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García ÁC, Hauptmann P, Neubauer P. Molecular genetic approaches to decrease the uncontrolled misincorporation of non-canonical branched chain amino acids into recombinant mini-proinsulin expressed in Escherichia coli. Microb Cell Fact 2022; 21:30. [PMID: 35246127 PMCID: PMC8896088 DOI: 10.1186/s12934-022-01756-x] [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: 11/19/2021] [Accepted: 02/09/2022] [Indexed: 05/31/2023] Open
Abstract
The uncontrolled incorporation of non-canonical branched chain amino acids (ncBCAAs) such as norleucine, norvaline and β-methylnorleucine into recombinant proteins in E. coli production processes is a crucial problem in the pharmaceutical industry, since it can lead to the production of altered proteins with non-optimal characteristics. Despite various solutions, to date there are no engineered strains that exhibit a reduced accumulation of these ncBAAs. In this study, novel E. coli K-12 BW25113 strains with exogenous tunable expression of target genes of the BCAA biosynthetic pathway were developed. For this purpose, single gene knock-outs for thrA, ilvA, leuA, ilvIH, ilvBN, ilvGM and ilvC were complemented with plasmids containing the respective genes under control of an arabinose promoter. These clones were screened in a mL-bioreactor system in fed-batch mode under both standard cultivation conditions and with pyruvate pulses, and induction of a min-proinsulin. Screening was performed by comparing the impurity profile of the recombinant mini-proinsulin expressed of each clone with the E. coli BW25113 WT strain, and the most promising clones were cultivated in a 15L Screening showed that up-regulation of ilvC, ilvIH and ilvGM, and downregulation of leuA and ilvBN trigger a reduction of norvaline and norleucine accumulation and misincorporation into mini-proinsulin. The stirred tank bioreactor cultivations confirmed that up-regulation of ilvIH and ilvGM were most effective to reduce the ncBCAA misincorporation. This novel approach for a reduced ncBCAA misincorporation may be solution to this old challenging problem in the large-scale production of human therapeutics.
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Affiliation(s)
| | | | - Peter Neubauer
- Chair of Bioprocess Engineering, Department of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, 10623, Berlin, Germany.
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Le T, Park S. Development of efficient microbial cell factory for whole-cell bioconversion of L-threonine to 2-hydroxybutyric acid. BIORESOURCE TECHNOLOGY 2022; 344:126090. [PMID: 34634464 DOI: 10.1016/j.biortech.2021.126090] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/29/2021] [Accepted: 10/01/2021] [Indexed: 06/13/2023]
Abstract
Production of 2-hydroxybutyric acid (2-HBA) was attempted in recombinant Escherichia coli W3110 Δtdh ΔilvIH (over)expressing a homologous and mutated threonine dehydratase (ilvA*) and a heterologous 2-ketobutyric acid (2-KBA) reductase from Alcaligenes eutrophus H16 (Ae_ldh). To prevent the degradation of 2-KBA, the aceE, poxB and pflB genes were deleted, and for blocking the 2-HBA degradation, the lldD and dld genes were disrupted. In addition, for efficient NADH regeneration/supply, a heterologous formate dehydrogenase from Candida boidinii (Cb_fdh) was overexpressed. Under anaerobic condition, E. coli W3110 Δtdh ΔilvIH ΔaceE ΔpoxB ΔlldD Δdld ΔpflB could produce > 400 mM 2-HBA in 33 h with the yield of ∼ 0.95 mol/mol. Furthermore, by enhancing the expression of a mutant Cb_fdh, the titer could be increased to ∼ 650 mM in 33 h. This study provides an efficient microbial cell factory for the bioconversion of threonine to 2-HBA with a high yield.
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Affiliation(s)
- Thai Le
- Department of Chemical Engineering, School of Energy and Chemical Engineering, College of Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of South Korea
| | - Sunghoon Park
- Department of Chemical Engineering, School of Energy and Chemical Engineering, College of Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of South Korea.
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3
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Fang Y, Zhang S, Wang J, Yin L, Zhang H, Wang Z, Song J, Hu X, Wang X. Metabolic Detoxification of 2-Oxobutyrate by Remodeling Escherichia coli Acetate Bypass. Metabolites 2021; 11:metabo11010030. [PMID: 33406667 PMCID: PMC7824062 DOI: 10.3390/metabo11010030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/22/2020] [Accepted: 12/28/2020] [Indexed: 12/03/2022] Open
Abstract
2-Oxobutyrate (2-OBA), as a toxic metabolic intermediate, generally arrests the cell growth of most microorganisms and blocks the biosynthesis of target metabolites. In this study, we demonstrated that using the acetate bypass to replace the pyruvate dehydrogenase complex (PDHc) in Escherichia coli could recharge the intracellular acetyl-CoA pool to alleviate the metabolic toxicity of 2-OBA. Furthermore, based on the crystal structure of pyruvate oxidase (PoxB), two candidate residues in the substrate-binding pocket of PoxB were predicted by computational simulation. Site-directed saturation mutagenesis was performed to attenuate 2-OBA-binding affinity, and one of the variants, PoxBF112W, exhibited a 20-fold activity ratio of pyruvate/2-OBA in substrate selectivity. PoxBF112W was employed to remodel the acetate bypass in E. coli, resulting in l-threonine (a precursor of 2-OBA) biosynthesis with minimal inhibition from 2-OBA. After metabolic detoxification of 2-OBA, the supplies of intracellular acetyl-CoA and NADPH (nicotinamide adenine dinucleotide phosphate) used for l-threonine biosynthesis were restored. Therefore, 2-OBA is the substitute for pyruvate to engage in enzymatic reactions and disturbs pyruvate metabolism. Our study makes a straightforward explanation of the 2-OBA toxicity mechanism and gives an effective approach for its metabolic detoxification.
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Affiliation(s)
- Yu Fang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Y.F.); (S.Z.); (J.W.); (Z.W.); (J.S.); (X.H.)
| | - Shuyan Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Y.F.); (S.Z.); (J.W.); (Z.W.); (J.S.); (X.H.)
| | - Jianli Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Y.F.); (S.Z.); (J.W.); (Z.W.); (J.S.); (X.H.)
| | - Lianghong Yin
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou 311300, China;
| | - Hailing Zhang
- Department of Biological Engineering, College of Life Science, Yantai University, Yantai 264005, China;
| | - Zhen Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Y.F.); (S.Z.); (J.W.); (Z.W.); (J.S.); (X.H.)
| | - Jie Song
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Y.F.); (S.Z.); (J.W.); (Z.W.); (J.S.); (X.H.)
| | - Xiaoqing Hu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Y.F.); (S.Z.); (J.W.); (Z.W.); (J.S.); (X.H.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Y.F.); (S.Z.); (J.W.); (Z.W.); (J.S.); (X.H.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
- Correspondence: ; Tel./Fax: +86-510-85329239
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4
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Hao Y, Ma Q, Liu X, Fan X, Men J, Wu H, Jiang S, Tian D, Xiong B, Xie X. High-yield production of L-valine in engineered Escherichia coli by a novel two-stage fermentation. Metab Eng 2020; 62:198-206. [DOI: 10.1016/j.ymben.2020.09.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 08/24/2020] [Accepted: 09/16/2020] [Indexed: 01/27/2023]
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5
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Zabel BE, Gerdes S, Evans KC, Nedveck D, Singles SK, Volk B, Budinoff C. Strain-specific strategies of 2'-fucosyllactose, 3-fucosyllactose, and difucosyllactose assimilation by Bifidobacterium longum subsp. infantis Bi-26 and ATCC 15697. Sci Rep 2020; 10:15919. [PMID: 32985563 PMCID: PMC7522266 DOI: 10.1038/s41598-020-72792-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/02/2020] [Indexed: 02/07/2023] Open
Abstract
Human milk provides essential nutrients for infant nutrition. A large proportion of human milk is composed of human milk oligosaccharides (HMOs), which are resistant to digestion by the infant. Instead, HMOs act as a bioactive and prebiotic enriching HMO-utilizing bacteria and cause systematic changes in the host. Several species of Bifidobacterium have been shown to utilize HMOs by conserved, as well as species-specific pathways, but less work has been done to study variation within species or sub-species. B. longum subsp. infantis is a prevalent species in the breast-fed infant gut and the molecular mechanisms of HMO utilization for the type strain B. longum subsp. infantis ATCC 15697 (type strain) have been well characterized. We used growth, transcriptomic, and metabolite analysis to characterize key differences in the utilization of 2'FL, 3FL and DFL (FLs) between B. longum subsp. infantis Bi-26 (Bi-26) and the type strain. Bi-26 grows faster, produces unique metabolites, and has a distinct global gene transcription response to FLs compared to the type strain. Taken together the findings demonstrate major strain specific adaptations in Bi-26 to efficient utilization of FLs.
