1
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Hao Y, Pan X, You J, Li G, Xu M, Rao Z. Microbial production of branched chain amino acids: Advances and perspectives. BIORESOURCE TECHNOLOGY 2024; 397:130502. [PMID: 38417463 DOI: 10.1016/j.biortech.2024.130502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 02/23/2024] [Accepted: 02/25/2024] [Indexed: 03/01/2024]
Abstract
Branched-chain amino acids (BCAAs) such as L-valine, L-leucine, and L-isoleucine are widely used in food and feed. To comply with sustainable development goals, commercial production of BCAAs has been completely replaced with microbial fermentation. However, the efficient production of BCAAs by microorganisms remains a serious challenge due to their staggered metabolic networks and cell growth. To overcome these difficulties, systemic metabolic engineering has emerged as an effective and feasible strategy for the biosynthesis of BCAA. This review firstly summarizes the research advances in the microbial synthesis of BCAAs and representative engineering strategies. Second, systematic methods, such as high-throughput screening, adaptive laboratory evolution, and omics analysis, can be used to analyses the synthesis of BCAAs at the whole-cell level and further improve the titer of target chemicals. Finally, new tools and engineering strategies that may increase the production output and development direction of the microbial production of BCAAs are discussed.
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Affiliation(s)
- Yanan Hao
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xuewei Pan
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jiajia You
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Guomin Li
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Meijuan Xu
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhiming Rao
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
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2
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Sullivan JR, Courtine C, Taylor L, Solomon O, Behr MA. Loss of allosteric regulation in α-isopropylmalate synthase identified as an antimicrobial resistance mechanism. NPJ ANTIMICROBIALS AND RESISTANCE 2023; 1:7. [PMID: 38686213 PMCID: PMC11057210 DOI: 10.1038/s44259-023-00005-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/18/2023] [Indexed: 05/02/2024]
Abstract
Despite our best efforts to discover new antimicrobials, bacteria have evolved mechanisms to become resistant. Resistance to antimicrobials can be attributed to innate, inducible, and acquired mechanisms. Mycobacterium abscessus is one of the most antimicrobial resistant bacteria and is known to cause chronic pulmonary infections within the cystic fibrosis community. Previously, we identified epetraborole as an inhibitor against M. abscessus with in vitro and in vivo activities and that the efficacy of epetraborole could be improved with the combination of the non-proteinogenic amino acid norvaline. Norvaline demonstrated activity against the M. abscessus epetraborole resistant mutants thus, limiting resistance to epetraborole in wild-type populations. Here we show M. abscessus mutants with resistance to epetraborole can acquire resistance to norvaline in a leucyl-tRNA synthetase (LeuRS) editing-independent manner. After showing that the membrane hydrophobicity and efflux activity are not linked to norvaline resistance, whole-genome sequencing identified a mutation in the allosteric regulatory domain of α-isopropylmalate synthase (α-IPMS). We found that mutants with the α-IPMSA555V variant incorporated less norvaline in the proteome and produced more leucine than the parental strain. Furthermore, we found that leucine can rescue growth inhibition from norvaline challenge in the parental strain. Our results demonstrate that M. abscessus can modulate its metabolism through mutations in an allosteric regulatory site to upregulate the biosynthesis of the natural LeuRS substrate and outcompete norvaline. These findings emphasize the antimicrobial resistant nature of M. abscessus and describe a unique mechanism of substrate-inhibitor competition.
