METHOD OF PRODUCING SUCCINIC ACID AND OTHER CHEMICLAS USING FACILITATED DIFFUSION FOR SUGAR IMPORT

Abstract

This invention relates to the production of succinic acid and other chemicals derived from phosphoenolpyruvate (PEP) by fermentation with a microorganism in which the fermentation medium contains one or more sugars, and in which one or more of the sugars is imported into the cell by facilitated diffusion. As a specific example, succinic acid is produced from a glucose-containing renewable feedstock through fermentation using a biocatalyst. Examples of such a biocatalyst include microorganisms that have been enhanced in their ability to utilize glucose as a carbon and energy source. The biocatalysts of the present invention are derived from the genetic manipulation of parental strains that were originally constructed with the goal to produce one or more chemicals (for example succinic acid and/or a salt of succinic acid) at a commercial scale using feedstocks that include, for example, glucose, fructose, or sucrose. The genetic manipulations of the present invention involve the introduction of exogenous genes involved in the transport and metabolism of glucose or fructose into the parental strains. The genes involved in the transport and metabolism of glucose or fructose can also be introduced into a microorganism prior to developing the organism to produce a particular chemical. The genes involved in the transport and metabolism of sucrose can also be used to augment or improve the efficiency of sugar transport and metabolism by strains already known to have some ability for glucose utilization in biological fermentations.

Description

CROSS-REFERENCE TO RELATED APPLICATION

[0001] This application claims the priority of the U.S. Provisional Application Ser. No. 61/857,300, filed on Jul. 23, 2013.

FIELD OF THE INVENTION

[0002] The present invention is in the field of producing specialty and commodity organic chemicals using biocatalysts (bacteria and other microorganisms) that can be modified to increase their efficiency in using sugar-containing feedstocks. More specifically, the present invention is related to the genetic modifications of genes that encode functions involving transport and metabolism of sugars for the biological production of succinic acid and other chemicals.

BACKGROUND OF THE INVENTION

[0003] A large number of organic chemicals are currently derived from petrochemical feedstocks. There is a growing interest in producing many of these petrochemical-derived organic compounds through biological fermentation processes using renewable feedstocks. The list of organic compounds that can be derived from renewable feedstocks includes .alpha.,.omega.-diacids (succinic, fumaric, malic, glucaric, malonic, and maleic), 2,5-furan dicarboxylic acid, propionic acid, 3-hydroxy propionic acid, aspartic acid, glucaric acid, glutamic acid, itaconic acid, levulinic acid, 3-hydroxybutyrolactone, glycerol, and butanediols such as 1,4 butanediol (US Patent Application 20090047719), 1,3-butanediol (US Patent Application 20090253192), and 2,3-butanediol. Many other types of organic compounds, including, but not limited to, amino acids, vitamins, alcohols (such as ethanol, n-propanol, isopropanol, n-butanol, isobutanol, and higher alcohols), fatty acids, esters of fatty acids, hydrocarbons, isoprenoids, turpenes, carotenoids, amines, can also be produced using renewable feedstocks. Any such compound shall be referred to herein as a "desired compound". Although fermentation processes for many of these desired compounds have been developed, in order to compete with petrochemical processes, there is a constant need to improve the overall economics of fermentation, for example to improve product titer (final concentration in grams per liter of product) and product yield (grams of product per gram of carbon source such as glucose), and to reduce the titer of unwanted byproducts, such as acetate.

[0004] Many bacteria, including Escherichia coli, use a system for actively transporting glucose and other sugars into the cell called a phosphotransferase system (PTS). This system uses PEP (phosphoenol pyruvate) as the source of energy and phosphate for simultaneously transporting and phophorylating the sugar. PTS systems usually require four or more proteins that together function to import and phosphorylate the incoming sugar. Some of these proteins are common to all of the sugars that a given organism imports by a PTS, while other protein components of the PTS are specific for one or more particular sugars.

[0005] For example, in E. coli, the proteins that are common to all PTS pathways are PtsH and PtsI, encoded by the genes ptsH and ptsI, respectively. In addition to these two "common" PTS proteins, one or more additional sugar-specific PTS proteins are required to import and phosphorylate particular sugars. For example, import of glucose by the PTS requires two additional proteins named Crr and PtsG. Crr is a cytoplasmic protein with a single domain called A, and PtsG is a membrane protein with two domains named B and C. The phosphate group from PEP is relayed from protein to protein and is finally transferred to glucose as it is imported, at the 6 position to give glucose-6-phosphate inside the cell. The order of the relay starting with PEP is PtsI, PtsH, Crr, and finally PtsG. Historically, these proteins have also been called by other names, such as EI, HPr, EIIA.sup.Glc, and EIIBC, respectively. As another example from E. coli, fructose is imported by a similar relay using PtsI, PtsH, FruA, and FruB, the last two of which are also known as EII.sup.Fru and EII.sup.Fru, respectively. For some sugars, for example mannitol, the sugar-specific protein domains corresponding to A, B, and C as mentioned above for glucose are fused into one membrane bound polypeptide, while for other sugars, for example mannose, the A and B domains are fused into one cytoplasmic polypeptide, while the membrane bound component is comprised of two subunits called C and D.

[0006] In all cases, the system relies on the "common subunits" (PtsI and PtsH in E. coli), and PEP is the source of energy and phosphate. As a result, every molecule of sugar imported by a PTS system results in the utilization of one molecule of PEP and the production of one molecule of phosphorylated sugar and one molecule of pyruvate. However, PEP is also an obligate intermediate in several biochemical pathways, such as 1) formation of pyruvate and ATP by pyruvate kinase, 2) the anapleurotic pathways catalyzed by PEP carboxykinase and PEP carboxylase, which both feed carbon into the TCA (tricarboxylic acid) cycle, and 3) the entry into the common aromatic amino acid and aromatic vitamin biosynthetic pathway catalyzed by one or more isozymes of 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (DAHP synthase). Thus there is an inevitable competition for PEP between the PTS system for sugar import and the other pathways just mentioned.

[0007] Since many bacteria, including both Gram positives and Gram negatives, use a PTS system, it is obviously a system that has prevailed under many circumstances throughout evolution. However, under anaerobic conditions, production of ATP from sugars such as glucose is much less efficient than under aerobic conditions, and the so-called "substrate level" phosphorylation, for example, by pyruvate kinase, becomes a larger portion of the ATP production budget than under aerobic conditions where oxidative phosphorylation provides the majority of the ATP budget. As such, it is noteworthy that some organisms, such as Saccharomyces cerevisiae and Zymomonas mobilis, both of which are well adapted to anaerobic growth on glucose and other sugars, do not have a PTS system, but instead use a facilitated diffusion protein (also called a permease) to import glucose and other sugars. Furthermore, when organisms that natively use a PTS are genetically engineered to overproduce particular compounds by fermentation, the pathways in many cases use PEP as an intermediate, so that the PTS competes with the desired biosynthetic pathway for PEP. Alleviation from this competition by reducing the activity of the PTS is known to increase flux to a desired biosynthetic pathway.

[0008] For example, PEP is an intermediate in the reductive branch of the tricarboxylic acid (TCA) cycle that leads to succinate. During the metabolic evolution of KJ122, an E. coli succinate producer, a frameshift mutation arose in the ptsI gene, which resulted in an increase in succinate production from glucose. Reinstalling a wild type ptsI gene caused a drastic reduction in succinate production, proving that the ptsI mutation contributed strongly to the strain improvement.

[0009] For another example, aromatic amino acids are built from PEP and erythrose-4-phosphate. Deletion of three pts genes (.DELTA.ptsHI, crr) in an E. coli strain was shown to increase flux to the aromatic amino acid biosynthetic pathway when cells are grown on glucose as the carbon source.

[0010] In both of the above examples, import of glucose is presumably still accomplished at some level by the so-called galactose permease (GalP, encoded by the galP gene). In the first example, a mutation that reduced the activity of a repressor (GalS) of the galP gene was found to result from metabolic evolution (WO2011/123154). In the second example, one or more mutations occurred after deletion of pts genes that resulted in an increase in growth rate. The resulting strain depended on galP for significant growth on glucose, and one or more mutations in the strain could have been related to an increase in expression of galP (U.S. Pat. No. 6,962,794). However, the strains from this second example produced only low titers of aromatic amino acids after engineering the "Pts-/Glu+" strains for aromatic amino acid production. Phenylalanine, tyrosine, and tryptophan were produced at 1.7, 0.8, and 2.2 g/l respectively. Since these titers are nowhere near high enough to support an economically attractive commercial process, it is not clear that the invention disclosed in U.S. Pat. No. 6,962,794 is useful for commercial production. As such, there is still a need to improve fermentation parameters for economically viable commercial production of chemicals by fermentation.

[0011] Although the use of GalP for glucose import conserves PEP, it is a proton symporter, so it consumes about 1/3 of an ATP for each glucose molecule transported. Some microorganisms, for example the bacterium Zymomonas mobilis and the yeast Saccharomyces cerevisiae use facilitated diffusion for importing glucose. Z. mobilis has one facilitator protein that functions to import both glucose and fructose. S. cerevisiae has at least 14 different hexose importers, many of which import glucose and at least some of which import fructose as well. This mode for glucose import requires no ATP expenditure until the sugar is inside the cytoplasm, after which an ATP is consumed to form glucose-6-phophate to allow the sugar to enter glycolysis. Most importantly, unlike for the PTS system, no PEP is consumed. As such, facilitated diffusion clearly works well for some organisms, and costs the cell less in terms of PEP and ATP than either a PTS system or a proton symporter such as GalP. Ingram et al. (U.S. Pat. No. 5,602,030) demonstrated that the facilitated diffusion protein (Glf, encoded by the glf gene) from Zymomonas mobilis, together with a glucokinase (Glk, encoded by the glk gene), also from Zymomonas mobilis, expressed from those genes on a multicopy plasmid, could functionally replace the PTS to support growth in a minimal glucose medium of an E. coli strain, where the parent had no native glucose facilitated diffusion capability, and other glucose import systems had been disabled by mutation. The recombinant E. coli ptsG-, ptsM-, glk- strain ZSC113 containing the two Z. mobilis genes glf and glk on a plasmid could grow aerobically on minimal glucose medium.

[0012] These disclosures proved that the Z. mobilis proteins could function in E. coli enough to support growth aerobically with a specific growth rate of 0.53 hr-1. However, wild type E. coli using the native PTS for glucose import has an aerobic specific growth rate of 1.0 to 1.2 hr-1), so the strains engineered in U.S. Pat. No. 5,602,030 to use glf appear to be severely limited by glucose uptake. Moreover, the disclosures did not show that the facilitated diffusion system could support anaerobic growth. A number of important chemicals produced by fermentation require robust anaerobic growth to support an economically attractive commercial production system (WO2012/018699). The examples in U.S. Pat. No. 5,602,030 and Snoep et al (1994) showed that modest growth could be obtained by expressing glf and glk from a multicopy plasmid, but it was not demonstrated that growth could be supported by integrated copies of the glf and glk genes, yet it is often desirable for commercial scale production to use strains that do not contain a plasmid. Finally, U.S. Pat. No. 5,602,030 did not demonstrate that a glf-based system could support high titer production of a commodity chemical such as ethanol or succinate in E. coli or any other organism that does not natively use facilitated diffusion. As such, it was not clear from the disclosure of U.S. Pat. No. 5,602,030 alone that a glf could replace the PTS and result in an economically attractive fermentation processes for producing a desired chemical in a host strain that does not have a native facilitated diffusion system.

[0013] Tang et al (2013) went a couple steps further to show that anaerobic production of succinate could be achieved by expression of Z. mobilis glf in combination with a glucokinase in an E. coli strain background that was .DELTA.ptsI, .DELTA.ldhA, .DELTA.pflB, pck*. However, the best succinate production in this system was modest, only 220 mM (26 g/l) in 96 hours. Despite having optimized by combinatorial modulation the expression of glf and glk, this titer and productivity is nowhere near that of previously published strains that produced 83 g/l succinate without the use of glf. Thus, despite the more advanced work of Tang et al., it had still not been demonstrated that the use of facilitated diffusion for glucose import was useful for actually improving fermentation production parameters at levels that would be necessary for economically attractive commercial production, which would be at the benchmark of at least 83 g/l (WO2012/018699). To further complicate the potential replacement of a PTS by glf, in E. coli, and presumably in other bacteria, the components of the PTS have many diverse regulatory functions that affect many different metabolic pathways, so it is impossible to predict what the effects will be of a deletion in any one or more of the PTS genes on the overall physiology and fermentative properties of any resulting modified strain. Native Z. mobilis strains, which naturally use facilitated diffusion for glucose uptake, are capable of producing up to about 60 g/l ethanol and a similar quantity of carbon dioxide from glucose. An engineered strain of Z. mobilis is reported to produce 64 g/l succinate from glucose (EP20070715351). However, this fermentation required 10 of yeast extract in the fermentation medium, which is undesirable for commercial production of succinic acid, both because of its expense and the increased cost required for downstream purification of the succinate from the yeast extract components. Furthermore, Z. mobilis is often not a convenient or optimal host organism for use in fermentative processes.

[0014] Thus, to summarize the prior art, it had been shown that E. coli can be engineered to use facilitated diffusion of glucose to support aerobic growth to a modest rate, and to support a modest level of succinate production anaerobically, but there has been no disclosure of any bacterial strain or process that has been engineered to confer the non-native use of facilitated diffusion for glucose import and that is improved over strains using native glucose import systems such as PTS and/or GalP for production of a chemical by fermentation. Furthermore, there has been no disclosure of any bacterial strain or process that uses facilitated diffusion for glucose import and that is capable of producing succinate or any chemical other than ethanol and carbon dioxide at a titer, yield, and rate that is high enough in a medium that would be commercially attractive, such as a minimal glucose medium. As such, there is still a need for improved strains that can produce succinate and chemicals in a process that is economically attractive when all factors including productivity, cost of the medium, and downstream purification are taken into account.

SUMMARY OF THE INVENTION

[0015] This present invention provides biocatalysts (for example genetically engineered microorganisms) and methods for using facilitated diffusion of glucose for improving the fermentative production of commercially important products, for example, but not limited to, specialty and commodity chemicals. Specifically, the present invention is useful in the fermentative production of organic acids, amino acids, and other biochemicals that have PEP as a biochemical intermediate in their biosynthetic pathway, using sugar-containing renewable feedstocks. As a specific example, the present invention is useful in the fermentative production of succinic acid from a glucose, fructose, or sucrose-containing renewable feedstock using biocatalysts that have been constructed to use facilitated diffusion of a sugar. The principles of the present invention can be applied to many other desired chemical compounds that can be produced by fermentation, particularly chemicals intermediates of the TCA cycle or derivatives thereof, such as fumaric acid, malic acid, glutamate, derivatives of glutamate, aspartate, derivatives of aspartate, aromatic amino acids (phenylalanine, tyrosine, tryptophan), and compounds derived from intermediates in the central aromatic pathway, such as vitamins and cis, cis-muconic acid.

[0016] According to the present invention, genes coding for the proteins involved in facilitated diffusion of sugars such as glucose can be introduced into a wide variety of biocatalysts either to confer a new ability to the biocatalyst to import a sugar as a source of carbon and energy from the fermentation medium by facilitated diffusion, or to augment or improve an already existing capacity of the biocatalysts for sugar transport and metabolism. Strains engineered to have the added ability to import sugars by facilitated diffusion can have improved fermentation parameters when compared to parameters of the parent strain, such as increased titer (g/l of desired chemical product), increased yield (grams of product produced per gram of sugar consumed), increased specific productivity (g/l-hr of product formation), and/or decreased titer of unwanted byproducts such as acetate, pyruvate and/or amino acids. These improved parameters can result from conservation of energy (for example use of less ATP for formation of proton gradients to drive proton symporters such as GalP), conservation of PEP for pathways that use PEP as an intermediate, such as the succinate pathway(s), and decreasing of overflow metabolism into acetate production pathways or other unwanted pathways.

[0017] This approach is particularly advantageous for production of chemicals that are derived at least in part from or through PEP, such as succinate, malate, fumarate, lactate, ethanol, butanols, propane diols, 3-hydroxypropionic acid, acrylic acid, propionic acid, lactic acid, amino acids such as glutamate, aspartate, methionine, lysine, threonine, and isoleucine, compounds derived from the central aromatic pathway such as phenylalanine, tyrosine, tryptophan, aromatic vitamins, aromatic vitamin-like compounds, and any other compound that is derived from PEP as a biosynthetic intermediate.

[0018] In one embodiment, the present invention provides biocatalysts that do not natively have the ability to import a sugar by facilitated diffusion with an added heterologous gene (or genes) that confers a new ability to import a sugar by facilitated diffusion. In another embodiment, the present invention provides novel biocatalysts that produce a higher titer of a desired fermentation product than the parent biocatalyst. In another embodiment, the present invention provides novel biocatalysts that produce a higher yield of a desired fermentation product than the parent biocatalyst. In another embodiment, the present invention provides novel biocatalysts that produce a higher specific productivity for a desired fermentation product than the parent biocatalyst. In another embodiment, the present invention provides a novel biocatalyst that produces a lower titer of an undesired desired byproduct than the parent biocatalyst.

[0019] The gene or genes that code for the protein or proteins that function in the facilitated diffusion of a sugar can be derived from any organism that has the native ability to carry out facilitated diffusion of a sugar, the only requirement being that the protein or proteins are able to function in the new host. The gene encoding a sugar kinase, for example a glucokinase, that is required to phosphorylate the sugar after it enters the cytoplasm can be derived from the same donor from which came the gene(s) for facilitated diffusion, or a native sugar kinase gene from the recipient host can be used, or a combination of both sugar kinases can be used.

[0020] In another embodiment, the present invention provides for methods for producing a desired fermentation product comprising cultivating a genetically engineered microorganism that used facilitated diffusion to import a sugar.

