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Yang Y, Zou Y, Chen X, Sun H, Hua X, Johnston L, Zeng X, Qiao S, Ye C. Metabolic engineering of Escherichia coli for the production of 5-aminolevulinic acid based on combined metabolic pathway modification and reporter-guided mutant selection (RGMS). BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:82. [PMID: 38886801 PMCID: PMC11184883 DOI: 10.1186/s13068-024-02530-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 06/10/2024] [Indexed: 06/20/2024]
Abstract
BACKGROUND 5-Aminolevulinic acid (ALA) recently received much attention due to its potential application in many fields such as medicine, nutrition and agriculture. Metabolic engineering is an efficient strategy to improve microbial production of 5-ALA. RESULTS In this study, an ALA production strain of Escherichia coli was constructed by rational metabolic engineering and stepwise improvement. A metabolic strategy to produce ALA directly from glucose in this recombinant E. coli via both C4 and C5 pathways was applied herein. The expression of a modified hemARS gene and rational metabolic engineering by gene knockouts significantly improved ALA production from 765.9 to 2056.1 mg/L. Next, we tried to improve ALA production by RGMS-directed evolution of eamA gene. After RGMS, the ALA yield of strain A2-ASK reached 2471.3 mg/L in flask. Then, we aimed to improve the oxidation resistance of cells by overexpressing sodB and katE genes and ALA yield reached 2703.8 mg/L. A final attempt is to replace original promoter of hemB gene in genome with a weaker one to decrease its expression. After 24 h cultivation, a high ALA yield of 19.02 g/L was achieved by 108-ASK in a 5 L fermenter. CONCLUSIONS These results suggested that an industrially competitive strain can be efficiently developed by metabolic engineering based on combined rational modification and optimization of gene expression.
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Affiliation(s)
- Yuting Yang
- State Key Laboratory of Animal Nutrition and Feeding, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Bio-Feed Additives, Beijing, 100193, China
| | - Yuhong Zou
- State Key Laboratory of Animal Nutrition and Feeding, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Bio-Feed Additives, Beijing, 100193, China
| | - Xi Chen
- State Key Laboratory for Agro-Biotechnology, Ministry of Agriculture and Rural Affairs, Key Laboratory for Pest Monitoring and Green Management, Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Haidong Sun
- National Feed Engineering Technology Research Centre, Beijing, 100193, China
| | - Xia Hua
- State Key Laboratory for Agro-Biotechnology, Ministry of Agriculture and Rural Affairs, Key Laboratory for Pest Monitoring and Green Management, Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Lee Johnston
- Swine Nutrition and Production, West Central Research and Outreach Center, University of Minnesota, Morris, MN, 56267, USA
| | - Xiangfang Zeng
- State Key Laboratory of Animal Nutrition and Feeding, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Bio-Feed Additives, Beijing, 100193, China
| | - Shiyan Qiao
- State Key Laboratory of Animal Nutrition and Feeding, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Bio-Feed Additives, Beijing, 100193, China
| | - Changchuan Ye
- State Key Laboratory of Animal Nutrition and Feeding, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing, 100193, China.
- Department of Animal Science, College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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2
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Fatema N, Li X, Gan Q, Fan C. Characterizing lysine acetylation of glucokinase. Protein Sci 2024; 33:e4845. [PMID: 37996965 PMCID: PMC10731539 DOI: 10.1002/pro.4845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/16/2023] [Accepted: 11/18/2023] [Indexed: 11/25/2023]
Abstract
Glucokinase (GK) catalyzes the phosphorylation of glucose to form glucose-6-phosphate as the substrate of glycolysis for energy production. Acetylation of lysine residues in Escherichia coli GK has been identified at multiple sites by a series of proteomic studies, but the impact of acetylation on GK functions remains largely unknown. In this study, we applied the genetic code expansion strategy to produce site-specifically acetylated GK variants which naturally exist in cells. Enzyme assays and kinetic analyses showed that lysine acetylation decreases the GK activity, mostly resulting from acetylation of K214 and K216 at the entrance of the active site, which impairs the binding of substrates. We also compared results obtained from the glutamine substitution method and the genetic acetyllysine incorporation approach, showing that glutamine substitution is not always effective for mimicking acetylated lysine. Further genetic studies as well as in vitro acetylation and deacetylation assays were performed to determine acetylation and deacetylation mechanisms, which showed that E. coli GK could be acetylated by acetyl-phosphate without enzymes and deacetylated by CobB deacetylase.
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Affiliation(s)
- Nour Fatema
- Cell and Molecular Biology ProgramUniversity of ArkansasFayettevilleArkansasUSA
| | - Xinyu Li
- Cell and Molecular Biology ProgramUniversity of ArkansasFayettevilleArkansasUSA
| | - Qinglei Gan
- Department of Chemistry and BiochemistryUniversity of ArkansasFayettevilleArkansasUSA
| | - Chenguang Fan
- Cell and Molecular Biology ProgramUniversity of ArkansasFayettevilleArkansasUSA
- Department of Chemistry and BiochemistryUniversity of ArkansasFayettevilleArkansasUSA
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3
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Liu Z, Cai M, Zhou S, You J, Zhao Z, Liu Z, Xu M, Rao Z. High-efficient production of L-homoserine in Escherichia coli through engineering synthetic pathway combined with regulating cell division. BIORESOURCE TECHNOLOGY 2023; 389:129828. [PMID: 37806363 DOI: 10.1016/j.biortech.2023.129828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/03/2023] [Accepted: 10/03/2023] [Indexed: 10/10/2023]
Abstract
L-Homoserine is an important amino acid as a precursor in synthesizing many valuable products. However, the low productivity caused by slow L-homoserine production during active cell growth in fermentation hinders its potential applications. In this study, strategies of engineering the synthetic pathway combined with regulating cell division were employed in an L-homoserine-producing Escherichia coli strain for efficiently biomanufacturing L-homoserine. First, the flux-control genes in the L-homoserine degradation pathway were omitted to redistribute carbon flux. To drive more carbon flux into L-homoserine production, the phosphoenolpyruvate-pyruvate-oxaloacetate loop was redrawn. Subsequently, the cell division was engineered by using the self-regulated promoters to coordinate cell growth and L-homoserine production. The ultimate strain HOM23 produced 101.31 g/L L-homoserine with a productivity of 1.91 g/L/h, which presented the highest L-homoserine titer and productivity to date from plasmid-free strains. The strategies used in this study could be applied to constructing cell factories for producing other L-aspartate derivatives.
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Affiliation(s)
- Zhifei Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, Jiangsu 214200, China
| | - Mengmeng Cai
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, Jiangsu 214200, China
| | - Siquan Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, Jiangsu 214200, China
| | - Jiajia You
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, Jiangsu 214200, China
| | - Zhenqiang Zhao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, Jiangsu 214200, China
| | - Zuyi Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, Jiangsu 214200, China
| | - Meijuan Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, Jiangsu 214200, China
| | - Zhiming Rao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, Jiangsu 214200, China.
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4
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Taylor JE, Palur DSK, Zhang A, Gonzales JN, Arredondo A, Coulther TA, Lechner ABJ, Rodriguez EP, Fiehn O, Didzbalis J, Siegel JB, Atsumi S. Awakening the natural capability of psicose production in Escherichia coli. NPJ Sci Food 2023; 7:54. [PMID: 37838768 PMCID: PMC10576766 DOI: 10.1038/s41538-023-00231-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 10/02/2023] [Indexed: 10/16/2023] Open
Abstract
Due to the rampant rise in obesity and diabetes, consumers are desperately seeking for ways to reduce their sugar intake, but to date there are no options that are both accessible and without sacrifice of palatability. One of the most promising new ingredients in the food system as a non-nutritive sugar substitute with near perfect palatability is D-psicose. D-psicose is currently produced using an in vitro enzymatic isomerization of D-fructose, resulting in low yield and purity, and therefore requiring substantial downstream processing to obtain a high purity product. This has made adoption of D-psicose into products limited and results in significantly higher per unit costs, reducing accessibility to those most in need. Here, we found that Escherichia coli natively possesses a thermodynamically favorable pathway to produce D-psicose from D-glucose through a series of phosphorylation-epimerization-dephosphorylation steps. To increase carbon flux towards D-psicose production, we introduced a series of genetic modifications to pathway enzymes, central carbon metabolism, and competing metabolic pathways. In an attempt to maximize both cellular viability and D-psicose production, we implemented methods for the dynamic regulation of key genes including clustered regularly interspaced short palindromic repeats inhibition (CRISPRi) and stationary-phase promoters. The engineered strains achieved complete consumption of D-glucose and production of D-psicose, at a titer of 15.3 g L-1, productivity of 2 g L-1 h-1, and yield of 62% under test tube conditions. These results demonstrate the viability of whole-cell catalysis as a sustainable alternative to in vitro enzymatic synthesis for the accessible production of D-psicose.
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Affiliation(s)
- Jayce E Taylor
- Department of Chemistry, University of California, Davis, Davis, CA, 95616, USA
| | | | - Angela Zhang
- Department of Chemistry, University of California, Davis, Davis, CA, 95616, USA
| | - Jake N Gonzales
- Plant Biology Graduate Group, University of California, Davis, Davis, CA, 95616, USA
| | - Augustine Arredondo
- Department of Chemistry, University of California, Davis, Davis, CA, 95616, USA
| | | | | | - Elys P Rodriguez
- Department of Chemistry, University of California, Davis, Davis, CA, 95616, USA
- West Coast Metabolomics Center, UC Davis Genome Center, University of California, Davis, Davis, CA, 95616, USA
| | - Oliver Fiehn
- West Coast Metabolomics Center, UC Davis Genome Center, University of California, Davis, Davis, CA, 95616, USA
| | - John Didzbalis
- Mars, Incorporated, 6885 Elm Street, McLean, VA, 22101, USA
| | - Justin B Siegel
- Department of Chemistry, University of California, Davis, Davis, CA, 95616, USA
- Genome Center, University of California, Davis, Davis, CA, 95616, USA
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Sacramento, CA, 95616, USA
| | - Shota Atsumi
- Department of Chemistry, University of California, Davis, Davis, CA, 95616, USA.
- Plant Biology Graduate Group, University of California, Davis, Davis, CA, 95616, USA.