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Affiliation(s)
- Jaryd R. Sullivan
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1 Canada
- Department of Microbiology & Immunology, McGill University, Montreal, QC H3A 2B4 Canada
- McGill International TB Centre, Montreal, QC H4A 3S5 Canada
| | - Christophe Courtine
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1 Canada
- Department of Microbiology & Immunology, McGill University, Montreal, QC H3A 2B4 Canada
- Present Address: Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755 USA
| | - Lorne Taylor
- Clinical Proteomics Platform, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1 Canada
| | - Ori Solomon
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1 Canada
- Department of Microbiology & Immunology, McGill University, Montreal, QC H3A 2B4 Canada
- McGill International TB Centre, Montreal, QC H4A 3S5 Canada
| | - Marcel A. Behr
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1 Canada
- Department of Microbiology & Immunology, McGill University, Montreal, QC H3A 2B4 Canada
- McGill International TB Centre, Montreal, QC H4A 3S5 Canada
- Department of Medicine, McGill University Health Centre, Montreal, QC H3G 2M1 Canada
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3
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Tsukahara M, Isogai S, Azuma H, Tsukahara K, Toyokawa Y, Takagi H. Characterization of a new Saccharomyces cerevisiae isolated from banana stems and its mutant with l-leucine accumulation for awamori brewing. Biosci Biotechnol Biochem 2023; 87:240-244. [PMID: 36396349 DOI: 10.1093/bbb/zbac185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/10/2022] [Indexed: 11/19/2022]
Abstract
We isolated a new strain of the yeast Saccharomyces cerevisiae, 35a14, from banana stems in Okinawa. This strain did not belong to any industrial yeast groups in a phylogenetic tree and produced high levels of alcohol. Furthermore, awamori, an Okinawa's traditional distilled alcoholic beverage, brewed with an l-leucine overproducing mutant derived from 35a14 showed a high concentration of isoamyl acetate.
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Affiliation(s)
| | - Shota Isogai
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma, Nara, Japan
| | - Haruna Azuma
- BioJet Co., Ltd., 315 Shioya, Uruma, Okinawa, Japan
| | | | - Yoichi Toyokawa
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma, Nara, Japan
| | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma, Nara, Japan
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4
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Yan W, Zheng Y, Dou C, Zhang G, Arnaout T, Cheng W. The pathogenic mechanism of Mycobacterium tuberculosis: implication for new drug development. MOLECULAR BIOMEDICINE 2022; 3:48. [PMID: 36547804 PMCID: PMC9780415 DOI: 10.1186/s43556-022-00106-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), is a tenacious pathogen that has latently infected one third of the world's population. However, conventional TB treatment regimens are no longer sufficient to tackle the growing threat of drug resistance, stimulating the development of innovative anti-tuberculosis agents, with special emphasis on new protein targets. The Mtb genome encodes ~4000 predicted proteins, among which many enzymes participate in various cellular metabolisms. For example, more than 200 proteins are involved in fatty acid biosynthesis, which assists in the construction of the cell envelope, and is closely related to the pathogenesis and resistance of mycobacteria. Here we review several essential enzymes responsible for fatty acid and nucleotide biosynthesis, cellular metabolism of lipids or amino acids, energy utilization, and metal uptake. These include InhA, MmpL3, MmaA4, PcaA, CmaA1, CmaA2, isocitrate lyases (ICLs), pantothenate synthase (PS), Lysine-ε amino transferase (LAT), LeuD, IdeR, KatG, Rv1098c, and PyrG. In addition, we summarize the role of the transcriptional regulator PhoP which may regulate the expression of more than 110 genes, and the essential biosynthesis enzyme glutamine synthetase (GlnA1). All these enzymes are either validated drug targets or promising target candidates, with drugs targeting ICLs and LAT expected to solve the problem of persistent TB infection. To better understand how anti-tuberculosis drugs act on these proteins, their structures and the structure-based drug/inhibitor designs are discussed. Overall, this investigation should provide guidance and support for current and future pharmaceutical development efforts against mycobacterial pathogenesis.
