein into a cell. Introduced includes reference to the incorporation of a nucleic acid into a eukaryotic or prokaryotic cell where the nucleic acid may be incorporated into the genome of the cell, and includes reference to the transient provision of a nucleic acid or protein to the cell. Introduced includes reference to stable or transient transformation methods, as well as sexually crossing. Thus, “introduced” in the context of inserting a nucleic acid fragment (e.g., a recombinant construct/expression construct) into a cell, means “transfection” or “transformation” or “transduction” and includes reference to the incorporation of a nucleic acid fragment into a eukaryotic or prokaryotic cell where the nucleic acid fragment may be incorporated into the genome of the cell (e.g., chromosome, plasmid, plastid or mitochondrial DNA), converted into an autonomous replicon, or transiently expressed (e.g., transfected mRNA).
The term “homologous” refers to proteins or polypeptides of common evolutionary origin with similar catalytic function. The invention may include bacteria producing homologous proteins via recombinant technology.
Disclosed herein are recombinant E. coli that have the ability to produce glycerol and glycerol derived products and also have enhanced acetyl-CoA synthetase enzyme activity. The enhanced acetyl-CoA synthetase enzyme activity is due to overexpression of an acs gene encoding a polypeptide having acetyl-CoA synthetase activity. As a consequence of having enhanced acetyl-CoA synthetase enzyme activity, the recombinant E. coli disclosed herein produce less acetate during fermentation. The lower concentration of acetate in the fermentation broth simplifies the separation and purification of the desired products, i.e., glycerol and glycerol derived products such as 3-hydroxypropionic acid, methylglyoxal, 1,2-propanediol, or 1,3-propanediol.
The recombinant E. coli disclosed herein comprise a promoter operably linked to a nucleotide sequence encoding a polypeptide having acetyl-CoA synthetase enzyme activity. The promoter and nucleotide sequence encoding a polypeptide having acetyl-CoA synthetase enzyme activity are each independently either native or non-native. Specifically, the promoter can be non-native and the nucleotide sequence encoding a polypeptide having acetyl-CoA synthetase enzyme activity can be native; the promoter can be native and the nucleotide sequence encoding a polypeptide having acetyl-CoA synthetase enzyme activity can be non-native; both the promoter and the nucleotide sequence encoding a polypeptide having acetyl-CoA synthetase enzyme activity can be non-native; and both the promoter and the nucleotide sequence encoding a polypeptide having acetyl-CoA synthetase enzyme activity can be native if the recombinant E. coli comprises at least two copies of the promoter and the nucleotide sequence.
The acs gene is usually expressed at very low levels in E. coli K strains (Phue et al., J. Biotechnol. 109:21-30, 2004). One approach to enhancing the acetyl-Co synthetase activity in E. coli in order to reduce acetate accumulation during fermentation is to overexpress the native acs gene by replacing the native promoter with a non-native promoter. Therefore, in one embodiment the recombinant E. coli disclosed herein comprises a non-native promoter and a native nucleotide sequence encoding a polypeptide having acetyl-CoA synthetase enzyme activity.
In one embodiment, the native nucleotide sequence encoding a polypeptide having acetyl-CoA synthetase enzyme activity is the coding sequence of the acs gene from E. coli as set forth in SEQ ID NO:27, which encodes the polypeptide having the amino acid sequence set forth in SEQ ID NO:28. In one embodiment, the polypeptide having acetyl-CoA synthetase enzyme activity has at least 95% amino acid identity, based on the Clustal V method of alignment, when compared to the amino acid sequence set forth in SEQ ID NO:28.
Suitable non-native promoters are well known in the art and include, but are not limited to, CYC1, HIS3, GAL1, GAL10, ADH1, PGK, PHO5, GAPDH, ADC1, TRP1, URA3, LEU2, ENO, and lac, ara, tet, trp, IPL, IPR, T5, T7, tac, Pcat, and trc, amy, apr, and npr promoters. In one embodiment, the non-native promoter is a strong phage T5 promoter (Deuschle et al., EMBO 5:2987-2994, 1986). In one embodiment, the phage T5 promoter has a nucleotide sequence as set forth in SEQ ID NO:33. This sequence containing a T5 promoter, lacO site and ribosomal binding site can be synthesized from the pQE30 vector available from Qiagen (Valencia, Calif.). In another embodiment, the T5 promoter has a nucleotide sequence having at least 95% sequence identity, based on the BLASTN method of alignment, when compared to the nucleotide sequence set forth in SEQ ID NO:33
In another embodiment, the non-native promoter is a Pcat promoter found driving the expression of the chloramphenicol acetyl transferase encoding gene on plasmid R6/5 (Stuber et al., Proc. Natl. Acad. Sci. USA, 78:167-171, 1981). In one embodiment, the Pcat promoter has a nucleotide sequence as set forth in SEQ ID NO:34. In another embodiment, the Pcat promoter has a nucleotide sequence having at least 95% sequence identity, based on the BLASTN method of alignment, when compared to the nucleotide sequence set forth in SEQ ID NO:34.
In another embodiment, the recombinant E. coli disclosed herein comprises a non-native promoter and a non-native nucleotide sequence encoding a polypeptide having acetyl-CoA synthetase enzyme activity. Any of the non-native promoters listed above may be used. In one embodiment, the non-native promoter is a T5 promoter, as described above. In another embodiment, the promoter is a Pcat promoter, as described above.
The acs genes from various sources provide suitable non-native nucleotide sequences encoding a polypeptide having acetyl-CoA synthetase enzyme activity for use as disclosed herein. Examples of acs genes include, but are not limited to, acs genes from Yersinia pestis, Salmonella typhimurium, Pseudomonas fluorescens, and Saccharomyces cerevisiae. 
In one embodiment, the nucleotide sequence encoding a polypeptide having acetyl-CoA synthetase enzyme activity is the coding sequence of the acs1 gene from Saccharomyces cerevisiae as set forth in SEQ ID NO:29, which encodes the polypeptide having the amino acid sequence set forth in SEQ ID NO:30. In one embodiment, the polypeptide having acetyl-CoA synthetase enzyme activity has at least 95% amino acid identity, based on the Clustal V method of alignment, when compared to the amino acid sequence set forth in SEQ ID NO:30.
In another embodiment, the nucleotide sequence encoding a polypeptide having acetyl-CoA synthetase enzyme activity is the coding sequence of the acs2 gene from Saccharomyces cerevisiae as set forth in SEQ ID NO:31, which encodes the polypeptide having the amino acid sequence set forth in SEQ ID NO:32. In one embodiment, the polypeptide having acetyl-CoA synthetase enzyme activity has at least 95% amino acid identity, based on the Clustal V method of alignment, when compared to the amino acid sequence set forth in SEQ ID NO:32.
In another embodiment, the recombinant E. coli disclosed herein comprises a native promoter and a non-native nucleotide sequence encoding a polypeptide having acetyl-CoA synthetase enzyme activity. Any of the non-native nucleotide sequences encoding a polypeptide having acetyl-CoA synthetase enzyme activity discussed above may be used with the native promoter.
In another embodiment, the recombinant E. coli disclosed herein comprises at least two copies of the native promoter and the native nucleotide sequence encoding a polypeptide having acetyl-CoA synthetase enzyme activity. At least two copies are necessary in order for the recombinant E. coli to have enhanced acetyl-CoA synthetase enzyme activity relative to the parent E. coli strain, which contains one copy of the native acs gene.
The coding sequence of acs genes encoding polypeptides having acetyl-CoA synthetase enzyme activity may be used to isolate nucleotide sequences encoding homologous polypeptides from the same or other microbial species. For example, homologs of the genes may be identified using sequence analysis software, such as BLASTN, to search publicly available nucleic acid sequence databases. Additionally, the isolation of homologous genes using sequence-dependent protocols is well known in the art. Examples of sequence-dependent protocols include, but are not limited to, methods of nucleic acid hybridization, and methods of DNA and RNA amplification as exemplified by various uses of nucleic acid amplification technologies (e.g. polymerase chain reaction (PCR), Mullis et al., U.S. Pat. No. 4,683,202; ligase chain reaction (LCR), Tabor, S. et al., Proc. Acad. Sci. USA 82, 1074, 1985); or strand displacement amplification (SDA), Walker, et al., Proc. Natl. Acad. Sci. U.S.A., 89: 392, (1992)). For example, the nucleotide sequences encoding the polypeptides having acetyl-CoA synthetase enzyme activity described above may be employed as a hybridization probe for the identification of homologs.