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5
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Breger JC, Vranish JN, Oh E, Stewart MH, Susumu K, Lasarte-Aragonés G, Ellis GA, Walper SA, Díaz SA, Hooe SL, Klein WP, Thakur M, Ancona MG, Medintz IL. Self assembling nanoparticle enzyme clusters provide access to substrate channeling in multienzymatic cascades. Nat Commun 2023; 14:1757. [PMID: 36990995 PMCID: PMC10060375 DOI: 10.1038/s41467-023-37255-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 03/08/2023] [Indexed: 03/31/2023] Open
Abstract
Access to efficient enzymatic channeling is desired for improving all manner of designer biocatalysis. We demonstrate that enzymes constituting a multistep cascade can self-assemble with nanoparticle scaffolds into nanoclusters that access substrate channeling and improve catalytic flux by orders of magnitude. Utilizing saccharification and glycolytic enzymes with quantum dots (QDs) as a model system, nanoclustered-cascades incorporating from 4 to 10 enzymatic steps are prototyped. Along with confirming channeling using classical experiments, its efficiency is enhanced several fold more by optimizing enzymatic stoichiometry with numerical simulations, switching from spherical QDs to 2-D planar nanoplatelets, and by ordering the enzyme assembly. Detailed analyses characterize assembly formation and clarify structure-function properties. For extended cascades with unfavorable kinetics, channeled activity is maintained by splitting at a critical step, purifying end-product from the upstream sub-cascade, and feeding it as a concentrated substrate to the downstream sub-cascade. Generalized applicability is verified by extending to assemblies incorporating other hard and soft nanoparticles. Such self-assembled biocatalytic nanoclusters offer many benefits towards enabling minimalist cell-free synthetic biology.
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Affiliation(s)
- Joyce C Breger
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA
| | - James N Vranish
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA
- Department of Chemistry, Engineering, and Physics, Franciscan University of Steubenville, Steubenville, OH, 43952, USA
| | - Eunkeu Oh
- Optical Sciences Division, Code 5611, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA
| | - Michael H Stewart
- Optical Sciences Division, Code 5611, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5611, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA
| | - Guillermo Lasarte-Aragonés
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA
- College of Science, George Mason University, Fairfax, VA, 22030, USA
| | - Gregory A Ellis
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA
| | - Scott A Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA
| | - Shelby L Hooe
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA
- National Research Council, Washington, D.C., 20001, USA
| | - William P Klein
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA
- National Research Council, Washington, D.C., 20001, USA
| | - Meghna Thakur
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA
- College of Science, George Mason University, Fairfax, VA, 22030, USA
| | - Mario G Ancona
- Electronic Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA
- Department of Electrical and Computer Engineering, Florida State University, Tallahassee, FL, 32310, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, USA.
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6
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Shakir NA, Aslam M, Bibi T, Falak S, Rashid N. Functional analyses of a highly thermostable hexokinase from Pyrobaculum calidifontis. Carbohydr Res 2023; 523:108711. [PMID: 36395717 DOI: 10.1016/j.carres.2022.108711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/11/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
Abstract
The gene encoding a repressor open reading frame sugar kinase (ROK) family protein from hyperthermophilic crenarchaeon Pyrobaculum calidifontis, Pcal-HK, was cloned and expressed in Escherichia coli. The recombinant protein was produced in soluble and highly active form. Purified Pcal-HK was highly thermostable and existed in a monomeric form in solution. The enzyme was specific to ATP as phosphoryl donor but showed broad specificity to phosphoryl acceptors. It catalyzed the phosphorylation of a number of hexoses, including glucose, glucosamine, N-acetyl glucosamine, fructose and mannose, at nearly the same rate and similar affinity. The enzyme was metal ion dependent exhibiting highest activity at 90-95 °C and pH 8.5. Mg2+ was most effective metal ion, which could be partially replaced by Mn2+, Ni2+ or Zn2+. Kinetic parameters were determined at 90 °C and the enzyme showed almost similar catalytic efficiency (kcat/Km) towards the above mentioned hexoses. To the best of our knowledge, Pcal-HK is the most active thermostable ROK family hexokinase characterized to date which catalyzes the phosphorylation of various hexoses with nearly similar affinity.
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Affiliation(s)
- Nisar Ahmed Shakir
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan
| | - Mehwish Aslam
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan
| | - Tahira Bibi
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan
| | - Samia Falak
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan
| | - Naeem Rashid
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan.
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7
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Fung V, Xiao Y, Tan ZJD, Ma X, Zhou JFJ, Panda S, Yan N, Zhou K. Producing aromatic amino acid from corn husk by using polyols as intermediates. Biomaterials 2022; 287:121661. [PMID: 35842981 DOI: 10.1016/j.biomaterials.2022.121661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 06/21/2022] [Accepted: 06/28/2022] [Indexed: 11/22/2022]
Abstract
Agricultural biomass remains as one of the commonly found waste on Earth. Although valorisation of these wastes has been studied in detail, the fermentation-based processes still need improvement due to the high cost of hydrolysing enzymes, and the presence of growth inhibitors which constrains the fermentation to produce high-value products. To address these challenges, we developed an integrated process in this study combining abiotic- and bio-catalysis to produce l-tyrosine from corn husk. The first step involved a one-pot hydrolytic hydrogenation tandem reaction without the use of the expensive enzymes, which yielded a mixture of polyols and sugars. Without any purification, these crude hydrolysates can be almost completely utilized by an engineered Escherichia coli strain, which did not exhibit any growth inhibition. The strain produced 0.44 g/L l-tyrosine from 10 g/L crude corn husk hydrolysates, demonstrating the feasibility of converting agricultural biomass into a valuable aromatic amino acid via an integrated process.
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Affiliation(s)
- Vincent Fung
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Singapore
| | - Yiying Xiao
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Singapore; Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University, Binhai New City, Fuzhou, 350207, China
| | - Zhi Jun Daniel Tan
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Singapore
| | - Xiaoqiang Ma
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Singapore
| | - Jie Fu J Zhou
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Singapore
| | - Smaranika Panda
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Singapore
| | - Ning Yan
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Singapore.
| | - Kang Zhou
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Singapore.
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8
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Wang J, Ma S, Li W, Wang X, Huang D, Jiang L, Feng L. Salmonella enterica Serovar Typhi Induces Host Metabolic Reprogramming to Increase Glucose Availability for Intracellular Replication. Int J Mol Sci 2021; 22:ijms221810003. [PMID: 34576166 PMCID: PMC8467381 DOI: 10.3390/ijms221810003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 11/18/2022] Open
Abstract
Salmonella enterica serovar Typhi (S. Typhi) is a human-limited intracellular pathogen and the cause of typhoid fever, a severe systemic disease. Pathogen–host interaction at the metabolic level affects the pathogenicity of intracellular pathogens, but it remains unclear how S. Typhi infection influences host metabolism for its own benefit. Herein, using metabolomics and transcriptomics analyses, combined with in vitro and in vivo infection assays, we investigated metabolic responses in human macrophages during S. Typhi infection, and the impact of these responses on S. Typhi intracellular replication and systemic pathogenicity. We observed increased glucose content, higher rates of glucose uptake and glycolysis, and decreased oxidative phosphorylation in S. Typhi-infected human primary macrophages. Replication in human macrophages and the bacterial burden in systemic organs of humanized mice were reduced by either the inhibition of host glucose uptake or a mutation of the bacterial glucose uptake system, indicating that S. Typhi utilizes host-derived glucose to enhance intracellular replication and virulence. Thus, S. Typhi promotes its pathogenicity by inducing metabolic changes in host macrophages and utilizing the glucose that subsequently accumulates as a nutrient for intracellular replication. Our findings provide the first metabolic signature of S. Typhi-infected host cells and identifies a new strategy utilized by S. Typhi for intracellular replication.
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Affiliation(s)
- Jingting Wang
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China; (J.W.); (S.M.); (W.L.); (X.W.); (D.H.)
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
| | - Shuai Ma
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China; (J.W.); (S.M.); (W.L.); (X.W.); (D.H.)
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
| | - Wanwu Li
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China; (J.W.); (S.M.); (W.L.); (X.W.); (D.H.)
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
| | - Xinyue Wang
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China; (J.W.); (S.M.); (W.L.); (X.W.); (D.H.)
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
| | - Di Huang
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China; (J.W.); (S.M.); (W.L.); (X.W.); (D.H.)
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
| | - Lingyan Jiang
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China; (J.W.); (S.M.); (W.L.); (X.W.); (D.H.)
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- Correspondence: (L.J.); (L.F.)
| | - Lu Feng
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China; (J.W.); (S.M.); (W.L.); (X.W.); (D.H.)
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- Correspondence: (L.J.); (L.F.)
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9
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Usvalampi A, Li H, Frey AD. Production of Glucose 6-Phosphate From a Cellulosic Feedstock in a One Pot Multi-Enzyme Synthesis. Front Bioeng Biotechnol 2021; 9:678038. [PMID: 34150734 PMCID: PMC8206812 DOI: 10.3389/fbioe.2021.678038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/07/2021] [Indexed: 12/04/2022] Open
Abstract
Glucose 6-phosphate is the phosphorylated form of glucose and is used as a reagent in enzymatic assays. Current production occurs via a multi-step chemical synthesis. In this study we established a fully enzymatic route for the synthesis of glucose 6-phosphate from cellulose. As the enzymatic phosphorylation requires ATP as phosphoryl donor, the use of a cofactor regeneration system is required. We evaluated Escherichia coli glucokinase and Saccharomyces cerevisiae hexokinase (HK) for the phosphorylation reaction and Pseudomonas aeruginosa polyphosphate kinase 2 (PPK2) for ATP regeneration. All three enzymes were characterized in terms of temperature and pH optimum and the effects of substrates and products concentrations on enzymatic activities. After optimization of the conditions, we achieved a 85% conversion of glucose into glucose 6-phosphate using the HK/PPK2 activities within a 24 h reaction resulting in 12.56 g/l of glucose 6-phosphate. Finally, we demonstrated the glucose 6-phosphate formation from microcrystalline cellulose in a one-pot reaction comprising Aspergillus niger cellulase for glucose release and HK/PPK2 activities. We achieved a 77% conversion of released glucose into glucose 6-phosphate, however at the expense of a lower glucose 6-phosphate yield of 1.17 g/l. Overall, our study shows an alternative approach for synthesis of glucose 6-phosphate that can be used to valorize biomass derived cellulose.
