甘油脱氢酶基因在大肠杆菌中的密码子优化表达

[目的]利用密码子优化技术,提高甘油脱氢酶基因gldA在大肠杆菌中的表达水平.[方法]针对gldA起始密码子下游区域,优先选择AT含量最高的同义密码子,从而在不改变氨基酸序列的前提下,提高该区域的AT含量.利用大引物PCR的方法对野生型gldA-WT进行定点突变,获得优化型基因gldA-4,与pET-32a(+)连接后...     

克雷伯杆菌甘油脱氢酶基因的克隆表达与纯化

以克雷伯杆菌(Klebsiella pneumoniae)基因组DNA为模板, 运用PCR扩增得到编码甘油脱氢酶(GDH)的基因(gldA), 并克隆到pMD-18T载体上, 构建克隆载体pMD-gldA。经测序正确后, 将gldA亚克隆至表达载体pET-32a(+)上构建表达质粒pET-32gldA。在乳糖诱导下, 携带pET-32gldA的E. coli BL21 (DE3)高效表达分子量约为54 kD的可溶性蛋白。表达产物带有His6-tag标记, 选用Ni柱对表达产物进行纯化, 纯化后酶液的比活为188 u/mg, 纯化倍数和回收率分别为3倍和67.5%。     

克雷伯杆菌甘油脱氢酶基因的克隆表达与纯化

以克雷伯杆菌(Klebsiella pneumoniae)基因组DNA为模板, 运用PCR扩增得到编码甘油脱氢酶(GDH)的基因(gldA), 并克隆到pMD-18T载体上, 构建克隆载体pMD-gldA。经测序正确后, 将gldA亚克隆至表达载体pET-32a(+)上构建表达质粒pET-32gldA。在乳糖诱导下, 携带pET-32gldA的E. coli BL21 (DE3)高效表达分子量约为54 kD的可溶性蛋白。表达产物带有His6-tag标记, 选用Ni柱对表达产物进行纯化, 纯化后酶液的比活为188 u/mg, 纯化倍数和回收率分别为3倍和67.5%。     

Metabolic engineering of a 1,2-propanediol pathway in Escherichia coli

1,2-Propanediol (1,2-PD) is a major commodity chemical that is currently derived from propylene, a nonrenewable resource. A goal of our research is to develop fermentation routes to 1,2-PD from renewable resources. Here we report the production of enantiomerically pure R-1,2-PD from glucose in Escherichia coli expressing NADH-linked glycerol dehydrogenase genes (E. coli gldA or Klebsiella pneumoniae dhaD). We also show that E. coli overexpressing the E. coli methylglyoxal synthase gene (mgs) produced 1,2-PD. The expression of either glycerol dehydrogenase or methylglyoxal synthase resulted in the anaerobic production of approximately 0.25 g of 1,2-PD per liter. R-1,2-PD production was further improved to 0.7 g of 1,2-PD per liter when methylglyoxal synthase and glycerol dehydrogenase (gldA) were coexpressed. In vitro studies indicated that the route to R-1,2-PD involved the reduction of methylglyoxal to R-lactaldehyde by the recombinant glycerol dehydrogenase and the reduction of R-lactaldehyde to R-1, 2-PD by a native E. coli activity. We expect that R-1,2-PD production can be significantly improved through further metabolic and bioprocess engineering.     

Quantitative analysis of the fermentative metabolism of glycerol in Escherichia coli

Availability, low price, and high degree of reduction have made glycerol a highly attractive and exploited carbon source for the production of fuels and reduced chemicals. Here we report the quantitative analysis of the fermentative metabolism of glycerol in Escherichia coli through the use of kinetic modeling and metabolic control analysis (MCA) to gain a better understanding of glycerol fermentation and identify key targets for genetic manipulation that could enhance product synthesis. The kinetics of glycerol fermentation in a batch culture was simulated using a dynamic model consisting of mass balances for glycerol, ethanol, biomass, and 11 intracellular metabolites, along with the corresponding kinetic expressions for the metabolism of each species. The model was then used to calculate metabolic control coefficients and elucidate the control structure of the pathways involved in glycerol utilization and ethanol synthesis. The calculated flux control coefficients indicate that the glycolytic flux during glycerol fermentation is almost exclusively controlled by the enzymes glycerol dehydrogenase (encoded by gldA) and dihydroxyacetone kinase (DHAK) (encoded by dhaKLM). In agreement with the MCA findings, overexpression of gldA and dhaKLM led to significant increase in glycerol utilization and ethanol synthesis fluxes. Moreover, overexpression of other enzymes involved in the pathways that mediate glycerol utilization and its conversion to ethanol had no significant impact on glycerol utilization and ethanol synthesis, further validating the MCA predictions. These findings were then applied as a means of increasing the production of ethanol: overexpression of glycerol dehyrdogenase and DHAK enabled the production of 20 g/L ethanol from crude glycerol, a by-product of biodiesel production, indicating the potential for industrial scale conversion of waste glycerol to ethanol under anaerobic conditions.     