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Affiliation(s)
- Weizhu Yan
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Yanhui Zheng
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Chao Dou
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Guixiang Zhang
- grid.13291.380000 0001 0807 1581Division of Gastrointestinal Surgery, Department of General Surgery and Gastric Cancer center, West China Hospital, Sichuan University, No. 37. Guo Xue Xiang, Chengdu, 610041 China
| | - Toufic Arnaout
- Kappa Crystals Ltd., Dublin, Ireland ,MSD Dunboyne BioNX, Co. Meath, Ireland
| | - Wei Cheng
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
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5
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Bai Y, Jiao W, Vörster J, Parker EJ. Conformational interdomain flexibility in a bacterial α-isopropylmalate synthase is necessary for leucine biosynthesis. J Biol Chem 2022; 299:102789. [PMID: 36509144 PMCID: PMC9860122 DOI: 10.1016/j.jbc.2022.102789] [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: 09/29/2022] [Revised: 12/01/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
α-Isopropylmalate synthase (IPMS) catalyzes the first step in leucine (Leu) biosynthesis and is allosterically regulated by the pathway end product, Leu. IPMS is a dimeric enzyme with each chain consisting of catalytic, accessory, and regulatory domains, with the accessory and regulatory domains of each chain sitting adjacent to the catalytic domain of the other chain. The IPMS crystal structure shows significant asymmetry because of different relative domain conformations in each chain. Owing to the challenges posed by the dynamic and asymmetric structures of IPMS enzymes, the molecular details of their catalytic and allosteric mechanisms are not fully understood. In this study, we have investigated the allosteric feedback mechanism of the IPMS enzyme from the bacterium that causes meningitis, Neisseria meningitidis (NmeIPMS). By combining molecular dynamics simulations with small-angle X-ray scattering, mutagenesis, and heterodimer generation, we demonstrate that Leu-bound NmeIPMS is in a rigid conformational state stabilized by asymmetric interdomain polar interactions. Furthermore, we found removing these polar interactions by mutagenesis impaired the allosteric response without compromising Leu binding. Our results suggest that the allosteric inhibition of NmeIPMS is achieved by restricting the flexibility of the accessory and regulatory domains, demonstrating that significant conformational flexibility is required for catalysis.
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Affiliation(s)
- Yu Bai
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Wanting Jiao
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Jan Vörster
- School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Emily J. Parker
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand,For correspondence: Emily J. Parker
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6
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Wang C, Wang Y, Chen J, Liu L, Yang M, Li Z, Wang C, Pichersky E, Xu H. Synthesis of 4-methylvaleric acid, a precursor of pogostone, involves a 2-isobutylmalate synthase related to 2-isopropylmalate synthase of leucine biosynthesis. THE NEW PHYTOLOGIST 2022; 235:1129-1145. [PMID: 35485988 DOI: 10.1111/nph.18186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/19/2022] [Indexed: 06/14/2023]
Abstract
We show here that the side chain of pogostone, one of the major components of patchouli oil obtained from Pogostemon cablin and possessing a variety of pharmacological activities, is derived from 4-methylvaleric acid. We also show that 4-methylvaleric acid is produced through the one-carbon α-ketoacid elongation pathway with the involvement of the key enzyme 2-isobutylmalate synthase (IBMS), a newly identified enzyme related to isopropylmalate synthase (IPMS) of leucine (Leu) biosynthesis. Site-directed mutagenesis identified Met132 in the N-terminal catalytic region as affecting the substrate specificity of PcIBMS1. Even though PcIBMS1 possesses the C-terminal domain that in IPMS serves to mediate Leu inhibition, it is insensitive to Leu. The observation of the evolution of IBMS from IPMS, as well as previously reported examples of IPMS-related genes involved in making glucosinolates in Brassicaceae, acylsugars in Solanaceae, and flavour compounds in apple, indicate that IPMS genes represent an important pool for the independent evolution of genes for specialised metabolism.
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Affiliation(s)
- Chu Wang
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Ying Wang
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Jing Chen
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Lang Liu
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Mingxia Yang
- The Center for Microbes, Development and Health, Institute Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Zhengguo Li
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Chengyuan Wang
- The Center for Microbes, Development and Health, Institute Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Eran Pichersky
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Haiyang Xu
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
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7
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Takagi H, Yamamoto K, Matsuo Y, Furuie M, Kasayuki Y, Ohtani R, Shiotani M, Hasegawa T, Ohnishi T, Ohashi M, Johzuka K, Kurata A, Uegaki K. Influence of mutation in the regulatory domain of α-isopropylmalate synthase from Saccharomyces cerevisiae on its activity and feedback inhibition. Biosci Biotechnol Biochem 2022; 86:755-762. [PMID: 35333283 DOI: 10.1093/bbb/zbac045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/16/2022] [Indexed: 11/14/2022]
Abstract
Isoamyl alcohol (i-AmOH) is produced from α-ketoisocaproate in the l-leucine biosynthetic pathway in yeast and controlled by the negative feedback regulation of α-isopropylmalate synthase (IPMS), which senses the accumulation of l-leucine. It is known that i-AmOH production increases when mutations in the regulatory domain reduce the susceptibility to feedback inhibition. However, the impact of mutations in this domain on the IPMS activity has not been examined. In this study, we obtained 5 IPMS mutants, encoding the LEU4 gene, N515D/S520P/S542F/A551D/A551V, that are tolerant to 5,5,5-trifluoro-dl-leucine. All mutant proteins were purified and examined for both IPMS activity and negative feedback activity by in vitro experiments. The results showed that not only the negative-feedback regulation by l-leucine was almost lost in all mutants, but also the IPMS activity was greatly decreased and the difference in IPMS activity among Leu4 mutants in the presence of l-leucine was significantly correlated with i-AmOH production.