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Affiliation(s)
- Anne Usvalampi
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Espoo, Finland
| | - He Li
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Espoo, Finland
| | - Alexander D Frey
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Espoo, Finland
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10
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Pan Q, Li Z, Ju X, Hou C, Xiao Y, Shi R, Fu C, Danchin A, You C. Escherichia coli segments its controls on carbon-dependent gene expression into global and specific regulations. Microb Biotechnol 2021; 14:1084-1106. [PMID: 33650807 PMCID: PMC8085971 DOI: 10.1111/1751-7915.13776] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 02/05/2021] [Accepted: 02/05/2021] [Indexed: 01/20/2023] Open
Abstract
How bacteria adjust gene expression to cope with variable environments remains open to question. Here, we investigated the way global gene expression changes in E. coli correlated with the metabolism of seven carbon substrates chosen to trigger a large panel of metabolic pathways. Coarse-grained analysis of gene co-expression identified a novel regulation pattern: we established that the gene expression trend following immediately the reduction of growth rate (GR) was correlated to its initial expression level. Subsequent fine-grained analysis of co-expression demonstrated that the Crp regulator, coupled with a change in GR, governed the response of most GR-dependent genes. By contrast, the Cra, Mlc and Fur regulators governed the expression of genes responding to non-glycolytic substrates, glycolytic substrates or phosphotransferase system transported sugars following an idiosyncratic way. This work allowed us to expand additional genes in the panel of gene complement regulated by each regulator and to elucidate the regulatory functions of each regulator comprehensively. Interestingly, the bulk of genes controlled by Cra and Mlc were, respectively, co-regulated by Crp- or GR-related effect and our quantitative analysis showed that each factor took turns to work as the primary one or contributed equally depending on the conditions.
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Affiliation(s)
- Qing Pan
- Shenzhen Key Laboratory of Microbial Genetic EngineeringCollege of Life Sciences and OceanologyShenzhen UniversityShenzhen, GuangdongChina
- Shandong Provincial Key Laboratory of Energy GeneticsKey Laboratory of BiofuelsQingdao Engineering Research Center of Biomass Resources and EnvironmentQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdao, ShandongChina
| | - Zongjin Li
- Shenzhen Key Laboratory of Microbial Genetic EngineeringCollege of Life Sciences and OceanologyShenzhen UniversityShenzhen, GuangdongChina
| | - Xian Ju
- Shenzhen Key Laboratory of Microbial Genetic EngineeringCollege of Life Sciences and OceanologyShenzhen UniversityShenzhen, GuangdongChina
| | - Chaofan Hou
- Shenzhen Key Laboratory of Microbial Genetic EngineeringCollege of Life Sciences and OceanologyShenzhen UniversityShenzhen, GuangdongChina
| | - Yunzhu Xiao
- Shenzhen Key Laboratory of Microbial Genetic EngineeringCollege of Life Sciences and OceanologyShenzhen UniversityShenzhen, GuangdongChina
| | - Ruoping Shi
- Shenzhen Key Laboratory of Microbial Genetic EngineeringCollege of Life Sciences and OceanologyShenzhen UniversityShenzhen, GuangdongChina
| | - Chunxiang Fu
- Shandong Provincial Key Laboratory of Energy GeneticsKey Laboratory of BiofuelsQingdao Engineering Research Center of Biomass Resources and EnvironmentQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdao, ShandongChina
| | - Antoine Danchin
- Kodikos Labs/Stellate TherapeuticsInstitut Cochin24 rue du Faubourg Saint‐JacquesParis75014France
| | - Conghui You
- Shenzhen Key Laboratory of Microbial Genetic EngineeringCollege of Life Sciences and OceanologyShenzhen UniversityShenzhen, GuangdongChina
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11
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Xiong B, Zhu Y, Tian D, Jiang S, Fan X, Ma Q, Wu H, Xie X. Flux redistribution of central carbon metabolism for efficient production of l-tryptophan in Escherichia coli. Biotechnol Bioeng 2021; 118:1393-1404. [PMID: 33399214 DOI: 10.1002/bit.27665] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/24/2020] [Accepted: 12/30/2020] [Indexed: 01/22/2023]
Abstract
Microbial production of l-tryptophan (l-trp) has received considerable attention because of its diverse applications in food additives and pharmaceuticals. Overexpression of rate-limiting enzymes and blockage of competing pathways can effectively promote microbial production of l-trp. However, the biosynthetic process remains suboptimal due to imbalanced flux distribution between central carbon and tryptophan metabolism, presenting a major challenge to further improvement of l-trp yield. In this study, we redistributed central carbon metabolism to improve phosphoenolpyruvate (PEP) and erythrose-4-phosphate (E4P) pools in an l-trp producing strain of Escherichia coli for efficient l-trp synthesis. To do this, a phosphoketolase from Bifidobacterium adolescentis was introduced to strengthen E4P formation, and the l-trp titer and yield increased to 10.8 g/L and 0.148 g/g glucose, respectively. Next, the phosphotransferase system was substituted with PEP-independent glucose transport, meditated by a glucose facilitator from Zymomonas mobilis and native glucokinase. This modification improved l-trp yield to 0.164 g/g glucose, concomitant with 58% and 40% decreases of acetate and lactate accumulation, respectively. Then, to channel more central carbon flux to the tryptophan biosynthetic pathway, several metabolic engineering strategies were applied to rewire the PEP-pyruvate-oxaloacetate node. Finally, the constructed strain SX11 produced 41.7 g/L l-trp with an overall yield of 0.227 g/g glucose after 40 h fed-batch fermentation in 5-L bioreactor. This is the highest overall yield of l-trp ever reported from a rationally engineered strain. Our results suggest the flux redistribution of central carbon metabolism to maintain sufficient supply of PEP and E4P is a promising strategy for efficient l-trp biosynthesis, and this strategy would likely also increase the production of other aromatic amino acids and derivatives.
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Affiliation(s)
- Bo Xiong
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, China.,College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Yongduo Zhu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, China.,College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Daoguang Tian
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, China.,College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Shuai Jiang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, China.,College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Xiaoguang Fan
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, China.,College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Qian Ma
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, China.,College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Heyun Wu
- College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin, China
| | - Xixian Xie
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, China.,College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
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12
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Evolution of an Escherichia coli PTS - strain: a study of reproducibility and dynamics of an adaptive evolutive process. Appl Microbiol Biotechnol 2020; 104:9309-9325. [PMID: 32954454 DOI: 10.1007/s00253-020-10885-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 08/12/2020] [Accepted: 09/04/2020] [Indexed: 10/23/2022]
Abstract
Adaptive laboratory evolution (ALE) has been used to study and solve pressing questions about evolution, especially for the study of the development of mutations that confer increased fitness during evolutionary processes. In this contribution, we investigated how the evolutionary process conducted with the PTS- mutant of Escherichia coli PB11 in three parallel batch cultures allowed the restoration of rapid growth with glucose as the carbon source. The significant findings showed that genomic sequence analysis of a set of newly evolved mutants isolated from ALE experiments 2-3 developed some essential mutations, which efficiently improved the fast-growing phenotypes throughout different fitness landscapes. Regulator galR was the target of several mutations such as SNPs, partial and total deletions, and insertion of an IS1 element and thus indicated the relevance of a null mutation of this gene in the adaptation of the evolving population of PB11 during the parallel ALE experiments. These mutations resulted in the selection of MglB and GalP as the primary glucose transporters by the evolving population, but further selection of at least a second adaptive mutation was also necessary. We found that mutations in the yfeO, rppH, and rng genes improved the fitness advantage of evolving PTS- mutants and resulted in amplification of leaky activity in Glk for glucose phosphorylation and upregulation of glycolytic and other growth-related genes. Notably, we determined that these mutations appeared and were fixed in the evolving populations between 48 and 72 h of cultivation, which resulted in the selection of fast-growing mutants during one ALE experiments in batch cultures of 80 h duration.Key points• ALE experiments selected evolved mutants through different fitness landscapes in which galR was the target of different mutations: SNPs, deletions, and insertion of IS.• Key mutations in evolving mutants appeared and fixed at 48-72 h of cultivation.• ALE experiments led to increased understanding of the genetics of cellular adaptation to carbon source limitation.
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13
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ABC Transporters Required for Hexose Uptake by Clostridium phytofermentans. J Bacteriol 2019; 201:JB.00241-19. [PMID: 31109990 DOI: 10.1128/jb.00241-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 05/13/2019] [Indexed: 01/02/2023] Open
Abstract
The mechanisms by which bacteria uptake solutes across the cell membrane broadly impact their cellular energetics. Here, we use functional genomic, genetic, and biophysical approaches to reveal how Clostridium (Lachnoclostridium) phytofermentans, a model bacterium that ferments lignocellulosic biomass, uptakes plant hexoses using highly specific, nonredundant ATP-binding cassette (ABC) transporters. We analyze the transcription patterns of its 173 annotated sugar transporter genes to find those upregulated on specific carbon sources. Inactivation of these genes reveals that individual ABC transporters are required for uptake of hexoses and hexo-oligosaccharides and that distinct ABC transporters are used for oligosaccharides versus their constituent monomers. The thermodynamics of sugar binding shows that substrate specificity of these transporters is encoded by the extracellular solute-binding subunit. As sugars are not phosphorylated during ABC transport, we identify intracellular hexokinases based on in vitro activities. These mechanisms used by Clostridia to uptake plant hexoses are key to understanding soil and intestinal microbiomes and to engineer strains for industrial transformation of lignocellulose.IMPORTANCE Plant-fermenting Clostridia are anaerobic bacteria that recycle plant matter in soil and promote human health by fermenting dietary fiber in the intestine. Clostridia degrade plant biomass using extracellular enzymes and then uptake the liberated sugars for fermentation. The main sugars in plant biomass are hexoses, and here, we identify how hexoses are taken in to the cell by the model organism Clostridium phytofermentans We show that this bacterium uptakes hexoses using a set of highly specific, nonredundant ABC transporters. Once in the cell, the hexoses are phosphorylated by intracellular hexokinases. This study provides insight into the functioning of abundant members of soil and intestinal microbiomes and identifies gene targets to engineer strains for industrial lignocellulosic fermentation.
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14
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Zhu JS, Stiers KM, Winter SM, Garcia AD, Versini AF, Beamer LJ, Jakeman DL. Synthesis, Derivatization, and Structural Analysis of Phosphorylated Mono-, Di-, and Trifluorinated d-Gluco-heptuloses by Glucokinase: Tunable Phosphoglucomutase Inhibition. ACS OMEGA 2019; 4:7029-7037. [PMID: 31179410 PMCID: PMC6547622 DOI: 10.1021/acsomega.9b00008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 04/08/2019] [Indexed: 05/16/2023]
Abstract
Glucokinase phosphorylated a series of C-1 fluorinated α-d-gluco-heptuloses. These phosphorylated products were discovered to be inhibitors of α-phosphomannomutase/phosphoglucomutase (αPMM/PGM) and β-phosphoglucomutase (βPGM). Inhibition potency with both mutases inversely correlated to the degree of fluorination. Structural analysis with αPMM demonstrated the inhibitor binding to the active site, with the phosphate in the phosphate binding site and the anomeric hydroxyl directed to the catalytic site.