[0021] In another embodiment, the present invention provides for methods for improving fermentation performance parameters (titer, yield, specific productivity, minimizing byproduct formation) of strains engineered to use facilitated diffusion.

[0022] In another embodiment, the present invention provides for methods for achieving an improved balance of facilitated diffusion and sugar kinase activity leading to improved growth and fermentation parameters in genetically engineered microorganism that used facilitated diffusion to import a sugar.

[0023] According to the present invention, one approach is to genetically transfer a facilitated diffusion system for importing a sugar from a second donor organism that naturally contains the relevant genes (for example glf or glk or a combination thereof) into a first recipient organism that does not naturally contain said relevant genes, so as to confer on said first recipient organism a new ability to import said sugar by facilitated diffusion. In a preferred embodiment, the first recipient has been previously engineered or constructed to be devoid of, or substantially reduced in, its ability to import said sugar by any native system or systems present in a parent or ancestor of said first recipient strain. In such an embodiment, the resulting strain is in effect forced to use facilitated diffusion for growth on said sugar.

[0024] In a preferred embodiment, the first recipient strain is an E. coli strain, and the second donor strain is Zymomonas mobilis CP4. In a more preferred embodiment, said first strain is WG53, which in turn is derived from KJ122 by deletion of ptsH, ptsI, and galP. The exact nature of the deletions of ptsH, ptsI, and galP can vary widely, the only important criterion being that the activities of the PtsH, PtsI, and GalP proteins are eliminated or substantially reduced.

[0025] The first recipient organism of the invention can vary widely, the only criterion being that it does not natively contain a protein that functions in facilitated diffusion for a sugar such as glucose. In addition to E. coli, examples of first recipient organisms include, but are not limited to: Gluconobacter oxydans, Gluconobacter asaii, Achromobacter delmarvae, Achromobacter viscosus, Achromobacter lacticum, Agrobacterium tumefaciens, Agrobacterium radiobacter, Alcaligenes faecalis, Arthrobacter citreus, Arthrobacter tumescens, Arthrobacter paraffineus, Arthrobacter hydrocarboglutamicus, Arthrobacter oxydans, Aureobacterium saperdae, Azotobacter indicus, Brevibacterium ammoniagenes, divaricatum, Brevibacterium lactofermentum, Brevibacterium flavum, Brevibacterium globosum, Brevibacterium fuscum, Brevibacterium ketoglutamicum, Brevibacterium helcolum, Brevibacterium pusillum, Brevibacterium testaceum, Brevibacterium roseum, Brevibacterium immariophilium, Brevibacterium linens, Brevibacterium protopharmiae, Corynebacterium acetophilum, Corynebacterium glutamicum, Corynebacterium callunae, Corynebacterium acetoacidophilum, Corynebacterium acetoglutamicum, Enterobacter aerogenes, Erwinia amylovora, Erwinia carotovora, Erwinia herbicola, Erwinia chrysanthemi, Flavobacterium peregrinum, Flavobacterium fucatum, Flavobacterium aurantinum, Flavobacterium rhenanum, Flavobacterium sewanense, Flavobacterium breve, Flavobacterium meningosepticum, Micrococcus sp. CCM825, Morganella morganii, Nocardia opaca, Nocardia rugosa, Planococcus eucinatus, Proteus rettgeri, Propionibacterium shermanii, Pseudomonas synxantha, Pseudomonas azotoformans, Pseudomonas fluorescens, Pseudomonas ovalis, Pseudomonas stutzeri, Pseudomonas acidovolans, Pseudomonas mucidolens, Pseudomonas testosteroni, Pseudomonas aeruginosa, Rhodococcus erythropolis, Rhodococcus rhodochrous, Rhodococcus sp. ATCC 15592, Rhodococcus sp. ATCC 19070, Sporosarcina ureae, Staphylococcus aureus, Vibrio metschnikovii, Vibrio tyrogenes, Actinomadura madurae, Actinomyces violaceochromogenes, Kitasatosporia parulosa, Streptomyces coelicolor, Streptomyces flavelus, Streptomyces griseolus, Streptomyces lividans, Streptomyces olivaceus, Streptomyces tanashiensis, Streptomyces virginiae, Streptomyces antibioticus, Streptomyces cacaoi, Streptomyces lavendulae, Streptomyces viridochromogenes, Aeromonas salmonicida, Bacillus pumilus, Bacillus circulans, Bacillus thiaminolyticus, Escherichia freundii, Microbacterium ammoniaphilum, Serratia marcescens, Salmonella typhimurium, Salmonella schottmulleri, Bacillus subtilis, Bacillus licheniformis, Bacillus amylolliquefaciens, Klebsiella oxytoca, Klebsiella pneumoniae, Acinetobacter baylyi, Corynebacterium glutamicum Brevibacteium flavum, Mannhemia succiniproducens and Anaerobiospirilum succiniproducens, and Xanthomonas citri.

[0026] Examples of second donor organisms are any strain or species that has a native facilitated diffusion system for a sugar, for example Zymomonas mobilis strains (in addition to strain CP4), Homo sapiens, Azospirillum amazonense, Flavobacteriaceae bacterium S85, Saccharomyces cerevisiae or other yeast genera.

[0027] In another embodiment, a first parent strain is first constructed to use facilitated diffusion for importing a sugar, and then the resulting stain is further engineered to overproduce a chemical of commercial interest such as succinic acid.

[0028] Novel aspects of this invention are that the glf gene from a non-pathogenic, robust sugar utilizer has been stably integrated into the chromosome of a bacterium, such that the newly constructed bacterium can produce a commercially viable product with an economically viable process. The titer, yield and/or specific productivity of product from glucose or another sugar is greater than those parameters of the parent organism. The glf gene is integrated at a site in the chromosome that does not interfere with any relevant aspect of growth or product production. The acetate titer is less than that of the parent strain at about 45 to 48 hours in a representative fermentation, allowing a 2 day fermentation cycle time, unlike a prior art example. Strains in the prior art that used facilitated diffusion for sugar import did not produce sufficient titers of the desired product to be economically attractive. Another novel aspect of this invention is that by using facilitated diffusion for sugar import, it was unexpectedly found that the production of the unwanted byproduct acetate or acetic acid was significantly reduced. The prior art strain KJ122 produces about 5 to 7 g/l acetate in a typical fed glucose fermentation (WO2012/018699), while new strains of the invention produce only about 4.2 g/l or less.

[0029] Additional advantages of this invention will become readily apparent from the ensuing description.

BRIEF DESCRIPTION OF THE DRAWINGS

[0030] FIG. 1 Structure of plasmid pAC19, a source of an expression cassette for Z. mobilis glf and glk.

[0031] FIG. 2 Structure of plasmid pAC21, a source of a selectable and counter-selectable cassette containing cat (chloramphenicol resistance) and sacB (levan sucrase) genes.

[0032] FIG. 3 Structure of plasmid pSS2, a source of an expression cassette for Z. mobilis glf without glk.

[0033] FIG. 4 Structure of plasmid pMH68, a source of an expression cassette for integration of a second copy of the E. coli crr gene at the pflD locus.

[0034] Table 1. Production of succinate by AC15 in 7 liter fermentors

[0035] Table 2. Production of succinate by red mutants of AC15 in 500 ml microaerobic fermentors.

[0036] Table 3. Production of succinate by two isolates of SS8 in 500 ml microaerobic fermentors.

[0037] Table 4. Production of succinate by YSS41 in 20 liter microaerobic fermentors.

[0038] Table 5. Production of succinate by MH141 in 500 ml microaerobic fermentors.

[0039] Table 6. Succinate production by E. coli strains KJ122 and YSS41 in 20 liter fermentors under optimized aeration conditions for both strains.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

Definitions

[0040] When the phrase "for example" or "such as" is used, the subsequently mentioned items are meant to be illustrative examples for the idea or concept being disclosed. The subsequently mentioned items are not meant to be limited to the examples given, since any other specific item or example that would fall under the generalization of the idea or concept is meant to be included. For any given compound, it might be more appropriate to produce a salt of said compound, so for example, succinic acid might be produced at pH near 7 as a salt of sodium, potassium, calcium, magnesium, ammonium, etc., while lysine might be produced as a salt of chloride, sulfate, bicarbonate, etc. As such, any time a compound is named herein, any salt of said compound is meant to be included, and any time a salt is named, the free acid or free base is also meant to be included. Thus, for example, "succinate" is meant to include "succinic acid" and vice versa, and "acetate" is meant to include "acetic acid" and vice versa.

[0041] "Facilitated diffusion" means the action of a system, typically comprising an integral membrane protein situated in a biological membrane (for example the inner membrane of a Gram negative bacterium or the single membrane of a Gram positive bacterium), or a complex of more than one protein molecules situated in a biological membrane, that functions to specifically allow one or more chemicals called the "substrate" (for example glucose and/or fructose), but not chemicals in general (for example water and cytoplasmic metabolites other than the specific substrate), to cross through the membrane without any energy (such as that provided by hydrolysis of ATP or PEP) or gradient of a different chemical (for example a proton gradient) provided directly to the system by the cell. If there is a concentration gradient, for example if the concentration of a substrate is higher outside the cell than inside the cell, there will be a net flux of that substrate into the cell at a rate that is faster than would occur if the facilitated diffusion system were absent. The protein(s) that function for facilitated diffusion typically have a binding affinity that is specific for one or more substrates and allows the system to assist passing the substrate across the membrane at relatively low concentrations of several millimolar or less. Some types of facilitated diffusion can function by creating a pore or channel through the membrane that discriminates in favor of a substrate, and in other types the protein(s) can bind the substrate on one side of the membrane and then rotate through the membrane to release the substrate on the opposite side of the membrane. A facilitated diffusion protein (sometimes called simply a facilitator) is a protein component of such a system. Thus, the thermodynamic driving force for facilitated diffusion is a gradient of substrate concentration, in which the substrate (for example a sugar) flows from a higher concentration outside of a cell to a lower concentration inside the cell. We shall use the genetic symbols Glf and glf to respectively mean a facilitated diffusion protein and a gene encoding such a protein that has specificity for glucose. We usually consider Glf to be a comprised of a single polypeptide chain, but a Glf could be a complex comprised of more than one polypeptide chain. Although the specific examples of Glf written herein are bacterial in origin, our definition is meant to include facilitated diffusion system derived from any organism. For example, it is well known that the yeast Saccharomyces cerevisiae and other yeasts have one or more facilitated diffusion proteins for importing hexoses (for example glucose and fructose) named HXT1, HXT2, HTX3, HTX4, HTX5, HTX6, HTX7, etc.), and human erythrocytes use facilitated diffusion to import and export glucose via a protein named GLUT1. The mechanism of action of Glf's can vary widely, including pore-facilitated transport and carrier-facilitated transport. Although the specific examples given in this specification disclose a Glf that has good specificity for glucose, it is known in the art that a Glf protein can be active on more than one sugar, for example Glf from Zymomonas mobilis and Saccharomyces cerevisiae can be active on fructose as well as glucose.

[0042] Proton symport is defined as a system for importing a substrate across a biological membrane that uses a proton gradient as a driving force. A higher concentration of protons outside of the cell has a thermodynamic tendency to diffuse back into the cell. This thermodynamic pressure is used to carry in a substrate such as a sugar. A proton symporter is a protein or complex of proteins that functions to provide proton symport. An example of a proton symporter is the GalP protein of E. coli, which is well known to function in the import of galactose, glucose, and other sugars.

[0043] A glucokinase and a fructokinase are enzymes that catalyze phosphorylation of glucose, fructose, or other sugar, usually at the 6.sup.th carbon position, but alternatively possibly at the 1.sup.st carbon or another position. We shall use the genetic symbols Glk and glk to respectively mean a glucokinase and a gene that encodes a glucokinase. Frk and frk mean a fructokinase and a gene that encodes a fructokinase, respectively.

[0044] A crr gene is a gene that encodes an EIIA.sup.glc component of a PTS, such as the crr gene of an E. coli strain or of a Bacillus subtilis strain or a homolog of such a crr gene.

[0045] A PTS (phosphotransferase system) is a group of proteins that act together to pump a sugar into a cytoplasm and simultaneously phosphorylate the sugar, using PEP as the source of phosphate and energy. Examples of genes encoding PTS proteins from E. coli include ptsH, ptsI, crr, ptsG, fruA, fruB, manX, manY, and manZ. The corresponding proteins are named PtsH, PtsI, Crr, PtsG, FruA, FruB, ManX, ManY, and ManZ. However, there are many more examples from E. coli and other prokaryotes, and these proteins can have alternate names, for example Crr is sometimes named EIIA.sup.glc. Some of the PTS proteins are more specific to one or more particular sugars than to other sugars, while some PTS proteins, for example PtsH and PtsI from E. coli, are used in common for many different sugars.

[0046] In this specification, the term "microaerobic" means that the feed rate of air is less than 0.1 volume of air per volume of liquid culture per minute. In 7 and 20 liter fermentor examples disclosed herein, this is accomplished with a sparger and flow meter, or by allowing the tank to breathe through a sterile membrane attached to the top of the tank without any forced air flow. In 500 ml fermentor tank examples disclosed herein, no air is deliberately introduced, but a small amount of air is introduced from leakage, feeding of the base solution, and taking of samples.

[0047] A "minimal medium" is a microbial growth medium comprised of water, a pure carbon source (such as a substantially pure sugar or mixture of substantially pure sugars), mineral salts (for example potassium, sodium, magnesium, calcium, bicarbonate plus carbonate, phosphate, sulfate and chloride), a pure nitrogen source such as ammonium or urea, trace metals (iron, copper, zinc, manganese, cobalt, molybdenum, and optionally borate), optionally glycine betaine (also known as simply betaine), and optionally an antifoam agent. Minimal media do not contain any complex (also known as "rich") nutrient source such as yeast extract, corn steep liquor, soy hydrolysate, broth, casein hydrolysate, grain, legume, or any other "undefined" mixture of nutrients that typically would be derived from an agricultural source without any physical or chemical purification or separation steps. Reasonably pure sugars derived from sugar cane, corn starch, sorghum starch, tapioca starch, or any other reasonably pure starch source is considered to be acceptable for a minimal medium. A minimal medium can contain one or a few pure chemicals to satisfy a particular growth requirement (auxotrophy or bradytrophy) or to enhance a biochemical pathway. For example, some strains require a vitamin such as biotin, which can be added at small concentrations without a significant negative impact on a process. As another example, addition of a vitamin such as thiamine, while not absolutely required for growth, can nonetheless enhance growth or a biochemical pathway. Minimal media are preferable for fermentative production of many chemicals due to the relatively low cost of the components, and due producing cleaner fermentations broths that allows for more favorable economics for downstream purification of the desired chemical. Ethanol production is an exception, since downstream purification can be accomplished with distillation, an economically attractive method for purification of the desired product even from complex media.

[0048] An aromatic biochemical means any one or more of the following: phenylalanine, tyrosine, or tryptophan, or any derivative thereof (such as L-dihyroxyphenylalanine, melatonin, indole, indole acetic acid, indigo, serotonin, cinnamic acid, hydroxy styrene), a vitamin or vitamin-like compound containing an aromatic moiety (such as p-hydroxybenzoic acid, 2,3-dihyroxybenzoic acid, p-amino benzoic acid, folate, tocopherol, pyrroloquinoline quinone).

[0049] A homolog of a first gene or protein is defined as a second gene or protein in which the second protein or the protein inferred to be translated from the second gene has the same or a similar biochemical function as the first protein or protein inferred to be translated from the first gene, and in which an alignment of the first and second proteins or first and second inferred translated proteins results in a 25% or greater identity or similarity for a region of at least 50 amino acids in length, when using the default parameters of a publically available computer alignment program such as BLAST.

[0050] A mutation is any change in a DNA sequence relative to the DNA sequence of the related wild type or native gene. A mutation can be a single or multiple base change that introduces a premature stop codon or an amino acid that is different from the wild type amino acid at that position. A mutation can be an insertion or deletion of one or more bases that creates a frame shift that results in a protein that is significantly different from the wild type protein. A mutation can be a deletion that removes much, most, or all of a coding region (also known as an open reading frame or orf). One type of mutation removes one or more entire orfs plus additional non-coding DNA either upstream or downstream from the coding region, or both. A mutation can result from insertion of a relatively large DNA sequence (more than about 100 bases), for example an insertion element (for example IS186 or IS4) or a transposon (for example Tn10). When the intent is to remove a function, a preferable mutation is a deletion of all or most of an orf, however, smaller mutations such as single base changes or insertions can often accomplish removal of a function for all practical purposes. Mutations can be spontaneous, induced by mutagenesis, or constructed by genetic engineering. Some mutations, when desired to accomplish a strain improvement, are mutations that decrease or eliminate a biological function, such as particular elements of a PTS. However, some mutations, when desired to accomplish a strain improvement, are mutations that increase a biological function, for example a "promoter up mutation" can increase the expression of a desired gene, such as a glf gene.

[0051] "Exogenous" means a gene or protein derived from a second genus that has been installed in a first genus, where said second genus is a different genus from said first genus.

[0052] A gene is defined as a region of a chromosome that encodes a protein or enzyme, and is meant to include both the open reading frame that corresponds to the protein or enzyme and any DNA sequences surrounding the open reading frame that contribute to controlling the level or rate of production of the protein or enzyme, such as promoters, ribosome binding sites, operators, regulatory protein binding sites, DNA corresponding to 5' untranslated mRNA leader sequences, terminators, and antiterminator sites. When two or more open reading frames that correspond to protein coding DNA sequences are under the control of a single promoter and a single terminator, the whole region encompassing the promoter, open reading frames corresponding to protein coding DNA sequences and the terminator is referred as an operon. For example, when the exogenous genes glf and glk are under the control of a single promoter and a single terminator, it is referred as glf-glk operon.