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Affiliation(s)
- Hironobu Takagi
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, 3327-204 Nakamachi, Nara, Japan
| | - Kazuki Yamamoto
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, 3327-204 Nakamachi, Nara, Japan
| | - Yoshifumi Matsuo
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, 3327-204 Nakamachi, Nara, Japan
| | - Miki Furuie
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, 3327-204 Nakamachi, Nara, Japan
| | - Yasuha Kasayuki
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, 3327-204 Nakamachi, Nara, Japan
| | - Rina Ohtani
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, 3327-204 Nakamachi, Nara, Japan
| | - Mizuki Shiotani
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, 3327-204 Nakamachi, Nara, Japan
| | - Tetsuya Hasegawa
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, 3327-204 Nakamachi, Nara, Japan
| | - Toru Ohnishi
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, 3327-204 Nakamachi, Nara, Japan
| | - Masataka Ohashi
- Nara Prefecture Institute of Industrial Development, 129-1 Kashiwagi, Nara, Japan
| | - Katsuki Johzuka
- Astrobiology Center, National Institutes of Natural Sciences, 38 Nishigonaka, Myodaiji, Aichi, Japan
| | - Atsushi Kurata
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, 3327-204 Nakamachi, Nara, Japan
| | - Koichi Uegaki
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, 3327-204 Nakamachi, Nara, Japan.,Agricultural Technology and Innovation Research Institute, Kindai University, 3327-204 Nakamachi, Nara, Japan
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8
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Fukuda N, Takeuchi M. Complete dominant inheritance of intracellular leucine accumulation traits in polyploid yeasts. Yeast 2022; 39:272-282. [PMID: 35315123 DOI: 10.1002/yea.3700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 02/04/2022] [Accepted: 02/22/2022] [Indexed: 11/11/2022] Open
Abstract
The yeast Saccharomyces cerevisiae is widely used for ethanol production. In the production of alcoholic beverages, flavours are affected mainly by yeast metabolism in the fermentation process. To increase the contents of initial scented fruity flavours, such as isoamyl alcohol and isoamyl acetate, leucine accumulation in yeast cells is induced by a decrease of leucine feedback inhibition in the l-leucine synthetic pathway using conventional mutagenesis. Diploid strains are commonly used in sake brewing because of better fermentation performance, such as vitality and endurance, compared with those of haploid strains. Heterozygous mutations are mostly detected in target genes of brewing yeasts generated through mutation breeding. Here we describe that an allele of the LEU4 gene, LEU4G516S , dominantly induced leucine accumulation even in triploid and tetraploid yeasts as with in diploid yeasts. Importantly, we demonstrated that there is no difference in the intracellular amount of branched-chain amino acids between LEU4G516S /LEU4 heterozygous diploids and LEU4G516S /LEU4G516S homozygous diploids. The approach to increase isoamyl alcohol and isoamyl acetate by intracellular leucine accumulation can potentially be applied to a variety of yeast strains, including aneuploid and polyploid yeasts.