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Affiliation(s)
- Jian-She Zhu
- College
of Pharmacy, Dalhousie University, 5968 College Street, Halifax, Nova Scotia B3H 4R2, Canada
| | - Kyle M. Stiers
- Biochemistry
Department, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, United States
| | - Sherany M. Winter
- College
of Pharmacy, Dalhousie University, 5968 College Street, Halifax, Nova Scotia B3H 4R2, Canada
- Department
of Chemistry, Hogeschool Leiden (UAS Leiden), Zernikedreef 11, CK Leiden 2333, The Netherlands
| | - Anthony D. Garcia
- College
of Pharmacy, Dalhousie University, 5968 College Street, Halifax, Nova Scotia B3H 4R2, Canada
- École
Nationale Supérieure de Chimie de Rennes, 11 Allée de Beaulieu, CS 50837, Rennes Cedex 7 35708, France
| | - Antoine F. Versini
- College
of Pharmacy, Dalhousie University, 5968 College Street, Halifax, Nova Scotia B3H 4R2, Canada
- École
Supérieure de Physique et de Chimie Industrielles de la Ville
de Paris, 10 rue Vauquelin, Paris 75005, France
| | - Lesa J. Beamer
- College
of Pharmacy, Dalhousie University, 5968 College Street, Halifax, Nova Scotia B3H 4R2, Canada
- E-mail: (L.J.B.)
| | - David L. Jakeman
- College
of Pharmacy, Dalhousie University, 5968 College Street, Halifax, Nova Scotia B3H 4R2, Canada
- Department
of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- E-mail: (D.L.J.)
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15
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Abstract
SIGNIFICANCE Hexokinases are key enzymes that are responsible for the first reaction of glycolysis, but they also moonlight other cellular processes, including mitochondrial redox signaling regulation. Modulation of hexokinase activity and spatiotemporal location by reactive oxygen and nitrogen species as well as other gasotransmitters serves as the basis for a unique, underexplored method of tight and flexible regulation of these fundamental enzymes. Recent Advances: Redox modifications of thiols serve as a molecular code that enables the precise and complex regulation of hexokinases. Redox regulation of hexokinases is also used by multiple parasites to cause widespread and severe diseases, including malaria, Chagas disease, and sleeping sickness. Redox-active molecules affect each other, and the moonlighting activity of hexokinases provides another feedback loop that affects the cellular redox status and is hijacked in malignantly transformed cells. CRITICAL ISSUES Several compounds affect the redox status of hexokinases in vivo. These include the dehydroascorbic acid (oxidized form of vitamin C), pyrrolidinium porrolidine-1-carbodithioate (contraceptive), peroxynitrite (product of ethanol metabolism), alloxan (a glucose analog), and isobenzothiazolinone ebselen. However, very limited information is available regarding which amino acid residues in hexokinases are affected by redox signaling. Except in cases of monogenic diabetes, direct evidence is absent for disease phenotypes that are associated with variations within motifs that are susceptible to redox signaling. FUTURE DIRECTIONS Further studies should address the propensity of hexokinases and their disease-associated variants to participate in redox regulation. Robust and straightforward proteomic methods are needed to understand the context and consequences of hexokinase-mediated redox regulation in health and disease.
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Affiliation(s)
- Petr Heneberg
- Third Faculty of Medicine, Charles University , Prague, Czech Republic
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16
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Abstract
Carbohydrate kinases activate a wide variety of monosaccharides by adding a phosphate group, usually from ATP. This modification is fundamental to saccharide utilization, and it is likely a very ancient reaction. Modern organisms contain carbohydrate kinases from at least five main protein families. These range from the highly specialized inositol kinases, to the ribokinases and galactokinases, which belong to families that phosphorylate a wide range of substrates. The carbohydrate kinases utilize a common strategy to drive the reaction between the sugar hydroxyl and the donor phosphate. Each sugar is held in position by a network of hydrogen bonds to the non-reactive hydroxyls (and other functional groups). The reactive hydroxyl is deprotonated, usually by an aspartic acid side chain acting as a catalytic base. The deprotonated hydroxyl then attacks the donor phosphate. The resulting pentacoordinate transition state is stabilized by an adjacent divalent cation, and sometimes by a positively charged protein side chain or the presence of an anion hole. Many carbohydrate kinases are allosterically regulated using a wide variety of strategies, due to their roles at critical control points in carbohydrate metabolism. The evolution of a similar mechanism in several folds highlights the elegance and simplicity of the catalytic scheme.
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17
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Lu Y, Wang L, Teng F, Zhang J, Hu M, Tao Y. Production of myo-inositol from glucose by a novel trienzymatic cascade of polyphosphate glucokinase, inositol 1-phosphate synthase and inositol monophosphatase. Enzyme Microb Technol 2018; 112:1-5. [DOI: 10.1016/j.enzmictec.2018.01.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 12/20/2017] [Accepted: 01/15/2018] [Indexed: 02/06/2023]
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18
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Construction and evolution of an Escherichia coli strain relying on nonoxidative glycolysis for sugar catabolism. Proc Natl Acad Sci U S A 2018; 115:3538-3546. [PMID: 29555759 PMCID: PMC5889684 DOI: 10.1073/pnas.1802191115] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
We constructed an Escherichia coli strain that does not use glycolysis for sugar catabolism. Instead, it uses the synthetic nonoxidative glycolysis cycle to directly synthesize stoichiometric amounts of the two-carbon building block (acetyl-CoA), which is then converted to three-carbon metabolites to support growth. The resulting strain grows aerobically in glucose minimal medium and can achieve near-complete carbon conservation in the production of acetyl-CoA–derived products during anaerobic fermentation. This strain improves the theoretical carbon yield from 66.7% to 100% in acetyl-CoA–derived product formation. The Embden–Meyerhoff–Parnas (EMP) pathway, commonly known as glycolysis, represents the fundamental biochemical infrastructure for sugar catabolism in almost all organisms, as it provides key components for biosynthesis, energy metabolism, and global regulation. EMP-based metabolism synthesizes three-carbon (C3) metabolites before two-carbon (C2) metabolites and must emit one CO2 in the synthesis of the C2 building block, acetyl-CoA, a precursor for many industrially important products. Using rational design, genome editing, and evolution, here we replaced the native glycolytic pathways in Escherichia coli with the previously designed nonoxidative glycolysis (NOG), which bypasses initial C3 formation and directly generates stoichiometric amounts of C2 metabolites. The resulting strain, which contains 11 gene overexpressions, 10 gene deletions by design, and more than 50 genomic mutations (including 3 global regulators) through evolution, grows aerobically in glucose minimal medium but can ferment anaerobically to products with nearly complete carbon conservation. We confirmed that the strain metabolizes glucose through NOG by 13C tracer experiments. This redesigned E. coli strain represents a different approach for carbon catabolism and may serve as a useful platform for bioproduction.
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19
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Rexer TFT, Schildbach A, Klapproth J, Schierhorn A, Mahour R, Pietzsch M, Rapp E, Reichl U. One pot synthesis of GDP-mannose by a multi-enzyme cascade for enzymatic assembly of lipid-linked oligosaccharides. Biotechnol Bioeng 2017; 115:192-205. [PMID: 28922469 PMCID: PMC5765510 DOI: 10.1002/bit.26454] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/08/2017] [Accepted: 09/11/2017] [Indexed: 12/22/2022]
Abstract
Glycosylation of proteins is a key function of the biosynthetic‐secretory pathway in the endoplasmic reticulum (ER) and Golgi apparatus. Glycosylated proteins play a crucial role in cell trafficking and signaling, cell‐cell adhesion, blood‐group antigenicity, and immune response. In addition, the glycosylation of proteins is an important parameter in the optimization of many glycoprotein‐based drugs such as monoclonal antibodies. In vitro glycoengineering of proteins requires glycosyltransferases as well as expensive nucleotide sugars. Here, we present a designed pathway consisting of five enzymes, glucokinase (Glk), phosphomannomutase (ManB), mannose‐1‐phosphate‐guanyltransferase (ManC), inorganic pyrophosphatase (PmPpA), and 1‐domain polyphosphate kinase 2 (1D‐Ppk2) expressed in E. coli for the cell‐free production and regeneration of GDP‐mannose from mannose and polyphosphate with catalytic amounts of GDP and ADP. It was shown that GDP‐mannose is produced at various conditions, that is pH 7–8, temperature 25–35°C and co‐factor concentrations of 5–20 mM MgCl2. The maximum reaction rate of GDP‐mannose achieved was 2.7 μM/min at 30°C and 10 mM MgCl2 producing 566 nmol GDP‐mannose after a reaction time of 240 min. With respect to the initial GDP concentration (0.8 mM) this is equivalent to a yield of 71%. Additionally, the cascade was coupled to purified, transmembrane‐deleted Alg1 (ALG1ΔTM), the first mannosyltransferase in the ER‐associated lipid‐linked oligosaccharide (LLO) assembly. Thereby, in a one‐pot reaction, phytanyl‐PP‐(GlcNAc)2‐Man1 was produced with efficient nucleotide sugar regeneration for the first time. Phytanyl‐PP‐(GlcNAc)2‐Man1 can serve as a substrate for the synthesis of LLO for the cell‐free in vitro glycosylation of proteins. A high‐performance anion exchange chromatography method with UV and conductivity detection (HPAEC‐UV/CD) assay was optimized and validated to determine the enzyme kinetics. The established kinetic model enabled the optimization of the GDP‐mannose regenerating cascade and can further be used to study coupling of the GDP‐mannose cascade with glycosyltransferases. Overall, the study envisages a first step towards the development of a platform for the cell‐free production of LLOs as precursors for in vitro glycoengineering of proteins.
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Affiliation(s)
- Thomas F T Rexer
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Anna Schildbach
- Department of Downstream Processing, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Jan Klapproth
- Department of Downstream Processing, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Angelika Schierhorn
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Reza Mahour
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Markus Pietzsch
- Department of Downstream Processing, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany.,Otto-von-Guericke University Magdeburg, Chair of Bioprocess Engineering, Magdeburg, Germany
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20
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Sánchez-Pascuala A, de Lorenzo V, Nikel PI. Refactoring the Embden-Meyerhof-Parnas Pathway as a Whole of Portable GlucoBricks for Implantation of Glycolytic Modules in Gram-Negative Bacteria. ACS Synth Biol 2017; 6:793-805. [PMID: 28121421 PMCID: PMC5440799 DOI: 10.1021/acssynbio.6b00230] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
The
Embden–Meyerhof–Parnas (EMP) pathway is generally
considered to be the biochemical standard for glucose catabolism.