Engineering Escherichia coli for the efficient conversion of glycerol to ethanol and co-products

Given its availability, low prices, and high degree of reduction, glycerol has become an ideal feedstock for producing reduced compounds via anaerobic fermentation. We recently identified environmental conditions enabling the fermentative metabolism of glycerol in E. coli, along with the pathways and mechanisms mediating this metabolic process. In this work, we used the knowledge base created in previous studies to engineer E. coli for the efficient conversion of crude glycerol to ethanol. Our strategy capitalized on the high degree of reduction of carbon in glycerol, thus enabling the production of not only ethanol but also co-products hydrogen and formate. Two strains were created for the co-production of ethanol-hydrogen and ethanol-formate: SY03 and SY04, respectively. High ethanol yields were achieved in both strains by minimizing the synthesis of by-products succinate and acetate through mutations that inactivated fumarate reductase (DeltafrdA) and phosphate acetyltransferase (Deltapta), respectively. Strain SY04, which produced ethanol-formate, also contained a mutation that inactivated formate-hydrogen lyase (DeltafdhF), thus preventing the conversion of formate to CO(2) and H(2). High rates of glycerol utilization and product synthesis were achieved by simultaneous overexpression of glycerol dehydrogenase (gldA) and dihydroxyacetone kinase (dhaKLM), which are the enzymes responsible for the conversion of glycerol to glycolytic intermediate dihydroxyacetone phosphate. The resulting strains, SY03 (pZSKLMgldA) and SY04 (pZSKLMgldA), produced ethanol-hydrogen and ethanol-formate from unrefined glycerol at yields exceeding 95% of the theoretical maximum and specific rates in the order of 15-30 mmol/gcell/h. These yields and productivities are superior to those reported for the conversion of glycerol to ethanol-H(2) or ethanol-formate by other organisms and equivalent to those achieved in the production of ethanol from sugars using E. coli.     

大肠杆菌甘油激酶基因(glpK)和甘油脱氢酶基因(gldA)的敲除及其对甘油产量的影响

利用Red重组系统构建了大肠杆菌JM109甘油激酶基因(glpK)和甘油脱氢酶基因(gldA)缺失的双突变菌株JM109B,然后将表达酿酒酵母3-磷酸甘油脱氢酶基因(GPD1)和3-磷酸甘油酯酶基因(HOR2)的质粒pSE-gpd1-hor2转化到JM109B突变菌株中,在含1%葡萄糖的摇瓶发酵培养基中37℃发酵24 h,甘油的最高产量为5.61 g/L,是原始菌株JM109/pSE-gpd1-hor2甘油产量的1.59倍;在30 L发酵罐中发酵28 h,甘油的最高产量为103.12 g/L,是原始菌株JM109/pSE-gpd1-hor2甘油产量的1.59倍,是原始菌株BL21/pSE-gpd1-hor2甘油产量的1.41倍,葡萄糖转化率为50.39%。     

重组依赖辅酶B12的甘油脱水酶基因表达系统构建

采用PCR方法从肺炎克雷伯氏杆菌基因组中分别扩增得到了编码依赖辅酶B12的甘油脱水酶α、β、γ三个亚基的基因gldA、gldB、gld将gldBC基因克隆至pSIM—T载体上,经测序正确后亚克隆至pGEX-4T-1载体中。将gldA进行T-A克隆后测定核苷酸序列正确,亚克隆至连有gldBC基因的pGEX-4T-1载体中。从而成功的构建了gldABC基因的同向串联原核融合表达载体pGEX—gldABC。     

Role of GldA in dihydroxyacetone and methylglyoxal metabolism of Escherichia coli K12