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Affiliation(s)
- Nobuo Fukuda
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Osaka, Japan
| | - Mio Takeuchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Osaka, Japan
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9
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Vigueras-Meneses LG, Escalera-Fanjul X, El-Hafidi M, Montalvo-Arredondo J, Gomez-Hernandez N, Colón M, Granados E, Campero-Basaldua C, Riego-Ruiz L, Scazzocchio C, González A, Quezada H. Two alpha isopropylmalate synthase isozymes with similar kinetic properties are extant in the yeast Lachancea kluyveri. FEMS Yeast Res 2022; 22:6546212. [PMID: 35266531 DOI: 10.1093/femsyr/foac016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/22/2022] [Accepted: 03/08/2022] [Indexed: 11/13/2022] Open
Abstract
The first committed step in the leucine biosynthetic pathway is catalyzed by α-isopropylmalate synthase (α-IPMS, EC 2.3.3.13), which in the Saccaromycotina subphylum of Ascomycete yeasts is frequently encoded by duplicated genes. Following a gene duplication event, the two copies may be preserved presumably because the encoded proteins diverge in either functional properties and/or cellular localization. The genome of the petite-negative budding yeast Lachancea kluyveri includes two SAKL0E10472 (LkLEU4) and SAKL0F05170g (LKLEU4BIS) paralogous genes, which are homologous to other yeast α-IPMS sequences. Here, we investigate whether these paralogous genes encode functional α-IPMS isozymes and whether their functions have diverged. Molecular phylogeny suggested that the LkLeu4 isozyme is located in the mitochondria and LkLeu4BIS in the cytosol. Comparison of growth rates, leucine intracellular pools and mRNA levels, indicate that the LkLeu4 isozyme is the predominant α-IPMS enzyme during growth on glucose as carbon source. Determination of the kinetic parameters indicates that the isozymes have similar affinities for the substrates and for the feedback inhibitor leucine. Thus, the diversification of the physiological roles of the genes LkLEU4 and LKLEU4BIS involves preferential transcription of the LkLEU4 gene during growth on glucose and different subcellular localization, although ligand interactions have not diverged.
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Affiliation(s)
- Liliana Guadalupe Vigueras-Meneses
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ximena Escalera-Fanjul
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Mohammed El-Hafidi
- Departamento de Biomedicina Cardiovascular, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | - Javier Montalvo-Arredondo
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), San Luis Potosí, Mexico
| | - Nicolás Gomez-Hernandez
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), San Luis Potosí, Mexico
| | - Maritrini Colón
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Estefany Granados
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Carlos Campero-Basaldua
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Lina Riego-Ruiz
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), San Luis Potosí, Mexico
| | - Claudio Scazzocchio
- Department of Microbiology, Imperial College London, London, United Kingdom.,Institut de Biologie Intégrative de la Cellule (I2BC), Gif-sur-Yvette, France
| | - Alicia González
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Héctor Quezada
- Laboratorio de Investigación en Inmunología y Proteómica, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
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10
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Regulation of the Leucine Metabolism in Mortierella alpina. J Fungi (Basel) 2022; 8:jof8020196. [PMID: 35205950 PMCID: PMC8880518 DOI: 10.3390/jof8020196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 12/20/2022] Open
Abstract
The oleaginous fungus Mortierella alpina is a safe source of polyunsaturated fatty acids (PUFA) in industrial food and feed production. Besides PUFA production, pharmaceutically relevant surface-active and antimicrobial oligopeptides were isolated from this basal fungus. Both production of fatty acids and oligopeptides rely on the biosynthesis and high turnover of branched-chain-amino acids (BCAA), especially l-leucine. However, the regulation of BCAA biosynthesis in basal fungi is largely unknown. Here, we report on the regulation of the leucine, isoleucine, and valine metabolism in M. alpina. In contrast to higher fungi, the biosynthetic genes for BCAA are hardly transcriptionally regulated, as shown by qRT-PCR analysis, which suggests a constant production of BCAAs. However, the enzymes of the leucine metabolism are tightly metabolically regulated. Three enzymes of the leucine metabolism were heterologously produced in Escherichia coli, one of which is inhibited by allosteric feedback loops: The key regulator is the α-isopropylmalate synthase LeuA1, which is strongly disabled by l-leucine, α-ketoisocaproate, and propionyl-CoA, the precursor of the odd-chain fatty acid catabolism. Its gene is not related to homologs from higher fungi, but it has been inherited from a phototrophic ancestor by horizontal gene transfer.