One of ordinary skill in the art will appreciate that genes encoding these polypeptides isolated from other sources may also be used in the recombinant E. coli disclosed herein. Additionally, variations in the nucleotide sequences encoding the polypeptides may be made without affecting the amino acid sequence of the encoded polypeptide due to codon degeneracy, and that amino acid substitutions, deletions or additions that produce a substantially similar protein may be included in the encoded protein.
The nucleotide sequences encoding polypeptides having acetyl-CoA synthetase enzyme activity may be isolated using PCR (see, e.g., U.S. Pat. No. 4,683,202) and primers designed to bound the desired sequence, if this sequence is known. Other methods of gene isolation are well known to one skilled in the art such as by using degenerate primers or heterologous probe hybridization. The nucleotide sequences can also be chemically synthesized or purchased from vendors such as DNA2.0 Inc. (Menlo Park, Calif.).
Overexpression of an acs gene encoding a polypeptide having acetyl CoA synthetase enzyme activity may be effected using one of many methods known to one skilled in the art. For example, the native or non-native nucleotide sequence encoding the polypeptide described above may be introduced into the E. coli bacterium on at least one multicopy plasmid, or by integrating one or more copies of the nucleotide sequence into the host genome. The introduced coding region(s) that is (are) either on a plasmid(s) or in the genome may be expressed from at least one highly active promoter, as described above. An integrated coding region may either be introduced as a part of a chimeric gene having its own promoter, or it may be integrated adjacent to a highly active promoter that is endogenous to the genome or in a highly expressed operon.
In one embodiment, the recombinant E. coli disclosed herein are capable of producing glycerol. Biological processes for the preparation of glycerol using carbohydrates or sugars are known in yeasts and in some bacteria, other fungi, and algae. Both bacteria and yeasts produce glycerol by converting glucose or other carbohydrates through the fructose-1,6-bisphosphate pathway in glycolysis. In the method of producing glycerol disclosed herein, host E. coli may be used that naturally produce glycerol. In addition, E. coli may be engineered for production of glycerol and glycerol derivatives. The capacity for glycerol production from a variety of substrates may be provided through the expression of the enzyme activities glycerol-3-phosphate dehydrogenase (G3PDH) and/or glycerol-3-phosphatase as described in U.S. Pat. No. 7,005,291. Genes encoding these proteins that may be used for expressing the enzyme activities in a host bacterium are described in U.S. Pat. No. 7,005,291. Suitable examples of genes encoding polypeptides having glycerol-3-phosphate dehydrogenase activity include, but are not limited to, GPD1 from Saccharomyces cerevisiae (coding sequence set forth in SEQ ID NO:1, encoded protein sequence set forth in SEQ ID NO:2) and GPD2 from Saccharomyces cerevisiae (coding sequence set forth in SEQ ID NO:3, encoded protein sequence set forth in SEQ ID NO:4). Suitable examples of genes encoding polypeptides having glycerol-3-phosphatase activity include, but are not limited to, GPP1 from Saccharomyces cerevisiae (coding sequence set forth in SEQ ID NO:5, encoded protein sequence set forth in SEQ ID NO:6) and GPP2 from Saccharomyces cerevisiae (coding sequence set forth in SEQ ID NO:7, encoded protein sequence set forth in SEQ ID NO:8).
Increased production of glycerol may be attained through reducing expression of target endogenous genes. Down-regulation of endogenous genes encoding glycerol kinase and glycerol dehydrogenase activities further enhance glycerol production as described in U.S. Pat. No. 7,005,291. Increased channeling of carbon to glycerol may be accomplished by reducing the expression of the endogenous gene encoding glyceraldehyde 3-phosphate dehydrogenase, as described in U.S. Pat. No. 7,371,558. Down-regulation may be accomplished by using any method known in the art, for example, the methods described above for down-regulation of genes of the PTS system.
Glycerol provides a substrate for microbial production of useful products. Examples of such products, i.e., glycerol derivatives include, but are not limited to, 3-hydroxypropionic acid, methylglyoxal, 1,2-propanediol, and 1,3-propanediol.
In another embodiment, the recombinant E. coli disclosed herein are capable of producing 1,3-propanediol. The glycerol derivative 1,3-propanediol is a monomer having potential utility in the production of polyester fibers and the manufacture of polyurethanes and cyclic compounds. 1,3-Propanediol can be produced by a single microorganism by bioconversion of a carbon substrate other than glycerol or dihydroxyacetone, as described in U.S. Pat. No. 5,686,276. In this bioconversion, glycerol is produced from the carbon substrate, as described above. Glycerol is converted to the intermediate 3-hydroxypropionaldehyde by a dehydratase enzyme, which can be encoded by the host bacterium or can be introduced into the host by recombination. The dehydratase can be glycerol dehydratase (EC 4.2.1.30), diol dehydratase (EC 4.2.1.28) or any other enzyme able to catalyze this conversion. A suitable example of genes encoding the “α” (alpha), “β” (beta), and “γ” (gamma) subunits of a glycerol dehydratase include, but are not limited to dhaB1 (coding sequence set forth in SEQ ID NO:9), dhaB2 (coding sequence set forth in SEQ ID NO:11), and dhaB3 (coding sequence set forth in SEQ ID NO:13), respectively, from Klebsiella pneumoniae. The further conversion of 3-hydroxypropionaldehyde to 1,3-propandeiol can be catalyzed by 1,3-propanediol dehydrogenase (EC 1.1.1.202) or other alcohol dehydrogenases. A suitable example of a gene encoding a 1,3-propanediol dehydrogenase is dhaT from Klebsiella pneumoniae (coding sequence set forth in SEQ ID NO:23, encoded protein sequence set forth in SEQ ID NO:24).
E. coli can be recombinantly engineered to provide more efficient production of glycerol and the glycerol derivative 1,3-propanediol. For example, U.S. Pat. No. 7,005,291 discloses transformed microorganisms and a method for production of glycerol and 1,3-propanediol with advantages derived from expressing exogenous activities of one or both of glycerol-3-phosphate dehydrogenase and glycerol-3-phosphate phosphatase while disrupting one or both of endogenous activities glycerol kinase and glycerol dehydrogenase.
U.S. Pat. No. 6,013,494 describes a process for the production of 1,3-propanediol using a single microorganism comprising exogenous glycerol-3-phosphate dehydrogenase, glycerol-3-phosphate phosphatase, dehydratase, and 1,3-propanediol oxidoreductase (e.g., dhaT). U.S. Pat. No. 6,136,576 discloses a method for the production of 1,3-propanediol comprising a recombinant microorganism further comprising a dehydratase and protein X (later identified as being a dehydratase reactivation factor peptide).
U.S. Pat. No. 6,514,733 describes an improvement to the process where a significant increase in titer (grams product per liter) is obtained by virtue of a non-specific catalytic activity (distinguished from 1,3-propanediol oxidoreductase encoded by dhaT) to convert 3-hydroxypropionaldehyde to 1,3-propanediol. Additionally, U.S. Pat. No. 7,132,527 discloses vectors and plasmids useful for the production of 1,3-propanediol.
Increased production of 1,3-propanediol may be achieved by further modifications to a host bacterium, including down-regulating expression of some target genes and up-regulating, expression of other target genes, as described in U.S. Pat. No. 7,371,558. For utilization of glucose as a carbon source in a PTS minus host, expression of glucokinase activity may be increased.
Additional genes whose increased or up-regulated expression increases 1,3-propanediol production include genes encoding:

    
    
        phosphoenolpyruvate carboxylase typically characterized as EC 4.1.1.31
        cob(I)alamin adenosyltransferase, typically characterized as EC 2.5.1.17
        non-specific catalytic activity that is sufficient to catalyze the interconversion of 3-HPA and 1,3-propanediol, and specifically excludes 1,3-propanediol oxidoreductase(s), typically these enzymes are alcohol dehydrogenases
    
    


Genes whose reduced or down-regulated expression increases 1,3-propanediol production include genes encoding:

    
    
        aerobic respiration control protein
        methylglyoxal synthase
        acetate kinase
        phosphotransacetylase
        aldehyde dehydrogenase A
        aldehyde dehydrogenase B
        triosephosphate isomerase
        phosphogluconate dehydratase
    
    


In another embodiment, the recombinant E. coli disclosed herein are capable of producing 3-hydroxypropionic acid. 3-Hydroxypropionic acid has utility for specialty synthesis and can be converted to commercially important intermediates by known art in the chemical industry, e.g., acrylic acid by dehydration, malonic acid by oxidation, esters by esterification reactions with alcohols, and 1,3-propanediol by reduction. 3-Hydroxypropionic acid may be produced biologically from a fermentable carbon source by a single microorganism, as described in copending and commonly owned U.S. patent application Ser. No. 12/815,461. In one representative biosynthetic pathway, a carbon substrate is converted to 3-hydroxypropionaldehyde, as described above for the production of 1,3-propanediol. The 3-hydroxypropionaldehyde is converted to 3-hydroxypropionic acid by an aldehyde dehydrogenase. Suitable examples of aldehyde dehydrogenases include, but are not limited to, AldB (SEQ ID NO:16), encoded by the E. coli gene aldB (coding sequence set forth in SEQ ID NO:15); AldA (SEQ ID NO:18), encoded by the E. coli gene aldA (coding sequence set forth in SEQ ID NO:17); and AldH (SEQ ID NO:20), encoded by the E. coli gene aldH (coding sequence asset forth in SEQ ID NO:19).
Many of the modifications described above to improve 1,3-propanediol production by a recombinant E. coli can also be made to improve 3-hydroxypropionic acid production. For example, the elimination of glycerol kinase prevents glycerol, formed from G3P by the action of G3P phosphatase, from being re-converted to G3P at the expense of ATP. Also, the elimination of glycerol dehydrogenase (for example, gldA) prevents glycerol, formed from DHAP by the action of NAD-dependent glycerol-3-phosphate dehydrogenase, from being converted to dihydroxyacetone. Mutations can be directed toward a structural gene so as to impair or improve the activity of an enzymatic activity or can be directed toward a regulatory gene, including promoter regions and ribosome binding sites, so as to modulate the expression level of an enzymatic activity.
Up-regulation or down-regulation may be achieved by a variety of methods which are known to those skilled in the art. It is well understood that up-regulation or down-regulation of a gene refers to an alteration in the level of activity present in a cell that is derived from the protein encoded by that gene relative to a control level of activity, for example, by the activity of the protein encoded by the corresponding (or non-altered) wild-type gene.
Specific genes involved in an enzyme pathway may be up-regulated to increase the activity of their encoded function(s). For example, additional copies of selected genes may be introduced into the host cell on multicopy plasmids such as pBR322. Such genes may also be integrated into the chromosome with appropriate regulatory sequences that result in increased activity of their encoded functions. The target genes may be modified so as to be under the control of non-native promoters or altered native promoters. Endogenous promoters can be altered in vivo by mutation, deletion, and/or substitution.
Alternatively, it may be useful to reduce or eliminate the expression of certain genes relative to a given activity level. Methods of down-regulating (disrupting) genes are known to those of skill in the art.
Down-regulation can occur by deletion, insertion, or alteration of coding regions and/or regulatory (promoter) regions. Specific down regulations may be obtained by random mutation followed by screening or selection, or, where the gene sequence is known, by direct intervention by molecular biology methods known to those skilled in the art. A particularly useful, but not exclusive, method to effect down-regulation is to alter promoter strength.
Furthermore, down-regulation of gene expression may be used to either prevent expression of the protein of interest or result in the expression of a protein that is non-functional. This may be accomplished for example, by 1) deleting coding regions and/or regulatory (promoter) regions, 2) inserting exogenous nucleic acid sequences into coding regions and/regulatory (promoter) regions, and 3) altering coding regions and/or regulatory (promoter) regions (for example, by making DNA base pair changes). Specific disruptions may be obtained by random mutation followed by screening or selection, or, in cases where the gene sequences in known, specific disruptions may be obtained by direct intervention using molecular biology methods know to those skilled in the art. A particularly useful method is the deletion of significant amounts of coding regions and/or regulatory (promoter) regions.
Methods of altering recombinant protein expression are known to those skilled in the art, and are discussed in part in Baneyx, Curr. Opin. Biotechnol. (1999) 10:411; Ross, et al., J. Bacteriol. (1998) 180:5375; deHaseth, et al., J. Bacteriol. (1998) 180:3019; Smolke and Keasling, Biotechnol. Bioeng. (2002) 80:762; Swartz, Curr. Opin. Biotech. (2001) 12:195; and Ma, et al., J. Bacteriol. (2002) 184:5733.
Recombinant E. coli containing the necessary changes in gene expression for overexpression of acs and production of microbial products including glycerol and glycerol derivatives, as described above, may be constructed using techniques well known in the art, some of which are exemplified in the Examples herein.
The construction of the recombinant E. coli disclosed herein may be accomplished using a variety of vectors and transformation and expression cassettes suitable for the cloning, transformation and expression of coding regions of acs genes and the genes necessary to produce glycerol and glycerol-derived products, as described above. Suitable vectors are those which are compatible with the bacterium employed. Suitable vectors can be derived, for example, from a bacterium, a virus (such as bacteriophage T7 or a M-13 derived phage), a cosmid, a yeast or a plant. Protocols for obtaining and using such vectors are known to those skilled in the art (Sambrook et al., supra).
Initiation control regions, or promoters, which are useful to drive expression of coding regions for the instant invention in the desired host bacterium are numerous and familiar to those skilled in the art. Virtually any promoter capable of driving expression is suitable for use herein. For example, any of the promoters listed above may be used.
Termination control regions may also be derived from various genes native to the preferred hosts. Optionally, a termination site may be unnecessary; however, it is most preferred if included.
For effective expression of a polypeptide having acetyl-CoA synthetase enzyme activity, the nucleotide sequence encoding the polypeptide is linked operably through initiation codons to selected expression control regions such that expression results in the formation of the appropriate messenger RNA.
Particularly useful in the present invention are the vectors pSYCO101, pSYCO103, pSYCO106, and pSYCO109, described in U.S. Pat. No. 7,371,558, and pSYCO400/AGRO, described in U.S. Pat. No. 7,524,660. The essential elements of these vectors are derived from the dha regulon isolated from Klebsiella pneumoniae and from Saccharomyces cerevisiae. Each vector contains the open reading frames dhaB1, dhaB2, dhaB3, dhaX (coding sequence set forth in SEQ ID NO:25), orfX, DAR1, and GPP2 arranged in three separate operons. The nucleotide sequences of pSYCO101, pSYCO103, pSYCO106, pSYCO109, and pSYCO400/AGRO are set forth in SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:38, and SEQ ID NO:39, respectively. The differences between the vectors are illustrated in the chart below [the prefix “p-” indicates a promoter; the open reading frames contained within each “( )” represent the composition of an operon]:
pSYCO101 (SEQ ID NO:35):