[0053] The present invention provides biocatalysts for succinic acid production in high titer, yield and productivity using a minimal medium with a sugar as a carbon source. The term "yield" as defined in this invention refers to the number of grams of product (such as succinic acid) produced per gram of sugar (such as glucose or sucrose) consumed. The term "productivity" as defined in this present invention refers to the number of grams of product (such as succinic acid) produced per liter of culture per hour. The term "titer" is defined as the concentration of product (such as succinic acid) in the fermentation broth in grams per liter. The desirable yield for succinic acid is in the range of 0.8-1.2 grams of succinic acid produced per gram of sugar consumed. The desirable productivity for succinic acid in this present invention is in the range of 1 gram or more of succinic acid produced per liter per hour. The desirable titer of succinic acid is greater than 26 g/l, or more preferably greater than 64 g/l, and most preferably greater than 83 g/l in a fermentation time of 48 hours or less.

[0054] The bacterial growth rate is measured in terms of the rate of increase in the optical density at 550 or 600 nanometers of a liquid culture resulting from the bacterial multiplication. The bacterial growth rate is also expressed in terms of time required for doubling of bacterial cells. In the bacterial cells suitable for the present invention, the bacterial cells are expected to have a doubling time of between 20 minutes and 3 hours.

[0055] According to the present invention, the biocatalyst for succinic acid production can be developed in two different ways. Under the first approach, a wild type bacterial species is genetically manipulated and, optionally, evolved, to grow efficiently using facilitated diffusion for import of glucose or other sugar. Once such a strain is constructed, subsequent genetic manipulations are carried out in the metabolic pathways to obtain a bacterial strain that produces succinic acid or another desired chemical with high titer, yield and productivity, for example, by following methods known in the art.

[0056] The patent applications published under Patent Cooperation Treaty with the publication No. WO 2010/115067 and United States Patent Application Publication No. US 20100184171 provide the details about the genetic engineering techniques useful in generating a strain of E. coli with improved succinic acid production capacity. These two patent applications are incorporated herein by reference.

[0057] Under the second approach, a bacterial strain already developed to have a commercially attractive yield and productivity for a chemical such as succinic acid as described in the patent application publications US 20100184171 and WO 2010/115067 is used as a parental strain. Further genetic manipulations, and optionally, evolution, are then carried out with this strain to obtain a bacterial strain that has the ability to use facilitated diffusion to import glucose or another sugar to produce succinic acid at a commercially attractive titer, yield, and productivity.

[0058] As a specific example, this present invention discloses biocatalysts and methods that have improved ability over that of the prior art to produce succinic acid at high enough titer, yield and productivity while gaining the new ability to import a sugar by facilitated diffusion. For example, the KJ122 strain of E. coli described by Jantama et al. can be selected as the starting strain for the present invention. The KJ122 strain of E. coli is reported to have the ability to produce succinic acid in a minimal medium at high titer and productivity.

[0059] The KJ122 strain of E. coli was derived from the E. coli C strain through gene deletions and metabolic evolution as described in US Patent Application Publication No. 20100184171 and in the International Patent Application Publication No. WO 2010/115067. These two patent application publication documents providing details about the genetic changes that led to the development of the KJ122 strain of E. coli are incorporated herein by reference. KJ122 does not have any substantial ability to import glucose as a source of carbon by facilitated diffusion in the production of succinic acid. The absence of this function in KJ122 is attributable to the lack of a gene that encodes a Glf protein. The inventors have discovered genetic approaches that enable KJ122 to more efficiently use glucose as a source of carbohydrate while retaining or improving its original ability to produce succinic acid at high titer, yield, and productivity in a minimal medium.

[0060] The term "carbohydrate" as used in this invention includes mono-saccharides such as glucose, fructose, xylose, and arabinose, disaccharides such as sucrose, melibiose, maltose and lactose, trisaccharides such as raffinose and maltotriose, and higher oligosaccharides, and hydrolysates derived from the enzymatic or chemical digestion of polysaccharides such as starch, cellulose, and biomass. Simple carbohydrates, those with from one to three saccharide units, are referred to herein as "sugars", for example glucose, fructose, sucrose, maltose, etc.

[0061] The terms "PTS.sup.+ organism" or "PTS.sup.+ bacterium" refers to a bacterium which has the capacity for a carbohydrate transport based on a PTS. The term "non-PTS organism," or "non-PTS bacterium" or "PTS.sup.-" bacterium refers to bacterial cells that are mutated in one or more genes that encode a PTS function, such that the activity of the PTS is decreased relative to that of the wild type PTS.

[0062] In one aspect, the present invention discloses the addition of genes to an organism in order to install or increase the activity of one or more proteins and/or enzymes involved in the import and conversion of a sugar into metabolic intermediates such as glucose 6-phosphate, glucose 1-phosphate, fructose 6-phosphate, or fructose 1-phosphate that can be further metabolized by the cell. The genes that encode relevant proteins or enzymes are chosen from a group consisting of a glf gene, an HXT gene, a glk gene, and a frk gene.

[0063] In another embodiment, the present invention provides a process for producing succinic acid or another chemical using facilitated diffusion to import a sugar such as glucose as a renewable feedstock. In one aspect, the present invention provides a process for producing succinic acid from a sugar-containing medium that makes use of a biocatalyst that has a decreased activity in at least one protein of the organism's native PTS system relative to that of the ancestral or parental strain. In another aspect, the present invention provides a process for producing succinic acid or other chemical in a sugar-containing medium that makes use of a biocatalyst that has a decreased activity in at least one protein of the organism's native sugar import system relative to that of the ancestral or parental strain involving use of a protein symport system, such as GalP.

[0064] The present invention provides ways to manipulate a PTS and in turn the bacterial carbohydrate uptake system. Since EI and HPr proteins function as "general" or "common" components of the PTS system, inactivation of either the ptsI gene coding for EI protein or the ptsH gene coding for HPr protein would lead to the complete inactivation of a PTS. There will be substantially less carbohydrate transport through the PTS system in bacterial cells where the activity of ptsH or ptsI or both has been decreased or eliminated. When the PTS is partially or completely inactivated, the bacterial cell has to depend on one or more other alternative permease systems for carbohydrate transport.

[0065] When there is active glucose transport through PTS, the EIIA.sup.Glc remains unphosphorylated as there is a carbohydrate substrate for accepting its phosphate group. However, when there is no glucose in the medium, the phosphorylated form of EIIA.sup.Glc cannot transfer its phosphate group to glucose and therefore it remains in its phosphorylated state. The unphosphorylated EIIA.sup.Glc mediates the phenomenon generally known as carbon catabolite repression (CCR). Under CCR, when glucose is present in the growth medium, the transport and/or utilization of other carbohydrates in the medium is prevented until the glucose in the medium is decreased to a low concentration. The carbon catabolite repression results from the inhibitory effect of unphosphorylated EIIA.sup.Glc on permease systems or other systems of carbon source utilization. A number of permeases involved in the carbohydrate transport are known to be inhibited by unphosphorylated EIIA.sup.Glc, for example, LacY or lactose permease. In addition, the unphosphorylated EIIA.sup.Glc is known to have a negative effect on the transcription of number of genes involved in carbohydrate transport and metabolism through its influence on the adenylate cyclase system.

[0066] Strain KJ122, good succinate producer, contains a frameshift mutation in the ptsI gene, and this mutation is important for good succinate production. Thus it was surprising in the context of the current invention that further improvements in succinate production could be made by deleting ptsHI and galP, and then installing a facilitated diffusion system.

[0067] In another embodiment, the present invention provides a non-naturally occurring duplication of the crr gene that encodes the EIIA.sup.Glc protein. The inventors discovered that strains containing a ptsHI deletion, a galP mutation, and an installation of a functional glf gene, have an unexpected tendency to acquire a mutation in the crr gene which causes a decrease or elimination in function of the EIIA.sup.Glc protein, which in turn causes an unexpected undesirable decrease in succinate production parameters. Duplication of the crr gene by integrating a second copy of crr at a locus separate from the native crr locus solves this problem by greatly reducing the frequency of mutants that become phenotypically crr negative.

[0068] The present invention will be explained in detail below. An example bacterium belonging to the genus Escherichia of the present invention is a strain which is constructed from a parental strain that is not initially capable of using facilitated diffusion for sugar import, but which after genetic engineering as disclosed herein harbors a glf gene, and optionally an exogenous glk gene, and has the ability to use facilitated diffusion for import of glucose and fructose.

[0069] The exogenous genes introduced into the cell can be maintained within the cell on a self-replicating plasmid. A plasmid can be maintained through antibiotic selection or complementation of a chromosomal mutation. However, when the exogenous genes are maintained within the biocatalyst on a self-replicating plasmid within the cell, it is necessary to assure the there is no unnecessary waste of energy and materials leading to the inhibition of growth, and a decrease in the yield or productivity of the organic material being manufactured using the biocatalyst. Preferentially, the exogenous genes are integrated into the host chromosome so that there is no need to add any antibiotics to maintain the plasmids within the cell, and little or no metabolic burden is placed on the cell for plasmid maintenance. There are many possible locations within the cell for the integration of the exogenous genes. The preferential locations for integrating the exogenous genes within the E. coli chromosomal DNA include regions that do not encode an essential function for growth and product formation under commercial fermentation conditions.

[0070] When the exogenous genes are obtained as an operon, it is preferable to remove any possible negative regulatory genes or proteins from the operon. It is ideal to have only the genes and proteins that function positively in facilitated diffusion and metabolism. Thus, expression of a facilitated diffusion gene is preferably not inhibited by a repressor or by carbon catabolite repression.

[0071] The following examples are provided as a way of illustrating the present invention and not as a limitation.

[0072] Any bacterium that does not natively use a facilitated diffusion system for sugar import can be improved according to the present invention.

[0073] A bacterium of the present invention may be obtained by introduction of one or more genes that enables utilization of facilitated diffusion into a succinic acid producing strain such as KJ122 or other strain previously engineered to produce a desired chemical. Alternatively a bacterium of the present invention may be obtained by conferring an ability to produce succinic acid or other desired chemical to a bacterium in which utilization of facilitated diffusion has already been enabled by genetic engineering, and optionally by evolution. This latter alternative can be accomplished, for example, by following all the steps used for constructing KJ122 but starting with strain ATCC 9637 or a K-12 type E. coli strain, or any other safe E. coli strain, instead of starting with strain ATCC 8739.

Example 1

Construction of AC15, a Derivative of KJ122 that Contains the Glf and Glk Genes from Gene Cluster from Zymomonas mobilis CP4

[0074] All manipulations of DNA and plasmids, polymerase chain reaction (PCR), transformation, and chromosomal integration were accomplished by standard methods that are well known in the art, It is well known that DNA sequences can be cloned and joined together to form new combinations that cannot be easily found in nature. In addition to the more traditional methods involving restriction enzymes and DNA ligase, newer methods using recombineering in yeast, the so-called "Gibson Method" of in vitro splicing of DNA, or any other appropriate method can be used to construct such novel DNA sequences. The DNA fragments needed can be obtained from libraries of clones or by PCR from appropriate template DNA. It is also understood that many desired DNA sequences can be designed and synthesized from chemical precursors. Such a service is supplied by a number of commercial companies, for example DNA 2.0 and GeneArt (Invitrogen).

[0075] Plasmid pAC19 was constructed to contain an artificial operon containing the glf and glk genes from Z. mobilis, driven by the P.sub.26 promoter from the Bacillus subtilis phage SP01. This operon was embedded between an upstream sequence homologous to the E. coli C tdcC gene and a downstream sequence homologous to the E. coli C tdcE gene, to foster integration into the tdcCDE locus of strains to be engineered. The cassette described above is carried on a low copy plasmid vector derived from pCL1921, which contains the pSC101 origin of replication and a spectinomycin resistance gene. The components for the cassette were obtained by PCR using appropriate synthetic DNA primers obtained from commercial suppliers such as Sigma and Integrated DNA Technologies (IDT). The source for the Zymomonas genes was pLOI1740, which originally contained a zwf and edd gene in addition to the desired glf and glk genes. The glf, zwf, edd, glk cluster was transferred to pCL1921, and then the unnecessary zwf and edd genes were deleted by inside out PCR. The upstream and downstream tdc sequences were obtained by PCR from KJ122 chromosomal DNA as template. The P.sub.26 promoter was obtained from bacteriophage SP01. The sequence of pAC19 is given as SEQ ID #1.

[0076] All constructions were done while growing strains on LB medium (10 grams Bacto-tryptone, 5 grams Bacto-yeast extract, and 5 grams sodium chloride) supplemented as appropriate with antibiotic or sucrose. To construct strain AC15, the cassette containing the artificial operon of pAC19 was integrated into the chromosome of strain WG53, using a two step gene replacement method previously described The cat, sacB cassette for the first step was contained on plasmid pAC21, SEQ ID #2. pAC21 is similar to pAC19, except that the artificial operon is replaced with a cat, sacB cassette that contains a chloramphenicol resistance gene and a counterselectable sacB gene encoding levan sucrase The transforming DNA was obtained by PCR form pAC21 for the first step and by PCR from pAC19 for the second step.

[0077] Strain WG53 was obtained by deleting the ptsH, ptsI, and galP genes from succinate producing strain KJ122, using a two step gene replacement method similar to that described in the above paragraph. The DNA sequence spanning the ptsHI deletion is given as SEQ ID #3. Note that this deletion leaves the crr gene intact, as well as native promoters that naturally exist upstream from the ptsH gene. The DNA sequence spanning the galP deletion is given as SEQ ID #4.

[0078] While intermediate strain WG53 grew extremely poorly on minimal glucose medium, strains KJ122 and AC15 grew well on minimal glucose medium, demonstrating that 1) the ptsHI and galP genes had been successfully deleted in WG53, and 2) the glf, glk cassette was functional in AC15 allowing glucose to be imported.

Example 2

Strain AC15 Produces Succinate as Well as Parent KJ122

[0079] Strains KJ122 and AC15 were grown under microaerobic condition in 7 liter fermentors (New Brunswick Scientific) at 39.degree. C. using a minimal medium with glucose fed batch system. The starting volume of 3 liters contained potassium phosphate monobasic (18 mM), magnesium sulfate (2 mM), betaine (1.33 mM), trace elements, Antifoam 204 (8 ppm) and 25 g/l glucose. The pH was adjusted initially to pH 7.0 and thereafter was maintained at pH 6.5 as acid was produced by addition of the ammonium hydroxide/ammonium bicarbonate solution described below. The 150 ml inocula were grown aerobically and contained a minimal medium similar to the above described medium, except that glucose was at 20 g/l and calcium chloride was added to a final concentration of 0.1 mM. Agitation was set at 750 RPM (revolutions per minute). When glucose decreased to 5 g/l, a 650 g/l glucose feed was started and maintained at a rate aimed to keep the glucose concentration at about 5 g/l or less. The stock solution used for neutralization contained both ammonium hydroxide and ammonium bicarbonate (7 N NH.sub.4OH and 3M NH.sub.4HCO.sub.3). AC15 was aerated at 35 ml/min, while KJ122 was not given air other than what was present in the head space, which was equilibrated with the atmosphere through a breathable sterile membrane filter. These were conditions that had been shown to work well for each strain. Sugars, succinate, and byproducts from 48 hour samples were assayed by HPLC. The results of averaged duplicates are shown in Table 1. AC15 produced about the same titer as parent KJ122, but the acetate byproduct was significantly lower, and the yield on glucose was higher for AC15.

Example 3

Spontaneous "Red Mutants" Derived from AC15

[0080] KJ122 is able to ferment lactose, as evidenced by formation of red colonies on MacConkey lactose plates (Beckton-Dickinson, Franklin Lakes, N.J.). However, AC15 does not ferment lactose, as evidence by producing "white" (beige) colonies on MacConkey lactose plates. This white colony phenotype of AC15 results from binding and inhibition of lactose permease (LacY) by unphosphorylated EIIA.sup.Glc protein. This white colony phenotype is present in all strains deleted for ptsHI, since the enzymes required to phosphorylate EIIA.sup.Glc are absent, and as a result, all EIIA.sup.Glc present in the cells remains unphosphorylated. Thus, ironically, E. coli ptsHI mutants are phenotypically Lac.sup.-, even though lactose is not imported by the PTS system in E. coli.

[0081] The inventors noticed by chance that when MacConkey lactose plates were streaked with AC15 and allowed to incubate overnight at 37.degree. C., and then for an extra day at room temperature (about 22.degree. C.), a large number of red colonies emerged from the lawn of white colonies that had grown over the denser part of the streak. Upon restreaking of several of the red colonies, it was observed that two classes of red colonies had evolved. We shall call the first class "solid red", since the individual colonies were uniformly red across the entire colony. A second class shall be called "fried egg red", since the individual colonies were red in the center, but the outer portion of the colonies were white or beige. We shall call the strains giving rise to all types of red colonies on MacConkey lactose collectively "red mutants".

[0082] A white colony of AC15, and four red mutants, named AC15-R1, -R2, -R3, and -R4 (two of which are solid red and two of which are fried egg red), were tested for succinate production in 500 ml microaerobic fermentors (Fleakers, Corning Glass, Corning, N.Y.) using a medium and method similar to those described above for the 7 liter fermentors, with the differences being that the starting volume of the minimal medium was 200 ml, the glucose was all batched in the starting medium at 100 g/l, no glucose was fed, agitation was with a magnetic stirring bar at 350 RPM, and no air was deliberately introduced or removed. The results are shown in Table 2. The two fried egg mutants performed similarly to parent AC15, while the two solid red mutants performed significantly worse than parent AC15.

[0083] Genome sequencing of the parent AC15 and the four red mutants, using the Illumina HiSeq2000 system, revealed that both solid red mutants had acquired one mutation each, and both of these mutations were in the crr gene, which encodes EIIA.sup.Glc. Both were judged to be null mutations. Both fried egg red mutants had acquired one mutation each, and both of these mutations were in the lactose operon. Both of these were judged to be mutations that would lead to a higher level of expression of the lactose operon (one was a mutation in the lacO operator, and the other was a frameshift in lacI, the gene that encodes the Lac repressor. All four mutations made sense in that they could explain the observed phenotype of increased ability to ferment lactose. The crr null mutations relieved the inhibition of the LacY permease, as would be expected, while the lactose operon mutations would be expected to overproduce LacY, allowing at least some escape from the inhibition. However, the crr null mutations clearly had an additional pleiotropic effect, causing a decrease in the cells' ability to produce succinate under our fermentation conditions. This was an unexpected effect that was not predicted.