The metabolic pathway involving dihydroxyacetone is poorly characterized although novel enzymes associated with this metabolite have recently been demonstrated. The role of GldA in dihydroxyacetone and methylglyoxal metabolism was investigated by purifying the enzyme and characterizing its catalytic ability using nuclear magnetic resonance (NMR) spectroscopy. At neutral pH, the enzyme exhibits much higher affinities towards dihydroxyacetone, methylglyoxal, and glycolaldehyde than glycerol with K(m) values of 0.30, 0.50, 0.85, and 56 mM, respectively. This is consistent with NMR data with crude extracts, showing that the conversion from dihydroxyacetone to glycerol by GldA is far more efficient than the reverse reaction. Dihydroxyacetone was found to be lethal at higher concentration with an LC(50) value of 28 mM compared with 0.4 mM of methylglyoxal, while lactaldehyde was found to exhibit significant growth inhibition in Escherichia coli cells. The toxicity of dihydroxyacetone appears to be due to its intracellular conversion to an aldehyde compound, presumably methylglyoxal, since the glyoxalase mutant becomes sensitive to dihydroxyacetone. Based on information that gldA is preceded in an operon by the ptsA homolog and talC gene encoding fructose 6-phosphate aldolase, this study proposes that the primary role of gldA is to remove toxic dihydroxyacetone by converting it into glycerol.     

Enhanced production of (R)-1,2-propanediol by metabolically engineered Escherichia coli

1,2-Propanediol (1,2-PD) is a major commodity chemical currently derived from propylene. Previously, we have demonstrated the production of enantiomerically pure (R)-1,2-propanediol from glucose by an engineered E. coli expressing genes for NADH-linked glycerol dehydrogenase and methylglyoxal synthase. In this work, we investigate three methods to improve 1,2-PD in E. coli. First, we investigated improving the host by eliminating production of a byproduct, lactate. To do this, we constructed strains with mutations in two enzymes involved in lactate production, lactate dehydrogenase and glyoxalase I. (Surprisingly, when mutations were made in its ability to produce lactate, one strain of E. coli [MM294], produced a small amount of 1,2-PD without any added genes.) Second, we constructed a complete pathway to 1,2-PD from the glycolytic intermediate, dihydroxyacetone phosphate. Our previous 1, 2-PD producing strains relied on at least one endogenous E. coli activity and only produced 0.7 g/L of 1,2-PD. The complete pathway involved the coexpression of methylglyoxal synthase (mgs), glycerol dehydrogenase (gldA), and either yeast alcohol dehydrogenase (adhI) or E. coli 1,2-propanediol oxidoreductase (fucO). Third, we investigated bioprocessing improvements by carrying out a fed-batch fermentation with the best engineered strain (expressing mgs, gldA, and fucO). A final titer of 4.5 g/L of (R)-1,2-PD was produced, with a final yield of 0.19 g of 1,2-PD per gram of glucose consumed. This work provides a basis for further strain and process improvement.     

Production of 1,2-propanediol from glycerol in Saccharomyces cerevisiae

Glycerol has become an attractive carbon source in the biotechnology industry owing to its low price and reduced state. However, glycerol is rarely used as a carbon source in Saccharomyces cerevisiae because of its low utilization rate. In this study, we used glycerol as a main carbon source in S. cerevisiae to produce 1,2-propanediol. Metabolically engineered S. cerevisiae strains with overexpression of glycerol dissimilation pathway genes, including glycerol kinase (GUT1), glycerol 3-phosphate dehydrogenase (GUT2), glycerol dehydrogenase (gdh), and a glycerol transporter gene (GUP1), showed increased glycerol utilization and growth rate. More significant improvement of glycerol utilization and growth rate was accomplished by introducing 1,2-propanediol pathway genes, mgs (methylglyoxal synthase) and gldA (glycerol dehydrogenase) from Escherichia coli. By engineering both glycerol dissimilation and 1,2-propanediol pathways, the glycerol utilization and growth rate were improved 141% and 77%, respectively, and a 2.19 g 1,2- propanediol/l titer was achieved in 1% (v/v) glycerolcontaining YEPD medium in engineered S. cerevisiae.     