    
    
        p-trc (Dar1_GPP2) in opposite orientation compared to the other 2 pathway operons,
        p-1.6 long GI (dhaB1_dhaB2_dhaB3_dhaX), and
        p-1.6 long GI (orfY_orfX_orfW).

pSYCO103 (SEQ ID NO:36):

        p-trc (Dar1_GPP2) same orientation compared to the other 2 pathway operons,
        p-1.5 long GI (dhaB1_dhaB2_dhaB3_dhaX), and
        p-1.5 long GI (orfY_orfX_orfW).

pSYCO106 (SEQ ID NO:37):

        p-trc (Dar1_GPP2) same orientation compared to the other 2 pathway operons,
        p-1.6 long GI (dhaB1_dhaB2_dhaB3_dhaX), and
        p-1.6 long GI (orfY_orfX_orfW).

pSYCO109 (SEQ ID NO:38):

        p-trc (Dar1_GPP2) same orientation compared to the other 2 pathway operons,
        p-1.6 long GI (dhaB1_dhaB2_dhaB3_dhaX), and
        p-1.6 long GI (orfY_orfX).

pSYCO400/AGRO (SEQ ID NO:39):

        p-trc (Dar1_GPP2) same orientation compared to the other 2 pathway operons,
        p-1.6 long GI (dhaB1_dhaB2_dhaB3_dhaX), and
        p-1.6 long GI (orfY_orfX).
        p-1.20 short/long GI (scrK) opposite orientation compared to the pathway operons.
    
    


Once suitable expression cassettes are constructed, they are used to transform appropriate host bacterium. Introduction of the cassette containing the coding regions into the host bacterium may be accomplished by known procedures such as by transformation (e.g., using calcium-permeabilized cells, or electroporation) or by transfection using a recombinant phage virus (Sambrook et al., supra). Expression cassettes may be maintained on a stable plasmid in a host cell. In addition, expression cassettes may be integrated into the genome of the host bacterium through homologous or random recombination using vectors and methods well known to those skilled in the art. Site-specific recombination systems may also be used for genomic integration of expression cassettes.
In addition to the cells exemplified, cells having single or multiple mutations specifically designed to enhance the production of microbial products including glycerol and/or its derivatives may also be used. Cells that normally divert a carbon feed stock into non-productive pathways, or that exhibit significant catabolite repression may be mutated to avoid these phenotypic deficiencies.
Methods of creating mutants are common and well known in the art. A summary of some methods is presented in U.S. Pat. No. 7,371,558. Specific methods for creating mutants using radiation or chemical agents are well documented in the art. See, for example, Thomas D. Brock in Biotechnology: A Textbook of Industrial Microbiology, Second Edition (1989) Sinauer Associates, Inc., Sunderland, Mass., or Deshpande, Mukund V., Appl. Biochem. Biotechnol. 36, 227 (1992).
After mutagenesis has occurred, mutants having the desired phenotype may be selected by a variety of methods. Random screening is most common where the mutagenized cells are selected for the ability to produce the desired product or intermediate. Alternatively, selective isolation of mutants can be performed by growing a mutagenized population on selective media where only resistant colonies can develop. Methods of mutant selection are highly developed and well known in the art of industrial microbiology. See, for example, Brock, Supra; DeMancilha et al., Food Chem. 14, 313 (1984).
Fermentation media in the present invention comprise a suitable carbon substrate. Suitable carbon substrates include, but are not limited to, monosaccharides such as glucose and fructose, oligosaccharides such as lactose or sucrose, and polysaccharides. In one embodiment, the carbon substrate is glucose.
In addition to the carbon substrate, a suitable fermentation medium contains, for example, suitable minerals, salts, cofactors, buffers and other components, known to those skilled in the art, suitable for the growth of the cultures and promotion of the enzymatic pathway necessary for production of glycerol and its derivatives, for example 1,3-propanediol. Particular attention is given to Co(II) salts and/or vitamin B12 or precursors thereof in production of 1,3-propanediol.
Adenosyl-cobalamin (coenzyme B12) is an important cofactor for dehydratase activity. Synthesis of coenzyme B12 is found in prokaryotes, some of which are able to synthesize the compound de novo, for example, Escherichia blattae, Klebsiella species, Citrobacter species, and Clostridium species, while others can perform partial reactions. E. coli, for example, cannot fabricate the corrin ring structure, but is able to catalyze the conversion of cobinamide to corrinoid and can introduce the 5′-deoxyadenosyl group. Thus, it is known in the art that a coenzyme B12 precursor, such as vitamin B12, needs be provided in E. coli fermentations. Vitamin B12 may be added continuously to E. coli fermentations at a constant rate or staged as to coincide with the generation of cell mass, or may be added in single or multiple bolus additions.
Typically bacterial cells are grown at 25 to 40° C. in an appropriate medium. Examples of suitable growth media for use herein are common commercially prepared media such as Luria Bertani (LB) broth, Sabouraud Dextrose (SD) broth or Yeast medium (YM) broth. Other defined or synthetic growth media may also be used, and the appropriate medium for growth of the particular bacterium will be known by someone skilled in the art of microbiology or fermentation science. The use of agents known to modulate catabolite repression directly or indirectly, e.g., cyclic adenosine 2′:3′-monophosphate, may also be incorporated into the reaction media. Similarly, the use of agents known to modulate enzymatic activities (e.g., methyl viologen) that lead to enhancement of 1,3-propanediol production may be used in conjunction with or as an alternative to genetic manipulations with 1,3-propanediol production strains.
Suitable pH ranges for the fermentation are between pH 5.0 to pH 9.0, where pH 6.0 to pH 8.0 is typical as the initial condition.
Reactions may be performed under aerobic, anoxic, or anaerobic conditions depending on the requirements of the recombinant bacterium. Fed-batch fermentations may be performed with carbon feed, for example, carbon substrate, limited or excess.
Batch fermentation is a commonly used method. Classical batch fermentation is a closed system where the composition of the medium is set at the beginning of the fermentation and is not subject to artificial alterations during the fermentation. Thus, at the beginning of the fermentation, the medium is inoculated with the desired bacterium and fermentation is permitted to occur adding nothing to the system. Typically, however, “batch” fermentation is batch with respect to the addition of carbon source, and attempts are often made at controlling factors such as pH and oxygen concentration. In batch systems, the metabolite and biomass compositions of the system change constantly up to the time the fermentation is stopped. Within batch cultures, cells moderate through a static lag phase to a high growth log phase and finally to a stationary phase where growth rate is diminished or halted. If untreated, cells in the stationary phase will eventually die. Cells in log phase generally are responsible for the bulk of production of end product or intermediate.
A variation on the standard batch system is the Fed-Batch system. Fed-Batch fermentation processes are also suitable for use herein and comprise a typical batch system with the exception that the substrate is added in increments as the fermentation progresses. Fed-Batch systems are useful when catabolite repression is apt to inhibit the metabolism of the cells and where it is desirable to have limited amounts of substrate in the media. Measurement of the actual substrate concentration in Fed-Batch systems is difficult and is therefore estimated on the basis of the changes of measurable factors such as pH, dissolved oxygen and the partial pressure of waste gases such as CO2. Batch and Fed-Batch fermentations are common and well known in the art and examples may be found in Brock, supra.
Continuous fermentation is an open system where a defined fermentation medium is added continuously to a bioreactor and an equal amount of conditioned medium is removed simultaneously for processing. Continuous fermentation generally maintains the cultures at a constant high density where cells are primarily in log phase growth.
Continuous fermentation allows for the modulation of one factor or any number of factors that affect cell growth or end product concentration. For example, one method will maintain a limiting nutrient such as the carbon source or nitrogen level at a fixed rate and allow all other parameters to moderate. In other systems, a number of factors affecting growth can be altered continuously while the cell concentration, measured by the turbidity of the medium, is kept constant. Continuous systems strive to maintain steady state growth conditions, and thus the cell loss due to medium being drawn off must be balanced against the cell growth rate in the fermentation. Methods of modulating nutrients and growth factors for continuous fermentation processes as well as techniques for maximizing the rate of product formation are well known in the art of industrial microbiology and a variety of methods are detailed by Brock, supra.
It is contemplated that the present invention may be practiced using batch, fed-batch or continuous processes and that any known mode of fermentation would be suitable. Additionally, it is contemplated that cells may be immobilized on a substrate as whole cell catalysts and subjected to fermentation conditions for production of glycerol and glycerol derivatives, such as 1,3-propanediol.
In one embodiment, a process for making glycerol, 1,3-propanediol, and/or 3-hydroxypropionic acid using the recombinant E. coli described above is provided. The process comprises the steps of culturing a recombinant E. coli, as described above, in a suitable growth medium, and optionally recovering the glycerol, 1,3-propanediol, and/or 3-hydroxypropionic acid produced. The product may be recovered using methods known in the art. For example, solids may be removed from the fermentation medium by centrifugation, filtration, decantation, or the like. Then, the product may be isolated from the fermentation medium, which has been treated to remove solids as described above, using methods such as distillation, liquid-liquid extraction, or membrane-based separation. For example, 1,3-propanediol can be purified from the fermentation broth using the methods disclosed by Adkesson et al. (U.S. Patent Application Publication No. 2005/0069997).
EXAMPLES
The present invention is further defined in the following Examples. It should be understood that these Examples, while indicating preferred embodiments of the invention, are given by way of illustration only. From the above discussion and these Examples, one skilled in the art can ascertain the essential characteristics of this invention, and without departing from the spirit and scope thereof, can make various changes and modifications of the invention to adapt it to various uses and conditions.
General Methods
Standard recombinant DNA and molecular cloning techniques described in the Examples are well known in the art and are described by Sambrook, J., Fritsch, E. F. and Maniatis, T. Molecular Cloning: A Laboratory Manual; Cold Spring Harbor Laboratory Press: Cold Spring Harbor, (1989) (Maniatis) and by T. J. Silhavy, M. L. Bennan, and L. W. Enquist, Experiments with Gene Fusions, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1984) and by Ausubel, F. M. et al., Current Protocols in Molecular Biology, pub. by Greene Publishing Assoc. and Wiley-Interscience (1987).
Materials and Methods suitable for the maintenance and growth of bacterial cultures are well known in the art. Techniques suitable for use in the following Examples may be found as set out in Manual of Methods for General Bacteriology (Phillipp Gerhardt, R. G. E. Murray, Ralph N. Costilow, Eugene W. Nester, Willis A. Wood, Noel R. Krieg and G. Briggs Phillips, eds), American Society for Microbiology, Washington, D.C. (1994)) or by Thomas D. Brock in Biotechnology: A Textbook of Industrial Microbiology, Second Edition, Sinauer Associates, Inc., Sunderland, Mass. (1989). All reagents, restriction enzymes and materials described for the growth and maintenance of bacterial cells may be obtained from Aldrich Chemicals (Milwaukee, Wis.), BD Diagnostic Systems (Sparks, Md.), Life Technologies (Rockville, Md.), New England Biolabs (Beverly, Mass.), or Sigma Chemical Company (St. Louis, Mo.).
The meaning of abbreviations is as follows: “sec” means second(s), “min” means minute(s), “h” means hour(s), “nm” means nanometer(s), “μL” means microliter(s), “mL” means milliliter(s), “L” means liter(s), “mM” means millimolar, “M” means molar, “g” means gram(s), “μg” means microgram(s), “ng” means nanogram(s), “bp” means base pair(s), “kbp” means kilobase pair(s), “rpm” means revolutions per minute, “ATCC” means American Type Culture Collection, Manassas, Va., “OD” means optical density, “OD550” means the optical density measured at 550 nm, “g” means the gravitation constant, “HPLC” means high performance liquid chromatography.