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Affiliation(s)
- Bryan E Zabel
- Genomics and Microbiome Science, DuPont Nutrition and Biosciences, Madison, WI, USA.
| | - Svetlana Gerdes
- Genomics and Microbiome Science, DuPont Nutrition and Biosciences, Madison, WI, USA
| | - Kara C Evans
- Genomics and Microbiome Science, DuPont Nutrition and Biosciences, Madison, WI, USA
| | - Derek Nedveck
- Genomics and Microbiome Science, DuPont Nutrition and Biosciences, Madison, WI, USA
| | | | - Barbara Volk
- Advanced Analytical, DuPont Nutrition and Biosciences, Wilmington, DE, USA
| | - Charles Budinoff
- Genomics and Microbiome Science, DuPont Nutrition and Biosciences, Madison, WI, USA
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Liang YF, Yan LT, Yue Q, Zhao JK, Luo CY, Gao F, Li H, Gao WY. Preparation of a whole cell catalyst overexpressing acetohydroxyacid synthase of Thermotoga maritima and its application in the syntheses of α-hydroxyketones. Sci Rep 2020; 10:15404. [PMID: 32958806 PMCID: PMC7505981 DOI: 10.1038/s41598-020-72416-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 08/31/2020] [Indexed: 11/30/2022] Open
Abstract
The large catalytic subunit of acetohydroxyacid synthase (AHAS, EC 2.2.1.6) of Thermotoga maritima (TmcAHAS) was prepared in this study. It possesses high specific activity and excellent stability. The protein and a whole cell catalyst overexpressing the protein were applied to the preparation of α-hydroxyketones including acetoin (AC), 3-hydroxy-2-pentanone (HP), and (R)-phenylacetylcarbinol (R-PAC). The results show that AC and HP could be produced in high yields (84% and 62%, respectively), while R-PAC could be synthesized in a high yield (about 78%) with an R/S ratio of 9:1. Therefore, TmcAHAS and the whole cell catalyst overexpressing the protein could be practically useful bio-catalysts in the preparation of α-hydroxyketones including AC, HP, and R-PAC. To the best of our knowledge, this is the first time that bacterial AHAS was used as a catalyst to prepare HP with a good yield, and also the first time that TmcAHAS was employed to synthesize AC and R-PAC.
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Affiliation(s)
- Yan-Fei Liang
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, 710069, Shaanxi, People's Republic of China
| | - Le-Tian Yan
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, 710069, Shaanxi, People's Republic of China
| | - Qiao Yue
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, 710069, Shaanxi, People's Republic of China
| | - Ji-Kui Zhao
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, 710069, Shaanxi, People's Republic of China
| | - Cai-Yun Luo
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, 710069, Shaanxi, People's Republic of China
| | - Feng Gao
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, 710069, Shaanxi, People's Republic of China
| | - Heng Li
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, 710069, Shaanxi, People's Republic of China.
| | - Wen-Yun Gao
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, 710069, Shaanxi, People's Republic of China.
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7
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Bansal A, Karanth NM, Demeler B, Schindelin H, Sarma SP. Crystallographic Structures of IlvN·Val/Ile Complexes: Conformational Selectivity for Feedback Inhibition of Aceto Hydroxy Acid Synthases. Biochemistry 2019; 58:1992-2008. [PMID: 30887800 PMCID: PMC6668035 DOI: 10.1021/acs.biochem.9b00050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Conformational factors that predicate selectivity for valine or isoleucine binding to IlvN leading to the regulation of aceto hydroxy acid synthase I (AHAS I) of Escherichia coli have been determined for the first time from high-resolution (1.9-2.43 Å) crystal structures of IlvN·Val and IlvN·Ile complexes. The valine and isoleucine ligand binding pockets are located at the dimer interface. In the IlvN·Ile complex, among residues in the binding pocket, the side chain of Cys43 is 2-fold disordered (χ1 angles of gauche- and trans). Only one conformation can be observed for the identical residue in the IlvN·Val complexes. In a reversal, the side chain of His53, located at the surface of the protein, exhibits two conformations in the IlvN·Val complex. The concerted conformational switch in the side chains of Cys43 and His53 may play an important role in the regulation of the AHAS I holoenzyme activity. A significant result is the establishment of the subunit composition in the AHAS I holoenzyme by analytical ultracentrifugation. Solution nuclear magnetic resonance and analytical ultracentrifugation experiments have also provided important insights into the hydrodynamic properties of IlvN in the ligand-free and -bound states. The structural and biophysical data unequivocally establish the molecular basis for differential binding of the ligands to IlvN and a rationale for the resistance of IlvM to feedback inhibition by the branched-chain amino acids.
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Affiliation(s)
- Akanksha Bansal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - N. Megha Karanth
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Borries Demeler
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, Mailcode 7760, 7703 Floyd Curl Drive, San Antonio, Texas 78229-3900, United States
| | - Hermann Schindelin
- Rudolf Virchow Centre for Experimental Biomedicine, Institute of Structural Biology, University of Wuerzburg, Josef-Schneider-Strasse 2, D-97080 Wuerzburg, Germany
| | - Siddhartha P. Sarma
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
- NMR Research Center, Indian Institute of Science, Bangalore, Karnataka 560012, India
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8
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Xu JM, Li JQ, Zhang B, Liu ZQ, Zheng YG. Fermentative production of the unnatural amino acid L-2-aminobutyric acid based on metabolic engineering. Microb Cell Fact 2019; 18:43. [PMID: 30819198 PMCID: PMC6393993 DOI: 10.1186/s12934-019-1095-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 02/25/2019] [Indexed: 01/13/2023] Open
Abstract
Background l-2-aminobutyric acid (l-ABA) is an unnatural amino acid that is a key intermediate for the synthesis of several important pharmaceuticals. To make the biosynthesis of l-ABA environmental friendly and more suitable for the industrial-scale production. We expand the nature metabolic network of Escherichia coli using metabolic engineering approach for the production of l-ABA. Results In this study, Escherichia coli THR strain with a modified pathway for threonine-hyperproduction was engineered via deletion of the rhtA gene from the chromosome. To redirect carbon flux from 2-ketobutyrate (2-KB) to l-ABA, the ilvIH gene was deleted to block the l-isoleucine pathway. Furthermore, the ilvA gene from Escherichia coli W3110 and the leuDH gene from Thermoactinomyces intermedius were amplified and co-overexpressed. The promoter was altered to regulate the expression strength of ilvA* and leuDH. The final engineered strain E. coli THR ΔrhtAΔilvIH/Gap-ilvA*-Pbs-leuDH was able to produce 9.33 g/L of l-ABA with a yield of 0.19 g/L/h by fed-batch fermentation in a 5 L bioreactor. Conclusions This novel metabolically tailored strain offers a promising approach to fulfill industrial requirements for production of l-ABA. Electronic supplementary material The online version of this article (10.1186/s12934-019-1095-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jian-Miao Xu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Jian-Qiang Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Bo Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Zhi-Qiang Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China.
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
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9
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Borchert AJ, Downs DM. Analyses of variants of the Ser/Thr dehydratase IlvA provide insight into 2-aminoacrylate metabolism in Salmonella enterica. J Biol Chem 2018; 293:19240-19249. [PMID: 30327426 PMCID: PMC6302184 DOI: 10.1074/jbc.ra118.005626] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 10/11/2018] [Indexed: 12/12/2022] Open
Abstract
RidA is a conserved and broadly distributed protein that has enamine deaminase activity. In a variety of organisms tested thus far, lack of RidA results in the accumulation of the reactive metabolite 2-aminoacrylate (2AA), an obligate intermediate in the catalytic mechanism of several pyridoxal 5'-phosphate (PLP)-dependent enzymes. This study reports the characterization of variants of the biosynthetic serine/threonine dehydratase (EC 4.3.1.19; IlvA), which is a significant generator of 2AA in the bacteria Salmonella enterica, Escherichia coli, and Pseudomonas aeruginosa and the yeast Saccharomyces cerevisiae Two previously identified mutations, ilvA3210 and ilvA3211, suppressed the phenotypic growth consequences of 2AA accumulation in S. enterica Characterization of the respective protein variants suggested that they affect 2AA metabolism in vivo by two different catalytic mechanisms, both leading to an overall reduction in serine dehydratase activity. To emphasize the physiological relevance of the in vitro enzyme characterization, we sought to explain in vivo phenotypes using these data. A simple mathematical model describing the impact these catalytic deficiencies had on 2AA production was generally supported by our data. However, caveats arose when kinetic parameters, determined in vitro, were used to predict formation of the isoleucine precursor 2-ketobutyrate and model in vivo (growth) behaviors. Altogether, our data support the need for a holistic approach, including in vivo and in vitro analyses, to generate data used in understanding and modeling metabolism.