Application of sequential integration for metabolic engineering of 1,2-propanediol production in yeast

The yeast species Saccharomyces cerevisiae was engineered to produce 1,2-propanediol (1,2-PD) using the delta/UB sequential gene integration method. To study the effects of increased copy number, 2 genes (mgs and gldA from Escherichia coli) were sequentially integrated into the chromosomes of S. cerevisiae strains of opposite mating type. The resulting strains (containing 0-3 copies of either mgs or gldA) were mated to create all possible combinations of the 2 genes introduced for 1,2-PD production. Enzyme activities were generally correlated with copy number, although there was greater variation in GldA activity in the diploid cells. The integrated genes were confirmed by Southern blot and 1,2-PD production was analyzed by HPLC. The strain containing 3 copies of mgs and gldA showed the highest level of 1,2-PD; however, 1,2-PD concentration was not clearly related to gene copy number. 1,2-PD production did correlate with Mgs specific activity, and high GldA specific activity was found to be inhibitory.     

Clostridium beijerinckii and Clostridium difficile detoxify methylglyoxal by a novel mechanism involving glycerol dehydrogenase

In contrast to gram-negative bacteria, little is known about the mechanisms by which gram-positive bacteria degrade the toxic metabolic intermediate methylglyoxal (MG). Clostridium beijerinckii BR54, a Tn1545 insertion mutant of the NCIMB 8052 strain, formed cultures that contained significantly more (free) MG than wild-type cultures. Moreover, BR54 was more sensitive to growth inhibition by added MG than the wild type, suggesting that it has a reduced ability to degrade MG. The single copy of Tn1545 in this strain lies just downstream from gldA, encoding glycerol dehydrogenase. As a result of antisense RNA production, cell extracts of BR54 possess significantly less glycerol dehydrogenase activity than wild-type cell extracts (H. Liyanage, M. Young, and E. R. Kashket, J. Mol. Microbiol. Biotechnol. 2:87-93, 2000). Inactivation of gldA in both C. beijerinckii and Clostridium difficile gave rise to pinpoint colonies that could not be subcultured, indicating that glycerol dehydrogenase performs an essential function in both organisms. We propose that this role is detoxification of MG. To our knowledge, this is the first report of targeted gene disruption in the C. difficile chromosome.     

Location of the maltose A and B loci on the genetic map of Escherichia coli

Schwartz, Maxime (Institut Pasteur, Paris, France). Location of the maltose A and B loci on the genetic map of Escherichia coli. J. Bacteriol. 92:1083-1089. 1966.-All of the mutations impairing maltose metabolism that have been found in Escherichia coli map in one of the two loci, malA and malB. The position of malA in relation to the streptomycin, diaminopimelic acid + homoserine, and glycerol D loci were established both by sexual crosses and by P1 transduction. A new biotin marker was also shown to be located in this region. The position of malB was studied in relation to the loci for arginine F, methionine A, ultraviolet radiation A, and the origin of transfer of Hfr P10.     

The 6.9-A structure of GlpF: a basis for homology modeling of the glycerol channel from Escherichia coli

The three-dimensional structure of GlpF, the glycerol facilitator of Escherichia coli, was determined by cryo-electron microscopy. The 6.9-A density map calculated from images of two-dimensional crystals shows the GlpF helices to be similar to those of AQP1, the erythrocyte water channel. While the helix arrangement of GlpF does not reflect the larger pore diameter as seen in the projection map, additional peripheral densities observed in GlpF are compatible with the 31 additional residues in loops C and E, which accordingly do not interfere with the inner channel construction. Therefore, the atomic structure of AQP1 was used as a basis for homology modeling of the GlpF channel, which is predicted to be free of bends, wider, and more vertically oriented than the AQP1 channel. Furthermore, the residues facing the GlpF channel exhibit an amphiphilic nature, being hydrophobic on one side and hydrophilic on the other side. This property may partially explain the contradiction of glycerol diffusion but limited water permeation capacity.     

Mutation affecting resistance of Escherichia coli K12 to nalidixic acid

A new mutation, nalD, determining resistance of Escherichia coli to nalidixic acid (NAL) is reported. The nalD mutant described is resistant to NAL at 37 degrees C but sensitive at 30 degrees C. It is defective in penetration of NAL and glycerol through the outer membrane at 37 degrees C. The nalD mutation is located half-way between 89 and 89.5 min on the E. coli genetic map.     