TABLE 1







Primers used in the Examples











SEQ ID


Primer
Sequence
NO:





acsPdown-
CGATGTTGGCAGGAATGGTGTGTTTGTGAA
40


catR
TTTGGCTCATTTTAGCTTCCTTAGCTCCTG



 


acsPdown-
CGATGTTGGCAGGAATGGTGTGTTTGTGAA
41


T5R
TTTGGCTCATATGAGTTAATTTCTCCTCTT



 


acsPup-
GTTGTCTTTAATCAATTGTAAGTGCATGTA
42


loxKan5′
AAATACCACTGTGCGTAGTCGTTGGCAAGC



 


Pcat up
ATAAGAATGCGGCCGCTGACATTAACCTAT
43



AAAAATAGGCGTATC



 


T5 up
ATAAGAATGCGGCCGCCTATAAAAATAGGC
44



GTATCACGAGGC-CCTTTC



 


acs down
CCAGCTTTGTTTAAACTTACGATGGCATCG
45



CGATAGCCTGCTTC



 


Pcat down
TGTACGGCAGAGGGCGACATTTTAGCTTCC
46


acs1
TTAGCTCCTG



 


Pcat down
TTATGTTCCTTGATTGTCATTTTAGCTTCC
47


acs2
TTAGCTCCTG



 


acs1 up
CAGGAGCTAAGGAAGCTAAAATGTCGCCCT
48



CTGCCGTACA



 


acs1 down
CCAGCTTTGTTTAAACTTACAACTTGACCG
49



AATCAATTAGAT GTC



 


acs2 up
CAGGAGCTAAGGAAGCTAAAATGACAATCA
50



AGGAACATAA



 