Alas, its native genomic organization and the control of gene expression
in Escherichia coli are both very intricate, which
limits the portability of the EMP pathway to other biotechnologically
important bacterial hosts that lack the route. In this work, the genes
encoding all the enzymes of the linear EMP route have been individually
recruited from the genome of E. coli K-12, edited in silico to remove their endogenous regulatory signals,
and synthesized de novo following a standard (GlucoBrick)
that enables their grouping in the form of functional modules at the
user’s will. After verifying their activity in several glycolytic
mutants of E. coli, the versatility of these
GlucoBricks was demonstrated in quantitative physiology tests and
biochemical assays carried out in Pseudomonas putida KT2440 and P. aeruginosa PAO1 as the heterologous
hosts. Specific configurations of GlucoBricks were also adopted to
streamline the downward circulation of carbon from hexoses to pyruvate
in E. coli recombinants, thereby resulting in
a 3-fold increase of poly(3-hydroxybutyrate) synthesis from glucose.
Refactoring whole metabolic blocks in the fashion described in this
work thus eases the engineering of biochemical processes where the
optimization of carbon traffic is facilitated by the operation of
the EMP pathway—which yields more ATP than other glycolytic
routes such as the Entner–Doudoroff pathway.
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Affiliation(s)
- Alberto Sánchez-Pascuala
- Systems and Synthetic Biology
Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Víctor de Lorenzo
- Systems and Synthetic Biology
Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Pablo I. Nikel
- Systems and Synthetic Biology
Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
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21
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Liu Z, Zhang Y, Jia X, Hu M, Deng Z, Xu Y, Liu T. In Vitro Reconstitution and Optimization of the Entire Pathway to Convert Glucose into Fatty Acid. ACS Synth Biol 2017; 6:701-709. [PMID: 28080041 DOI: 10.1021/acssynbio.6b00348] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Glucose and fatty acids play essential physiological roles in nearly all living organisms, and the pathway that converts glucose into fatty acid is pivotal to the central metabolic network. We have successfully reconstituted a pathway that converts glucose to fatty acid in vitro using 30 purified proteins. Through systematic titration and optimization of the glycolytic pathway and pyruvate dehydrogenase, we increased the yield of free fatty acid from nondetectable to a level that exceeded 9% of the theoretical yield. We also reconstituted the entire pentose-phosphate pathway of Escherichia coli and established a pentose phosphate-glycolysis hybrid pathway, replacing GAPDH to enhance NADPH availability. Our efforts provide a useful platform for research involving these core biochemical transformations.
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Affiliation(s)
- Zheng Liu
- Department
of Endocrinology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Yuchen Zhang
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
| | - Xiaoge Jia
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
| | - Mengzhu Hu
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
| | - Zixin Deng
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
| | - Yancheng Xu
- Department
of Endocrinology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Tiangang Liu
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
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22
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Hayes CA, Dalia TN, Dalia AB. Systematic genetic dissection of PTS in Vibrio cholerae uncovers a novel glucose transporter and a limited role for PTS during infection of a mammalian host. Mol Microbiol 2017; 104:568-579. [PMID: 28196401 DOI: 10.1111/mmi.13646] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2017] [Indexed: 12/26/2022]
Abstract
A common mechanism for high affinity carbohydrate uptake in microbial species is the phosphoenolpyruvate-dependent phosphotransferase system (PTS). This system consists of a shared component, EI, which is required for all PTS transport, and numerous carbohydrate uptake transporters. In Vibrio cholerae, there are 13 distinct PTS transporters. Due to genetic redundancy within this system, the carbohydrate specificity of each of these transporters is not currently defined. Here, using multiplex genome editing by natural transformation (MuGENT), we systematically dissect PTS transport in V. cholerae. Specifically, we generated a mutant strain that lacks all 13 PTS transporters, and from this strain, we created a panel of mutants where each expresses a single transporter. Using this panel, we have largely defined the carbohydrate specificities of each PTS transporter. In addition, this analysis uncovered a novel glucose transporter. We have further defined the mechanism of this transporter and characterized its regulation. Using our 13 PTS transporter mutant, we also provide the first clear evidence that carbohydrate transport by the PTS is not essential during infection in an infant mouse model of cholera. In summary, this study shows how multiplex genome editing can be used to rapidly dissect complex biological systems and genetic redundancy in microbial systems.
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Affiliation(s)
- Chelsea A Hayes
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Triana N Dalia
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Ankur B Dalia
- Department of Biology, Indiana University, Bloomington, IN, USA
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Engineering Corynebacterium glutamicum for fast production of l-lysine and l-pipecolic acid. Appl Microbiol Biotechnol 2016; 100:8075-90. [DOI: 10.1007/s00253-016-7682-6] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 06/07/2016] [Accepted: 06/13/2016] [Indexed: 11/25/2022]
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24
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Kwan DH, Jin Y, Jiang J, Chen HM, Kötzler MP, Overkleeft HS, Davies GJ, Withers SG. Chemoenzymatic synthesis of 6-phospho-cyclophellitol as a novel probe of 6-phospho-β-glucosidases. FEBS Lett 2016; 590:461-8. [DOI: 10.1002/1873-3468.12059] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 12/19/2015] [Accepted: 12/22/2015] [Indexed: 11/10/2022]
Affiliation(s)
- David H. Kwan
- Department of Chemistry; University of British Columbia; BC Canada
| | - Yi Jin
- York Structural Biology Laboratory; Department of Chemistry; University of York; UK
| | - Jianbing Jiang
- Department of Bioorganic Synthesis; Leiden Institute of Chemistry; Leiden University; the Netherlands
| | - Hong-Ming Chen
- Department of Chemistry; University of British Columbia; BC Canada
| | | | - Herman S. Overkleeft
- Department of Bioorganic Synthesis; Leiden Institute of Chemistry; Leiden University; the Netherlands
| | - Gideon J. Davies
- York Structural Biology Laboratory; Department of Chemistry; University of York; UK
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25
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Biochemistry and regulatory functions of bacterial glucose kinases. Arch Biochem Biophys 2015; 577-578:1-10. [DOI: 10.1016/j.abb.2015.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 04/30/2015] [Accepted: 05/02/2015] [Indexed: 11/19/2022]
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26
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Bowden SD, Hopper-Chidlaw AC, Rice CJ, Ramachandran VK, Kelly DJ, Thompson A. Nutritional and metabolic requirements for the infection of HeLa cells by Salmonella enterica serovar Typhimurium. PLoS One 2014; 9:e96266. [PMID: 24797930 PMCID: PMC4010460 DOI: 10.1371/journal.pone.0096266] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 04/07/2014] [Indexed: 12/04/2022] Open
Abstract
Salmonella is the causative agent of a spectrum of human and animal diseases ranging from gastroenteritis to typhoid fever. It is a food - and water - borne pathogen and infects via ingestion followed by invasion of intestinal epithelial cells and phagocytic cells. In this study we employed a mutational approach to define the nutrients and metabolic pathways required by Salmonella enterica serovar Typhimurium during infection of a human epithelial cell line (HeLa). We deleted the key glycolytic genes, pfkA and pfkB to show that S. Typhimurium utilizes glycolysis for replication within HeLa cells; however, glycolysis was not absolutely essential for intracellular replication. Using S. Typhimurium strains deleted for genes encoding components of the phosphotransferase system and glucose transport, we show that glucose is a major substrate required for the intracellular replication of S. Typhimurium in HeLa cells. We also deleted genes encoding enzymes involved in the utilization of gluconeogenic substrates and the glyoxylate shunt and show that neither of these pathways were required for intracellular replication of S. Typhimurium within HeLa cells.
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Affiliation(s)
- Steven D. Bowden
- Institute of Food Research, Norwich Research Park, Colney, Norwich, United Kingdom
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | | | | | - Vinoy K. Ramachandran
- Institute of Food Research, Norwich Research Park, Colney, Norwich, United Kingdom
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - David J. Kelly
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Arthur Thompson
- Institute of Food Research, Norwich Research Park, Colney, Norwich, United Kingdom
- * E-mail:
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Production of glucose-6-phosphate by glucokinase coupled with an ATP regeneration system. World J Microbiol Biotechnol 2013; 30:1123-8. [PMID: 24165747 DOI: 10.1007/s11274-013-1534-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 10/21/2013] [Indexed: 10/26/2022]
Abstract
A process of glucose-6-phosphate (G-6-P) production coupled with an adenosine triphosphate (ATP) regeneration system was constructed that utilized acetyl phosphate (ACP) via acetate kinase (ACKase). The genes glk and ack from Escherichia coli K12 were amplified and cloned into pET-28a(+), then transformed into E. coli BL21 (DE3) and the recombinant strains were named pGLK and pACK respectively. Glucokinase (glkase) in pGLK and ACKase in pACK were both overexpressed in soluble form. G-6-P was efficiently produced from glucose and ACP using a very small amount of ATP. The conversion yield was greater than 97 % when the reaction solution containing 10 mM glucose, 20 mM ACP-Na₂, 0.5 mM ATP, 5 mM Mg²⁺, 50 mM potassium phosphate buffer (pH 7.0), 4.856 U glkase and 3.632 U ACKase were put into 37 °C water bath for 1 h.
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Revealing in vivo glucose utilization of Gluconobacter oxydans 621H Δmgdh strain by mutagenesis. Microbiol Res 2013; 169:469-75. [PMID: 24035043 DOI: 10.1016/j.micres.2013.08.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 08/05/2013] [Accepted: 08/10/2013] [Indexed: 11/22/2022]
Abstract
Gluconobacter oxydans, belonging to acetic acid bacteria, is widely used in industrial biotechnology. In our previous study, one of the main glucose metabolic pathways in G. oxydans 621H was blocked by the disruption of the mgdh gene, which is responsible for glucose oxidation to gluconate on cell membrane. The resulting 621H Δmgdh mutant strain showed an enhanced growth and biomass yield on glucose. In order to further understand the intracellular utilization of glucose by 621H Δmgdh, the functions of four fundamental genes, namely glucokinase-encoding glk1 gene, soluble glucose dehydrogenase-encoding sgdh gene, galactose-proton symporter-encoding galp1 and galp2 genes, were investigated. The obtained metabolic characteristics of 621H Δmgdh Δglk1 and 621H Δmgdh Δsgdh double-gene knockout mutants showed that, in vivo, glucose is preferentially phosphorylated to glucose-6-phosphate by glucokinase rather than being oxidized to gluconate by soluble glucose dehydrogenase. In addition, although the galactose-proton symporter-encoding genes were proved to be glucose transporter genes in other organisms, both galp genes (galp 1 and galp2) in G. oxydans were not found to be involved in glucose uptake system, implying that other unknown transporters might be responsible for transporting glucose into the cells.