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11
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Wang Y, Xu J, Jin Z, Xia X, Zhang W. Improvement of acetyl-CoA supply and glucose utilization increases l-leucine production in Corynebacterium glutamicum. Biotechnol J 2021; 17:e2100349. [PMID: 34870372 DOI: 10.1002/biot.202100349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 11/11/2022]
Abstract
BACKGROUND l-Leucine is one of important essential amino acids with multiple industrial applications, whose market requirements cannot be met because of the lower productivity. MAIN METHODS AND MAJOR RESULTS In this study, a strain of Corynebacterium glutamicum with high l-leucine yield was constructed to enhance its acetyl-CoA supply and glucose utilization. One copy of leuA under the control of a strong promoter was incorporated into the C. glutamicum genome. Then, acetyl-CoA supply was increased by the integration of a terminator in front of gltA and by the heterogeneous overexpression of acetyl-CoA synthetase (Acs) and deacetylase (CobB) derived from Escherichia coli. Next, the transcriptional regulator SugR was deleted to enhance glucose uptake via a phosphotransferase-mediated route. In fed-batch fermentation performed in a 5-L reactor, l-leucine production of 40.11±0.73 g/L was achieved under the optimized conditions, with the l-leucine yield and productivity of 0.25 g/g glucose and 0.59 g/L/h, respectively. CONCLUSIONS AND IMPLICATIONS These results represent a significant improvement in the l-leucine titer of C. glutamicum, indicating that the process possesses highly potential for industrial application. These strategies can be also expanded to enable the production of other value-added biochemicals derived from the intermediates of central carbon metabolism. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yingyu Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, WuXi, 214122, China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, WuXi, 214122, China
| | - Jianzhong Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, WuXi, 214122, China
| | - Zhengyu Jin
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, WuXi, 214122, China
| | - Xiaole Xia
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, WuXi, 214122, China
| | - Weiguo Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, WuXi, 214122, China
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12
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Kitainda V, Jez JM. Structural Studies of Aliphatic Glucosinolate Chain-Elongation Enzymes. Antioxidants (Basel) 2021; 10:antiox10091500. [PMID: 34573132 PMCID: PMC8468904 DOI: 10.3390/antiox10091500] [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: 07/06/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 11/25/2022] Open
Abstract
Plants evolved specialized metabolic pathways through gene duplication and functional divergence of enzymes involved in primary metabolism. The results of this process are varied pathways that produce an array of natural products useful to both plants and humans. In plants, glucosinolates are a diverse class of natural products. Glucosinolate function stems from their hydrolysis products, which are responsible for the strong flavors of Brassicales plants, such as mustard, and serve as plant defense molecules by repelling insects, fighting fungal infections, and discouraging herbivory. Additionally, certain hydrolysis products such as isothiocyanates can potentially serve as cancer prevention agents in humans. The breadth of glucosinolate function is a result of its great structural diversity, which comes from the use of aliphatic, aromatic and indole amino acids as precursors and elongation of some side chains by up to nine carbons, which, after the formation of the core glucosinolate structure, can undergo further chemical modifications. Aliphatic methionine-derived glucosinolates are the most abundant form of these compounds. Although both elongation and chemical modification of amino acid side chains are important for aliphatic glucosinolate diversity, its elongation process has not been well described at the molecular level. Here, we summarize new insights on the iterative chain-elongation enzymes methylthioalkylmalate synthase (MAMS) and isopropylmalate dehydrogenase (IPMDH).
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13
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Qureshi NA, Bakhtiar SM, Faheem M, Shah M, Bari A, Mahmood HM, Sohaib M, Mothana RA, Ullah R, Jamal SB. Genome-Based Drug Target Identification in Human Pathogen Streptococcus gallolyticus. Front Genet 2021; 12:564056. [PMID: 33841489 PMCID: PMC8027347 DOI: 10.3389/fgene.2021.564056] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 02/16/2021] [Indexed: 12/21/2022] Open
Abstract
Streptococcus gallolysticus (Sg) is an opportunistic Gram-positive, non-motile bacterium, which causes infective endocarditis, an inflammation of the inner lining of the heart. As Sg has acquired resistance with the available antibiotics, therefore, there is a dire need to find new therapeutic targets and potent drugs to prevent and treat this disease. In the current study, an in silico approach is utilized to link genomic data of Sg species with its proteome to identify putative therapeutic targets. A total of 1,138 core proteins have been identified using pan genomic approach. Further, using subtractive proteomic analysis, a set of 18 proteins, essential for bacteria and non-homologous to host (human), is identified. Out of these 18 proteins, 12 cytoplasmic proteins were selected as potential drug targets. These selected proteins were subjected to molecular docking against drug-like compounds retrieved from ZINC database. Furthermore, the top docked compounds with lower binding energy were identified. In this work, we have identified novel drug and vaccine targets against Sg, of which some have already been reported and validated in other species. Owing to the experimental validation, we believe our methodology and result are significant contribution for drug/vaccine target identification against Sg-caused infective endocarditis.