Example 4

[0084] The Zymomonas mobilis glk gene is not essential for functioning of the glf gene in E. coli (084) Plasmid pSS2 was constructed using methods similar to those described above for pAC19. The only differences between pSS2 and pAC19 is that the, Z. mobilis glk gene was deleted from the artificial operon. In other aspects, such as vector backbone, the promoter driving expression of glf, embedding the artificial operon in the tdc flanking sequences, and orientation of the various components, pSS2 is similar to pAC19. The DNA sequence of pSS2 is given as SEQ ID #5.

[0085] The artificial operon from pSS2 was integrated at the tdc locus of KJ122 as described above for the operon from pAC19, using the two step gene replacement method. Two isolates, which are presumably identical to each other were named SS8-9 and SS8-11. These two new strains were compared to AC15 in 500 ml microaerobic fermentors as described above in Example 3. The results, which are averages of duplicate fermentors assayed at 48 hours, are shown in Table 3. SS8-9 and SS8-11 both gave growth and succinate titers similar to that of AC15, while the acetate production of both SS8 isolates was somewhat lower than that of AC15. Thus, the Z. mobilis glk gene is unnecessary for functioning of the glf gene in this context, and the Z. mobilis glk gene might even be slightly harmful to the fermentation parameters. Presumably, the SS8 isolates are using the endogenous E. coli glk gene to phosphorylate glucose.

Example 5

Metabolic Evolution of Strain AC15

[0086] As noted above in Example 3, strain AC15 preferred to receive a higher level of aeration than parent KJ122 in 7 liter fermentors. In order to obtain a derivative of AC15 that could thrive on less air, AC15 was subjected to metabolic evolution in 500 ml fermentors with a starting volume of 200 ml and no deliberate supply of aeration. The conditions were microaerobic, since no measures were taken to remove oxygen. A small amount of air was assumed to leak into the fermentation vessels during the course of the evolution. The conditions for growth were as described in Example 3. After 48 hours of growth, the culture was diluted 1:100 into a fresh fermentor containing 200 ml of fresh medium, and this step was then repeated 40 more times. Each one of these inoculations to fresh medium shall be called a "transfer". Thus, the strain was subjected to a total of 41 transfers to fresh medium. Each transfer corresponds to about 7 generations of cell division. A sample of the liquid culture from the last transfer was plated on a MacConkey lactose agar petri plate, and a single white colony was chosen and named YSS41.

[0087] By varying the rate of aeration in 7 liter fermentors, it was determined that YSS41 performed well for succinate production with 5 ml/min of air, which was substantially less than the 35 ml/min required for optimal performance of the parent AC15. With 5 ml/min air flow, YSS41 produced 94 g/l succinate and 1.3 g/l acetate, for a succinate yield of 0.95 g/g glucose in 48 hours in a 7 liter fermentor.

[0088] YSS41 was compared to KJ122 for succinate production in a 20 liter fermentor. The fermentation protocol was similar to that described above for 7 liter fermentors, except that the starting volume was 9 liters, and the aeration rate was 25 ml/min for both strains, conditions that had been determined to be productive for both strains. The results for 48 hour samples are shown in Table 4. The succinate titer for YSS41 was 100 g/l (significantly higher than for KJ122), the acetate as 2.2 g/l (significantly lower than for KJ122), and the succinate yield was 0.95 g/g glucose (a little lower than for KJ122). Thus, the evolved strain YSS41 was able to perform well in a 20 liter fermentor with an aeration requirement that was no higher than for the ancestor strain KJ122.

Example 6

Stabilizing YSS41 Against Mutations in the Crr Gene

[0089] When streaked on MacConkey lactose plates, YSS41 still gave rise to red mutants, both of the solid red type and of the fried egg red type. The crr gene was sequenced for one isolate of each type. Strain MYR222, a fried egg type had a wild type crr gene sequence. MYR223, a solid red type, had an insertion element inserted in the crr open reading frame. The DNA sequence of the insertion element matched that of IS186. Thus, the pattern established for AC15 red mutants appeared to apply also to YSS41 red mutants. In 500 ml microaerobic fermentors, grown as in Example 4, MYR222 performed similarly to YSS41, while MYR223 performed more poorly (see Table 5). Thus the potential loss of performance due to accumulation of solid red mutants in a population remained a possibility with strain YSS41.

[0090] In order to solve this potential loss, a second copy of the crr gene was integrated into a site distant form the native crr locus. The crr gene, together with its flanking promoters and terminator were amplified by PCR using YSS41 chromosomal DNA as a template, and primers BY249 (SEQ ID #6) and BY250 (SEQ ID #7). The resulting blunt fragment was then ligated into a low copy plasmid derived from pCL1921 that contained a clone of a portion of the pflDC region from E. coli C at the unique BstZ171 restriction site in the pflD open reading frame. The pflDC genes are homologous to the pflBA genes that encode pyruvate-formate lyase and the pyruvate-formate lyase activating enzyme. The pflDC genes are not essential for E. coli, and deletion of either pflD or pflC has no significant effect on growth, so it was reasoned that insertion of a cassette at that locus would not have any negative consequence for growth or succinate production. The resulting low copy plasmid, pMH68, contains the crr gene from YSS41 embedded in flanking sequences from pflDC, in a low copy plasmid. The DNA sequence of pMH68 is given as SEQ ID #8.

[0091] The integration cassette from pMH68 was amplified by PCR using primers BY124 (SEQ ID #9) and BY125 (SEQ ID #10), which were the same primers used to clone the pflDC genes to begin with. The integration cassette was then integrated into the chromosome of YSS41, using the two step gene replacement method. The resulting strain was named MH141, which is now a merodiploid for crr, meaning that it contains two copies of a wild type crr gene in two distant locations on the chromosome, one at its native locus, and the second inserted in the pflD open reading frame.

[0092] As expected, strain MH141 produced white colonies on MacConkey lactose plates. If a heavy streak is made, and the plates are and allowed to incubate overnight at 37.degree. C., and then for an extra day at room temperature, red colonies emerged from the lawn of white colonies that had grown over the denser part of the streak. However, the number of red mutants arising from MH141 was significantly lower than for a similar streak of YSS41 made on the same plate. 23 red mutants were picked from YSS41 and 12 red mutants were picked from MH141, and all were restreaked on MacConkey lactose plates. When scored for the type of red mutant, 12 of the 23 YSS41 red mutants were of the solid red type, while the other 11 of the 23 were of the fried egg type. In contrast, all 12 of the MH141 red mutants were of the fried egg type. Thus, by duplicating the crr gene in the chromosome, the rate of formation of the solid red mutants has been decreased by at least a factor of ten. One fried egg red mutant isolated from MH141 was named MH141-R1 and tested in 500 ml microaerobic fermentors as described above (see Table 5). Both MH141 and MH141-R1 performed similarly to parent YSS41 with respect to growth, succinate titer, and acetate titer. Thus, a more stable strain, MH141, has been constructed that uses facilitated diffusion for glucose import, and which produces a higher titer of succinate and a lower titer of the byproduct acetate when compared to the ancestor strain KJ122, which uses a the GalP system for glucose import.

Example 7

YSS41 Acquired Mutations in the Glf, Glk Cassette During Metabolic Evolution

[0093] The DNA sequences of the glf, glk expression cassettes in AC15 and YSS41 were determined. The regions were amplified by PCR and the resulting fragments were sequenced over the glf and glk genes and more than 200 base pairs upstream and downstream, by the dideoxy chain termination method. The sequenced region corresponds to bases 4976 to 7920 of pAC19, given in SEQ ID #1. Two mutations were found that were acquired during the evolution of YSS41. The first mutation was a G to A change at base number 7742 of SEQ ID #1. This base is in the 5' untranslated region of the glf, glk mRNA transcript, just upstream from the glf open reading frame, and results in a C to U change at base -22 relative to the ATG start codon, or +15 relative to the start of transcription, in the glf mRNA (messenger RNA). This mutation is expected to increase or decrease the rate of translation of the glf open reading frame. The second mutation was a G to A change at base number 6173 of SEQ ID #1. This base is in the 5' untranslated region just upstream from the glk open reading frame, and results in a C to U change at base -15 relative to the ATG start codon in the glk mRNA. This mutation is expected to increase or decrease the rate of translation of the glk open reading frame. Thus, the evolution of YSS41 resulted in a more optimal balance of expression between the glf and glk open reading frames, to result in a strain that outgrew and outperformed the parent strain AC15.

[0094] Other mutations that alter the rate of transcription or expression of the glf and glk genes, or that alter the concentration, specific activity, or stability of the glf and glk proteins, can similarly achieve a more optimal balance between the two encoded proteins will also benefit growth and production of a desired chemical. These other alternative mutations can be obtained by the using the method described above for YSS41. This method can also be applied to strains engineered to produce products other than succinate, where the ability to use facilitated diffusion or sugar import has been engineered into the strain.

Example 8

[0095] Fermentation of KJ122 and YSS41 after optimization of air flow rate for YSS41 (095) The optimum air flow rate for parent strain KJ122 had been determined to be 25 ml/minute in a 20 liter fermentor. At the air flow rate of 25 ml/min, YSS41 strain showed better succinate titer and yield when compared to that of KJ122. Further improvement in succinate yield and titer with YSS41 strain was obtained by increasing the air flow rate to 50 ml/min. Thus the optimal air flow rate for YSS41 strain with reference to succinate yield and titer seems to be different from that of KJ122. Table 6 provides fermentation results in the 20 liter fermentor under the optimized air flow conditions for each strain. YSS41 outperformed parent KJ122 in titer, yield, and acetate byproduct formation. The initial volume of the fermentation was 9500 ml. After feeding glucose and neutralizing with base the final volume was 12500 ml.

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TABLE-US-00001

[0138] TABLE 1 Production of Succinate by AC15 in 7 Liter Fermentors Relevant Aeration Succinate Acetate Yield g/g Strain genotype ml/min g/l g/l glucose KJ122 parent, ptsI*, 0 87 5.2 0.83 galP+ AC15 KJ122, .DELTA.ptsHI, 35 87 2.7 0.88 .DELTA.galP, P.sub.26-glf, glk

TABLE-US-00002 TABLE 2 Production of succinate by AC15 red mutants in 500 ml microaerobic fermentors Colony phenotype on MacConkey Succinate Acetate Mutation Strain lactose g/l g/l OD.sub.600 found AC15 white 74 2.4 7.5 none AC15-R1 solid red 51 9.0 6.5 crr Lys16 frameshift AC15-R3 solid red 65 6.6 7.0 crr Met1Ile AC15-R2 fried egg red 73 2.4 8.0 lacO G11A AC15-R4 fried egg red 73 3.0 7.5 lacI Asp300 frameshift

TABLE-US-00003 TABLE 3 Succinate production by SS8 isolates in 500 ml microaerobic fermentors Succinate Acetate Strain Relevant genotype g/l g/l OD.sub.600 AC15 KJ122, .DELTA.ptsHI, .DELTA.galP, 64 6.0 7.5 P.sub.26-glf, glk SS8-9 KJ122, .DELTA.ptsHI, .DELTA.galP, 64 4.2 8.5 P.sub.26-glf SS8-11 KJ122, .DELTA.ptsHI, .DELTA.galP, 64 3.6 8.2 P.sub.26-glf

TABLE-US-00004 TABLE 4 Succinic acid production by YSS-41, in a 20 liter fermentor Air flow Yield on Relevant rate Succinate Acetate glucose Strain genotype ml/min g/l g/l g/g KJ122 ptsI* 25 87 6.8 1.00 KJ122 ptsI* 25 85 6.8 0.98 YSS41 KJ122.quadrature..quadrature..DELTA.ptsHI, 25 100. 2.2 0.95 .DELTA.galP, P.sub.26-glf, glk, evolved

TABLE-US-00005 TABLE 5 Succinate production in 500 ml microaerobic fermentors by MH141, a merodiploid for crr+. Colony phenotype Relevant on MacConkey Succinate Acetate Strain genotype lactose g/l g/l OD.sub.600 YSS41 AC15, white 67 3.9 10.0 evolved, crr.sup.+ MH141 YSS41, white 68 3.2 8.5 .DELTA.pflD::crr.sup.+

TABLE-US-00006 TABLE 6 Succinate production by E. coli strains KJ122 and YSS41 in 20 liter fermentors under optimized aeration conditions for both strains Succinate Air flow Succinate yield on Acetate Cell rate titer glucose titer mass as Strain (ml/min) (g/l) (g/g) (g/l) OD600 KJ122 25 81 0.86 3.9 12 YSS41 50 96 0.98 2.5 13 YSS41 25 93 0.98 2.5 13