acs2 down
CCAGCTTTGTTTAAACTTATTTCTTTTTTT
51



GAGAGA










Example 1
Recombinant E. Coli Strains in which the Native acs Promoter is Replaced with Stronger Constitutive Promoters
This Example describes increasing the expression of the acs gene in E. coli by replacing the native acs promoter with stronger constitutive promoters.
The constitutive phage T5 (PT5) promoter (SEQ ID NO:33) (Yuan, L. Z., et al, 2006, Metab. Eng. 8, 79-90) and the Pcat promoter (SEQ ID NO:34) upstream of the chloramphenicol resistance gene from pBHR1 (MoBiTec GmbH, Goettingen, Germany), were synthesized by DNA 2.0 (Menlo Park, Calif.). The 157 bp PT5 promoter and the 253 bp Pcat promoter were cloned into the FseI and PstI sites of pMODlinker-Kan. The pMODlinker-Kan plasmid was constructed from pMODlinker-Spec, which is described by Viitanen et al. (U.S. Patent Application Publication No. 2009/0246876, Example 6). A DNA fragment, containing a Kanr gene and its promoter, that confers resistance to kanamycin (Kanr) was inserted between the NotI and PacI sites of the pMOD-Linker-Spec plasmid, replacing the DNA fragment that confers resistance to spectinomycin (Specr). The source of the Kanr gene and its promoter was plasmid pZB188/kan-XylA, which is described by Viitanen et al. (U.S. Pat. No. 7,741,119, Example 4). The resulting plasmids pDCQ702 (SEQ ID NO:52) and pDCQ703 (SEQ ID NO:53) contained the PT5 or Pcat promoter, respectively, downstream of the KanR gene flanked by loxP sites. Plasmids pDCQ702 or pDCQ703 were used as the template to amplify the 1255 bp loxP-KanR-loxP-PT5 cassette (SEQ ID NO:54) or the 1351 bp loxP-KanR-loxP-Pcat cassette (SEQ ID NO:55) by PCR. For the reaction with pDCQ702 as template, the primers were acsPup-loxKan5′ and acsPdown-T5R (see Table 1). For the reaction with pDCQ703 as template, the primers were acsPup-loxKan5′ primer and acsPdown-catR (see Table 1).
PCR was done using the following cycling conditions: 95° C. for 5 min, 35 cycles of 95° C. for 30 sec, 58° C. for 30 sec, 72° C. for 2 min and 72° C. for 10 min. High fidelity PfuUltra® II Fusion HS DNA polymerase (Stratagene; La Jolla, Calif.) was used in the PCR reaction. The PCR products were purified using QIAquick PCR Purification kit (Qiagen; Valencia, Calif.). The purified loxP-KanR-loxP-PT5 cassette or the loxP-KanR-loxP-Pcat cassette was integrated upstream of the acs locus in an E. coli K12 strain by Lambda Red recombination (Datsenko, K. A., and Wanner, B. L. 2000, Proc. Natl. Acad. Sci. USA 97, 6640-6645). This E. coli strain was a derivative of MG1655 (ATCC No. 47076) comprising disruptions in the endogenous araBAD operon and the poxB gene in the chromosome. Disruptions of the araBAD operon and the poxB gene are not relevant to the acs promoter replacement described here. Briefly, the purified PCR products were transformed into the MG1655-derived host strain containing the pRedET1 plasmid (Gene Bridges, Germany) encoding the lambda Red recombinases. The integrants were selected on Luria-Bertani (LB) plates containing 25 μg/mL kanamycin. PCR was used to confirm integration of the cassette upstream of the acs gene. The KanR marker flanked by the loxP sites was removed by Cre recombinase introduced from the temperature sensitive pCre-tet plasmid (Gene Bridges, Germany). The resulting strains were designated QC1549 (Pcat promoter) and QC1550 (PT5 promoter).
Example 2
Cloning of the Overexpressed E. Coli acs Gene on pMTP1.6fucP Plasmid
The acs gene operably linked to either the PT5 or Pcat promoter was cloned into the pMTP1.6fucP plasmid, a fucP overexpression vector, downstream of the fucP gene.
Construction of the pMTP1.6fucP Plasmid
The origin of replication of the large native plasmid pMT100, described in U.S. Patent Application Publication No. 2008/0194032, from E. coli strain ATCC No. 13281 was amplified by PCR using primers MTori1, set forth in SEQ ID NO:56, and MTori2, set forth in SEQ ID NO:57. A HindIII restriction enzyme recognition site was present in one of the PCR primers. The resulting PCR product was digested with the restriction enzymes DraI and HindIII and ligated to the SspI/HindIII fragment of pK194, described by Jobling and Holmes (Nucleic Acids Res. 18:5315, 1990), that contains a multiple cloning site and a kanamycin resistance gene. The resulting plasmid was named pMTori. To make plasmids pMTP1.5 and pMTP1.6, the EcoRI/HindIII fragment from pMTori1 was replaced with the EcoRI/HindIII fragment from the respective pMP38 plasmid, described in U.S. Pat. No. 7,132,527. The designations “1.5” and “1.6” refer to the variants of the glucose isomerase promoter described in U.S. Pat. No. 7,132,527. The coding sequence of the E. coli fucP gene, set forth in SEQ ID NO:58 was amplified by PCR from genomic DNA from E. coli strain MG1655 (available from The American Type Culture Collection as ATCC No: 47076) using the primer pair set forth in SEQ ID NOs:59 and 60. The resulting blunt fragment was ligated with HindIII-digested and blunted pMTP1.5 to generate pMTP1.5fucP (SEQ ID NO:61). The sequence of the plasmid was verified.
A pmeI restriction site was added to pMTP1.5fucP by ligation of a synthetic linker sequence (set forth in SEQ ID NO:62) with ScaI and NotI digested pMTP1.5fucP plasmids. The synthetic linker sequence had an overhang of ccgg at the 5′ end of the reverse strand. The resulting plasmid was designated as pMTP1.5fucPpmeI.
The plasmid pMTP1.6fucP (SEQ ID NO: 63) was generated by digesting pMTP1.5fucPpmeI and pMTP1.6 with BstEII. The larger fragment from the pMTP1.5fucPpmeI digest and the smaller fragment from the pMTP1.6 digest were then ligated. The sequence of the resulting plasmid was verified.
Cloning of the Overexpressed E. coli acs Gene
Genomic DNA of QC1549 and QC1550 (described in Example 1) was used as the template for separate PCR reactions. Primers Pcat up and acs down (see Table 1) were used to amplify the Pcat-acs from QC1549. Primers T5 up and acs down were used to amplify the PT5-acs from QC1550. The PCR conditions were similar to those described in Example 1. The PCR products were purified, and digested with NotI and PmeI. The vector plasmid pMTP1.6fucP was also digested with NotI and PmeI, and ligated with the Pcat-acs or PT5-acs fragment. The resulting plasmids were designated pDCQ804 (SEQ ID NO:64) and pDCQ805 (SEQ ID NO:65), respectively. Plasmid sequences were confirmed by sequencing.
Examples 3-6
Production of 1,3-Propanediol by Strains Overexpressing acs
E. coli strain TTab/pSYCO400Agro is a strain that is capable of producing 1,3-propanediol (PDO) and glycerol. TTab/pSYCO400Agro was transformed with the acs overexpression plasmids pDCQ804 and pDCQ805, or pMTP1.6fucP.
E. Coli Strain TTab pSYCO400/AGRO (a PTS Minus Strain)
Strain TTab was generated by deletion of the aldB gene from strain TT aldA, described in U.S. Pat. No. 7,371,558 (Example 17). Briefly, an aldB deletion was made by first replacing 1.5 kbp of the coding region of aldB in E. coli strain MG1655 with the FRT-CmR-FRT cassette of the pKD3 plasmid (Datsenko and Wanner, Proc. Natl. Acad. Sci. USA 97:6640-6645, 2000). A replacement cassette was amplified with the primer pair SEQ ID NO:66 and SEQ ID NO:67 using pKD3 as the template. The primer SEQ ID NO:66 contains 80 bp of homology to the 5′-end of aldB and 20 bp of homology to pKD3. Primer SEQ ID NO:67 contains 80 bp of homology to the 3′ end of aldB and 20 bp homology to pKD3. The PCR products were gel-purified and electroporated into MG1655/pKD46 competent cells (U.S. Pat. No. 7,371,558). Recombinant strains were selected on LB plates with 12.5 mg/L of chloroamphenicol. The deletion of the aldB gene was confirmed by PCR, using the primer pair SEQ ID NO:68 and SEQ ID NO:69. The wild-type strain gave a 1.5 kbp PCR product while the recombinant strain gave a characteristic 1.1 kbp PCR product. A P1 lysate was prepared and used to move the mutation to the TT aldA strain to form the TT aldAΔaldB::Cm strain. A chloramphenicol-resistant clone was checked by genomic PCR with the primer pair SEQ ID NO:68 and SEQ ID NO:69 to ensure that the mutation was present. The chloramphenicol resistance marker was removed using the FLP recombinase (Datsenko and Wanner, supra) to create TTab. Strain TTab was then transformed with pSYCO400/AGRO (set forth in SEQ ID NO:39), described in U.S. Pat. No. 7,524,660 (Example 4), to generate strain TTab pSYCO400/AGRO.
As described in the cited references, strain TTab is a derivative of E. coli strain FM5 (ATCC No. 53911) containing the following modifications:
deletion of glpK, gldA, ptsHI, crr, edd, arcA, mgsA, qor, ackA, pta, aldA and aldB genes;
upregulation of galP, glk, btuR, ppc, and yqhD genes; and
downregulation of gapA gene.
Plasmid pSYCO400/AGRO contains genes encoding a glycerol production pathway (DAR1 and GPP2) and genes encoding a glycerol dehydratase and associated reactivating factor (dhaB123, dhaX, orfX, orfY), as well as a gene encoding a fructokinase (scrK).
Transformation of E. Coli Strain TTab pSYCO400/AGRO with acs Overexpression Plasmids
TTab/pSYCO400Agro was transformed with the acs overexpression plasmids pDCQ804 and pDCQ805, or pMTP1.6fucP (Example 2), and transformants were selected by growth on LB-Agar containing 25 μg/mL kanamycin. The successful transformants were designated PDO3043, PDO3044 and PDO3042, respectively. Multiple transformants of each strain were picked and their growth phenotype was examined initially using a Bioscreen C growth chamber [Bioscreen, Helsinki, Finland].
Colonies of each strain from the transformation plates were first grown in 150 μL of LA medium (1% tryptone, 0.5% yeast extract, 0.05% sodium chloride) containing 100 μg/mL spectinomycin and 25 μg/mL kanamycin in a Costar 96-well U bottom plate (Corning Inc., Corning, N.Y.). The plate was incubated at 37° C. with shaking. The fresh overnight cultures were diluted 1:100 into MOPS-TM3 medium containing 10 g/L glucose in a Bioscreen honeycomb plate. MOPS-TM3 is a minimal medium containing 50 mM MOPS buffer pH6.8, 6.0 mM potassium phosphate buffer pH 6.8, 2.04 g/L citric acid dihydrate, 2 g/L magnesium sulfate heptahydrate, 0.033 g/L ferric ammonium citrate, 0.5 g/L yeast extract, 3 g/L ammonium sulfate, 0.002 g/L CaCl2.2H2O, 0.03 g MnSO4.H2O, 0.51 g/L NaCl, 1 mg/L FeSO4.7H2O, 1 mg/L CoCl2.6H2O, 1 mg/L ZnSO4.7H2O, 0.1 mg/L CuSO4.5H2O, 0.1 mg/L H3BO4, 0.1 mg/L NaMoO4.2H2O and sufficient NH4OH to provide a final pH of 6.8. Vitamin B12 and spectinomycin were added to the medium to a concentration of 0.1 mg/L and 100 μg/mL, respectively. The honeycomb plate was placed into the Bioscreen C instrument according to the manufacturer's instructions. The plate was incubated at 33° C. with constant shaking and the OD was recorded every 15 min. Growth curve data indicated that most isolates grew at a rate similar to the control strain, PDO3042.
Six independent clones from each strain and the TTab/pSYCO400Agro parent were selected for shake flask analysis. Fresh overnight cultures were inoculated into 12.5 mL MOPS-TM3 medium containing 10 g/L glucose plus 100 ng/mL Vitamin B12 and 100 μg/mL spectinomycin in shake flasks to an initial OD of 0.01. Cells were grown at 33° C. with shaking at 250 rpm for 24 hours. Cultures were centrifuged and the supernatants were added to 0.22 μm Spin-X centrifuge tube filters (Corning Inc., Corning, N.Y.) and centrifuged at 10,000 g for 1 min. The filtrates were analyzed by HPLC using a Waters Alliance 2690 HPLC system with refractive index detection. Samples were injected onto a Shodex SH-1011 column (8 mm×300 mm, purchased from Waters, Milford, Mass.) equipped with a Shodex SH-G guard column (6 mm×50 mm), temperature controlled at 50° C., using 0.01 N H2SO4 as mobile phase at a flow rate of 0.5 mL/min. Typically, the retention times of PDO and glycerol were 25.4 min and 20.1 min, respectively. The retention time of acetic acid was 22.4 min.
The results of the HPLC analyses are summarized in Table 2. Each value in the table represents the average of six cultures, except for TTab/pSYCO400Agro (Example 3, Comparative), where only one culture was grown. Standard deviations are indicated in parentheses. The results show that strain PDO3042 (Example 4, Comparative) containing the plasmid without acs accumulated similar amount of acetate as the parent TTab/pSYCO400Agro (Example 3, Comparative). Strains PDO3043 (Example 5) and PDO3044 (Example 6) with acs overexpression exhibited about 20% and 40% acetate reduction, respectively, relative to the control, strain PDO3042 (Example 4, Comparative). Furthermore, production of PDO and glycerol was not negatively affected in these acs overexpression strains. Strain PDO3044 (Example 6) with acs expressed by the stronger PT5 promoter showed more acetate reduction, consistent with the higher level of expression (see Example 7).