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Solomon KV, Moon TS, Ma B, Sanders TM, Prather KLJ. Tuning primary metabolism for heterologous pathway productivity. ACS Synth Biol 2013; 2:126-35. [PMID: 23656436 DOI: 10.1021/sb300055e] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Tuning expression of competing endogenous pathways has been identified as an effective strategy in the optimization of heterologous production pathways. However, intervention at the first step of glycolysis, where no alternate routes of carbon utilization exist, remains unexplored. In this work we have engineered a viable E. coli host that decouples glucose transport and phosphorylation, enabling independent control of glucose flux to a heterologous pathway of interest through glucokinase (glk) expression. Using community sourced and curated promoters, glk expression was varied over a 3-fold range while maintaining cellular viability. The effects of glk expression on the productivity of a model glucose-consuming pathway were also studied. Through control of glycolytic flux we were able to explore a number of cellular phenotypes and vary the yield of our model pathway by up to 2-fold in a controllable manner.
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Affiliation(s)
- Kevin V. Solomon
- Department of Chemical Engineering,
Synthetic Biology Engineering Research Center (SynBERC), Massachusetts Institute of Technology, Cambridge, Massachusetts
02139, United States
| | - Tae Seok Moon
- Department of Chemical Engineering,
Synthetic Biology Engineering Research Center (SynBERC), Massachusetts Institute of Technology, Cambridge, Massachusetts
02139, United States
| | - Brian Ma
- Department of Chemical Engineering,
Synthetic Biology Engineering Research Center (SynBERC), Massachusetts Institute of Technology, Cambridge, Massachusetts
02139, United States
- California
Institute of Technology
Summer Undergraduate Research Fellow (SURF), Department of Bioengineering, California Institute of Technology, Pasadena, California
91125, United States
| | - Tarielle M. Sanders
- Department of Chemical Engineering,
Synthetic Biology Engineering Research Center (SynBERC), Massachusetts Institute of Technology, Cambridge, Massachusetts
02139, United States
- Amgen
Scholars Program, Department
of Chemistry, Norfolk State University,
Norfolk, Virginia 23504, United States
| | - Kristala L. J. Prather
- Department of Chemical Engineering,
Synthetic Biology Engineering Research Center (SynBERC), Massachusetts Institute of Technology, Cambridge, Massachusetts
02139, United States
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30
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Lakshmi HP, Yeswanth S, Prasad UV, Vasu D, Swarupa V, Kumar PS, Narasu ML, Krishna Sarma PVG. Cloning, expression and characterization of glucokinase gene involved in the glucose-6- phosphate formation in Staphylococcus aureus. Bioinformation 2013; 9:169-73. [PMID: 23519063 PMCID: PMC3602885 DOI: 10.6026/97320630009169] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 01/28/2013] [Indexed: 11/23/2022] Open
Abstract
Glucose-6-phosphate (G-6-P) formation in Staphylococcus aureus is catalysed by glucokinase (glkA) gene under high glucose
concentration leading to upregulation of various pathogenic factors; therefore the present study is aimed in the cloning and
characterization of glk A gene from S. aureus ATCC12600. The glk A gene was cloned in the Sma I site of pQE 30, sequenced
(Accession number: JN645812) and expressed in E. coli DH5α. The recombinant glk A expressed from the resultant glk A 1 clone
was purified using nickel metal chelate chromatography, the pure enzyme gave single band in SDS-PAGE with molecular weight
of 33kDa. The rglk A showed very high affinity to glucose Km 5.1±0.06mM with Hill coefficient of 1.66±0.032mM. Analysis of
glucokinase sequence of S. aureus showed presence of typical ATP binding site and ROK motif CNCGRSGCIE. Sequentially and
phylogenetically S. aureus glk A exhibited low identity with other bacterial glk A and 21% homology with human glucokinase
(GCK). Functionally, S. aureus glk A showed higher rate of G-6-P formation compared to human GCK which may have profound
role in the pathogenesis.
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31
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Implantation of unmarked regulatory and metabolic modules in Gram-negative bacteria with specialised mini-transposon delivery vectors. J Biotechnol 2013; 163:143-54. [DOI: 10.1016/j.jbiotec.2012.05.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 05/01/2012] [Accepted: 05/09/2012] [Indexed: 11/23/2022]
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Glucokinase contributes to glucose phosphorylation in d-lactic acid production by Sporolactobacillus inulinus Y2-8. ACTA ACUST UNITED AC 2012; 39:1685-92. [DOI: 10.1007/s10295-012-1176-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 07/12/2012] [Indexed: 10/28/2022]
Abstract
Abstract
Sporolactobacillus inulinus, a homofermentative lactic acid bacterium, is a species capable of efficient industrial d-lactic acid production from glucose. Glucose phosphorylation is the key step of glucose metabolism, and fine-tuned expression of which can improve d-lactic acid production. During growth on high-concentration glucose, a fast induction of high glucokinase (GLK) activity was observed, and paralleled the patterns of glucose consumption and d-lactic acid accumulation, while phosphoenolpyruvate phosphotransferase system (PTS) activity was completely repressed. The transmembrane proton gradient of 1.3–1.5 units was expected to generate a large proton motive force to the uptake of glucose. This suggests that the GLK pathway is the major route for glucose utilization, with the uptake of glucose through PTS-independent transport systems and phosphorylation of glucose by GLK in S. inulinus d-lactic acid production. The gene encoding GLK was cloned from S. inulinus and expressed in Escherichia coli. The amino acid sequence revealed significant similarity to GLK sequences from Bacillaceae. The recombinant GLK was purified and shown to be a homodimer with a subunit molecular mass of 34.5 kDa. Strikingly, it demonstrated an unusual broad substrate specificity, catalyzing phosphorylation of 2-deoxyglucose, mannitol, maltose, galactose and glucosamine, in addition to glucose. This report documented the key step concerning glucose phosphorylation of S. inulinus, which will help to understand the regulation of glucose metabolism and d-lactic acid production.
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33
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Solomon KV, Sanders TM, Prather KL. A dynamic metabolite valve for the control of central carbon metabolism. Metab Eng 2012; 14:661-71. [DOI: 10.1016/j.ymben.2012.08.006] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2012] [Revised: 08/22/2012] [Accepted: 08/26/2012] [Indexed: 11/26/2022]
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Recruiting alternative glucose utilization pathways for improving succinate production. Appl Microbiol Biotechnol 2012; 97:2513-20. [PMID: 22895848 DOI: 10.1007/s00253-012-4344-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 07/28/2012] [Accepted: 07/30/2012] [Indexed: 01/14/2023]
Abstract
The phosphoenolpyruvate (PEP): carbohydrate phosphotransferase system (PTS) of Escherichia coli was usually inactivated to increase PEP supply for succinate production. However, cell growth and glucose utilization rate decreased significantly with PTS inactivation. In this work, two glucose transport proteins and two glucokinases (Glk) from E. coli and Zymomonas mobilis were recruited in PTS(-) strains, and their impacts on glucose utilization and succinate production were compared. All PTS(-) strains recruiting Z. mobilis glucose facilitator Glf had higher glucose utilization rates than PTS(-) strains using E. coli galactose permease (GalP), which was suggested to be caused by higher glucose transport velocity and lower energetic cost of Glf. The highest rate obtained by combinatorial modulation of glf and glk E. coli (2.13 g/L•h) was 81 % higher than the wild-type E. coli and 30 % higher than the highest rate obtained by combinatorial modulation of galP and glk E. coli . On the other hand, although glucokinase activities increased after replacing E. coli Glk with isoenzyme of Z. mobilis, glucose utilization rate decreased to 0.58 g/L•h, which was assumed due to tight regulation of Z. mobilis Glk by energy status of the cells. For succinate production, using GalP led to a 20 % increase in succinate productivity, while recruiting Glf led to a 41 % increase. These efficient alternative glucose utilization pathways obtained in this work can also be used for production of many other PEP-derived chemicals, such as malate, fumarate, and aromatic compounds.
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35
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Bujara M, Panke S. In silico assessment of cell-free systems. Biotechnol Bioeng 2012; 109:2620-9. [DOI: 10.1002/bit.24534] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Revised: 04/08/2012] [Accepted: 04/10/2012] [Indexed: 11/08/2022]
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36
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Chan S, Kanchanatawee S, Jantama K. Production of succinic acid from sucrose and sugarcane molasses by metabolically engineered Escherichia coli. BIORESOURCE TECHNOLOGY 2012; 103:329-336. [PMID: 22023966 DOI: 10.1016/j.biortech.2011.09.096] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2011] [Revised: 09/22/2011] [Accepted: 09/23/2011] [Indexed: 05/31/2023]
Abstract
Sucrose-utilizing genes (cscKB and cscA) from Escherichia coli KO11 were cloned and expressed in a metabolically engineered E. coli KJ122 to enhance succinate production from sucrose. KJ122 harboring a recombinant plasmid, pKJSUC, was screened for the efficient sucrose utilization by growth-based selection and adaptation. KJ122-pKJSUC-24T efficiently utilized sucrose in a low-cost medium to produce high succinate concentration with less accumulation of by-products. Succinate concentrations of 51 g/L (productivity equal to 1.05 g/L/h) were produced from sucrose in anaerobic bottles, and concentrations of 47 g/L were produced in 10L bioreactor within 48 h. Antibiotics had no effect on the succinate production by KJ122-pKJSUC-24T. In addition, succinate concentrations of 62 g/L were produced from sugarcane molasses in anaerobic bottles, and concentrations of 56 g/L in 10 L bioreactor within 72 h. These results demonstrated that KJ122-pKJSUC-24T would be a potential strain for bio-based succinate production from sucrose and sugarcane molasses.