Sequence CWU 1

1

1219430DNAEscherichia colipAC19(1)..(9430)Plasmid used to install a glf-glk casette at the tdc locus of bacterial strain KJ122 1gttgacagta agacgggtaa gcctgttgat gataccgctg ccttactggg tgcattagcc 60agtctgaatg acctgtcacg ggataatccg aagtggtcag actggaaaat cagagggcag 120gaactgctga acagcaaaaa gtcagatagc accacatagc agacccgcca taaaacgccc 180tgagaagccc gtgacgggct tttcttgtat tatgggtagt ttccttgcat gaatccataa 240aaggcgcctg tagtgccatt tacccccatt cactgccaga gccgtgagcg cagcgaactg 300aatgtcacga aaaagacagc gactcaggtg cctgatggtc ggagacaaaa ggaatattca 360gcgatttgcc cgagcttgcg agggtgctac ttaagccttt agggttttaa ggtctgtttt 420gtagaggagc aaacagcgtt tgcgacatcc ttttgtaata ctgcggaact gactaaagta 480gtgagttata cacagggctg ggatctattc tttttatctt tttttattct ttctttattc 540tataaattat aaccacttga atataaacaa aaaaaacaca caaaggtcta gcggaattta 600cagagggtct agcagaattt acaagttttc cagcaaaggt ctagcagaat ttacagatac 660ccacaactca aaggaaaagg actagtaatt atcattgact agcccatctc aattggtata 720gtgattaaaa tcacctagac caattgagat gtatgtctga attagttgtt ttcaaagcaa 780atgaactagc gattagtcgc tatgacttaa cggagcatga aaccaagcta attttatgct 840gtgtggcact actcaacccc acgattgaaa accctacaag gaaagaacgg acggtatcgt 900tcacttataa ccaatacgct cagatgatga acatcagtag ggaaaatgct tatggtgtat 960tagctaaagc aaccagagag ctgatgacga gaactgtgga aatcaggaat cctttggtta 1020aaggctttga gattttccag tggacaaact atgccaagtt ctcaagcgaa aaattagaat 1080tagtttttag tgaagagata ttgccttatc ttttccagtt aaaaaaattc ataaaatata 1140atctggaaca tgttaagtct tttgaaaaca aatactctat gaggatttat gagtggttat 1200taaaagaact aacacaaaag aaaactcaca aggcaaatat agagattagc cttgatgaat 1260ttaagttcat gttaatgctt gaaaataact accatgagtt taaaaggctt aaccaatggg 1320ttttgaaacc aataagtaaa gatttaaaca cttacagcaa tatgaaattg gtggttgata 1380agcgaggccg cccgactgat acgttgattt tccaagttga actagataga caaatggatc 1440tcgtaaccga acttgagaac aaccagataa aaatgaatgg tgacaaaata ccaacaacca 1500ttacatcaga ttcctaccta cgtaacggac taagaaaaac actacacgat gctttaactg 1560caaaaattca gctcaccagt tttgaggcaa aatttttgag tgacatgcaa agtaagcatg 1620atctcaatgg ttcgttctca tggctcacgc aaaaacaacg aaccacacta gagaacatac 1680tggctaaata cggaaggatc tgaggttctt atggctcttg tatctatcag tgaagcatca 1740agactaacaa acaaaagtag aacaactgtt caccgttaca tatcaaaggg aaaactgtcc 1800atatgcacag atgaaaacgg tgtaaaaaag atagatacat cagagctttt acgagttttt 1860ggtgcattta aagctgttca ccatgaacag atcgacaatg taacagatga acagcatgta 1920acacctaata gaacaggtga aaccagtaaa acaaagcaac tagaacatga aattgaacac 1980ctgagacaac ttgttacagc tcaacagtca cacatagaca gcctgaaaca ggcgatgctg 2040cttatcgaat caaagctgcc gacaacacgg gagccagtga cgcctcccgt ggggaaaaaa 2100tcatggcaat tctggaagaa atagcgcttt cagccggcaa acctgaagcc ggatctgcga 2160ttctgataac aaactagcaa caccagaaca gcccgtttgc gggcagcaaa acccgttatg 2220cttgtaaacc gttttgtgaa aaaattttta aaataaaaaa ggggacctct agggtcccca 2280attaattagt aatataatct attaaaggtc attcaaaagg tcatccaccg gatcaattcc 2340cctgctcgcg caggctgggt gccaagctct cgggtaacat caaggcccga tccttggagc 2400ccttgccctc ccgcacgatg atcgtgccgt gatcgaaatc cagatccttg acccgcagtt 2460gcaaaccctc actgatccgc atgcccgttc catacagaag ctgggcgaac aaacgatgct 2520cgccttccag aaaaccgagg atgcgaacca cttcatccgg ggtcagcacc accggcaagc 2580gccgcgacgg ccgaggtctt ccgatctcct gaagccaggg cagatccgtg cacagcacct 2640tgccgtagaa gaacagcaag gccgccaatg cctgacgatg cgtggagacc gaaaccttgc 2700gctcgttcgc cagccaggac agaaatgcct cgacttcgct gctgcccaag gttgccgggt 2760gacgcacacc gtggaaacgg atgaaggcac gaacccagtg gacataagcc tgttcggttc 2820gtaagctgta atgcaagtag cgtatgcgct cacgcaactg gtccagaacc ttgaccgaac 2880gcagcggtgg taacggcgca gtggcggttt tcatggcttg ttatgactgt ttttttgggg 2940tacagtctat gcctcgggca tccaagcagc aagcgcgtta cgccgtgggt cgatgtttga 3000tgttatggag cagcaacgat gttacgcagc agggcagtcg ccctaaaaca aagttaaaca 3060tcatgaggga agcggtgatc gccgaagtat cgactcaact atcagaggta gttggcgtca 3120tcgagcgcca tctcgaaccg acgttgctgg ccgtacattt gtacggctcc gcagtggatg 3180gcggcctgaa gccacacagt gatattgatt tgctggttac ggtgaccgta aggcttgatg 3240aaacaacgcg gcgagctttg atcaacgacc ttttggaaac ttcggcttcc cctggagaga 3300gcgagattct ccgcgctgta gaagtcacca ttgttgtgca cgacgacatc attccgtggc 3360gttatccagc taagcgcgaa ctgcaatttg gagaatggca gcgcaatgac attcttgcag 3420gtatcttcga gccagccacg atcgacattg atctggctat cttgctgaca aaagcaagag 3480aacatagcgt tgccttggta ggtccagcgg cggaggaact ctttgatccg gttcctgaac 3540aggatctatt tgaggcgcta aatgaaacct taacgctatg gaactcgccg cccgactggg 3600ctggcgatga gcgaaatgta gtgcttacgt tgtcccgcat ttggtacagc gcagtaaccg 3660gcaaaatcgc gccgaaggat gtcgctgccg actgggcaat ggagcgcctg ccggcccagt 3720atcagcccgt catacttgaa gctagacagg cttatcttgg acaagaagaa gatcgcttgg 3780cctcgcgcgc agatcagttg gaagaatttg tccactacgt gaaaggcgag atcaccaagg 3840tagtcggcaa ataatgtcta acaattcgtt caagccgacg ccgcttcgcg gcgcggctta 3900actcaagcgt tagatgcact aagcacataa ttgctcacag ccaaactatc aggtcaagtc 3960tgcttttatt atttttaagc gtgcataata agccctacac aaattgggag atatatcatg 4020aaaggctggc tttttcttgt tatcgcaata gttggcgaag taatcgcaac atccgcatta 4080aaatctagcg agggctttac taagctgatc cggtggatga ccttttgaat gacctttaat 4140agattatatt actaattaat tggggaccct agaggtcccc ttttttattt taaaaatttt 4200ttcacaaaac ggtttacaag catacgttgg ccgattcatt aatgcagctg gcacgacagg 4260tttcccgact ggaaagcggg cagtgagcgc aacgcaatta atgtgagtta gctcactcat 4320taggcacccc aggctttaca ctttatgctt ccggctcgta tgttgtgtgg aattgtgagc 4380ggataacaat ttcacacagg aaacagctat gaccatgatt acgccaagct tgcatgcctg 4440caggtcgact ctagaggatc ccccccgccg ccgacagagt aataggtttt acttaatagc 4500tcttcctgtc ccttccaggc agtgatccgc attccgttct catggcgagg caacatttcg 4560ggatggaaga taatgttctt tgctacagga aaatcaacaa tatgcgcacc agatgccact 4620ggcagccgcc cgctgcgcgt tactaactct ataaatgcag ggatctcatc aatgacaaca 4680tcctgcggac tgtttcctgc cagtcccatg atgatggcga catccgtggc atggcctttg 4740cccgtcagtg acaacgaccc gtacagatcg accacaatat ggctcgtcgc ggttaataag 4800ccgctacttt ccagccgatc aataaaactt tttccggcat tcattggccc cacggtatgc 4860gaactggagg gaccaatccc aattttgaaa atatcgaatg cactaatcat atccacaccc 4920tcggattgcc gttcagtgaa gtggagcgga acgaccttac gaccgtcccg ctcacgaggc 4980tttacgcact acgtactgcg atggcttcaa tttccagcgg gagggcggat ccactaatac 5040aaaatatatc aaaagttaat aataatatta ttcttactta agactttttt gtcttcattt 5100tttagtaaaa aatataaaaa aggccacctc ccgattttat cggaaggcag cctcttaaat 5160tcagttcata atattaaaaa atattattca acttcagaat atttgttggc ataggcagct 5220gccgcaccca acagtccagg ctgcggataa gtaatcaact taaccggaat cttggacatg 5280acgcgttcaa agcgtccttt tgaaacaaag cgctgacgga aaccagattc tggcaaatgg 5340gaagcgatac gaagaccgac accaccgcca ataacaacac tggttcgacc ctgtgccaaa 5400gcaagatcac cagcgatagc gccaaggctc aagcagaagc gatccaaagc ggcttcagca 5460aggttgtctt taccttccaa agccatctgc cataatttaa tatcatccag caagctgaac 5520ggaacgcctt caatggcagc cagtgcttcg tagatattac caagacccgg gccagaaata 5580atgcgttcga tagaaacgcg gcggaaacgt tcacgtaaac gtgccagaat tttgtcttca 5640agtctgtcaa gcggagcaaa gtcgatatga ccgccttcag tttcgatgac gaaataacgg 5700ccttcagtcc gcaacagatg ggcaacaccc aagcccgttc ccggaccaag aatagtgata 5760acaccatcgc taggaagcgc ttcatcagga ccacaaatat gatccagata agaagaatcc 5820atatgcgcaa ccgcgtgggc aaccgcgccg aagtcattga tcagaacatg cgtatcgatg 5880tccagctttt cattcagagt agctggtctt aatacccaag ggttattggt aagttttaaa 5940acttcaccat gaaccgggcc agcccatgca atagctgcgg cacgtggcag aggacgaccc 6000agtttttcac cgaaacgttc ccaagctaac tgcaagctag catgttctgc cgttttaaaa 6060gttgtttctt ctccaagaga aagaacccga ccattgctta cttccgcaat agagaaacgc 6120gcatgcgttc caccgatgtc aatcgcaaca atttccataa taattccttt ctgaaatcag 6180aaggctaccc aacaggtaaa ataagtccgc ccgctttata ccatcgttgt aaacaaaaag 6240tataattggt taagacttat ctaaaaaaga caaaaggatt cagccaaagc aagtttaact 6300acttctggga gcgccacatc tcctcgattt catccaggct ccgacctttg gtttccggca 6360cgaagcgagc aacaatcaag ccacctaaga tacttaatgc tgcgaaaacg agataggaga 6420aaccgtggtt gaaagtctga ttcaatgctg gagaaccatc ggcaacctta aacaggaagt 6480taaccaagat attagctaac cattgtccgg taacagcgat aggcatagct gcgcccttga 6540tggaactcgg gaacatttct gacagaacaa cccagcagac agggccccat gacataccaa 6600agactgcaat ataaagaagc acagaagcca aaggcaaaac accaccgact ttgaaccaga 6660aacagcagcc taaaacagcc atcattgcag ccataccgag agcaccccaa ataagcagag 6720gtttacggcc gaagcggtca acaacacggg aagcaatcat ggtgaagatg aagttcacaa 6780caccgataga gatggtctgc aataatgccg tatcagctcc aaaacctaaa ttctggaaca 6840tctgcggtgc ataatacagc acggcgttaa taccgactaa ctgctggaag gcagcaacgg 6900atacaccggc aaaaacaacg gtgataccaa aagcaaacaa acctgcgctg cttttgtcca 6960tggctttatc aaagccagct ttaatctttt gaatcgtcag attaggatcg gcttgcggtt 7020ccagacgagc aaggattttg ctagcctcgg aatgacgtcc cttcatcacc aaccaatgcg 7080gcgtatccgg tgcggttaac agcagcaata agaaggcaat accgatcagg ccttctgaag 7140ccggagacca gcaccaacca ctggcattaa cccaatcgat agaaccgaaa tgagccagta 7200accaggtaaa gatataaccg gttaaagcac ccgtcacaat ggccatctgc tgaccagaaa 7260ccatctgacc acgtttgtct ggcggagcaa tttcagcaat ataggttggg gtcaaggttg 7320aaacgacacc gatacctaaa ccggcaagaa accggaaaaa gcaaaaaatt tgtaaagccg 7380aaccaccggt tccaaataat ttttcggtta acgcagcacc aaaaccggcg gcgacgaaac 7440aaatggaact catcaacaat ccgccgcgac gaccgaagcg aataccaatc cagccagaca 7500gcaaagaacc ggtaacacaa ccgaccaaaa cagcaacaac gaccatccca gaaagggaag 7560ccgcagccgt agcagacagg tgacgagggg caataaaatg gatatcaacc ggtgtaccga 7620ttgcagcgat aaccgctgaa tcgtaaccga aaagcaagcc gcctatagca gcgattaggg 7680ctagtcgcgt gactagaccc tgactacttt cagaactcat ggcgattcct ctccctctag 7740agcgtcctgc tgttgttaag attattatac cacaccttgt agataaagtc aacaactttt 7800tgcaaaattt ttcaggaatt ttagcagagg ttgttctgga tgtagaacaa aacatctttc 7860cgctcttgtg ctgttaggat atctttcttg gaagctaggt aggcctcgag ttatggcagt 7920tggttaaaag gaaacaaaaa gaccgttttc acacaaaacg gtctttttcg atttcttttt 7980acagtcacag ccacttttgc accaattaag gccacgctgt catttaaact ccgtttttcc 8040agttcaaatg caattgcctt caatgcacct tcgtagctgt ggtgagccag cggtgctggc 8100tctcccccat ttacggataa gaatgcattt tccgagttaa taccgtcggc aatacctgac 8160attaatactt cacagtcgct ggcatcgagt acggaaaact taatcgaaga cgaaccacag 8220ttaataacca aaacaaccgg aaattcattc atctcttttc tcatcctgag ttacggatta 8280aaacagtttg tatacgatgt tcaggatggt cagcagacca atcacggtaa caaacacgtt 8340atccagacga ccacggtatt tcgccagaga cggcgcttta cggatggcat acatcggcaa 8400caggcacagc agggatgcga taatcggtgc gcccatggct tcaatcaggt cgaggatgtt 8460cgggttggcg taggcaacaa cccaggtgga gcccatgatg aagatcatgc tgagagtatt 8520cagtttaccc agcgacactt tggttttgtc acctttataa ccgaacttca gaatcagacc 8580attcaagcct tccagcgtcc ccagatagtg accgaagaaa gatttgaaga tagccacgag 8640tgcgatgatg gaagccgcat attccagtgt aatcgcgaac gttgttttgg taccggtcat 8700ggacgcaaag tggttagcca gataagaaag cactggaata ttctgcgctt tggcttccgc 8760catgttggcc ggagacagag taaacaggca gctaaaggca aagaacatca ccactgcaac 8820catcagcatg ctggcacgag aaatgatttg ggaacattta cgttcggtga agtcgcgacc 8880gaagtctttc tcatactctt cacgtttaga aaccacgaag gaagagacga ttggcgagaa 8940gttaaaggag aaaaccatga tggaaatccc cagccagaca gtgatcagga taccgtcatg 9000accggttaac gacagcgaac cgaggtcaac ctggtcgata actgcagagt tccagtaagg 9060gatcagcgac aaagaaatca gcaccaggct ggcgataaac ggccatacca ggtagctcag 9120ggtaccgagc tcgaattcac tggccgtcgt tttacaacgt cgtgactggg aaaaccctgg 9180cgttacccaa cttaatcgcc ttgcagcaca tccccctttc gccagctggc gtaatagcga 9240agaggcccgc accgatcgcc cttcccaaca gttgcgcagc ctgaatggcg aatggcgcct 9300gatgcggtat tttctcctta cgcatctgtg cggtatttca caccgcatat ggtgcactct 9360cagtacaatc tgctctgatg ccgcatagtt aagccagccc cgacacccgc caacacccgc 9420tgacgaattc 943029462DNAEscherichia colipAC21(1)..(9462)Pplasmid used to install a slectable and counterselectable cat-sacB cassette at the tdc locus of strain KJ122 2gttgacagta agacgggtaa gcctgttgat gataccgctg ccttactggg tgcattagcc 60agtctgaatg acctgtcacg ggataatccg aagtggtcag actggaaaat cagagggcag 120gaactgctga acagcaaaaa gtcagatagc accacatagc agacccgcca taaaacgccc 180tgagaagccc gtgacgggct tttcttgtat tatgggtagt ttccttgcat gaatccataa 240aaggcgcctg tagtgccatt tacccccatt cactgccaga gccgtgagcg cagcgaactg 300aatgtcacga aaaagacagc gactcaggtg cctgatggtc ggagacaaaa ggaatattca 360gcgatttgcc cgagcttgcg agggtgctac ttaagccttt agggttttaa ggtctgtttt 420gtagaggagc aaacagcgtt tgcgacatcc ttttgtaata ctgcggaact gactaaagta 480gtgagttata cacagggctg ggatctattc tttttatctt tttttattct ttctttattc 540tataaattat aaccacttga atataaacaa aaaaaacaca caaaggtcta gcggaattta 600cagagggtct agcagaattt acaagttttc cagcaaaggt ctagcagaat ttacagatac 660ccacaactca aaggaaaagg actagtaatt atcattgact agcccatctc aattggtata 720gtgattaaaa tcacctagac caattgagat gtatgtctga attagttgtt ttcaaagcaa 780atgaactagc gattagtcgc tatgacttaa cggagcatga aaccaagcta attttatgct 840gtgtggcact actcaacccc acgattgaaa accctacaag gaaagaacgg acggtatcgt 900tcacttataa ccaatacgct cagatgatga acatcagtag ggaaaatgct tatggtgtat 960tagctaaagc aaccagagag ctgatgacga gaactgtgga aatcaggaat cctttggtta 1020aaggctttga gattttccag tggacaaact atgccaagtt ctcaagcgaa aaattagaat 1080tagtttttag tgaagagata ttgccttatc ttttccagtt aaaaaaattc ataaaatata 1140atctggaaca tgttaagtct tttgaaaaca aatactctat gaggatttat gagtggttat 1200taaaagaact aacacaaaag aaaactcaca aggcaaatat agagattagc cttgatgaat 1260ttaagttcat gttaatgctt gaaaataact accatgagtt taaaaggctt aaccaatggg 1320ttttgaaacc aataagtaaa gatttaaaca cttacagcaa tatgaaattg gtggttgata 1380agcgaggccg cccgactgat acgttgattt tccaagttga actagataga caaatggatc 1440tcgtaaccga acttgagaac aaccagataa aaatgaatgg tgacaaaata ccaacaacca 1500ttacatcaga ttcctaccta cgtaacggac taagaaaaac actacacgat gctttaactg 1560caaaaattca gctcaccagt tttgaggcaa aatttttgag tgacatgcaa agtaagcatg 1620atctcaatgg ttcgttctca tggctcacgc aaaaacaacg aaccacacta gagaacatac 1680tggctaaata cggaaggatc tgaggttctt atggctcttg tatctatcag tgaagcatca 1740agactaacaa acaaaagtag aacaactgtt caccgttaca tatcaaaggg aaaactgtcc 1800atatgcacag atgaaaacgg tgtaaaaaag atagatacat cagagctttt acgagttttt 1860ggtgcattta aagctgttca ccatgaacag atcgacaatg taacagatga acagcatgta 1920acacctaata gaacaggtga aaccagtaaa acaaagcaac tagaacatga aattgaacac 1980ctgagacaac ttgttacagc tcaacagtca cacatagaca gcctgaaaca ggcgatgctg 2040cttatcgaat caaagctgcc gacaacacgg gagccagtga cgcctcccgt ggggaaaaaa 2100tcatggcaat tctggaagaa atagcgcttt cagccggcaa acctgaagcc ggatctgcga 2160ttctgataac aaactagcaa caccagaaca gcccgtttgc gggcagcaaa acccgttatg 2220cttgtaaacc gttttgtgaa aaaattttta aaataaaaaa ggggacctct agggtcccca 2280attaattagt aatataatct attaaaggtc attcaaaagg tcatccaccg gatcaattcc 2340cctgctcgcg caggctgggt gccaagctct cgggtaacat caaggcccga tccttggagc 2400ccttgccctc ccgcacgatg atcgtgccgt gatcgaaatc cagatccttg acccgcagtt 2460gcaaaccctc actgatccgc atgcccgttc catacagaag ctgggcgaac aaacgatgct 2520cgccttccag aaaaccgagg atgcgaacca cttcatccgg ggtcagcacc accggcaagc 2580gccgcgacgg ccgaggtctt ccgatctcct gaagccaggg cagatccgtg cacagcacct 2640tgccgtagaa gaacagcaag gccgccaatg cctgacgatg cgtggagacc gaaaccttgc 2700gctcgttcgc cagccaggac agaaatgcct cgacttcgct gctgcccaag gttgccgggt 2760gacgcacacc gtggaaacgg atgaaggcac gaacccagtg gacataagcc tgttcggttc 2820gtaagctgta atgcaagtag cgtatgcgct cacgcaactg gtccagaacc ttgaccgaac 2880gcagcggtgg taacggcgca gtggcggttt tcatggcttg ttatgactgt ttttttgggg 2940tacagtctat gcctcgggca tccaagcagc aagcgcgtta cgccgtgggt cgatgtttga 3000tgttatggag cagcaacgat gttacgcagc agggcagtcg ccctaaaaca aagttaaaca 3060tcatgaggga agcggtgatc gccgaagtat cgactcaact atcagaggta gttggcgtca 3120tcgagcgcca tctcgaaccg acgttgctgg ccgtacattt gtacggctcc gcagtggatg 3180gcggcctgaa gccacacagt gatattgatt tgctggttac ggtgaccgta aggcttgatg 3240aaacaacgcg gcgagctttg atcaacgacc ttttggaaac ttcggcttcc cctggagaga 3300gcgagattct ccgcgctgta gaagtcacca ttgttgtgca cgacgacatc attccgtggc 3360gttatccagc taagcgcgaa ctgcaatttg gagaatggca gcgcaatgac attcttgcag 3420gtatcttcga gccagccacg atcgacattg atctggctat cttgctgaca aaagcaagag 3480aacatagcgt tgccttggta ggtccagcgg cggaggaact ctttgatccg gttcctgaac 3540aggatctatt tgaggcgcta aatgaaacct taacgctatg gaactcgccg cccgactggg 3600ctggcgatga gcgaaatgta gtgcttacgt tgtcccgcat ttggtacagc gcagtaaccg 3660gcaaaatcgc gccgaaggat gtcgctgccg actgggcaat ggagcgcctg ccggcccagt 3720atcagcccgt catacttgaa gctagacagg cttatcttgg acaagaagaa gatcgcttgg 3780cctcgcgcgc agatcagttg gaagaatttg tccactacgt gaaaggcgag atcaccaagg 3840tagtcggcaa ataatgtcta acaattcgtt caagccgacg ccgcttcgcg gcgcggctta 3900actcaagcgt tagatgcact aagcacataa ttgctcacag ccaaactatc aggtcaagtc 3960tgcttttatt atttttaagc gtgcataata agccctacac aaattgggag atatatcatg 4020aaaggctggc tttttcttgt tatcgcaata gttggcgaag taatcgcaac atccgcatta 4080aaatctagcg agggctttac taagctgatc cggtggatga ccttttgaat gacctttaat 4140agattatatt actaattaat tggggaccct agaggtcccc ttttttattt taaaaatttt 4200ttcacaaaac ggtttacaag catacgttgg ccgattcatt aatgcagctg gcacgacagg 4260tttcccgact ggaaagcggg cagtgagcgc aacgcaatta atgtgagtta gctcactcat 4320taggcacccc aggctttaca ctttatgctt ccggctcgta tgttgtgtgg aattgtgagc 4380ggataacaat ttcacacagg aaacagctat gaccatgatt acgccaagct tgcatgcctg 4440caggtcgact ctagaggatc ccccccgccg ccgacagagt aataggtttt acttaatagc 4500tcttcctgtc ccttccaggc agtgatccgc attccgttct catggcgagg caacatttcg 4560ggatggaaga taatgttctt tgctacagga aaatcaacaa tatgcgcacc agatgccact 4620ggcagccgcc cgctgcgcgt tactaactct ataaatgcag ggatctcatc aatgacaaca 4680tcctgcggac tgtttcctgc cagtcccatg atgatggcga catccgtggc atggcctttg 4740cccgtcagtg acaacgaccc gtacagatcg accacaatat ggctcgtcgc ggttaataag 4800ccgctacttt ccagccgatc aataaaactt tttccggcat tcattggccc cacggtatgc 4860gaactggagg gaccaatccc aattttgaaa atatcgaatg cactaatcat gtgacggaag 4920atcacttcgc agaataaata aatcctggtg tccctgttga taccgggaag ccctgggcca 4980acttttggcg aaaatgagac gttgatcggc acgtaagagg ttccaacttt caccataatg 5040aaataagatc actaccgggc gtattttttg agttatcgag attttcagga gctaaggaag 5100ctaaaatgga gaaaaaaatc actggatata ccaccgttga tatatcccaa tggcatcgta 5160aagaacattt tgaggcattt cagtcagttg ctcaatgtac ctataaccag accgttcagc 5220tggatattac ggccttttta aagaccgtaa agaaaaataa gcacaagttt tatccggcct 5280ttattcacat tcttgcccgc ctgatgaatg ctcatccgga