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Affiliation(s)
- Andrew J Borchert
- From the Department of Microbiology, University of Georgia, Athens, Georgia 30602
| | - Diana M Downs
- From the Department of Microbiology, University of Georgia, Athens, Georgia 30602
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Shifts in the Gut Metabolome and Clostridium difficile Transcriptome throughout Colonization and Infection in a Mouse Model. mSphere 2018; 3:mSphere00089-18. [PMID: 29600278 PMCID: PMC5874438 DOI: 10.1128/msphere.00089-18] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 02/23/2018] [Indexed: 12/12/2022] Open
Abstract
Clostridium difficile is a bacterial pathogen of global significance that is a major cause of antibiotic-associated diarrhea. Antibiotics deplete the indigenous gut microbiota and change the metabolic environment in the gut to one favoring C. difficile growth. Here we used metabolomics and transcriptomics to define the gut environment after antibiotics and during the initial stages of C. difficile colonization and infection. We show that amino acids, in particular, proline and branched-chain amino acids, and carbohydrates decrease in abundance over time and that C. difficile gene expression is consistent with their utilization by the bacterium in vivo. We employed an integrated approach to analyze the metabolome and transcriptome to identify associations between metabolites and transcripts. This highlighted the importance of key nutrients in the early stages of colonization, and the data provide a rationale for the development of therapies based on the use of bacteria that specifically compete for nutrients that are essential for C. difficile colonization and disease. Antibiotics alter the gut microbiota and decrease resistance to Clostridium difficile colonization; however, the mechanisms driving colonization resistance are not well understood. Loss of resistance to C. difficile colonization due to antibiotic treatment is associated with alterations in the gut metabolome, specifically, with increases in levels of nutrients that C. difficile can utilize for growth in vitro. To define the nutrients that C. difficile requires for colonization and pathogenesis in vivo, we used a combination of mass spectrometry and RNA sequencing (RNA Seq) to model the gut metabolome and C. difficile transcriptome throughout an acute infection in a mouse model at the following time points: 0, 12, 24, and 30 h. We also performed multivariate-based integration of the omics data to define the signatures that were most important throughout colonization and infection. Here we show that amino acids, in particular, proline and branched-chain amino acids, and carbohydrates decrease in abundance over time in the mouse cecum and that C. difficile gene expression is consistent with their utilization in vivo. This was also reinforced by the multivariate-based integration of the omics data where we were able to discriminate the metabolites and transcripts that support C. difficile physiology between the different time points throughout colonization and infection. This report illustrates how important the availability of amino acids and other nutrients is for the initial stages of C. difficile colonization and progression of disease. Future studies identifying the source of the nutrients and engineering bacteria capable of outcompeting C. difficile in the gut will be important for developing new targeted bacterial therapeutics. IMPORTANCEClostridium difficile is a bacterial pathogen of global significance that is a major cause of antibiotic-associated diarrhea. Antibiotics deplete the indigenous gut microbiota and change the metabolic environment in the gut to one favoring C. difficile growth. Here we used metabolomics and transcriptomics to define the gut environment after antibiotics and during the initial stages of C. difficile colonization and infection. We show that amino acids, in particular, proline and branched-chain amino acids, and carbohydrates decrease in abundance over time and that C. difficile gene expression is consistent with their utilization by the bacterium in vivo. We employed an integrated approach to analyze the metabolome and transcriptome to identify associations between metabolites and transcripts. This highlighted the importance of key nutrients in the early stages of colonization, and the data provide a rationale for the development of therapies based on the use of bacteria that specifically compete for nutrients that are essential for C. difficile colonization and disease.
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11
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Uncovering the role of branched-chain amino acid transaminases in Saccharomyces cerevisiae isobutanol biosynthesis. Metab Eng 2017; 44:302-312. [DOI: 10.1016/j.ymben.2017.10.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 09/29/2017] [Accepted: 10/02/2017] [Indexed: 12/20/2022]
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12
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Liu Y, Li Y, Wang X. Molecular evolution of acetohydroxyacid synthase in bacteria. Microbiologyopen 2017; 6. [PMID: 28782269 PMCID: PMC5727371 DOI: 10.1002/mbo3.524] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 06/21/2017] [Accepted: 06/29/2017] [Indexed: 11/16/2022] Open
Abstract
Acetohydroxyacid synthase (AHAS) is the key enzyme in the biosynthetic pathways of branched chain amino acids in bacteria. Since it does not exist in animal and plant cells, AHAS is an attractive target for developing antimicrobials and herbicides. In some bacteria, there is a single copy of AHAS, while in others there are multiple copies. Therefore, it is necessary to investigate the origin and evolutionary pathway of various AHASs in bacteria. In this study, all the available protein sequences of AHAS in bacteria were investigated, and an evolutionary model of AHAS in bacteria is proposed, according to gene structure, organization and phylogeny. Multiple copies of AHAS in some bacteria might be evolved from the single copy of AHAS, the ancestor. Gene duplication, domain deletion and horizontal gene transfer might occur during the evolution of this enzyme. The results show the biological significance of AHAS, help to understand the functions of various AHASs in bacteria, and would be useful for developing industrial production strains of branched chain amino acids or novel antimicrobials.
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Affiliation(s)
- Yadi Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yanyan Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China.,Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, China
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13
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Yang JE, Kim JW, Oh YH, Choi SY, Lee H, Park AR, Shin J, Park SJ, Lee SY. Biosynthesis of poly(2-hydroxyisovalerate-co-lactate) by metabolically engineeredEscherichia coli. Biotechnol J 2016; 11:1572-1585. [DOI: 10.1002/biot.201600420] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 08/22/2016] [Accepted: 09/06/2016] [Indexed: 01/10/2023]
Affiliation(s)
- Jung Eun Yang
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, and Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
| | - Je Woong Kim
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, and Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
| | - Young Hoon Oh
- Center for Bio-based Chemistry, Division of Convergence Chemistry; Korea Research Institute of Chemical Technology; Daejeon Republic of Korea
| | - So Young Choi
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, and Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
| | - Hyuk Lee
- Division of Drug Discovery Research; Korea Research Institute of Chemical Technology; Daejeon Republic of Korea
| | - A-Reum Park
- Division of Drug Discovery Research; Korea Research Institute of Chemical Technology; Daejeon Republic of Korea
| | - Jihoon Shin
- Center for Bio-based Chemistry, Division of Convergence Chemistry; Korea Research Institute of Chemical Technology; Daejeon Republic of Korea
| | - Si Jae Park
- Department of Environmental Engineering and Energy; Myongji University; Gyeonggido Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, and Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
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Liu Y, Li Y, Wang X. Acetohydroxyacid synthases: evolution, structure, and function. Appl Microbiol Biotechnol 2016; 100:8633-49. [DOI: 10.1007/s00253-016-7809-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 07/28/2016] [Accepted: 08/12/2016] [Indexed: 10/21/2022]
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15
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Li H, Liu N, Wang WT, Wang JY, Gao WY. Cloning and characterization of GST fusion tag stabilized large subunit of Escherichia coli acetohydroxyacid synthase I. J Biosci Bioeng 2016; 121:21-26. [DOI: 10.1016/j.jbiosc.2015.05.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 05/07/2015] [Accepted: 05/18/2015] [Indexed: 10/22/2022]
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16
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Milne N, van Maris AJA, Pronk JT, Daran JM. Comparative assessment of native and heterologous 2-oxo acid decarboxylases for application in isobutanol production by Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:204. [PMID: 26628917 PMCID: PMC4665922 DOI: 10.1186/s13068-015-0374-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 11/09/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND Decarboxylation of α-ketoisovalerate to isobutyraldehyde is a key reaction in metabolic engineering of Saccharomyces cerevisiae for isobutanol production with published studies relying on overexpression of either the native ARO10 gene or of the Lactococcus lactis kivD decarboxylase gene resulting in low enzymatic activities. Here, we compare relevant properties for isobutanol production of Aro10, KivD and an additional, less studied, L. lactis decarboxylase KdcA. RESULTS To eliminate interference by native decarboxylases, each 2-oxo acid decarboxylase was overexpressed in a 'decarboxylase-negative' (pdc1Δ pdc5Δ pdc6Δ aro10Δ) S. cerevisiae background. Kinetic analyses in cell extracts revealed a superior V max/K m ratio of KdcA for α-ketoisovalerate and a wide range of linear and branched-chain 2-oxo acids. However, KdcA also showed the highest activity with pyruvate which, in engineered strains, can contribute to formation of ethanol as a by-product. Removal of native decarboxylase genes eliminated growth on valine as sole nitrogen source and subsequent complementation of this growth impairment by expression of each decarboxylase indicated that based on the increased growth rate, the in vivo activity of KdcA with α-ketoisovalerate was higher than that of KivD and Aro10. Moreover, during oxygen-limited incubation in the presence of glucose, strains expressing kdcA or kivD showed a ca. twofold higher in vivo rate of conversion of α-ketoisovalerate into isobutanol than an ARO10-expressing strain. Finally, cell extracts from cultures grown on different nitrogen sources revealed increased activity of constitutively expressed KdcA after growth on both valine and phenylalanine, while KivD and Aro10 activity was only increased after growth on phenylalanine suggesting a difference in the regulation of these enzymes. CONCLUSIONS This study illustrates important differences in substrate specificity, enzyme kinetics and functional expression between different decarboxylases in the context of isobutanol production and identifies KdcA as a promising alternative decarboxylase not only for isobutanol production but also for other branched-chain and linear alcohols.
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Affiliation(s)
- N. Milne
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - A. J. A. van Maris
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - J. T. Pronk
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - J. M. Daran
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
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Abstract
The biosynthesis of serine, glycine, and one-carbon (C1) units constitutes a major metabolic pathway in Escherichia coli and Salmonella enterica serovar Typhimurium. C1 units derived from serine and glycine are used in the synthesis of purines, histidine, thymine, pantothenate, and methionine and in the formylation of the aminoacylated initiator fMet-TRNAfMet used to start translation in E. coli and serovar Typhimurium. The need for serine, glycine, and C1 units in many cellular functions makes it necessary for the genes encoding enzymes for their synthesis to be carefully regulated to meet the changing demands of the cell for these intermediates. This review discusses the regulation of the following genes: serA, serB, and serC; gly gene; gcvTHP operon; lpdA; gcvA and gcvR; and gcvB genes. Threonine utilization (the Tut cycle) constitutes a secondary pathway for serine and glycine biosynthesis. L-Serine inhibits the growth of E. coli cells in GM medium, and isoleucine releases this growth inhibition. The E. coli glycine transport system (Cyc) has been shown to transport glycine, D-alanine, D-serine, and the antibiotic D-cycloserine. Transport systems often play roles in the regulation of gene expression, by transporting effector molecules into the cell, where they are sensed by soluble or membrane-bound regulatory proteins.