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Affiliation(s)
- Sitha Chan
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, 111 University Ave., Suranaree, Muang, Nakhon Ratchasima 30000, Thailand
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37
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Substrate recognition mechanism and substrate-dependent conformational changes of an ROK family glucokinase from Streptomyces griseus. J Bacteriol 2011; 194:607-16. [PMID: 22101842 DOI: 10.1128/jb.06173-11] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Carbon catabolite repression (CCR) is a widespread phenomenon in many bacteria that is defined as the repression of catabolic enzyme activities for an unfavorable carbon source by the presence of a preferable carbon source. In Streptomyces, secondary metabolite production often is negatively affected by the carbon source, indicating the involvement of CCR in secondary metabolism. Although the CCR mechanism in Streptomyces still is unclear, glucokinase is presumably a central player in CCR. SgGlkA, a glucokinase from S. griseus, belongs to the ROK family glucokinases, which have two consensus sequence motifs (1 and 2). Here, we report the crystal structures of apo-SgGlkA, SgGlkA in complex with glucose, and SgGlkA in complex with glucose and adenylyl imidodiphosphate (AMPPNP), which are the first structures of an ROK family glucokinase. SgGlkA is divided into a small α/β domain and a large α+β domain, and it forms a dimer-of-dimer tetrameric configuration. SgGlkA binds a β-anomer of glucose between the two domains, and His157 in consensus sequence 1 plays an important role in the glucose-binding mechanism and anomer specificity of SgGlkA. In the structures of SgGlkA, His157 forms an HC3-type zinc finger motif with three cysteine residues in consensus sequence 2 to bind a zinc ion, and it forms two hydrogen bonds with the C1 and C2 hydroxyls of glucose. When the three structures are compared, the structure of SgGlkA is found to be modified by the binding of substrates. The substrate-dependent conformational changes of SgGlkA may be related to the CCR mechanism in Streptomyces.
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38
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Stevenson BJ, Liu JW, Kuchel PW, Ollis DL. Fermentative glycolysis with purified Escherichia coli enzymes for in vitro ATP production and evaluating an engineered enzyme. J Biotechnol 2011; 157:113-23. [PMID: 21963590 DOI: 10.1016/j.jbiotec.2011.09.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Revised: 09/13/2011] [Accepted: 09/16/2011] [Indexed: 10/17/2022]
Abstract
Each of the twelve enzymes for glycolytic fermentation, eleven from Escherichia coli and one from Saccharomyces cerevisiae, have been over-expressed in E. coli and purified with His-tags. Simple assays have been developed for each enzyme and they have been assembled for fermentation of glucose to ethanol. Phosphorus-31 NMR revealed that this in vitro reaction accumulates fructose 1,6-bisphosphate while recycling the cofactors NAD(+) and ATP. This reaction represents a defined ATP-regeneration system that can be tailored to suit in vitro biochemical reactions such as cell-free protein synthesis. The enzyme from S. cerevisiae, pyruvate decarboxylase 1 (Pdc1; EC 4.1.1.1), was identified as one of the major 'flux controlling' enzymes for the reaction and was replaced with an evolved version of Pdc1 that has over 20-fold greater activity under glycolysis reaction conditions. This substitution was only beneficial when the ratio of glycolytic enzymes was adjusted to suit greater Pdc1 activity.
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Affiliation(s)
- Bradley J Stevenson
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia.
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Miyazono KI, Tabei N, Marushima K, Ohnishi Y, Horinouchi S, Tanokura M. Purification, crystallization and preliminary X-ray analysis of glucokinase from Streptomyces griseus in complex with glucose. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:914-6. [PMID: 21821894 PMCID: PMC3151127 DOI: 10.1107/s1744309111022275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Accepted: 06/08/2011] [Indexed: 11/10/2022]
Abstract
Glucokinase catalyzes the phosphorylation of glucose using ATP to yield glucose 6-phosphate. SgGlkA is a bacterial group III glucokinase from Streptomyces griseus that seems to play a regulatory role in carbon catabolite repression in this organism. SgGlkA was expressed in Escherichia coli, purified and crystallized using the sitting-drop vapour-diffusion method at 293 K. A crystal of SgGlkA in complex with glucose was obtained using a reservoir solution consisting of 0.9 M sodium/potassium tartrate, 0.2 M NaCl and 0.1 M imidazole pH 8.1 and diffracted X-rays to 1.84 Å resolution. The crystal of SgGlkA in complex with glucose belonged to space group P6(2)22 or P6(4)22, with unit-cell parameters a = b = 109.19, c = 141.18 Å. The crystal contained one molecule in the asymmetric unit.
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Affiliation(s)
- Ken-ichi Miyazono
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Nobumitsu Tabei
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kazuya Marushima
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Sueharu Horinouchi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Masaru Tanokura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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Shimada T, Fujita N, Yamamoto K, Ishihama A. Novel roles of cAMP receptor protein (CRP) in regulation of transport and metabolism of carbon sources. PLoS One 2011; 6:e20081. [PMID: 21673794 PMCID: PMC3105977 DOI: 10.1371/journal.pone.0020081] [Citation(s) in RCA: 188] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Accepted: 04/18/2011] [Indexed: 12/17/2022] Open
Abstract
CRP (cAMP receptor protein), the global regulator of genes for carbon source utilization in the absence of glucose, is the best-studied prokaryotic transcription factor. A total of 195 target promoters on the Escherichia coli genome have been proposed to be under the control of cAMP-bound CRP. Using the newly developed Genomic SELEX screening system of transcription factor-binding sequences, however, we have identified a total of at least 254 CRP-binding sites. Based on their location on the E. coli genome, we predict a total of at least 183 novel regulation target operons, altogether with the 195 hitherto known targets, reaching to the minimum of 378 promoters as the regulation targets of cAMP-CRP. All the promoters selected from the newly identified targets and examined by using the lacZ reporter assay were found to be under the control of CRP, indicating that the Genomic SELEX screening allowed to identify the CRP targets with high accuracy. Based on the functions of novel target genes, we conclude that CRP plays a key regulatory role in the whole processes from the selective transport of carbon sources, the glycolysis-gluconeogenesis switching to the metabolisms downstream of glycolysis, including tricarboxylic acid (TCA) cycle, pyruvate dehydrogenase (PDH) pathway and aerobic respiration. One unique regulation mode is that a single and the same CRP molecule bound within intergenic regions often regulates both of divergently transcribed operons.
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Affiliation(s)
- Tomohiro Shimada
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, Japan
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41
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Reshamwala SMS, Noronha SB. Biofilm formation in Escherichia coli cra mutants is impaired due to down-regulation of curli biosynthesis. Arch Microbiol 2011; 193:711-22. [PMID: 21559929 DOI: 10.1007/s00203-011-0708-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 01/18/2011] [Accepted: 04/13/2011] [Indexed: 11/25/2022]
Abstract
Cra is a pleiotropic regulatory protein that controls carbon and energy flux in enteric bacteria. Recent studies have shown that Cra also regulates other cell processes and influences biofilm formation. The purpose of the present study was to investigate the role of Cra in biofilm formation in Escherichia coli. Congo red-binding studies suggested that curli biosynthesis is impaired in cra mutants. Microarray analysis of wild-type and mutant E. coli cultivated in conditions promoting biofilm formation revealed that the curli biosynthesis genes, csgBAC and csgDEFG, are poorly expressed in the mutant, suggesting that transcription of genes required for curli production is regulated by Cra. Four putative Cra-binding sites were identified in the curli intergenic region, which were experimentally validated by performing electromobility shift assays. Site-directed mutagenesis of three Cra-binding sites in the promoter region of the csgDEFG operon suggests that Cra activates transcription of this operon upon binding to operator regions both downstream and upstream of the transcription start site. Based on the Cra-binding sites identified in this and other studies, the Cra consensus sequence is refined.
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Affiliation(s)
- Shamlan M S Reshamwala
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra, 400076, India
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Optimization of a blueprint for in vitro glycolysis by metabolic real-time analysis. Nat Chem Biol 2011; 7:271-7. [PMID: 21423171 DOI: 10.1038/nchembio.541] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Accepted: 01/27/2011] [Indexed: 02/03/2023]
Abstract
Recruiting complex metabolic reaction networks for chemical synthesis has attracted considerable attention but frequently requires optimization of network composition and dynamics to reach sufficient productivity. As a design framework to predict optimal levels for all enzymes in the network is currently not available, state-of-the-art pathway optimization relies on high-throughput phenotype screening. We present here the development and application of a new in vitro real-time analysis method for the comprehensive investigation and rational programming of enzyme networks for synthetic tasks. We used this first to rationally and rapidly derive an optimal blueprint for the production of the fine chemical building block dihydroxyacetone phosphate (DHAP) via Escherichia coli's highly evolved glycolysis. Second, the method guided the three-step genetic implementation of the blueprint, yielding a synthetic operon with the predicted 2.5-fold-increased glycolytic flux toward DHAP. The new analytical setup drastically accelerates rational optimization of synthetic multienzyme networks.
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Novel members of the Cra regulon involved in carbon metabolism in Escherichia coli. J Bacteriol 2010; 193:649-59. [PMID: 21115656 DOI: 10.1128/jb.01214-10] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cra (catabolite repressor activator) is a global regulator of the genes for carbon metabolism in Escherichia coli. To gain insights into the regulatory roles of Cra, attempts were made to identify the whole set of regulation targets using an improved genomic SELEX (systematic evolution of ligands by exponential enrichment) system. Surprisingly, a total of 164 binding sites were identified for Cra, 144 (88%) of which were newly identified. The majority of known targets were included in the SELEX chip pattern. The promoters examined by the lacZ reporter assay in vivo were all regulated by Cra. These two lines of evidence indicate that a total of as many as 178 promoters are under the control of Cra. The majority of Cra targets are the genes coding for the enzymes involved in central carbon metabolism, covering all the genes for the enzymes involved in glycolysis and metabolism downstream of glycolysis, including the tricarboxylic acid (TCA) cycle and aerobic respiration. Taken together, we propose that Cra plays a key role in balancing the levels of the enzymes for carbon metabolism.
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Aklujkar M, Young ND, Holmes D, Chavan M, Risso C, Kiss HE, Han CS, Land ML, Lovley DR. The genome of Geobacter bemidjiensis, exemplar for the subsurface clade of Geobacter species that predominate in Fe(III)-reducing subsurface environments. BMC Genomics 2010; 11:490. [PMID: 20828392 PMCID: PMC2996986 DOI: 10.1186/1471-2164-11-490] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2010] [Accepted: 09/09/2010] [Indexed: 12/05/2022] Open
Abstract
Background Geobacter species in a phylogenetic cluster known as subsurface clade 1 are often the predominant microorganisms in subsurface environments in which Fe(III) reduction is the primary electron-accepting process. Geobacter bemidjiensis, a member of this clade, was isolated from hydrocarbon-contaminated subsurface sediments in Bemidji, Minnesota, and is closely related to Geobacter species found to be abundant at other subsurface sites. This study examines whether there are significant differences in the metabolism and physiology of G. bemidjiensis compared to non-subsurface Geobacter species. Results Annotation of the genome sequence of G. bemidjiensis indicates several differences in metabolism compared to previously sequenced non-subsurface Geobacteraceae, which will be useful for in silico metabolic modeling of subsurface bioremediation processes involving Geobacter species. Pathways can now be predicted for the use of various carbon sources such as propionate by G. bemidjiensis. Additional metabolic capabilities such as carbon dioxide fixation and growth on glucose were predicted from the genome annotation. The presence of different dicarboxylic acid transporters and two oxaloacetate decarboxylases in G. bemidjiensis may explain its ability to grow by disproportionation of fumarate. Although benzoate is the only aromatic compound that G. bemidjiensis is known or predicted to utilize as an electron donor and carbon source, the genome suggests that this species may be able to detoxify other aromatic pollutants without degrading them. Furthermore, G. bemidjiensis is auxotrophic for 4-aminobenzoate, which makes it the first Geobacter species identified as having a vitamin requirement. Several features of the genome indicated that G. bemidjiensis has enhanced abilities to respire, detoxify and avoid oxygen. Conclusion Overall, the genome sequence of G. bemidjiensis offers surprising insights into the metabolism and physiology of Geobacteraceae in subsurface environments, compared to non-subsurface Geobacter species, such as the ability to disproportionate fumarate, more efficient oxidation of propionate, enhanced responses to oxygen stress, and dependence on the environment for a vitamin requirement. Therefore, an understanding of the activity of Geobacter species in the subsurface is more likely to benefit from studies of subsurface isolates such as G. bemidjiensis than from the non-subsurface model species studied so far.