attccgtatg gcaatgaaag 5340acggtgagct ggtgatatgg gatagtgttc acccttgtta caccgttttc catgagcaaa 5400ctgaaacgtt ttcatcgctc tggagtgaat accacgacga tttccggcag tttctacaca 5460tatattcgca agatgtggcg tgttacggtg aaaacctggc ctatttccct aaagggttta 5520ttgagaatat gtttttcgtc tcagccaatc cctgggtgag tttcaccagt tttgatttaa 5580acgtggccaa tatggacaac ttcttcgccc ccgttttcac catgggcaaa tattatacgc 5640aaggcgacaa ggtgctgatg ccgctggcga ttcaggttca tcatgccgtt tgtgatggct 5700tccatgtcgg cagaatgctt aatgaattac aacagtactg cgatgagtgg cagggcgggg 5760cgtaattttt ttaaggcagt tattggtgcc cttaaacgcc tggtgctacg cctgaataag 5820tgataataag cggatgaatg gcagaaattc gaaagcaaat tcgacccggt cgtcggttca 5880gggcagggtc gttaaatagc cgcttatgtc tattgctggt ttantcggta cccggggatc 5940gcggccgcgg accggatccc atcacatata cctgccgttc actattattt agtgaaatga 6000gatattatga tattttctga attgtgatta aaaaggcaac tttatgccca tgcaacagaa 6060actataaaaa atacagagaa tgaaaagaaa cagatagatt ttttagttct ttaggcccgt 6120agtctgcaaa tccttttatg attttctatc aaacaaaaga ggaaaataga ccagttgcaa 6180tccaaacgag agtctaatag aatgaggtcg aaaagtaaat cgcgcgggtt tgttactgat 6240aaagcaggca agacctaaaa tgtgtaaagg gcaaagtgta tactttggcg tcacccctta 6300catattttag gtcttttttt attgtgcgta actaacttgc catcttcaaa caggagggct 6360ggaagaagca gaccgctaac acagtacata aaaaaggaga catgaacgat gaacatcaaa 6420aagtttgcaa aacaagcaac agtattaacc tttactaccg cactgctggc aggaggcgca 6480actcaagcgt ttgcgaaaga aacgaaccaa aagccatata aggaaacata cggcatttcc 6540catattacac gccatgatat gctgcaaatc cctgaacagc aaaaaaatga aaaatatcaa 6600gttcctgaat tcgattcgtc cacaattaaa aatatctctt ctgcaaaagg cctggacgtt 6660tgggacagct ggccattaca aaacgctgac ggcactgtcg caaactatca cggctaccac 6720atcgtctttg cattagccgg agatcctaaa aatgcggatg acacatcgat ttacatgttc 6780tatcaaaaag tcggcgaaac ttctattgac agctggaaaa acgctggccg cgtctttaaa 6840gacagcgaca aattcgatgc aaatgattct atcctaaaag accaaacaca agaatggtca 6900ggttcagcca catttacatc tgacggaaaa atccgtttat tctacactga tttctccggt 6960aaacattacg gcaaacaaac actgacaact gcacaagtta acgtatcagc atcagacagc 7020tctttgaaca tcaacggtgt agaggattat aaatcaatct ttgacggtga cggaaaaacg 7080tatcaaaatg tacagcagtt catcgatgaa ggcaactaca gctcaggcga caaccatacg 7140ctgagagatc ctcactacgt agaagataaa ggccacaaat acttagtatt tgaagcaaac 7200actggaactg aagatggcta ccaaggcgaa gaatctttat ttaacaaagc atactatggc 7260aaaagcacat cattcttccg tcaagaaagt caaaaacttc tgcaaagcga taaaaaacgc 7320acggctgagt tagcaaacgg cgctctcggt atgattgagc taaacgatga ttacacactg 7380aaaaaagtga tgaaaccgct gattgcatct aacacagtaa cagatgaaat tgaacgcgcg 7440aacgtcttta aaatgaacgg caaatggtac ctgttcactg actcccgcgg atcaaaaatg 7500acgattgacg gcattacgtc taacgatatt tacatgcttg gttatgtttc taattcttta 7560actggcccat acaagccgct gaacaaaact ggccttgtgt taaaaatgga tcttgatcct 7620aacgatgtaa cctttactta ctcacacttc gctgtacctc aagcgaaagg aaacaatgtc 7680gtgattacaa gctatatgac aaacagagga ttctacgcag acaaacaatc aacgtttgcg 7740ccgagcttcc tgctgaacat caaaggcaag aaaacatctg ttgtcaaaga cagcatcctt 7800gaacaaggac aattaacagt taacaaataa aaacgcaaaa gaaaatgcca atatcctatt 7860ggcattttct tttatttctt ccatttaaat ggatgcatgc gctagcggag tgtatactgg 7920cttactatgt tggcactgat gagggtgtca gtgaagtgct tcagcctcgt gagcgggacg 7980gtcgtaaggt cgttccgctc cacttcactg aacggcaatc cgagggtgtg gatccaatta 8040aggccacgct gtcatttaaa ttccgttttt ccagttcaaa tgcaattgcc ttcaatgcac 8100cttcgtagct gtggtgagcc agcggtgctg gctctccccc atttacggat aagaatgcat 8160tttccgagtt aataccgtcg gcaatacctg acattaatac ttcacagtcg ctggcatcga 8220gtacggaaaa cttaatcgaa gacgaaccac agttaataac caaaacaacc ggaaattcat 8280tcatctcttt tctcatcctg agttacggat taaaacagtt tgtatacgat gttcaggatg 8340gtcagcagac caatcacggt aacaaacacg ttatccagac gaccacggta tttcgccaga 8400gacggcgctt tacggatggc atacatcggc aacaggcaca gcagggatgc gataatcggt 8460gcgcccatgg cttcaatcag gtcgaggatg ttcgggttgg cgtaggcaac aacccaggtg 8520gagcccatga tgaagatcat gctgagagta ttcagtttac ccagcgacac tttggttttg 8580tcacctttat aaccgaactt cagaatcaga ccattcaagc cttccagcgt ccccagatag 8640tgaccgaaga aagatttgaa gatagccacg agtgcgatga tggaagccgc atattccagt 8700gtaatcgcga acgttgtttt ggtaccggtc atggacgcaa agtggttagc cagataagaa 8760agcactggaa tattctgcgc tttggcttcc gccatgttgg ccggagacag agtaaacagg 8820cagctaaagg caaagaacat caccactgca accatcagca tgctggcacg agaaatgatt 8880tgggaacatt tacgttcggt gaagtcgcga ccgaagtctt tctcatactc ttcacgttta 8940gaaaccacga aggaagagac gattggcgag aagttaaagg agaaaaccat gatggaaatc 9000cccagccaga cagtgatcag gataccgtca tgaccggtta acgacagcga accgaggtca 9060acctggtcga taactgcaga gttccagtaa gggatcagcg acaaagaaat cagcaccagg 9120ctggcgataa acggccatac caggtagctc agggtaccga gctcgaattc actggccgtc 9180gttttacaac gtcgtgactg ggaaaaccct ggcgttaccc aacttaatcg ccttgcagca 9240catccccctt tcgccagctg gcgtaatagc gaagaggccc gcaccgatcg cccttcccaa 9300cagttgcgca gcctgaatgg cgaatggcgc ctgatgcggt attttctcct tacgcatctg 9360tgcggtattt cacaccgcat atggtgcact ctcagtacaa tctgctctga tgccgcatag 9420ttaagccagc cccgacaccc gccaacaccc gctgacgaat tc 946231091DNAEscherichia coliptsHI(1)..(1091)Sequence surrounding the deletion of ptsHI. The fusion junction is in between the nucleotide positions 425 and 426. 3gcaacagtaa tgccagcttg ttaaaaatgc gtaaaaaagc acctttttag gtgctttttt 60gtggcctgct tcaaactttc gcccctcctg gcattgattc agcctgtcgg aactggtatt 120taaccagact aattattttg atgcgcgaaa ttaatcgtta caggaaaagc caaagctgaa 180tcgattttat gatttggttc aattcttcct ttagcggcat aatgtttaat gacgtacgaa 240acgtcagcgg tcaacacccg ccagcaatgg actgtattgc gctcttcgtg cgtcgcgtct 300gttaaaaact ggcgctaaca atacaggcta aagtcgaacc gccaggctag actttagttc 360cacaacacta aacctataag ttggggaaat acaatgttcc agcaagaagt taccattacc 420gctccacaat ctgctaatcc acgagatgcg gcccaattta ctgcttagga gaagatcatg 480ggtttgttcg ataaactgaa atctctggtt tccgacgaca agaaggatac cggaactatt 540gagatcattg ctccgctctc tggcgagatc gtcaatatcg aagacgtgcc ggatgtcgtt 600tttgcggaaa aaatcgttgg tgatggtatt gctatcaaac caacgggtaa caaaatggtc 660gcgccagtag acggcaccat tggtaaaatc tttgaaacca accacgcatt ctctatcgaa 720tctgatagcg gcgttgaact gttcgtccac ttcggtatcg acaccgttga actgaaaggc 780gaaggcttca agcgtattgc tgaagaaggt cagcgcgtga aagttggcga tactgtcatt 840gaatttgatc tgccgctgct ggaagagaaa gccaagtcta ccctgactcc ggttgttatc 900tccaacatgg acgaaatcaa agaactgatc aaactgtccg gtagcgtaac cgtgggtgaa 960accccggtta tccgcatcaa gaagtaattc tgccgcagtg aaaaatggcg cccatcggcg 1020ccattttttt atgcttccgc cagcggcggc aaaatcaatt catcgctctc atgctgctgg 1080gtgtagcgca t 1091466DNAEscherichia coligalP(1)..(66)Sequence surrounding the deletion of galP gene. The fusion junction is in between the nucelotide positions 48 and 49. 4atgcctgacg ctaaaaaaca ggggcggtca aacaaggcaa tgacgtttat aggcgctcac 60gattaa 6658446DNAEscherichia colipSS2(1)..(8446)Plasmid used to install a glf cassette at the tdc lcous of bacterial strain KJ122. 5gttgacagta agacgggtaa gcctgttgat gataccgctg ccttactggg tgcattagcc 60agtctgaatg acctgtcacg ggataatccg aagtggtcag actggaaaat cagagggcag 120gaactgctga acagcaaaaa gtcagatagc accacatagc agacccgcca taaaacgccc 180tgagaagccc gtgacgggct tttcttgtat tatgggtagt ttccttgcat gaatccataa 240aaggcgcctg tagtgccatt tacccccatt cactgccaga gccgtgagcg cagcgaactg 300aatgtcacga aaaagacagc gactcaggtg cctgatggtc ggagacaaaa ggaatattca 360gcgatttgcc cgagcttgcg agggtgctac ttaagccttt agggttttaa ggtctgtttt 420gtagaggagc aaacagcgtt tgcgacatcc ttttgtaata ctgcggaact gactaaagta 480gtgagttata cacagggctg ggatctattc tttttatctt tttttattct ttctttattc 540tataaattat aaccacttga atataaacaa aaaaaacaca caaaggtcta gcggaattta 600cagagggtct agcagaattt acaagttttc cagcaaaggt ctagcagaat ttacagatac 660ccacaactca aaggaaaagg actagtaatt atcattgact agcccatctc aattggtata 720gtgattaaaa tcacctagac caattgagat gtatgtctga attagttgtt ttcaaagcaa 780atgaactagc gattagtcgc tatgacttaa cggagcatga aaccaagcta attttatgct 840gtgtggcact actcaacccc acgattgaaa accctacaag gaaagaacgg acggtatcgt 900tcacttataa ccaatacgct cagatgatga acatcagtag ggaaaatgct tatggtgtat 960tagctaaagc aaccagagag ctgatgacga gaactgtgga aatcaggaat cctttggtta 1020aaggctttga gattttccag tggacaaact atgccaagtt ctcaagcgaa aaattagaat 1080tagtttttag tgaagagata ttgccttatc ttttccagtt aaaaaaattc ataaaatata 1140atctggaaca tgttaagtct tttgaaaaca aatactctat gaggatttat gagtggttat 1200taaaagaact aacacaaaag aaaactcaca aggcaaatat agagattagc cttgatgaat 1260ttaagttcat gttaatgctt gaaaataact accatgagtt taaaaggctt aaccaatggg 1320ttttgaaacc aataagtaaa gatttaaaca cttacagcaa tatgaaattg gtggttgata 1380agcgaggccg cccgactgat acgttgattt tccaagttga actagataga caaatggatc 1440tcgtaaccga acttgagaac aaccagataa aaatgaatgg tgacaaaata ccaacaacca 1500ttacatcaga ttcctaccta cgtaacggac taagaaaaac actacacgat gctttaactg 1560caaaaattca gctcaccagt tttgaggcaa aatttttgag tgacatgcaa agtaagcatg 1620atctcaatgg ttcgttctca tggctcacgc aaaaacaacg aaccacacta gagaacatac 1680tggctaaata cggaaggatc tgaggttctt atggctcttg tatctatcag tgaagcatca 1740agactaacaa acaaaagtag aacaactgtt caccgttaga tatcaaaggg aaaactgtcc 1800atatgcacag atgaaaacgg tgtaaaaaag atagatacat cagagctttt acgagttttt 1860ggtgcattta aagctgttca ccatgaacag atcgacaatg taacagatga acagcatgta 1920acacctaata gaacaggtga aaccagtaaa acaaagcaac tagaacatga aattgaacac 1980ctgagacaac ttgttacagc tcaacagtca cacatagaca gcctgaaaca ggcgatgctg 2040cttatcgaat caaagctgcc gacaacacgg gagccagtga cgcctcccgt ggggaaaaaa 2100tcatggcaat tctggaagaa atagcgcttt cagccggcaa acctgaagcc ggatctgcga 2160ttctgataac aaactagcaa caccagaaca gcccgtttgc gggcagcaaa acccgttatg 2220cttgtaaacc gttttgtgaa aaaattttta aaataaaaaa ggggacctct agggtcccca 2280attaattagt aatataatct attaaaggtc attcaaaagg tcatccaccg gatcaattcc 2340cctgctcgcg caggctgggt gccaagctct cgggtaacat caaggcccga tccttggagc 2400ccttgccctc ccgcacgatg atcgtgccgt gatcgaaatc cagatccttg acccgcagtt 2460gcaaaccctc actgatccgc atgcccgttc catacagaag ctgggcgaac aaacgatgct 2520cgccttccag aaaaccgagg atgcgaacca cttcatccgg ggtcagcacc accggcaagc 2580gccgcgacgg ccgaggtctt ccgatctcct gaagccaggg cagatccgtg cacagcacct 2640tgccgtagaa gaacagcaag gccgccaatg cctgacgatg cgtggagacc gaaaccttgc 2700gctcgttcgc cagccaggac agaaatgcct cgacttcgct gctgcccaag gttgccgggt 2760gacgcacacc gtggaaacgg atgaaggcac gaacccagtg gacataagcc tgttcggttc 2820gtaagctgta atgcaagtag cgtatgcgct cacgcaactg gtccagaacc ttgaccgaac 2880gcagcggtgg taacggcgca gtggcggttt tcatggcttg ttatgactgt ttttttgggg 2940tacagtctat gcctcgggca tccaagcagc aagcgcgtta cgccgtgggt cgatgtttga 3000tgttatggag cagcaacgat gttacgcagc agggcagtcg ccctaaaaca aagttaaaca 3060tcatgaggga agcggtgatc gccgaagtat cgactcaact atcagaggta gttggcgtca 3120tcgagcgcca tctcgaaccg acgttgctgg ccgtacattt gtacggctcc gcagtggatg 3180gcggcctgaa gccacacagt gatattgatt tgctggttac ggtgaccgta aggcttgatg 3240aaacaacgcg gcgagctttg atcaacgacc ttttggaaac ttcggcttcc cctggagaga 3300gcgagattct ccgcgctgta gaagtcacca ttgttgtgca cgacgacatc attccgtggc 3360gttatccagc taagcgcgaa ctgcaatttg gagaatggca gcgcaatgac attcttgcag 3420gtatcttcga gccagccacg atcgacattg atctggctat cttgctgaca aaagcaagag 3480aacatagcgt tgccttggta ggtccagcgg cggaggaact ctttgatccg gttcctgaac 3540aggatctatt tgaggcgcta aatgaaacct taacgctatg gaactcgccg cccgactggg 3600ctggcgatga gcgaaatgta gtgcttacgt tgtcccgcat ttggtacagc gcagtaaccg 3660gcaaaatcgc gccgaaggat gtcgctgccg actgggcaat ggagcgcctg ccggcccagt 3720atcagcccgt catacttgaa gctagacagg cttatcttgg acaagaagaa gatcgcttgg 3780cctcgcgcgc agatcagttg gaagaatttg tccactacgt gaaaggcgag atcaccaagg 3840tagtcggcaa ataatgtcta acaattcgtt caagccgacg ccgcttcgcg gcgcggctta 3900actcaagcgt tagatgcact aagcacataa ttgctcacag ccaaactatc aggtcaagtc 3960tgcttttatt atttttaagc gtgcataata agccctacac aaattgggag atatatcatg 4020aaaggctggc tttttcttgt tatcgcaata gttggcgaag taatcgcaac atccgcatta 4080aaatctagcg agggctttac taagctgatc cggtggatga ccttttgaat gacctttaat 4140agattatatt actaattaat tggggaccct agaggtcccc ttttttattt taaaaatttt 4200ttcacaaaac ggtttacaag catacgttgg ccgattcatt aatgcagctg gcacgacagg 4260tttcccgact ggaaagcggg cagtgagcgc aacgcaatta atgtgagtta gctcactcat 4320taggcacccc aggctttaca ctttatgctt ccggctcgta tgttgtgtgg aattgtgagc 4380ggataacaat ttcacacagg aaacagctat gaccatgatt acgccaagct tgcatgcctg 4440caggtcgact ctagaggatc ccccccgccg ccgacagagt aataggtttt acttaatagc 4500tcttcctgtc ccttccaggc agtgatccgc attccgttct catggcgagg caacatttcg 4560ggatggaaga taatgttctt tgctacagga aaatcaacaa tatgcgcacc agatgccact 4620ggcagccgcc cgctgcgcgt tactaactct ataaatgcag ggatctcatc aatgacaaca 4680tcctgcggac tgtttcctgc cagtcccatg atgatggcga catccgtggc atggcctttg 4740cccgtcagtg acaacgaccc gtacagatcg accacaatat ggctcgtcgc ggttaataag 4800ccgctacttt ccagccgatc aataaaactt tttccggcat tcattggccc cacggtatgc 4860gaactggagg gaccaatccc aattttgaaa atatcgaatg cactaatcat atccacaccc 4920tcggattgcc gttcagtgaa gtggagcgga acgaccttac gaccgtcccg ctcacgaggc 4980tttacgcact acgtactgcg atggcttcaa tttccagcgg gagggcggat ccactaatac 5040aaaatatatc aaaagttaat aataatatta ttcttactta agactttttt gtcttcattt 5100tttagtaaaa aatataaaaa aggccacctc ccgattttat cggaaggcag cctcttaaat 5160tcagttcata atattaaaaa atattattca acttcagatt atttgttggc ataggcagcg 5220ctccgcccgc tttataccat cgttgtaaac aaaaagtata attggttaag acttatctaa 5280aaaagacaaa aggattcagc caaagcaagt ttaactactt ctgggagcgc cacatctcct 5340cgatttcatc caggctccga cctttggttt ccggcacgaa gcgagcaaca atcaagccac 5400ctaagatact taatgctgcg aaaacgagat aggagaaacc gtggttgaaa gtctgattca 5460atgctggaga accatcggca accttaaaca ggaagttaac caagatatta gctaaccatt 5520gtccggtaac agcgataggc atagctgcgc ccttgatgga actcgggaac atttctgaca 5580gaacaaccca gcagacaggg ccccatgaca taccaaagac tgcaatataa agaagcacag 5640aagccaaagg caaaacacca ccgactttga accagaaaca gcagcctaaa acagccatca 5700ttgcagccat accgagagca ccccaaataa gcagaggttt acggccgaag cggtcaacaa 5760cacgggaagc aatcatggtg aagatgaagt tcacaacacc gatagagatg gtctgcaata 5820atgccgtatc agctccaaaa cctaaattct ggaacatctg cggtgcataa tacagcacgg 5880cgttaatacc gactaactgc tggaaggcag caacggatac accggcaaaa acaacggtga 5940taccaaaagc aaacaaacct gcgctgcttt tgtccatggc tttatcaaag ccagctttaa 6000tcttttgaat cgtcagatta ggatcggctt gcggttccag acgagcaagg attttgctag 6060cctcggaatg acgtcccttc atcaccaacc aatgcggcgt atccggtgcg gttaacagca 6120gcaataagaa ggcaataccg atcaggcctt ctgaagccgg agaccagcac caaccactgg 6180cattaaccca atcgatagaa ccgaaatgag ccagtaacca ggtaaagata taaccggtta 6240aagcacccgt cacaatggcc atctgctgac cagaaaccat ctgaccacgt ttgtctggcg 6300gagcaatttc agcaatatag gttggggtca aggttgaaac gacaccgata cctaaaccgg 6360caagaaaccg gaaaaagcaa aaaatttgta aagccgaacc accggttcca aataattttt 6420cggttaacgc agcaccaaaa ccggcggcga cgaaacaaat ggaactcatc aacaatccgc 6480cgcgacgacc gaagcgaata ccaatccagc cagacagcaa agaaccggta acacaaccga 6540ccaaaacagc aacaacgacc atcccagaaa gggaagccgc agccgtagca gacaggtgac 6600gaggggcaat aaaatggata tcaaccggtg taccgattgc agcgataacc gctgaatcgt 6660aaccgaaaag caagccgcct atagcagcga ttagggctag tcgcgtgact agaccctgac 6720tactttcaga actcatggcg attcctctcc ctctagagcg tcctgctgtt gttaagatta 6780ttataccaca ccttgtagat aaagtcaaca actttttgca aaatttttca ggaattttag 6840cagaggttgt tctggatgta gaacaaaaca tctttccgct cttgtgctgt taggatatct 6900ttcttggaag ctaggtaggc ctcgagttat ggcagttggt taaaaggaaa caaaaagacc 6960gttttcacac aaaacggtct ttttcgattt ctttttacag tcacagccac ttttgcacca 7020attaaggcca cgctgtcatt taaactccgt ttttccagtt caaatgcaat tgccttcaat 7080gcaccttcgt agctgtggtg agccagcggt gctggctctc ccccatttac ggataagaat 7140gcattttccg agttaatacc gtcggcaata cctgacatta atacttcaca gtcgctggca 7200tcgagtacgg aaaacttaat cgaagacgaa ccacagttaa taaccaaaac aaccggaaat 7260tcattcatct cttttctcat cctgagttac ggattaaaac agtttgtata cgatgttcag 7320gatggtcagc agaccaatca cggtaacaaa cacgttatcc agacgaccac ggtatttcgc 7380cagagacggc gctttacgga tggcatacat cggcaacagg cacagcaggg atgcgataat 7440cggtgcgccc atggcttcaa tcaggtcgag gatgttcggg ttggcgtagg caacaaccca 7500ggtggagccc atgatgaaga tcatgctgag agtattcagt ttacccagcg acactttggt 7560tttgtcacct ttataaccga acttcagaat cagaccattc aagccttcca gcgtccccag 7620atagtgaccg aagaaagatt tgaagatagc cacgagtgcg atgatggaag ccgcatattc 7680cagtgtaatc gcgaacgttg ttttggtacc ggtcatggac gcaaagtggt tagccagata 7740agaaagcact ggaatattct gcgctttggc ttccgccatg ttggccggag acagagtaaa 7800caggcagcta aaggcaaaga acatcaccac tgcaaccatc agcatgctgg cacgagaaat 7860gatttgggaa catttacgtt cggtgaagtc gcgaccgaag tctttctcat actcttcacg 7920tttagaaacc acgaaggaag agacgattgg cgagaagtta aaggagaaaa ccatgatgga 7980aatccccagc cagacagtga tcaggatacc gtcatgaccg gttaacgaca gcgaaccgag 8040gtcaacctgg tcgataactg cagagttcca gtaagggatc agcgacaaag aaatcagcac 8100caggctggcg ataaacggcc ataccaggta gctcagggta ccgagctcga attcactggc 8160cgtcgtttta caacgtcgtg actgggaaaa ccctggcgtt acccaactta atcgccttgc 8220agcacatccc cctttcgcca gctggcgtaa tagcgaagag gcccgcaccg atcgcccttc 8280ccaacagttg cgcagcctga atggcgaatg gcgcctgatg cggtattttc tccttacgca 8340tctgtgcggt atttcacacc gcatatggtg cactctcagt acaatctgct ctgatgccgc 8400atagttaagc cagccccgac acccgccaac acccgctgac gaattc 8446631DNAArtificial SequencePCR Primer BY249 for amplifying and cloning the crr gene of YSS41, together with BY249. 6gggcaacagt aatgccagct tgttaaaaat g 31725DNAArtificial SequencePCR Primer BY250 for amplifying and cloning the crr gene of YSS41 together with BY249. 7gggcgctaca cccagcagca tgaga 2588937DNAEscherichia colipMH68(1)..(8937)Plasmid used to install a second copy of teh crr gene from YSS41 at the pflD locus. 8gttgacagta agacgggtaa gcctgttgat gataccgctg ccttactggg tgcattagcc 60agtctgaatg acctgtcacg ggataatccg aagtggtcag actggaaaat cagagggcag 120gaactgctga acagcaaaaa gtcagatagc accacatagc agacccgcca taaaacgccc 180tgagaagccc gtgacgggct tttcttgtat tatgggtagt ttccttgcat gaatccataa 240aaggcgcctg tagtgccatt tacccccatt cactgccaga gccgtgagcg cagcgaactg 300aatgtcacga aaaagacagc gactcaggtg cctgatggtc ggagacaaaa ggaatattca