TABLE 2







Shake flask analysis of PDO production strains


with and without acs overexpression

















Acetic




Final
PDO
Glycerol
acid


EXAMPLE
Strain
OD550
(g/L)
(g/L)
(mg/L)















3, Compar-
TTab/
3.71
2.20
3.97
89.63


ative
pSYCO400Agro


4, Compar-
PDO3042
3.68
2.24
4.01
81.37


ative

(0.07)
(0.07)
(0.05)
(6.19)


5
PDO3043
3.85
2.26
3.91
67.11




(0.05)
(0.05)
(0.04)
(2.46)


6
PDO3044
2.42
2.75
4.00
48.21




(0.12)
(0.09)
(0.04)
(3.63)









Example 7
Analysis of acs Transcript Levels by Real-Time PCR
This Example demonstrates the increased expression of the acs gene in PDO3043 and PDO3044.
Fresh overnight cultures of strains TTab/pSYCO400Agro, PDO3042, PDO3043 and PDO3044 were inoculated into MOPS-TM3 medium containing 10 g/L glucose plus 100 ng/mL Vitamin B12 and appropriate antibiotics in shake flasks to an initial OD of 0.05. Cells were grown at 33° C. with shaking at 250 rpm for 4-5 hours until the OD reached approximately 0.5. A 2× volume of RNAprotect Bacteria Reagent (Qiagen, Valencia, Calif.) was immediately added to the cultures. The total RNA samples were prepared using RNeasy Mini Kit (Qiagen). Real time, reverse transcriptase (RT)-PCR was performed on an Applied Biosystems 7900 Sequence Detection System instrument using a two-step method (Applied Biosystems, Foster City, Calif.). In step 1, cDNA was synthesized from the provided RNA samples using random hexamers. The samples were first treated with DNase (Qiagen) for 15 min at room temperature, followed by inactivation for 5 min at 75° C. to eliminate any residual genomic DNA. The RNA was then reverse transcribed using the High Capacity cDNA Reverse Transcription Kit (Applied Biosystems) according to the manufacturer's recommended protocol. In step 2, the PCR reaction (20 μL) was run on the ABI 7900 using the following reagents: 10 μL of ABI TaqMan® Universal PCR Master Mix without UNG (uracil N-glycosylase; PN 4326614), 0.2 μL each of forward and reverse primers (100 μM), 0.05 μL TaqMan® probe (100 μM), 2 μL RNA and 7.55 μL RNase-free water. The PCR primers and dual labeled TaqMan® probes were designed using Primer Express v2.0 software from Applied Biosystems and were purchased from Sigma-Genosys. The primer and probe sequences are shown in Table 3.