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Affiliation(s)
- Muktak Aklujkar
- University of Massachusetts Amherst, Amherst, MA 01003, USA.
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Prediction of metabolic fluxes by incorporating genomic context and flux-converging pattern analyses. Proc Natl Acad Sci U S A 2010; 107:14931-6. [PMID: 20679215 DOI: 10.1073/pnas.1003740107] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Flux balance analysis (FBA) of a genome-scale metabolic model allows calculation of intracellular fluxes by optimizing an objective function, such as maximization of cell growth, under given constraints, and has found numerous applications in the field of systems biology and biotechnology. Due to the underdetermined nature of the system, however, it has limitations such as inaccurate prediction of fluxes and existence of multiple solutions for an optimal objective value. Here, we report a strategy for accurate prediction of metabolic fluxes by FBA combined with systematic and condition-independent constraints that restrict the achievable flux ranges of grouped reactions by genomic context and flux-converging pattern analyses. Analyses of three types of genomic contexts, conserved genomic neighborhood, gene fusion events, and co-occurrence of genes across multiple organisms, were performed to suggest a group of fluxes that are likely on or off simultaneously. The flux ranges of these grouped reactions were constrained by flux-converging pattern analysis. FBA of the Escherichia coli genome-scale metabolic model was carried out under several different genotypic (pykF, zwf, ppc, and sucA mutants) and environmental (altered carbon source) conditions by applying these constraints, which resulted in flux values that were in good agreement with the experimentally measured (13)C-based fluxes. Thus, this strategy will be useful for accurately predicting the intracellular fluxes of large metabolic networks when their experimental determination is difficult.
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Götz A, Goebel W. Glucose and glucose 6-phosphate as carbon sources in extra- and intracellular growth of enteroinvasive Escherichia coli and Salmonella enterica. MICROBIOLOGY-SGM 2010; 156:1176-1187. [PMID: 20075042 DOI: 10.1099/mic.0.034744-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
To study the role of carbohydrates, in particular glucose, glucose 6-phosphate and mannose, as carbon substrates for extra- and intracellular replication of facultative intracellular enteric bacteria, mutants of two enteroinvasive Escherichia coli (EIEC) strains and a Salmonella enterica serovar Typhimurium isolate were constructed that were defective in the uptake of glucose and mannose (DeltaptsG, manXYZ), glucose 6-phosphate (DeltauhpT) or all three carbohydrates (DeltaptsG, manXYZ, uhpT). The ability of these mutants to grow in RPMI medium containing the respective carbohydrates and in Caco-2 cells was compared with that of the corresponding wild-type strains. In the three strains, deletions of ptsG, manXYZ or uhpT resulted in considerably different levels of inhibition of growth in vitro in the presence of glucose, mannose and glucose 6-phosphate, respectively, but hardly reduced their capability for intracellular replication in Caco-2 cells. Even the triple mutants DeltaptsG, manXYZ, uhpT of the three enterobacterial strains were still able to replicate in Caco-2 cells, albeit at strain-specific lower rates than the corresponding wild-type strains.
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Affiliation(s)
- Andreas Götz
- Lehrstuhl für Mikrobiologie, Biozentrum der Universität Würzburg, D-97074 Würzburg, Germany
| | - Werner Goebel
- Lehrstuhl für Mikrobiologie, Biozentrum der Universität Würzburg, D-97074 Würzburg, Germany
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Bujara M, Schümperli M, Billerbeck S, Heinemann M, Panke S. Exploiting cell-free systems: Implementation and debugging of a system of biotransformations. Biotechnol Bioeng 2010; 106:376-89. [DOI: 10.1002/bit.22666] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Olvera L, Mendoza-Vargas A, Flores N, Olvera M, Sigala JC, Gosset G, Morett E, Bolívar F. Transcription analysis of central metabolism genes in Escherichia coli. Possible roles of sigma38 in their expression, as a response to carbon limitation. PLoS One 2009; 4:e7466. [PMID: 19838295 PMCID: PMC2759082 DOI: 10.1371/journal.pone.0007466] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Accepted: 09/18/2009] [Indexed: 11/29/2022] Open
Abstract
The phosphoenolpyruvate: carbohydrate transferase system (PTS) transports glucose in Escherichia coli. Previous work demonstrated that strains lacking PTS, such as PB11, grow slow on glucose. PB11 has a reduced expression of glycolytic, and upregulates poxB and acs genes as compared to the parental strain JM101, when growing on glucose. The products of the latter genes are involved in the production of AcetylCoA. Inactivation of rpoS that codes for the RNA polymerase σ38 subunit, reduces further (50%) growth of PB11, indicating that σ38 plays a central role in the expression of central metabolism genes in slowly growing cells. In fact, transcription levels of glycolytic genes is reduced in strain PB11rpoS− as compared to PB11. In this report we studied the role of σ70 and σ38 in the expression of the complete glycolytic pathway and poxB and acs genes in certain PTS− strains and their rpoS− derivatives. We determined the transcription start sites (TSSs) and the corresponding promoters, in strains JM101, PB11, its derivative PB12 that recovered its growth capacity, and in their rpoS− derivatives, by 5′RACE and pyrosequencing. In all these genes the presence of sequences resembling σ38 recognition sites allowed the proposition that they could be transcribed by both sigma factors, from overlapping putative promoters that initiate transcription at the same site. Fourteen new TSSs were identified in seventeen genes. Besides, more than 30 putative promoters were proposed and we confirmed ten previously reported. In vitro transcription experiments support the functionality of putative dual promoters. Alternatives that could also explain lower transcription levels of the rpoS− derivatives are discussed. We propose that the presence if real, of both σ70 and σ38 dependent promoters in all glycolytic genes and operons could allow a differential transcription of these central metabolism genes by both sigma subunits as an adaptation response to carbon limitation.
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Affiliation(s)
- Leticia Olvera
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología. Universidad Nacional Autónoma de México (UNAM), Cuernavaca Morelos, México
| | - Alfredo Mendoza-Vargas
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología. Universidad Nacional Autónoma de México (UNAM), Cuernavaca Morelos, México
| | - Noemí Flores
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología. Universidad Nacional Autónoma de México (UNAM), Cuernavaca Morelos, México
| | - Maricela Olvera
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología. Universidad Nacional Autónoma de México (UNAM), Cuernavaca Morelos, México
| | - Juan Carlos Sigala
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología. Universidad Nacional Autónoma de México (UNAM), Cuernavaca Morelos, México
| | - Guillermo Gosset
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología. Universidad Nacional Autónoma de México (UNAM), Cuernavaca Morelos, México
| | - Enrique Morett
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología. Universidad Nacional Autónoma de México (UNAM), Cuernavaca Morelos, México
- * E-mail: (EM); (FB)
| | - Francisco Bolívar
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología. Universidad Nacional Autónoma de México (UNAM), Cuernavaca Morelos, México
- * E-mail: (EM); (FB)
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Hold C, Panke S. Towards the engineering of in vitro systems. J R Soc Interface 2009; 6 Suppl 4:S507-21. [PMID: 19474076 PMCID: PMC2843965 DOI: 10.1098/rsif.2009.0110.focus] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2009] [Accepted: 04/29/2009] [Indexed: 01/16/2023] Open
Abstract
Synthetic biology aims at rationally implementing biological systems from scratch. Given the complexity of living systems and our current lack of understanding of many aspects of living cells, this is a major undertaking. The design of in vitro systems can be considerably easier, because they can consist of fewer constituents, are quasi time invariant, their parameter space can be better accessed and they can be much more easily perturbed and then analysed chemically and mathematically. However, even for simplified in vitro systems, following a comprehensively rational design procedure is still difficult. When looking at a comparatively simple system, such as a medium-sized enzymatic reaction network as it is represented by glycolysis, major issues such as a lack of comprehensive enzyme kinetics and of suitable knowledge on crucial design parameters remain. Nevertheless, in vitro systems are very suitable to overcome these obstacles and therefore well placed to act as a stepping stone to engineering living systems.
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Affiliation(s)
| | - Sven Panke
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26 4058, Basle, Switzerland
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Dashivets T, Wood N, Hergersberg C, Buchner J, Haslbeck M. Rapid matrix-assisted refolding of histidine-tagged proteins. Chembiochem 2009; 10:869-76. [PMID: 19235820 DOI: 10.1002/cbic.200800697] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The formation of inclusion bodies (IBs)--amorphous aggregates of misfolded insoluble protein--during recombinant protein expression, is still one of the biggest bottlenecks in protein science. We have developed and analyzed a rapid parallel approach for matrix-assisted refolding of recombinant His(6)-tagged proteins. Efficiencies of matrix-assisted refolding were screened in a 96-well format. The developed methodology allowed the efficient refolding of five different test proteins, including monomeric and oligomeric proteins. Compared to refolding in-solution, the matrix-assisted refolding strategy proved equal or better for all five proteins tested. Interestingly, specifically oligomeric proteins displayed significantly higher levels of refolding compared to refolding in-solution. Mechanistically, matrix-assisted folding seems to differ from folding in-solution, as the reaction proceeds more rapidly and shows a remarkably different concentration dependence--it allows refolding at up to 1000-fold higher protein concentration than folding in-solution.
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Affiliation(s)
- Tetyana Dashivets
- Munich Center for Integrated Protein Science and Chemistry Department, Technische Universität München, 85747 Garching, Germany
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