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Abstract
This review focuses on more recent studies concerning the systems biology of branched-chain amino acid biosynthesis, that is, the pathway-specific and global metabolic and genetic regulatory networks that enable the cell to adjust branched-chain amino acid synthesis rates to changing nutritional and environmental conditions. It begins with an overview of the enzymatic steps and metabolic regulatory mechanisms of the pathways and descriptions of the genetic regulatory mechanisms of the individual operons of the isoleucine-leucine-valine (ilv) regulon. This is followed by more-detailed discussions of recent evidence that global control mechanisms that coordinate the expression of the operons of this regulon with one another and the growth conditions of the cell are mediated by changes in DNA supercoiling that occur in response to changes in cellular energy charge levels that, in turn, are modulated by nutrient and environmental signals. Since the parallel pathways for isoleucine and valine biosynthesis are catalyzed by a single set of enzymes, and because the AHAS-catalyzed reaction is the first step specific for valine biosynthesis but the second step of isoleucine biosynthesis, valine inhibition of a single enzyme for this enzymatic step might compromise the cell for isoleucine or result in the accumulation of toxic intermediates. The operon-specific regulatory mechanisms of the operons of the ilv regulon are discussed in the review followed by a consideration and brief review of global regulatory proteins such as integration host factor (IHF), Lrp, and CAP (CRP) that affect the expression of these operons.
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Eram MS, Sarafuddin B, Gong F, Ma K. Characterization of acetohydroxyacid synthase from the hyperthermophilic bacterium Thermotoga maritima. Biochem Biophys Rep 2015; 4:89-97. [PMID: 29124191 PMCID: PMC5668897 DOI: 10.1016/j.bbrep.2015.08.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 08/24/2015] [Accepted: 08/24/2015] [Indexed: 11/30/2022] Open
Abstract
Acetohydroxyacid synthase (AHAS) is the key enzyme in branched chain amino acid biosynthesis pathway. The enzyme activity and properties of a highly thermostable AHAS from the hyperthermophilic bacterium Thermotoga maritima is being reported. The catalytic and regulatory subunits of AHAS from T. maritima were over-expressed in Escherichia coli. The recombinant subunits were purified using a simplified procedure including a heat-treatment step followed by chromatography. A discontinuous colorimetric assay method was optimized and used to determine the kinetic parameters. AHAS activity was determined to be present in several Thermotogales including T. maritima. The catalytic subunit of T. maritima AHAS was purified approximately 30-fold, with an AHAS activity of approximately 160±27 U/mg and native molecular mass of 156±6 kDa. The regulatory subunit was purified to homogeneity and showed no catalytic activity as expected. The optimum pH and temperature for AHAS activity were 7.0 and 85 °C, respectively. The apparent Km and Vmax for pyruvate were 16.4±2 mM and 246±7 U/mg, respectively. Reconstitution of the catalytic and regulatory subunits led to increased AHAS activity. This is the first report on characterization of an isoleucine, leucine, and valine operon (ilv operon) enzyme from a hyperthermophilic microorganism and may contribute to our understanding of the physiological pathways in Thermotogales. The enzyme represents the most active and thermostable AHAS reported so far. First report of AHAS from a hyperthermophilic bacterium. Catalytic and regulatory subunits of AHAS of T. maritima was expressed in E. coli. Recombinant proteins were purified using a simplified procedure. Enzyme represents the most active and thermostable AHAS reported so far. Kinetic parameters were determined for the purified recombinant enzyme
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Key Words
- AHAS, acetohydroxyacid synthase
- Acetohydroxyacid synthase
- BCAA, branched chain amino acid
- Branched-chain amino acids
- CCE, crude cell extract
- CFE, cell-free extract
- HTCCE, heat-treated crude cell extract
- Hyperthermophiles
- IB, inclusion body
- IMAC, immobilized metal affinity chromatography
- TPP, thiamine pyrophosphate
- Thermotogales
- TmAHAS, Thermotoga maritima acetohydroxyacid synthase
- ilv, isoleucine, leucine, valine
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Affiliation(s)
- Mohammad S Eram
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Benozir Sarafuddin
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Frank Gong
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Kesen Ma
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
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Characterization and modification of enzymes in the 2-ketoisovalerate biosynthesis pathway of Ralstonia eutropha H16. Appl Microbiol Biotechnol 2014; 99:761-74. [DOI: 10.1007/s00253-014-5965-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 07/15/2014] [Accepted: 07/16/2014] [Indexed: 11/27/2022]
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Co-Expression of Threonine Dehydratase and Acetolactate Synthase in Escherichia Coli for L-Isoleucine Production. ACTA ACUST UNITED AC 2014. [DOI: 10.4028/www.scientific.net/amr.989-994.997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Metabolic engineering ofCorynebacterium glutamicumhas sought to divert carbon into L-isoleucine. However, the fermentation period of this strain is long. TheC.glutamicumYILW strain (LeuL, AHVr, SGr, Leu-MEr) was previously derived by repeated compound mutagenesis which could accumulate 20.2 g/L L-isoleucine in a 5-L jar fermentor. Overexpression of the threonine dehydratase gene (ilvA) fromCorynebacterium glutamicumYILW and coexpression of threonine dehydratase and acetolactate synthase (ilvBN) from it were employed to divert carbon flux toward L-isoleucine. The strainE. coliTRFC with the expression ofilvA could accumulate L-isoleucine of 6.8 g/L without accumulation of any L-threonine by fed-batch fermentation in a 5-L jar fermentor. However, the production of L-isoleucine by the strainE.coliTRFC with the co-expression ofilvA andilvBN was decreased by 19.1%, and the production of L-valine was increased by 40% compared with that ofE. coliTRFC with the expression ofilvA.
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Feng Y, Cronan JE. PdhR, the pyruvate dehydrogenase repressor, does not regulate lipoic acid synthesis. Res Microbiol 2014; 165:429-38. [PMID: 24816490 PMCID: PMC4134263 DOI: 10.1016/j.resmic.2014.04.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 04/23/2014] [Accepted: 04/24/2014] [Indexed: 12/17/2022]
Abstract
Lipoic acid is a covalently-bound enzyme cofactor required for central metabolism all three domains of life. In the last 20 years the pathway of lipoic acid synthesis and metabolism has been established in Escherichia coli. Expression of the genes of the lipoic acid biosynthesis pathway was believed to be constitutive. However, in 2010 Kaleta and coworkers (BMC Syst. Biol. 4:116) predicted a binding site for the pyruvate dehydrogenase operon repressor, PdhR (referred to lipA site 1) upstream of lipA, the gene encoding lipoic acid synthase and concluded that PdhR regulates lipA transcription. We report in vivo and in vitro evidence that lipA is not controlled by PdhR and that the putative regulatory site deduced by the prior workers is nonfunctional and physiologically irrelevant. E. coli PdhR was purified to homogeneity and used for electrophoretic mobility shift assays. The lipA site 1 of Kaleta and coworkers failed to bind PdhR. The binding detected by these workers is due to another site (lipA site 3) located far upstream of the lipA promoter. Relative to the canonical PdhR binding site lipA site 3 is a half-palindrome and as expected had only weak PdhR binding ability. Manipulation of lipA site 3 to construct a palindrome gave significantly enhanced PdhR binding affinity. The native lipA promoter and the version carrying the artificial lipA3 palindrome were transcriptionally fused to a LacZ reporter gene to directly assay lipA expression. Deletion of pdhR gave no significant change in lipA promoter-driven β-galactosidase activity with either the native or constructed palindrome upstream sequences, indicating that PdhR plays no physiological role in regulation of lipA expression.
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Affiliation(s)
- Youjun Feng
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases & State Key Laboratory for Diagnosis and Treatment of Infectious Disease, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, PR China; Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, PR China; Department of Microbiology, University of Illinois at Urbana-Champaign, IL 61801, USA
| | - John E Cronan
- Department of Microbiology, University of Illinois at Urbana-Champaign, IL 61801, USA; Department of Biochemistry, University of Illinois at Urbana-Champaign, IL 61801, USA.
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23
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Braakman R, Smith E. Metabolic evolution of a deep-branching hyperthermophilic chemoautotrophic bacterium. PLoS One 2014; 9:e87950. [PMID: 24516572 PMCID: PMC3917532 DOI: 10.1371/journal.pone.0087950] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Accepted: 01/05/2014] [Indexed: 11/19/2022] Open
Abstract
Aquifex aeolicus is a deep-branching hyperthermophilic chemoautotrophic bacterium restricted to hydrothermal vents and hot springs. These characteristics make it an excellent model system for studying the early evolution of metabolism. Here we present the whole-genome metabolic network of this organism and examine in detail the driving forces that have shaped it. We make extensive use of phylometabolic analysis, a method we recently introduced that generates trees of metabolic phenotypes by integrating phylogenetic and metabolic constraints. We reconstruct the evolution of a range of metabolic sub-systems, including the reductive citric acid (rTCA) cycle, as well as the biosynthesis and functional roles of several amino acids and cofactors. We show that A. aeolicus uses the reconstructed ancestral pathways within many of these sub-systems, and highlight how the evolutionary interconnections between sub-systems facilitated several key innovations. Our analyses further highlight three general classes of driving forces in metabolic evolution. One is the duplication and divergence of genes for enzymes as these progress from lower to higher substrate specificity, improving the kinetics of certain sub-systems. A second is the kinetic optimization of established pathways through fusion of enzymes, or their organization into larger complexes. The third is the minimization of the ATP unit cost to synthesize biomass, improving thermodynamic efficiency. Quantifying the distribution of these classes of innovations across metabolic sub-systems and across the tree of life will allow us to assess how a tradeoff between maximizing growth rate and growth efficiency has shaped the long-term metabolic evolution of the biosphere.