TABLE 3







Primer and Probe Sequences Used for Real-Time PCR











Primer




Gene
Name
Direction
Sequence (5′ to 3′)





16S rRNA
16s-518F
Forward
CCAGCAGCCGCGGTAAT


E. coli


(SEQ ID NO: 70)



16s-579R
Reverse
TGCGCTTTACGCCCAGT





AAT (SEQ ID NO: 71)



16s-536T
Probe
CGGAGGGTGCAAGCGTT





AATCGG (SEQ ID NO:





72)


 


E.coli
acs-18F
Forward
ACACACCATTCCTGCCA


acs


ACA (SEQ ID NO:





73)



acs-89R
Reverse
TGTTGATACATCGCCTC





GTACTG (SEQ ID NO:





74)



acs-39T
Probe
CGCAGACCGTTGCCTGAT





AAACCC (SEQ ID NO:





75)









The following real time PCR thermal cycling conditions were used: 10 min at 95° C. followed by 40 cycles of 95° C. for 15 sec and 60° C. for 1 min. The samples were run at a concentration of 1 ng cDNA/reaction. A (−) reverse transcription RNA control of each sample was run with each primer set to confirm the absence of genomic DNA. All reactions were run in triplicate. The relative quantitation in the samples was calculated using the ΔΔCt method (see Applied Biosystems User Bulletin #2 “Relative Quantitation of Gene Expression”, Dec. 11, 1997, updated October 2001). A linear regression was performed for each primer and probe set and the efficiencies were within 95-100%. The 16S rRNA gene was used to normalize the quantitation of the target gene for differences in the amount of total RNA added to each reaction. The results are summarized in Table 4. The relative quantitation (RQ) value is the fold increase in acs expression in the samples relative to the parent strain TTab/pSYCO400Agro. As shown by the data in Table 4, PDO3042 containing the pMTP1.6fucP vector control had about the same acs expression as the control strain, PDO392. PDO3043 containing acs expressed by the Pcat promoter showed about 63-fold increase of acs expression. PDO3044 containing acs expressed by the PT5 promoter showed about 149-fold increase of acs expression







TABLE 4







Relative Expression of acs in PDO Production Strains










Strain
Relative Quantitation (RQ)














PDO392
1.00



PDO3044
148.7



PDO3043
63.15



PDO3042
1.21










Examples 8-10
Overexpression of Yeast acs Genes in a PDO Production Strain
The yeast acs1 (SEQ ID NO:29) and acs2 (SEQ ID NO:31) genes from Saccharomyces cerevisiae were expressed in E. coli strain TTab/pSYCO400Agro.
The yeast acs1 or acs2 gene expressed from the Pcat promoter was cloned into pMTP1.6fucP, resulting in pDCQ806 (SEQ ID NO:76) and pDCQ807 (SEQ ID NO:77), respectively. The Pcat-acs1 or the Pcat-acs2 fragment was assembled by overlapping PCR as described below. The first round of PCR was used to amplify the individual element. The Pcat promoter was amplified from QC1549 template (Example 1) using Pcat up primer with Pcat down acs1 or Pcat down acs2 primer. The acs1 or acs2 gene was amplified from yeast genomic DNA using acs1 up with acs1 down primers or acs2 up and acs2 down primers. The second round of PCR was used to assemble the Pcat with the acs1 or acs2 gene. For Pcat-acs1, the Pcat (acs1) and acs1 PCR products from the first round were both added as templates with Pcat up primer and acs1 down primer. For Pcat-acs2, the Pcat (acs2) and acs2 PCR products from the first round were both added as templates with Pcat up primer and acs2 down primer. The PCR products from the second round were purified, and digested with NotI and PmeI. The restricted fragments were ligated with NotI and PmeI digested pMTP1.6fucP. The resulting pDCQ806 and pDCQ807 were confirmed by sequencing. Separate transformations of TTab/pSYCO400Agro with pDCQ806 and pDCQ807 yielded strains PDO3045 and PDO3046, respectively.
The effect of expression of yeast acs1 or acs2 was determined using HPLC analysis, as described in Examples 3-6. The HPLC results are summarized in Table 5. Each value in the table represents the average of six cultures. Standard deviations are indicated in parentheses. Expression of the yeast acs1 gene (strain PDO3045, Example 9) or the acs2 gene (strain PDO3046, Example 10) by the Pcat promoter on pMTP1.6fucP showed about 20% reduction of acetate in the shake flask analysis relative to the strain without the acs gene (strain PDO03042, Example 8, Comparative). Production of PDO and glycerol was not negatively affected in these acs expression strains.







TABLE 5







Shake Flask Analysis of PDO Production Strains Expressing


the Yeast acs Genes by the Pcat Promoter

















Acetic




Final
PDO
Glycerol
acid


Example
Strain
OD550
(g/L)
(g/L)
(mg/L)















8, Compar-
PDO3042
3.34
2.45
3.87
76.62


ative

(0.05)
(0.10)
(0.08)
(5.18)


 9
PDO3045
3.28
2.47
3.89
63.27




(0.05)
(0.05)
(0.06)
(2.56)


10
PDO3046
3.19
2.53
3.86
60.66




(0.05)
(0.08)
(0.08)
(2.91)

## Claims

1. A recombinant Escherichia coli (E. coli) bacterium comprising a promoter operably linked to a nucleotide sequence encoding a polypeptide having acetyl-CoA synthetase enzyme activity, wherein the polypeptide has at least 95% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NO:28, SEQ ID NO:30, and SEQ ID NO:32, based on the Clustal V method of alignment and is classified as EC 6.2.1.1,
wherein the promoter and nucleotide sequence are each independently native or non-native, wherein said recombinant E. coli has enhanced acetyl-CoA synthetase enzyme activity compared to a parent E. coli from which the recombinant E. coli was obtained, and said recombinant E. coli produces glycerol, 1,3-propanediol and/or 3-hydroxypropionic acid, and wherein if the promoter and nucleotide sequence are both native, said recombinant E. coli comprises at least two copies of the promoter and nucleotide sequence.

2. The recombinant E. coli bacterium of claim 1, comprising a non-native promoter and a native nucleotide sequence encoding a polypeptide having acetyl-CoA synthetase enzyme activity.

3. The recombinant E. coli bacterium of claim 2, wherein the non-native promoter is a phage T5 promoter or a Pcat promoter.

4. The recombinant E. coli bacterium of claim 3, wherein the phage T5 promoter has a nucleotide sequence having at least 95% sequence identity to the nucleotide sequence of SEQ ID NO:33, based on the BLASTN method of alignment.

5. The recombinant E. coli bacterium of claim 3, wherein the Pcat promoter has a nucleotide sequence having at least 95% sequence identity to the nucleotide sequence of SEQ ID NO:34, based on the BLASTN method of alignment.

6. A process for making glycerol, 1,3-propanediol, and/or 3-hydroxypropionic acid comprising:
a) culturing the recombinant E. coli bacterium of claim 1 in a suitable growth medium; and
b) recovering the glycerol, 1,3-propanediol, and/or 3-hydroxypropionic acid produced.