Anaerobic growth of Escherichia coli on glycerol by importing genes of the dha regulon from Klebsiella pneumoniae

The dha regulon of Klebsiella pneumoniae specifying fermentative dissimilation of glycerol was mobilized by the broad-host-range plasmid RP4:mini Mu and introduced conjugatively into Escherichia coli. The recipient E. coli was enabled to grow anaerobically on glycerol without added hydrogen acceptors, although its cell yield was less than that of K. pneumoniae. The reduced cell yield was probably due to the lack of the coenzyme-B12-dependent glycerol dehydratase of the dha system. This enzyme initiates the first step in an auxiliary pathway for disposal of the extra reducing equivalents from glycerol. The lack of this enzyme would also account for the absence of 1,3-propanediol (a hallmark fermentation product of glycerol) in the spent culture medium. In a control experiment, a large quantity of this compound was detected in a similar culture medium following the growth of K. pneumoniae. The other three known enzymes of the dha system, glycerol dehydrogenase, dihydroxyacetone kinase and 1,3-propanediol oxidoreductase, however, were synthesized at levels comparable to those found in K. pneumoniae. Regulation of the dha system in E. coli appeared to follow the same pattern as in K. pneumoniae: the three acquired enzymes were induced by glycerol, catabolite repressed by glucose, and glycerol dehydrogenase was post-translationally inactivated during the shift from anaerobic to aerobic growth. The means by which the E. coli recipient can achieve redox balance without formation of 1,3-propanediol during anaerobic growth on glycerol remains to be discovered.     

1,3-Propanediol production by Escherichia coli expressing genes from the Klebsiella pneumoniae dha regulon.

The dha regulon in Klebsiella pneumoniae enables the organism to grow anaerobically on glycerol and produce 1,3-propanediol (1,3-PD). Escherichia coli, which does not have a dha system, is unable to grow anaerobically on glycerol without an exogenous electron acceptor and does not produce 1,3-PD. A genomic library of K. pneumoniae ATCC 25955 constructed in E. coli AG1 was enriched for the ability to grow anaerobically on glycerol and dihydroxyacetone and was screened for the production of 1,3-PD. The cosmid pTC1 (42.5 kb total with an 18.2-kb major insert) was isolated from a 1,3-PD-producing strain of E. coli and found to possess enzymatic activities associated with four genes of the dha regulon: glycerol dehydratase (dhaB), 1,3-PD oxidoreductase (dhaT), glycerol dehydrogenase (dhaD), and dihydroxyacetone kinase (dhaK). All four activities were inducible by the presence of glycerol. When E. coli AG1/pTC1 was grown on complex medium plus glycerol, the yield of 1,3-PD from glycerol was 0.46 mol/mol. The major fermentation by-products were formate, acetate, and D-lactate. 1,3-PD is an intermediate in organic synthesis and polymer production. The 1,3-PD fermentation provides a useful model system for studying the interaction of a biochemical pathway in a foreign host and for developing strategies for metabolic pathway engineering.     

1,3-Propanediol production by Escherichia coli expressing genes from the Klebsiella pneumoniae dha regulon.

The dha regulon in Klebsiella pneumoniae enables the organism to grow anaerobically on glycerol and produce 1,3-propanediol (1,3-PD). Escherichia coli, which does not have a dha system, is unable to grow anaerobically on glycerol without an exogenous electron acceptor and does not produce 1,3-PD. A genomic library of K. pneumoniae ATCC 25955 constructed in E. coli AG1 was enriched for the ability to grow anaerobically on glycerol and dihydroxyacetone and was screened for the production of 1,3-PD. The cosmid pTC1 (42.5 kb total with an 18.2-kb major insert) was isolated from a 1,3-PD-producing strain of E. coli and found to possess enzymatic activities associated with four genes of the dha regulon: glycerol dehydratase (dhaB), 1,3-PD oxidoreductase (dhaT), glycerol dehydrogenase (dhaD), and dihydroxyacetone kinase (dhaK). All four activities were inducible by the presence of glycerol. When E. coli AG1/pTC1 was grown on complex medium plus glycerol, the yield of 1,3-PD from glycerol was 0.46 mol/mol. The major fermentation by-products were formate, acetate, and D-lactate. 1,3-PD is an intermediate in organic synthesis and polymer production. The 1,3-PD fermentation provides a useful model system for studying the interaction of a biochemical pathway in a foreign host and for developing strategies for metabolic pathway engineering.