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Affiliation(s)
- Rogier Braakman
- Krasnow Institute for Advanced Study, George Mason University, Fairfax, Virginia, United States of America
- * E-mail:
| | - Eric Smith
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
- Krasnow Institute for Advanced Study, George Mason University, Fairfax, Virginia, United States of America
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Zhao Y, Niu C, Wen X, Xi Z. The minimum activation peptide from ilvH can activate the catalytic subunit of AHAS from different species. Chembiochem 2013; 14:746-52. [PMID: 23512804 DOI: 10.1002/cbic.201200680] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Indexed: 11/10/2022]
Abstract
Acetohydroxyacid synthases (AHASs), which catalyze the first step in the biosynthesis of branched-chain amino acids, are composed of a catalytic subunit (CSU) and a regulatory subunit (RSU). The CSU harbors the catalytic site, and the RSU is responsible for the activation and feedback regulation of the CSU. Previous results from Chipman and co-workers and our lab have shown that heterologous activation can be achieved among isozymes of Escherichia coli AHAS. It would be interesting to find the minimum peptide of ilvH (the RSU of E. coli AHAS III) that could activate other E. coli CSUs, or even those of ## species. In this paper, C-terminal, N-terminal, and C- and N-terminal truncation mutants of ilvH were constructed. The minimum peptide to activate ilvI (the CSU of E. coli AHAS III) was found to be ΔN 14-ΔC 89. Moreover, this peptide could not only activate its homologous ilvI and heterologous ilvB (CSU of E. coli AHAS I), but also heterologously activate the CSUs of AHAS from Saccharomyces cerevisiae, Arabidopsis thaliana, and Nicotiana plumbaginifolia. However, this peptide totally lost its ability for feedback regulation by valine, thus suggesting different elements for enzymatic activation and feedback regulation. Additionally, the apparent dissociation constant (Kd ) of ΔN 14-ΔC 89 when binding CSUs of different species was found to be 9.3-66.5 μM by using microscale thermophoresis. The ability of this peptide to activate different CSUs does not correlate well with its binding ability (Kd ) to these CSUs, thus implying that key interactions by specific residues is more important than binding ability in promoting enzymatic reactions. The high sequence similarity of the peptide ΔN 14-ΔC 89 to RSUs across species hints that this peptide represents the minimum activation motif in RSU and that it regulates all AHASs.
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Affiliation(s)
- Yuefang Zhao
- Department of Chemical Biology and State Key Laboratory of Elemento-organic Chemistry, Nankai University, Weijin 94, Tianjin 300071, China
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Park JH, Oh JE, Lee KH, Kim JY, Lee SY. Rational design of Escherichia coli for L-isoleucine production. ACS Synth Biol 2012; 1:532-40. [PMID: 23656230 DOI: 10.1021/sb300071a] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metabolic engineering of Escherichia coli was performed to construct a 100% rationally engineered strain capable of overproducing L-isoleucine, an important branched-chain amino acid. The thrABC (encoding L-threonine biosynthetic enzymes), ilvA (encoding feedback-resistant threonine dehydratase), ilvIH (encoding feedback-resistant acetohydroxy acid synthase III), and ygaZH (encoding branched-chain amino acid exporter) genes were amplified by plasmid-based overexpression. The ilvCED (encoding L-isoleucine biosynthetic enzymes) and lrp (encoding global regulator Lrp) genes were also amplified by chromosomal promoter replacement in order to further increase the flux toward L-isoleucine. The final engineered E. coli strain was able to produce 9.46 g/L of L-isoleucine with a yield of 0.14 g/g of glucose by fed-batch culture. The overall design principles described here for the production of highly regulated product should be useful in designing strains for the production of other similar bioproducts.
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Affiliation(s)
- Jin Hwan Park
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Program), Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| | - Jae Eun Oh
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Program), Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| | - Kwang Ho Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Program), Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| | - Ji Young Kim
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Program), Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Program), Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
- BioInformatics Research Center and BioProcess Engineering Research Center, KAIST, Daejeon 305-701, Republic of Korea
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26
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Zhao Y, Wen X, Niu C, Xi Z. Arginine 26 and Aspartic Acid 69 of the Regulatory Subunit are Key Residues of Subunits Interaction of Acetohydroxyacid Synthase Isozyme III fromE. coli. Chembiochem 2012; 13:2445-54. [DOI: 10.1002/cbic.201200362] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Indexed: 11/08/2022]
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Belenky I, Steinmetz A, Vyazmensky M, Barak Z, Tittmann K, Chipman DM. Many of the functional differences between acetohydroxyacid synthase (AHAS) isozyme I and other AHASs are a result of the rapid formation and breakdown of the covalent acetolactate-thiamin diphosphate adduct in AHAS I. FEBS J 2012; 279:1967-79. [DOI: 10.1111/j.1742-4658.2012.08577.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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28
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Gedi V, Yoon MY. Bacterial acetohydroxyacid synthase and its inhibitors - a summary of their structure, biological activity and current status. FEBS J 2012; 279:946-63. [DOI: 10.1111/j.1742-4658.2012.08505.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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29
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Vyazmensky M, Steinmetz A, Meyer D, Golbik R, Barak Z, Tittmann K, Chipman DM. Significant Catalytic Roles for Glu47 and Gln 110 in All Four of the C−C Bond-Making and -Breaking Steps of the Reactions of Acetohydroxyacid Synthase II. Biochemistry 2011; 50:3250-60. [DOI: 10.1021/bi102051h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maria Vyazmensky
- Ben-Gurion University of the Negev, Department of Life Sciences, Beer-Sheva 84105, Israel
| | - Andrea Steinmetz
- Georg-August University Göttingen, Albrecht-von-Haller-Institute and Göttingen Centre for Molecular Biosciences, Ernst-Caspari-Haus, Department of Bioanalytics, Justus-von-Liebig Weg 11, 37077 Göttingen, Germany
- Martin-Luther University Halle-Wittenberg, Institute for Biochemistry and Biotechnology, Kurt-Mothes-Strasse 3, 06120 Halle/Saale, Germany
| | - Danilo Meyer
- Georg-August University Göttingen, Albrecht-von-Haller-Institute and Göttingen Centre for Molecular Biosciences, Ernst-Caspari-Haus, Department of Bioanalytics, Justus-von-Liebig Weg 11, 37077 Göttingen, Germany
- Martin-Luther University Halle-Wittenberg, Institute for Biochemistry and Biotechnology, Kurt-Mothes-Strasse 3, 06120 Halle/Saale, Germany
| | - Ralph Golbik
- Martin-Luther University Halle-Wittenberg, Institute for Biochemistry and Biotechnology, Kurt-Mothes-Strasse 3, 06120 Halle/Saale, Germany
| | - Ze'ev Barak
- Ben-Gurion University of the Negev, Department of Life Sciences, Beer-Sheva 84105, Israel
| | - Kai Tittmann
- Georg-August University Göttingen, Albrecht-von-Haller-Institute and Göttingen Centre for Molecular Biosciences, Ernst-Caspari-Haus, Department of Bioanalytics, Justus-von-Liebig Weg 11, 37077 Göttingen, Germany
- Martin-Luther University Halle-Wittenberg, Institute for Biochemistry and Biotechnology, Kurt-Mothes-Strasse 3, 06120 Halle/Saale, Germany
| | - David M. Chipman
- Ben-Gurion University of the Negev, Department of Life Sciences, Beer-Sheva 84105, Israel
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Park JH, Jang YS, Lee JW, Lee SY. Escherichia coli W as a new platform strain for the enhanced production of L-valine by systems metabolic engineering. Biotechnol Bioeng 2011; 108:1140-7. [PMID: 21191998 DOI: 10.1002/bit.23044] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 12/12/2010] [Accepted: 12/14/2010] [Indexed: 11/11/2022]
Abstract
A less frequently employed Escherichia coli strain W, yet possessing useful metabolic characteristics such as less acetic acid production and high L-valine tolerance, was metabolically engineered for the production of L-valine. The ilvA gene was deleted to make more pyruvate, a key precursor for L-valine, available for enhanced L-valine biosynthesis. The lacI gene was deleted to allow constitutive expression of genes under the tac or trc promoter. The ilvBN(mut) genes encoding feedback-resistant acetohydroxy acid synthase (AHAS) I and the L-valine biosynthetic ilvCED genes encoding acetohydroxy acid isomeroreductase, dihydroxy acid dehydratase, and branched chain amino acid aminotransferase, respectively, were amplified by plasmid-based overexpression. The global regulator Lrp and L-valine exporter YgaZH were also amplified by plasmid-based overexpression. The engineered E. coli W (ΔlacI ΔilvA) strain overexpressing the ilvBN(mut) , ilvCED, ygaZH, and lrp genes was able to produce an impressively high concentration of 60.7 g/L L-valine by fed-batch culture in 29.5 h, resulting in a high volumetric productivity of 2.06 g/L/h. The most notable finding is that there was no other byproduct produced during L-valine production. The results obtained in this study suggest that E. coli W can be a good alternative to Corynebacterium glutamicum and E. coli K-12, which have so far been the most efficient L-valine producer. Furthermore, it is expected that various bioproducts including other amino acids might be more efficiently produced by this revisited platform strain of E. coli.