360gcgatttgcc cgagcttgcg agggtgctac ttaagccttt agggttttaa ggtctgtttt 420gtagaggagc aaacagcgtt tgcgacatcc ttttgtaata ctgcggaact gactaaagta 480gtgagttata cacagggctg ggatctattc tttttatctt tttttattct ttctttattc 540tataaattat aaccacttga atataaacaa aaaaaacaca caaaggtcta gcggaattta 600cagagggtct agcagaattt acaagttttc cagcaaaggt ctagcagaat ttacagatac 660ccacaactca aaggaaaagg actagtaatt atcattgact agcccatctc aattggtata 720gtgattaaaa tcacctagac caattgagat gtatgtctga attagttgtt ttcaaagcaa 780atgaactagc gattagtcgc tatgacttaa cggagcatga aaccaagcta attttatgct 840gtgtggcact actcaacccc acgattgaaa accctacaag gaaagaacgg acggtatcgt 900tcacttataa ccaatacgct cagatgatga acatcagtag ggaaaatgct tatggtgtat 960tagctaaagc aaccagagag ctgatgacga gaactgtgga aatcaggaat cctttggtta 1020aaggctttga gattttccag tggacaaact atgccaagtt ctcaagcgaa aaattagaat 1080tagtttttag tgaagagata ttgccttatc ttttccagtt aaaaaaattc ataaaatata 1140atctggaaca tgttaagtct tttgaaaaca aatactctat gaggatttat gagtggttat 1200taaaagaact aacacaaaag aaaactcaca aggcaaatat agagattagc cttgatgaat 1260ttaagttcat gttaatgctt gaaaataact accatgagtt taaaaggctt aaccaatggg 1320ttttgaaacc aataagtaaa gatttaaaca cttacagcaa tatgaaattg gtggttgata 1380agcgaggccg cccgactgat acgttgattt tccaagttga actagataga caaatggatc 1440tcgtaaccga acttgagaac aaccagataa aaatgaatgg tgacaaaata ccaacaacca 1500ttacatcaga ttcctaccta cgtaacggac taagaaaaac actacacgat gctttaactg 1560caaaaattca gctcaccagt tttgaggcaa aatttttgag tgacatgcaa agtaagcatg 1620atctcaatgg ttcgttctca tggctcacgc aaaaacaacg aaccacacta gagaacatac 1680tggctaaata cggaaggatc tgaggttctt atggctcttg tatctatcag tgaagcatca 1740agactaacaa acaaaagtag aacaactgtt caccgttaga tatcaaaggg aaaactgtcc 1800atatgcacag atgaaaacgg tgtaaaaaag atagatacat cagagctttt acgagttttt 1860ggtgcattta aagctgttca ccatgaacag atcgacaatg taacagatga acagcatgta 1920acacctaata gaacaggtga aaccagtaaa acaaagcaac tagaacatga aattgaacac 1980ctgagacaac ttgttacagc tcaacagtca cacatagaca gcctgaaaca ggcgatgctg 2040cttatcgaat caaagctgcc gacaacacgg gagccagtga cgcctcccgt ggggaaaaaa 2100tcatggcaat tctggaagaa atagcgcttt cagccggcaa acctgaagcc ggatctgcga 2160ttctgataac aaactagcaa caccagaaca gcccgtttgc gggcagcaaa acccgttatg 2220cttgtaaacc gttttgtgaa aaaattttta aaataaaaaa ggggacctct agggtcccca 2280attaattagt aatataatct attaaaggtc attcaaaagg tcatccaccg gatcaattcc 2340cctgctcgcg caggctgggt gccaagctct cgggtaacat caaggcccga tccttggagc 2400ccttgccctc ccgcacgatg atcgtgccgt gatcgaaatc cagatccttg acccgcagtt 2460gcaaaccctc actgatccgc atgcccgttc catacagaag ctgggcgaac aaacgatgct 2520cgccttccag aaaaccgagg atgcgaacca cttcatccgg ggtcagcacc accggcaagc 2580gccgcgacgg ccgaggtctt ccgatctcct gaagccaggg cagatccgtg cacagcacct 2640tgccgtagaa gaacagcaag gccgccaatg cctgacgatg cgtggagacc gaaaccttgc 2700gctcgttcgc cagccaggac agaaatgcct cgacttcgct gctgcccaag gttgccgggt 2760gacgcacacc gtggaaacgg atgaaggcac gaacccagtg gacataagcc tgttcggttc 2820gtaagctgta atgcaagtag cgtatgcgct cacgcaactg gtccagaacc ttgaccgaac 2880gcagcggtgg taacggcgca gtggcggttt tcatggcttg ttatgactgt ttttttgggg 2940tacagtctat gcctcgggca tccaagcagc aagcgcgtta cgccgtgggt cgatgtttga 3000tgttatggag cagcaacgat gttacgcagc agggcagtcg ccctaaaaca aagttaaaca 3060tcatgaggga agcggtgatc gccgaagtat cgactcaact atcagaggta gttggcgtca 3120tcgagcgcca tctcgaaccg acgttgctgg ccgtacattt gtacggctcc gcagtggatg 3180gcggcctgaa gccacacagt gatattgatt tgctggttac ggtgaccgta aggcttgatg 3240aaacaacgcg gcgagctttg atcaacgacc ttttggaaac ttcggcttcc cctggagaga 3300gcgagattct ccgcgctgta gaagtcacca ttgttgtgca cgacgacatc attccgtggc 3360gttatccagc taagcgcgaa ctgcaatttg gagaatggca gcgcaatgac attcttgcag 3420gtatcttcga gccagccacg atcgacattg atctggctat cttgctgaca aaagcaagag 3480aacatagcgt tgccttggta ggtccagcgg cggaggaact ctttgatccg gttcctgaac 3540aggatctatt tgaggcgcta aatgaaacct taacgctatg gaactcgccg cccgactggg 3600ctggcgatga gcgaaatgta gtgcttacgt tgtcccgcat ttggtacagc gcagtaaccg 3660gcaaaatcgc gccgaaggat gtcgctgccg actgggcaat ggagcgcctg ccggcccagt 3720atcagcccgt catacttgaa gctagacagg cttatcttgg acaagaagaa gatcgcttgg 3780cctcgcgcgc agatcagttg gaagaatttg tccactacgt gaaaggcgag atcaccaagg 3840tagtcggcaa ataatgtcta acaattcgtt caagccgacg ccgcttcgcg gcgcggctta 3900actcaagcgt tagatgcact aagcacataa ttgctcacag ccaaactatc aggtcaagtc 3960tgcttttatt atttttaagc gtgcataata agccctacac aaattgggag atatatcatg 4020aaaggctggc tttttcttgt tatcgcaata gttggcgaag taatcgcaac atccgcatta 4080aaatctagcg agggctttac taagctgatc cggtggatga ccttttgaat gacctttaat 4140agattatatt actaattaat tggggaccct agaggtcccc ttttttattt taaaaatttt 4200ttcacaaaac ggtttacaag catacgttgg ccgattcatt aatgcagctg gcacgacagg 4260tttcccgact ggaaagcggg cagtgagcgc aacgcaatta atgtgagtta gctcactcat 4320taggcacccc aggctttaca ctttatgctt ccggctcgta tgttgtgtgg aattgtgagt 4380gccaataccc gtgaaatctc gctggagcgg gcgctgcttt ataccgccag ccatcggcaa 4440accgaaggcg aaccggtgat attgcgccgg gcgaaagcaa cagcgtatat ccttgaacat 4500gttgaaattt cgattcgtga tgaagaactg attgccggta accgcaccgt aaaaccgcgc 4560gccgggatta tgtcgccgga aatggaccct tactggctgc tgaaagagct ggatcaattc 4620ccgacgcgtc cgcaggaccg ctttgctatc agcgaagaag ataaacgtat ctaccgcgaa 4680gagttgttcc cgtactggga aaaacgttcg atgaaagatt tcatcaacgg gcagatgaca 4740gatgaagtaa aagccgcgac cagcacgcag attttcagca tcaaccagac agataaaggc 4800caggggcaca ttattattga ttacccacgc ctgctgaatc acgggctggg ggagctggta 4860gcacagatgc agcaacattg tcagcaacag ccggagaatc acttttatca ggcagcgctg 4920ttactgctgg aagcctcgca gaaacacatt ttgcgttacg ccgaactggc ggaaacgatg 4980gcggcaaact gcacagatgc ccagcgtcgc gaagagctgc tgactattgc ggagatctcc 5040cgccataacg cgcaacataa gccgcagacg ttctggcagg cgtgccagtt attctggtac 5100atgaacatca ttctgcaata cgaatccaac gccagttcgc tatcgttggg gcgcttcgac 5160cagtatatgt tgccgttcta tcagacatca ttaacccagg gcgaagatgc ggcgttcctg 5220aaagaactgc tcgaatcttt atgggtgaaa tgcaacgaca tcgtgctgtt gcgctccacc 5280agcagcgcgc gttatttcgc cggtttcccg accggctata ccgcactgct cggcgggtta 5340accgagaacg gacgtagcgc ggtgaacgtg ctttcgttcc tttgccttga cgcctatcaa 5400agcgtgcaat taccgcaacc gaacctcggc gtgcgcacta acgccttgat cgacacgccg 5460ttcctgatga aaaccgccga aaccattcgc ctcggcaccg gtattccgca aatctttaac 5520gatgaagtgg tggtgccagc gttcctcaac cgtggcgttt cgctggaaga tgcgcgcgac 5580tattccgtag tgggctgtgt ggaattatct attcccggca gaacctacgg cttgcatgac 5640atcgcgatgt ttaacctgct gaaagtgatg gaaatctgcc tgcatgaaaa tgaaggcaat 5700gccgcgctga cttatgaagg tttactggaa cagatccgtg ccaagatcag ccactacatc 5760accctgatgg ttgaaggcag taatatttgc gatatcggcc atcgcgactg ggcacctgta 5820ccgctgctct cgtcttttat cagcgattgt ctggaaaaag gccgcgatat taccgatggc 5880ggcgcgcgtt ataacttctc cggcgtacag gggatcggta tcgccaacct gagcgattct 5940ctccatgcgt tgaaagggat ggtttttgat caacagcgtt taagttttga cgaattgctg 6000tcggtattaa aagccaactt tgcaacgcca gaaggcgaaa aagtccgcgc tcgcttaatt 6060aaccgctttg agaaatacgg taacgatatc gacgaggtgg ataacattag cgccgaactg 6120ttgcgccact actgcaaaga agtggaaaaa taccagaacc cgcgcggcgg ctacttcacg 6180ccgggatcgt agggcttcaa actttcgccc ctcctggcat tgattcagcc tgtcggaact 6240ggtatttaac cagactaatt attttgatgc gcgaaattaa tcgttacagg aaaagccaaa 6300gctgaatcga ttttatgatt tggttcaatt cttcctttag cggcataatg tttaatgacg 6360tacgaaacgt cagcggtcaa cacccgccag caatggactg tattgcgctc ttcgtgcgtc 6420gcgtctgtta aaaactggcg ctaacaatac aggctaaagt cgaaccgcca ggctagactt 6480tagttccaca acactaaacc tataagttgg ggaaatacaa tgttccagca agaagttacc 6540attaccgctc cgacaatctg ctaatccacg agatgcggcc caatttactg cttaggagaa 6600gatcatgggt ttgttcgata aactgaaatc tctggtttcc gacgacaaga aggataccgg 6660aactattgag atcattgctc cgctctctgg cgagatcgtc aatatcgaag acgtgccgga 6720tgtcgttttt gcggaaaaaa tcgttggtga tggtattgct atcaaaccaa cgggtaacaa 6780aatggtcgcg ccagtagacg gcaccattgg taaaatcttt gaaaccaacc acgcattctc 6840tatcgaatct gatagcggcg ttgaactgtt cgtccacttc ggtatcgaca ccgttgaact 6900gaaaggcgaa ggcttcaagc gtattgctga agaaggtcag cgcgtgaaag ttggcgatac 6960tgtcattgaa tttgatctgc cgctgctgga agagaaagcc aagtctaccc tgactccggt 7020tgttatctcc aacatggacg aaatcaaaga actgatcaaa ctgtccggta gcgtaaccgt 7080gggtgaaacc ccggttatcc gcatcaagaa gtaattcttg ccgcagtgaa aaatggcgcc 7140catcggcgcc atttttttat gcttccgcca gcggcggcaa aatcaattca tcgctctcat 7200gctgctgggt gtagcgccct accgtttctg ctcacgttcc gttgggatcg gtggttggcg 7260cgacgccaga cggtcgtttt gccggagaac agctggcaga cggcggcttg tcacctatgc 7320tgggtcagga cgcacaaggg ccaacggcgg tactgaagtc agtcagtaag ctcgataaca 7380cactgctgtc taacggtaca ttgctgaacg tgaaattcac tccggcgacc ctggaaggtg 7440aagcgggatt acgcaaactg gccgacttct tacgggcgtt tacccagctt aagttacaac 7500atattcagtt taacgtggtg aacgccgaca cgttgcggga agcgcaacag cgcccacaag 7560attatgccgg gctggtggtg cgcgttgccg gatacagcgc cttctttgtc gaactgtcga 7620aggagatcca ggatgacatc atccgccgga cagcgcatca gctgtaacgt tgtggaaacg 7680cgccgcaatg atgtggcgcg cattttcaac attcagcgtt attcactgaa tgacggtgag 7740ggcattcgta cggtggtctt ttttaaaggc tgtccgcatc tttgcccgtg gtgtgctaat 7800ccggagtcga tctccggcaa aatccagacg gtacgcagag aggcgaaatg tctgcactgt 7860gcgaaatgtt tgcgtgatgc ggatgaatgc ccctccgggg cgtttgaacg gattggtcgc 7920gatatcagcc ttgacgctct ggaacgggaa gtgatgaaag atgacatttt ttttcgcacg 7980tccggcggcg gcgtcacgct ttctggcggc gaagtgttaa tgcaggcgga gtttgctacc 8040cgttttttac agcgactgca gctgtggggt gtctcatgtg ccattgaaac tgccggagac 8100gcgccagcca gcaagctgtt accgctggcg aaattgtgcg atgaagtgtt gttcgattta 8160aaaatcatgg acgcgactca ggcgcgggat gtggtgaaga tgaacctgcc acgcgtgctg 8220gagaatctgc gtttgctggt gagtgagggc gtcaacgtga tcccgcgttt accgctgatc 8280cctggtttca cgctcagccg ggagaatatg cagcaggcgc tggatgtgct gatcccgctg 8340aatatcaggc agatccatct gttaccgttt catcagtacg gcgaaccgaa ataccgcctg 8400ctggggaaaa catggtcgat gaaagaggtg cctgcgccgt cgtcagccga tgtggcaacg 8460atgcgcgaaa tggcagaacg ggccggattt caggttaccg tgggaggtta aaatggcata 8520cctggtggca gtaaccgcct gcgtcagtgg cgtggcgcat acttatatgg cggcggaacg 8580gctggaaaag ttgtgcctgt tagagaagtg gggagtcagc attgaaactc agggcgctcg 8640aattcactgg ccgtcgtttt acaacgtcgt gactgggaaa accctggcgt tacccaactt 8700aatcgccttg cagcacatcc ccctttcgcc agctggcgta atagcgaaga ggcccgcacc 8760gatcgccctt cccaacagtt gcgcagcctg aatggcgaat ggcgcctgat gcggtatttt 8820ctccttacgc atctgtgcgg tatttcacac cgcatatggt gcactctcag tacaatctgc 8880tctgatgccg catagttaag ccagccccga cacccgccaa cacccgctga cgaattc 8937923DNAArtificial SequencePCR primer BY124 for amplifying and cloning teh pflDC geen of Escherichia coli C, or cassettes embedded in pflD, together with BY125. 9tgccaatacc cgtgaaatct cgc 231023DNAArtificial SequencePCR Primer BY125 for amplifying and cloning the pflDC genes of E. coli C, or cassettes embedded in pflD, together with BY124. 10cgccctgagt ttcaatgctg act 231126DNAArtificial SequencePCR primer AC74 for amplifying and clonig the tdcC-tdcG region of E. coli C and derivatives or cassettes embedded in teh tdcC-tdcG region,together with AC75. 11tgagctacct ggtatggccg tttatc 261222DNAArtificial SequencePCR primer Ac75 for amplifying and cloning the tdcC-tdcG region of E. coli C and derivatives, or cassettes embedded in teh tdcC-tdcG region, together with AC74. 12cccgccgccg acagagtaat ag 22