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Affiliation(s)
- Nosheen Afzal Qureshi
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
| | - Syeda Marriam Bakhtiar
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
| | - Muhammad Faheem
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Mohibullah Shah
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Ahmed Bari
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Hafiz M Mahmood
- Department of Pharmacology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Muhammad Sohaib
- Department of Soil Science, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Ramzi A Mothana
- Department of Pharmacognosy (MAPPRC), College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Riaz Ullah
- Department of Pharmacognosy (MAPPRC), College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Syed Babar Jamal
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
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14
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Biochemical characterization of 2-phosphinomethylmalate synthase from Streptomyces hygroscopicus: A member of the DRE-TIM metallolyase superfamily. Arch Biochem Biophys 2020; 691:108489. [PMID: 32697946 DOI: 10.1016/j.abb.2020.108489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 11/23/2022]
Abstract
2-Phosphinomethylmalate synthase (PMMS) from Streptomyces hygroscopicus catalyzes the first step in the biosynthesis of the herbicide bialophos using 3-phosphinopyruvic acid and acetyl coenzyme A as substrates to form 2-phosphinomethylmalic acid and coenzyme A. PMMS belongs to the Claisen condensation-like (CC-like) subgroup of the DRE-TIM metallolyase superfamily, which uses conserved active site architecture to catalyze a functionally-diverse set of reactions. Analysis of a sequence similarity network for the CC-like subgroup identified PMMS and the related R-citrate synthase in an early-diverging cluster suggesting that this group of sequences are more distinct in relation to other Claisen-condensation subgroup members. To better understand the structure/function landscape of the CC-like subgroup PMMS was recombinantly expressed in Escherichia coli, purified, and characterized with respect to its enzymatic properties. Using oxaloacetate as a substrate analog, the recombinantly-produced enzyme exhibited improved Michaelis constants relative to the previously reported natively-produced enzyme. Results from pH rate profiles and kinetic isotope effects were consistent with results from other members of the CC-like subgroup supporting acid-base chemistry and hydrolysis of the direct Claisen-condensation product as the rate-determining step. Results of site-directed mutagenesis experiments indicate that PMMS uses an active-site architecture similar to homocitrate synthase to select for a dicarboxylic acid substrate.
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15
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Suzuki T, Tomita T, Hirayama K, Suzuki M, Kuzuyama T, Nishiyama M. Involvement of subdomain II in the recognition of acetyl-CoA revealed by the crystal structure of homocitrate synthase from Sulfolobus acidocaldarius. FEBS J 2020; 288:1975-1988. [PMID: 32897601 DOI: 10.1111/febs.15527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 08/05/2020] [Accepted: 08/08/2020] [Indexed: 11/26/2022]
Abstract
Homocitrate synthase (HCS) catalyzes the aldol condensation of α-ketoglutarate and acetyl coenzyme A to form homocitrate, which is the first committed step of lysine biosynthesis through the α-aminoadipate pathway in yeast, fungi, and some prokaryotes. We determined the crystal structure of a truncated form of HCS from a hyperthermophilic acidophilic archaeon, Sulfolobus acidocaldarius, which lacks the RAM (Regulation of amino acid metabolism) domain at the C terminus serving as the regulatory domain for the feedback inhibition by lysine, in complex with α-ketoglutarate, Mg2+ , and CoA. This structure coupled with mutational analysis revealed that a subdomain, subdomain II, connecting the N-terminal catalytic domain and C-terminal RAM domain is involved in the recognition of acetyl-CoA. This is the first structural evidence of the function of subdomain II in the related enzyme family, which will lead to a better understanding of the catalytic mechanism of HCS. DATABASES: Structural data are available in the RCSB PDB database under the accession number 6KTQ.