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Affiliation(s)
- Jin Hwan Park
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Program), KAIST, Daejeon, Republic of Korea.
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Park JH, Lee SY. Metabolic pathways and fermentative production of L-aspartate family amino acids. Biotechnol J 2010; 5:560-77. [PMID: 20518059 DOI: 10.1002/biot.201000032] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The L-aspartate family amino acids (AFAAs), L-threonine, L-lysine, L-methionine and L-isoleucine have recently been of much interest due to their wide spectrum of applications including food additives, components of cosmetics and therapeutic agents, and animal feed additives. Among them, L-threonine, L-lysine and L-methionine are three major amino acids produced currently throughout the world. Recent advances in systems metabolic engineering, which combine various high-throughput omics technologies and computational analysis, are now facilitating development of microbial strains efficiently producing AFAAs. Thus, a thorough understanding of the metabolic and regulatory mechanisms of the biosynthesis of these amino acids is urgently needed for designing system-wide metabolic engineering strategies. Here we review the details of AFAA biosynthetic pathways, regulations involved, and export and transport systems, and provide general strategies for successful metabolic engineering along with relevant examples. Finally, perspectives of systems metabolic engineering for developing AFAA overproducers are suggested with selected exemplary studies.
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Affiliation(s)
- Jin Hwan Park
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 program), BioProcess Engineering Research Center, and Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, KAIST, Daejeon, Republic of Korea
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Steinmetz A, Vyazmensky M, Meyer D, Barak Z, Golbik R, Chipman DM, Tittmann K. Valine 375 and Phenylalanine 109 Confer Affinity and Specificity for Pyruvate as Donor Substrate in Acetohydroxy Acid Synthase Isozyme II from Escherichia coli. Biochemistry 2010; 49:5188-99. [DOI: 10.1021/bi100555q] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrea Steinmetz
- Albrecht-von-Haller-Institute and Göttingen Centre for Molecular Biosciences, Ernst-Caspari-Haus, Department of Bioanalytics, Georg-August University Göttingen, Justus-von-Liebig Weg 11, 37077 Göttingen, Germany
| | - Maria Vyazmensky
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Danilo Meyer
- Albrecht-von-Haller-Institute and Göttingen Centre for Molecular Biosciences, Ernst-Caspari-Haus, Department of Bioanalytics, Georg-August University Göttingen, Justus-von-Liebig Weg 11, 37077 Göttingen, Germany
| | - Ze′ev Barak
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Ralph Golbik
- Institute for Biochemistry and Biotechnology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle/Saale, Germany
| | - David M. Chipman
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Kai Tittmann
- Albrecht-von-Haller-Institute and Göttingen Centre for Molecular Biosciences, Ernst-Caspari-Haus, Department of Bioanalytics, Georg-August University Göttingen, Justus-von-Liebig Weg 11, 37077 Göttingen, Germany
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Nielsen DR, Yoon SH, Yuan CJ, Prather KLJ. Metabolic engineering of acetoin and meso-2, 3-butanediol biosynthesis in E. coli. Biotechnol J 2010; 5:274-84. [PMID: 20213636 DOI: 10.1002/biot.200900279] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- David R Nielsen
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Park JH, Lee SY. Fermentative production of branched chain amino acids: a focus on metabolic engineering. Appl Microbiol Biotechnol 2010; 85:491-506. [PMID: 19844702 DOI: 10.1007/s00253-009-2307-y] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Revised: 10/11/2009] [Accepted: 10/11/2009] [Indexed: 12/13/2022]
Abstract
The branched chain amino acids (BCAAs), L-valine, L-leucine, and L-isoleucine, have recently been attracting much attention as their potential to be applied in various fields, including animal feed additive, cosmetics, and pharmaceuticals, increased. Strategies for developing microbial strains efficiently producing BCAAs are now in transition toward systems metabolic engineering from random mutagenesis. The metabolism and regulatory circuits of BCAA biosynthesis need to be thoroughly understood for designing system-wide metabolic engineering strategies. Here we review the current knowledge on BCAAs including their biosynthetic pathways, regulations, and export and transport systems. Recent advances in the development of BCAA production strains are also reviewed with a particular focus on L-valine production strain. At the end, the general strategies for developing BCAA overproducers by systems metabolic engineering are suggested.
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Affiliation(s)
- Jin Hwan Park
- BioProcess Engineering Research Center, KAIST, Daejeon, Republic of Korea
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35
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Cann AF, Liao JC. Pentanol isomer synthesis in engineered microorganisms. Appl Microbiol Biotechnol 2010; 85:893-9. [PMID: 19859707 PMCID: PMC2804790 DOI: 10.1007/s00253-009-2262-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Revised: 09/11/2009] [Accepted: 09/11/2009] [Indexed: 01/05/2023]
Abstract
Pentanol isomers such as 2-methyl-1-butanol and 3-methyl-1-butanol are a useful class of chemicals with a potential application as biofuels. They are found as natural by-products of microbial fermentations from amino acid substrates. However, the production titer and yield of the natural processes are too low to be considered for practical applications. Through metabolic engineering, microbial strains for the production of these isomers have been developed, as well as that for 1-pentanol and pentenol. Although the current production levels are still too low for immediate industrial applications, the approach holds significant promise for major breakthroughs in production efficiency.
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Affiliation(s)
- Anthony F. Cann
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095 USA
| | - James C. Liao
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095 USA
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Chipman DM, Barak Z, Shaanan B, Vyazmensky M, Binshtein E, Belenky I, Temam V, Steinmetz A, Golbik R, Tittmann K. Origin of the specificities of acetohydroxyacid synthases and glyoxylate carboligase. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.molcatb.2009.03.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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37
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Vyazmensky M, Zherdev Y, Slutzker A, Belenky I, Kryukov O, Barak Z, Chipman DM. Interactions between large and small subunits of different acetohydroxyacid synthase isozymes of Escherichia coli. Biochemistry 2009; 48:8731-7. [PMID: 19653643 DOI: 10.1021/bi9009488] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The large, catalytic subunits (LSUs; ilvB, ilvG and ilvI, respectively) of enterobacterial acetohydroxyacid synthases isozymes (AHAS I, II and III) have molecular weights approximately 60 kDa and are paralogous with a family of other thiamin diphosphate dependent enzymes. The small, regulatory subunits (SSUs) of AHAS I and AHAS III (ilvN and ilvH) are required for valine inhibition, but ilvN and ilvH can only confer valine sensitivity on their own LSUs. AHAS II is valine resistant. The LSUs have only approximately 15, <<1 and approximately 3%, respectively, of the activity of their respective holoenzymes, but the holoenzymes can be reconstituted with complete recovery of activity. We have examined the activation of each of the LSUs by SSUs from different isozymes and ask to what extent such activation is specific; that is, is effective nonspecific interaction possible between LSUs and SSUs of different isozymes? To our surprise, the AHAS II SSU ilvM is able to activate the LSUs of all three of the isozymes, and the truncated AHAS III SSUs ilvH-Delta80, ilvH-Delta86 and ilvH-Delta89 are able to activate the LSUs of both AHAS I and AHAS III. However, none of the heterologously activated enzymes have any feedback sensitivity. Our results imply the existence of a common region in all three LSUs to which regulatory subunits may bind, as well as a similarity between the surfaces of ilvM and the other SSUs. This surface must be included within the N-terminal betaalphabetabetaalphabeta-domain of the SSUs, probably on the helical face of this domain. We suggest hypotheses for the mechanism of valine inhibition, and reject one involving induced dissociation of subunits.
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Affiliation(s)
- Maria Vyazmensky
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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Awasthy D, Gaonkar S, Shandil RK, Yadav R, Bharath S, Marcel N, Subbulakshmi V, Sharma U. Inactivation of the ilvB1 gene in Mycobacterium tuberculosis leads to branched-chain amino acid auxotrophy and attenuation of virulence in mice. MICROBIOLOGY-SGM 2009; 155:2978-2987. [PMID: 19542000 DOI: 10.1099/mic.0.029884-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Acetohydroxyacid synthase (AHAS) is the first enzyme in the branched-chain amino acid biosynthesis pathway in bacteria. Bioinformatics analysis revealed that the Mycobacterium tuberculosis genome contains four genes (ilvB1, ilvB2, ilvG and ilvX) coding for the large catalytic subunit of AHAS, whereas only one gene (ilvN or ilvH) coding for the smaller regulatory subunit of this enzyme was found. In order to understand the physiological role of AHAS in survival of the organism in vitro and in vivo, we inactivated the ilvB1 gene of M. tuberculosis. The mutant strain was found to be auxotrophic for all of the three branched-chain amino acids (isoleucine, leucine and valine), when grown with either C(6) or C(2) carbon sources, suggesting that the ilvB1 gene product is the major AHAS in M. tuberculosis. Depletion of these branched chain amino acids in the medium led to loss of viability of the DeltailvB1 strain in vitro, resulting in a 4-log reduction in colony-forming units after 10 days. Survival kinetics of the mutant strain cultured in macrophages maintained with sub-optimal concentrations of the branched-chain amino acids did not show any loss of viability, indicating either that the intracellular environment was rich in these amino acids or that the other AHAS catalytic subunits were functional under these conditions. Furthermore, the growth kinetics of the DeltailvB1 strain in mice indicated that although this mutant strain showed defective growth in vivo, it could persist in the infected mice for a long time, and therefore could be a potential vaccine candidate.