Claims

1. A bacterium producing more than 30 grams per liter of a desired chemical, wherein one of the biosynthetic intermediates for said desired chemical is phosphoenolpyruvate, and said bacterium contains at least one exogenous gene that encodes a protein that functions in the facilitated diffusion of a sugar.

2. The bacterium of claim 1, wherein the bacterium is selected from a group consisting of Gluconobacter oxydans, Gluconobacter asaii, Achromobacter delmarvae, Achromobacter viscosus, Achromobacter lacticum, Agrobacterium tumefaciens, Agrobacterium radiobacter, Alcaligenes faecalis, Arthrobacter citreus, Arthrobacter tumescens, Arthrobacter paraffineus, Arthrobacter hydrocarboglutamicus, Arthrobacter oxydans, Aureobacterium saperdae, Azotobacter indicus, Brevibacterium ammoniagenes, divaricatum, Brevibacterium lactofermentum, Brevibacterium flavum, Brevibacterium globosum, Brevibacterium fuscum, Brevibacterium ketoglutamicum, Brevibacterium helcolum, Brevibacterium pusillum, Brevibacterium testaceum, Brevibacterium roseum, Brevibacterium immariophilium, Brevibacterium linens, Brevibacterium protopharmiae, Corynebacterium acetophilum, Corynebacterium glutamicum, Corynebacterium callunae, Corynebacterium acetoacidophilum, Corynebacterium acetoglutamicum, Enterobacter aerogenes, Erwinia amylovora, Erwinia carotovora, Erwinia herbicola, Erwinia chrysanthemi, Flavobacterium peregrinum, Flavobacterium fucatum, Flavobacterium aurantinum, Flavobacterium rhenanum, Flavobacterium sewanense, Flavobacterium breve, Flavobacterium meningosepticum, Micrococcus sp. CCM825, Morganella morganii, Nocardia opaca, Nocardia rugosa, Planococcus eucinatus, Proteus rettgeri, Propionibacterium shermanii, Pseudomonas synxantha, Pseudomonas azotoformans, Pseudomonas fluorescens, Pseudomonas ovalis, Pseudomonas stutzeri, Pseudomonas acidovolans, Pseudomonas mucidolens, Pseudomonas testosteroni, Pseudomonas aeruginosa, Rhodococcus erythropolis, Rhodococcus rhodochrous, Rhodococcus sp. ATCC 15592, Rhodococcus sp. ATCC 19070, Sporosarcina ureae, Staphylococcus aureus, Vibrio metschnikovii, Vibrio tyrogenes, Actinomadura madurae, Actinomyces violaceochromogenes, Kitasatosporia parulosa, Streptomyces coelicolor, Streptomyces flavelus, Streptomyces griseolus, Streptomyces lividans, Streptomyces olivaceus, Streptomyces tanashiensis, Streptomyces virginiae, Streptomyces antibioticus, Streptomyces cacaoi, Streptomyces lavendulae, Streptomyces viridochromogenes, Aeromonas salmonicida, Bacillus pumilus, Bacillus circulans, Bacillus thiaminolyticus, Escherichia freundii, Microbacterium ammoniaphilum, Serratia marcescens, Salmonella typhimurium, Salmonella schottmulleri, Bacillus subtilis, Bacillus licheniformis, Bacillus amylolliquefaciens and Xanthomonas citri.

3. The bacterium of claim 1, wherein the bacterium is selected from a group consisting of Escherichia coli, Corynebacterium glutamicum Brevibacteium flavum, Mannhemia succiniproducens and Anaerobiospirilum succiniproducens.

4. The bacterium according to claim 1, wherein said desired chemical is selected from a group consisting of succinic acid, fumaric acid, glucaric acid, malonic acid, maleic acid, 2,5-furan dicarboxylic acid, propionic acid, 3-hydroxypropionic acid, aspartic acid, glucaric acid, glutamic acid, itaconic acid, levulinic acid, 3-hydroxybutryolactone, and butanediols such as 1,4 butnaediol, 1,3-butanediol and 2,3-butanediol.

5. The bacterium according to claim 1, wherein said desired chemical is succinate.

6. The bacterium according to claim 1, wherein said desired chemical is cis, cis-muconic acid.

7. The bacterium according to claim 1, wherein said desired chemical is an aromatic biochemical.

8. A bacterium according to claim 1, wherein the bacterium is a PTS.sup.- bacterial strain.

9. A bacterium according to claim 1, wherein the bacterium has a reduced level of phosphotransferase activity compared to a related wild type strain.

10. A bacterium of claim 1 further comprising a mutation or deletion in one or more genes that encode proteins that functions in a phosphotransferase system for sugar import, said mutated or deleted gene being other than a crr gene.

11. A Bacterium of claim 10 further comprising a deletion in a gene that encodes a sugar importer that functions using proton symport.

12. A bacterium of claim 10 wherein said mutated or deleted gene is a ptsH gene or a homolog thereof.

13. A bacterium of claim 10 wherein said mutated or deleted gene ptsI gene or a homolog thereof.

14. A bacterium of claim 10 wherein said mutated or deleted genes are selected from a group consisting of ptsH, ptsI, homolog of ptsH and homolog of ptsI.

15. A bacterium according to claim 1, wherein the bacterium is a galP.sup.- bacterial stain.

16. The bacterium of claim 1, wherein said exogenous gene is contained on a replicating plasmid.

17. The bacterium of claim 1, wherein said exogenous gene is integrated into the host chromosome.

18. The bacterium of claim 1 wherein said exogenous gene is a glf gene.

19. The bacterium of claim 1 wherein said exogenous genes are a glf and a glk genes.

20. The bacterium of claim 1 in which said exogenous genes are a glf gene and a frk gene.

21. The bacterium of claim 1 in which said exogenous gene is derived from a yeast.

22. The bacterium of claim 1 in which said exogenous gene or genes are derived from a strain of Zymomonas mobilis.

23. A bacterium of claim 1, wherein said bacterium is grown in minimal medium.

24. A bacterium of claim 1 wherein said bacterium produces more than 64 grams per liter of a desired chemical.

25. A bacterium of claim 1 wherein said bacterium produces more than 83 grams per liter of a desired chemical.

26. A bacterium containing two or more copies of a functional crr gene or a functional homolog of a crr gene.

27. A method for producing a desired chemical comprising the steps of: growing a bacterium of claim 1 in a minimal fermentation medium; and optionally purifying said chemical from the fermentation medium.

28. A method for producing succinic acid comprising the steps of: growing a bacterium comprising at least one exogenous gene that encodes a protein that function in the facilitated diffusion of sugar and producing at least 60 grams of succinate per liter and less than 4.2 grams of acetate per liter in a minimal fermentation medium; and optionally purifying succinic acid from the fermentation medium.

29. A method for improving the titer and yield of a desired chemical produced by a bacterial strain that has been engineered to use facilitated diffusion for import of a sugar, comprising the steps of: subjecting a parent strain to serial transfers into fresh liquid medium; plating the resulting culture for single colonies on a petri plate; and choosing a single colony.

30. A bacterial strain engineered to use facilitated diffusion for import of a sugar comprising a glf-glk operon, wherein said bacterial strain has been evolved for improved titer and yield for succinate production, and further comprising one or more mutations in the glf-glk operon.

31. A bacterial strain of claim 30 in which said one or more mutations alter bases in the DNA sequence that corresponds to the 5' untranslated leader region of an mRNA that encodes either of said glf or glk gene.

32. A bacterial strain engineered to use facilitated diffusion for import of a sugar comprising a glf gene, wherein said bacterial strain has been evolved for improved titer and yield for succinate production, and said glf gene comprises one or more mutations.

33. A bacterial strain engineered to use facilitated diffusion for import of a sugar comprising a glk gene, wherein said bacterial strain has been evolved for improved titer and yield for succinate production, and said glk gene comprises one or more mutations.

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