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Affiliation(s)
- Disha Awasthy
- AstraZeneca R&D, Bellary Road, Hebbal, Bangalore-560024, India
| | | | - R K Shandil
- AstraZeneca R&D, Bellary Road, Hebbal, Bangalore-560024, India
| | - Reena Yadav
- AstraZeneca R&D, Bellary Road, Hebbal, Bangalore-560024, India
| | - Sowmya Bharath
- AstraZeneca R&D, Bellary Road, Hebbal, Bangalore-560024, India
| | - Nimi Marcel
- AstraZeneca R&D, Bellary Road, Hebbal, Bangalore-560024, India
| | | | - Umender Sharma
- AstraZeneca R&D, Bellary Road, Hebbal, Bangalore-560024, India
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Cann AF, Liao JC. Production of 2-methyl-1-butanol in engineered Escherichia coli. Appl Microbiol Biotechnol 2008; 81:89-98. [PMID: 18758769 PMCID: PMC7419481 DOI: 10.1007/s00253-008-1631-y] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2008] [Revised: 07/18/2008] [Accepted: 07/24/2008] [Indexed: 11/04/2022]
Abstract
Recent progress has been made in the production of higher alcohols by harnessing the power of natural amino acid biosynthetic pathways. Here, we describe the first strain of Escherichia coli developed to produce the higher alcohol and potential new biofuel 2-methyl-1-butanol (2MB). To accomplish this, we explored the biodiversity of enzymes catalyzing key parts of the isoleucine biosynthetic pathway, finding that AHAS II (ilvGM) from Salmonella typhimurium and threonine deaminase (ilvA) from Corynebacterium glutamicum improve 2MB production the most. Overexpression of the native threonine biosynthetic operon (thrABC) on plasmid without the native transcription regulation also improved 2MB production in E. coli. Finally, we knocked out competing pathways upstream of threonine production (ΔmetA, Δtdh) to increase its availability for further improvement of 2MB production. This work led to a strain of E. coli that produces 1.25 g/L 2MB in 24 h, a total alcohol content of 3 g/L, and with yields of up to 0.17 g 2MB/g glucose.
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Affiliation(s)
- Anthony F Cann
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
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40
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Curien G, Biou V, Mas-Droux C, Robert-Genthon M, Ferrer JL, Dumas R. Amino acid biosynthesis: new architectures in allosteric enzymes. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2008; 46:325-339. [PMID: 18272376 DOI: 10.1016/j.plaphy.2007.12.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2007] [Indexed: 05/25/2023]
Abstract
This review focuses on the allosteric controls in the Aspartate-derived and the branched-chain amino acid biosynthetic pathways examined both from kinetic and structural points of view. The objective is to show the differences that exist among the plant and microbial worlds concerning the allosteric regulation of these pathways and to unveil the structural bases of this diversity. Indeed, crystallographic structures of enzymes from these pathways have been determined in bacteria, fungi and plants, providing a wonderful opportunity to obtain insight into the acquisition and modulation of allosteric controls in the course of evolution. This will be examined using two enzymes, threonine synthase and the ACT domain containing enzyme aspartate kinase. In a last part, as many enzymes in these pathways display regulatory domains containing the conserved ACT module, the organization of ACT domains in this kind of allosteric enzymes will be reviewed, providing explanations for the variety of allosteric effectors and type of controls observed.
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Affiliation(s)
- Gilles Curien
- Laboratoire de Physiologie Cellulaire Végétale, Université Joseph Fourier, Commissariat à l'Energie Atomique, Institut de Recherche et de Technologie des Sciences du Vivant, 38054 Grenoble, France
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41
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YjgF is required for isoleucine biosynthesis when Salmonella enterica is grown on pyruvate medium. J Bacteriol 2008; 190:3057-62. [PMID: 18296521 DOI: 10.1128/jb.01700-07] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The YjgF/YER057c/UK114 family of proteins is conserved across the three domains of life, yet no biochemical function has been clearly defined for any member of this family. In Salmonella enterica, a deletion of yjgF results in a requirement for isoleucine when the mutant strain is grown in glucose-serine or pyruvate medium. Feedback inhibition of IlvA is required for the curative effect of isoleucine on glucose-serine medium. On pyruvate medium, yjgF mutants are unable to synthesize enough isoleucine for growth. From this study, we conclude that the isoleucine requirement of a yjgF mutant on pyruvate is a consequence of the decreased transaminase B (IlvE) activity that has previously been characterized in these mutants.
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42
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Mitra A, Sarma SP. Escherichia coli ilvN interacts with the FAD binding domain of ilvB and activates the AHAS I enzyme. Biochemistry 2008; 47:1518-31. [PMID: 18193896 DOI: 10.1021/bi701893b] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The unique multidomain organization in the multimeric Escherichia coli AHAS I (ilvBN) enzyme has been exploited to generate polypeptide fragments which, when cloned and expressed, reassemble in the presence of cofactors to yield a catalytically competent enzyme. Multidimensional multinuclear NMR methods have been employed for obtaining near complete sequence specific NMR assignments for backbone HN, 15N, 13Calpha and 13Cbeta atoms of the FAD binding domain of ilvB on samples that were isotopically enriched in 2H, 13C and 15N. Unambiguous assignments were obtained for 169 of 177 backbone Calpha atoms and 127 of 164 side chain Cbeta atoms. The secondary structure determined on the basis of observed 13Calpha secondary chemical shifts and sequential NOEs agrees well with the structure of this domain in the catalytic subunit of yeast AHAS. Binding of ilvN to the ilvBalpha and ilvBbeta domains was studied by both circular dichroism and isotope edited solution nuclear magnetic resonance methods. Changes in CD spectra indicate that ilvN interacts with ilvBalpha and ilvBbeta domains of the catalytic subunit and not with the ilvBgamma domain. NMR chemical shift mapping methods show that ilvN binds close to the FAD binding site in ilvBbeta and proximal to the intrasubunit ilvBalpha/ilvBbeta domain interface. The implication of this interaction on the role of the regulatory subunit on the activity of the holoenzyme is discussed.
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Affiliation(s)
- Ashima Mitra
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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43
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Nelson DR, Duxbury T. The distribution of acetohydroxyacid synthase in soil bacteria. Antonie Van Leeuwenhoek 2007; 93:123-32. [PMID: 17624809 DOI: 10.1007/s10482-007-9186-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2007] [Accepted: 06/18/2007] [Indexed: 11/26/2022]
Abstract
Most bacteria possess the enzyme acetohydroxyacid synthase, which is used to produce branched-chain amino acids. Enteric bacteria contain several isozymes suited to different conditions, but the distribution of acetohydroxyacid synthase in soil bacteria is largely unknown. Growth experiments confirmed that Escherichia coli, Salmonella enterica serotype Typhimurium, and Enterobacter aerogenes contain isozymes of acetohydroxyacid synthase, allowing the bacteria to grow in the presence of valine (which causes feedback inhibition of AHAS I) or the sulfonylurea herbicide triasulfuron (which inhibits AHAS II) although a slight lag phase was observed in growth in the latter case. Several common soil isolates were inhibited by triasulfuron, but Pseudomonas fluorescens and Rhodococcus erythropolis were not inhibited by any combination of triasulfuron and valine. The extent of sulfonylurea-sensitive acetohydroxyacid synthase in soil was revealed when 21 out of 27 isolated bacteria in pure culture were inhibited by triasulfuron, the addition of isoleucine and/or valine reversing the effect in 19 cases. Primers were designed to target the genes encoding the large subunits (ilvB, ilvG and ilvI) of acetohydroxyacid synthase from available sequence data and a approximately 355 bp fragment in Bacillus subtilis, Arthrobacter globiformis, E. coli and S. enterica was subsequently amplified. The primers were used to create a small clone library of sequences from an agricultural soil. Phylogenetic analysis revealed significant sequence variation, but all 19 amino acid sequences were most closely related to published large subunit acetohydroxyacid synthase amino acid sequences within several phyla including the Proteobacteria and Actinobacteria. The results suggested the majority of soil microorganisms contain only one functional acetohydroxyacid synthase enzyme sensitive to sulfonylurea herbicides.
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Affiliation(s)
- Darryl R Nelson
- School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW, 2006, Australia.
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Sakai T, Nakamura N, Umitsuki G, Nagai K, Wachi M. Increased production of pyruvic acid by Escherichia coli RNase G mutants in combination with cra mutations. Appl Microbiol Biotechnol 2007; 76:183-92. [PMID: 17483940 DOI: 10.1007/s00253-007-1006-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2007] [Revised: 04/13/2007] [Accepted: 04/15/2007] [Indexed: 12/01/2022]
Abstract
The Escherichia coli RNase G is known as an endoribonuclease responsible for the 5'-end maturation of 16S rRNA and degradation of several specific mRNAs such as adhE and eno mRNAs. In this study, we found that an RNase G mutant derived from the MC1061 strain did not grow on a glucose minimal medium. Genetic analysis revealed that simultaneous defects of cra and ilvIH, encoding a transcriptional regulator of glycolysis/gluconeogenesis and one of isozymes of acetohydroxy acid synthase, respectively, were required for this phenomenon to occur. The results of additional experiments presented here indicate that the RNase G mutation, in combination with cra mutation, caused the increased production of pyruvic acid from glucose, which was then preferentially converted to valine due to the ilvIH mutation, resulting in depletion of isoleucine. In fact, the rng cra double mutant produced increased amount of pyruvate in the medium. These results suggest that the RNase G mutation could be applied in the breeding of producer strains of pyruvate and its derivatives such as valine.
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Affiliation(s)
- Taro Sakai
- Department of Bioengineering, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8503, Japan
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45
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Park JH, Lee KH, Kim TY, Lee SY. Metabolic engineering of Escherichia coli for the production of L-valine based on transcriptome analysis and in silico gene knockout simulation. Proc Natl Acad Sci U S A 2007; 104:7797-802. [PMID: 17463081 PMCID: PMC1857225 DOI: 10.1073/pnas.0702609104] [Citation(s) in RCA: 445] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The L-valine production strain of Escherichia coli was constructed by rational metabolic engineering and stepwise improvement based on transcriptome analysis and gene knockout simulation of the in silico genome-scale metabolic network. Feedback inhibition of acetohydroxy acid synthase isoenzyme III by L-valine was removed by site-directed mutagenesis, and the native promoter containing the transcriptional attenuator leader regions of the ilvGMEDA and ilvBN operon was replaced with the tac promoter. The ilvA, leuA, and panB genes were deleted to make more precursors available for L-valine biosynthesis. This engineered Val strain harboring a plasmid overexpressing the ilvBN genes produced 1.31 g/liter L-valine. Comparative transcriptome profiling was performed during batch fermentation of the engineered and control strains. Among the down-regulated genes, the lrp and ygaZH genes, which encode a global regulator Lrp and L-valine exporter, respectively, were overexpressed. Amplification of the lrp, ygaZH, and lrp-ygaZH genes led to the enhanced production of L-valine by 21.6%, 47.1%, and 113%, respectively. Further improvement was achieved by using in silico gene knockout simulation, which identified the aceF, mdh, and pfkA genes as knockout targets. The VAMF strain (Val DeltaaceF Deltamdh DeltapfkA) overexpressing the ilvBN, ilvCED, ygaZH, and lrp genes was able to produce 7.55 g/liter L-valine from 20 g/liter glucose in batch culture, resulting in a high yield of 0.378 g of L-valine per gram of glucose. These results suggest that an industrially competitive strain can be efficiently developed by metabolic engineering based on combined rational modification, transcriptome profiling, and systems-level in silico analysis.
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Affiliation(s)
- Jin Hwan Park
- *Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 program), BioProcess Engineering Research Center
- Center for Systems and Synthetic Biotechnology, Institute for the Biocentury, and
| | - Kwang Ho Lee
- *Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 program), BioProcess Engineering Research Center
- Center for Systems and Synthetic Biotechnology, Institute for the Biocentury, and
- R & D Center for Bioproducts, CJ Corporation, Seoul 157-724, Korea
| | - Tae Yong Kim
- *Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 program), BioProcess Engineering Research Center
- Center for Systems and Synthetic Biotechnology, Institute for the Biocentury, and
| | - Sang Yup Lee
- *Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 program), BioProcess Engineering Research Center
- Center for Systems and Synthetic Biotechnology, Institute for the Biocentury, and
- Department of BioSystems and Bioinformatics Research Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Korea; and
- To whom correspondence should be addressed. E-mail:
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46
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McCourt JA, Duggleby RG. Acetohydroxyacid synthase and its role in the biosynthetic pathway for branched-chain amino acids. Amino Acids 2006; 31:173-210. [PMID: 16699828 DOI: 10.1007/s00726-005-0297-3] [Citation(s) in RCA: 171] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2005] [Accepted: 12/09/2005] [Indexed: 11/25/2022]
Abstract
The branched-chain amino acids are synthesized by plants, fungi and microorganisms, but not by animals. Therefore, the enzymes of this pathway are potential target sites for the development of antifungal agents, antimicrobials and herbicides. Most research has focused upon the first enzyme in this biosynthetic pathway, acetohydroxyacid synthase (AHAS) largely because it is the target site for many commercial herbicides. In this review we provide a brief overview of the important properties of each enzyme within the pathway and a detailed summary of the most recent AHAS research, against the perspective of work that has been carried out over the past 50 years.
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Affiliation(s)
- J A McCourt
- School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Australia
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47
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Schloss JV. Acetolactate synthase, mechanism of action and its herbicide binding site. ACTA ACUST UNITED AC 2006. [DOI: 10.1002/ps.2780290305] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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48
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Vinogradov V, Vyazmensky M, Engel S, Belenky I, Kaplun A, Kryukov O, Barak Z, Chipman DM. Acetohydroxyacid synthase isozyme I from Escherichia coli has unique catalytic and regulatory properties. Biochim Biophys Acta Gen Subj 2006; 1760:356-63. [PMID: 16326011 DOI: 10.1016/j.bbagen.2005.10.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2005] [Revised: 09/27/2005] [Accepted: 10/20/2005] [Indexed: 11/30/2022]
Abstract
AHAS I is an isozyme of acetohydroxyacid synthase which is apparently unique to enterobacteria. It has been known for over 20 years that it has many properties which are quite different from those of the other two enterobacterial AHASs isozymes, as well as from those of "typical" AHASs which are single enzymes in a given organism. These include a unique mechanism for regulation of expression and the absence of a preference for forming acetohydroxybutyrate. We have cloned the two subunits, ilvB and ilvN, of this Escherichia coli isoenzyme and examined the enzymatic properties of the purified holoenzyme and the enzyme reconstituted from purified subunits. Unlike other AHASs, AHAS I demonstrates cooperative feedback inhibition by valine, and the kinetics fit closely to an exclusive binding model. The formation of acetolactate by AHAS I is readily reversible and acetolactate can act as substrate for alternative AHAS I-catalyzed reactions.
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Affiliation(s)
- Valerie Vinogradov
- Department of Life Sciences, Ben-Gurion University of the Negev, POB 657, Beer-Sheva 84105, Israel
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49
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Clark DP, Cronan JE. Two-Carbon Compounds and Fatty Acids as Carbon Sources. EcoSal Plus 2005; 1. [PMID: 26443509 DOI: 10.1128/ecosalplus.3.4.4] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2004] [Indexed: 06/05/2023]
Abstract
This review concerns the uptake and degradation of those molecules that are wholly or largely converted to acetyl-coenzyme A (CoA) in the first stage of metabolism in Escherichia coli and Salmonella enterica. These include acetate, acetoacetate, butyrate and longer fatty acids in wild type cells plus ethanol and some longer alcohols in certain mutant strains. Entering metabolism as acetyl-CoA has two important general consequences. First, generation of energy from acetyl-CoA requires operation of both the citric acid cycle and the respiratory chain to oxidize the NADH produced. Hence, acetyl-CoA serves as an energy source only during aerobic growth or during anaerobic respiration with such alternative electron acceptors as nitrate or trimethylamine oxide. In the absence of a suitable oxidant, acetyl-CoA is converted to a mixture of acetic acid and ethanol by the pathways of anaerobic fermentation. Catabolism of acetyl-CoA via the citric acid cycle releases both carbon atoms of the acetyl moiety as carbon dioxide and growth on these substrates as sole carbon source therefore requires the operation of the glyoxylate bypass to generate cell material. The pair of related two-carbon compounds, glycolate and glyoxylate are also discussed. However, despite having two carbons, these are metabolized via malate and glycerate, not via acetyl-CoA. In addition, mutants of E. coli capable of growth on ethylene glycol metabolize it via the glycolate pathway, rather than via acetyl- CoA. Propionate metabolism is also discussed because in many respects its pathway is analogous to that of acetate. The transcriptional regulation of these pathways is discussed in detail.
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Affiliation(s)
- David P Clark
- Department of Microbiology, Southern Illinois University, Carbondale, Illinois 62901
| | - John E Cronan
- Departments of Microbiology and Biochemistry, University of Illinois, B103 CLSL, 601 S. Goodwin Avenue, Urbana, Illinois 61801
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Abstract
Acetohydroxyacid synthase (AHAS) is the first common enzyme in the pathway for the biosynthesis of branched-chain amino acids. Interest in the enzyme has escalated over the past 20 years since it was discovered that AHAS is the target of the sulfonylurea and imidazolinone herbicides. However, several questions regarding the reaction mechanism have remained unanswered, particularly the way in which AHAS "chooses" its second substrate. A new method for the detection of reaction intermediates enables calculation of the microscopic rate constants required to explain this phenomenon.
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Affiliation(s)
- Jennifer A McCourt
- School of Molecular and Microbial Sciences, University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
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