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Affiliation(s)
- Tomohiro Suzuki
- Biotechnology Research Center, The University of Tokyo, Japan
| | - Takeo Tomita
- Biotechnology Research Center, The University of Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Japan
| | - Kenta Hirayama
- Biotechnology Research Center, The University of Tokyo, Japan
| | - Michio Suzuki
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
| | - Tomohisa Kuzuyama
- Biotechnology Research Center, The University of Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Japan
| | - Makoto Nishiyama
- Biotechnology Research Center, The University of Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Japan
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16
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Klünemann T, Henke S, Blankenfeldt W. The crystal structure of the heme d 1 biosynthesis-associated small c-type cytochrome NirC reveals mixed oligomeric states in crystallo. Acta Crystallogr D Struct Biol 2020; 76:375-384. [PMID: 32254062 PMCID: PMC7137109 DOI: 10.1107/s2059798320003101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/05/2020] [Indexed: 11/10/2022] Open
Abstract
Monoheme c-type cytochromes are important electron transporters in all domains of life. They possess a common fold hallmarked by three α-helices that surround a covalently attached heme. An intriguing feature of many monoheme c-type cytochromes is their capacity to form oligomers by exchanging at least one of their α-helices, which is often referred to as 3D domain swapping. Here, the crystal structure of NirC, a c-type cytochrome co-encoded with other proteins involved in nitrite reduction by the opportunistic pathogen Pseudomonas aeruginosa, has been determined. The crystals diffracted anisotropically to a maximum resolution of 2.12 Å (spherical resolution of 2.83 Å) and initial phases were obtained by Fe-SAD phasing, revealing the presence of 11 NirC chains in the asymmetric unit. Surprisingly, these protomers arrange into one monomer and two different types of 3D domain-swapped dimers, one of which shows pronounced asymmetry. While the simultaneous observation of monomers and dimers probably reflects the interplay between the high protein concentration required for crystallization and the structural plasticity of monoheme c-type cytochromes, the identification of conserved structural motifs in the monomer together with a comparison with similar proteins may offer new leads to unravel the unknown function of NirC.
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Affiliation(s)
- Thomas Klünemann
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Steffi Henke
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Wulf Blankenfeldt
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstrasse 7, 38106 Braunschweig, Germany
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17
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Abrahams RS, Pires JC, Schranz ME. Genomic Origin and Diversification of the Glucosinolate MAM Locus. FRONTIERS IN PLANT SCIENCE 2020; 11:711. [PMID: 32582245 PMCID: PMC7289053 DOI: 10.3389/fpls.2020.00711] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 05/05/2020] [Indexed: 05/06/2023]
Abstract
Glucosinolates are a diverse group of plant metabolites that characterize the order Brassicales. The MAM locus is one of the most significant QTLs for glucosinolate diversity. However, most of what we understand about evolution at the locus is focused on only a few species and not within a phylogenetic context. In this study, we utilize a micro-synteny network and phylogenetic inference to investigate the origin and diversification of the MAM/IPMS gene family. We uncover unique MAM-like genes found at the orthologous locus in the Cleomaceae that shed light on the transition from IPMS to MAM. In the Brassicaceae, we identify six distinct MAM clades across Lineages I, II, and III. We characterize the evolutionary impact and consequences of local duplications, transpositions, whole genome duplications, and gene fusion events, generating several new hypothesizes on the function and diversity of the MAM locus.
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Affiliation(s)
- R. Shawn Abrahams
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
- Biosystematics Group, Wageningen University, Wageningen, Netherlands
| | - J. Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - M. Eric Schranz
- Biosystematics Group, Wageningen University, Wageningen, Netherlands
- *Correspondence: M. Eric Schranz,
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18
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Maeda HA. Harnessing evolutionary diversification of primary metabolism for plant synthetic biology. J Biol Chem 2019; 294:16549-16566. [PMID: 31558606 DOI: 10.1074/jbc.rev119.006132] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Plants produce numerous natural products that are essential to both plant and human physiology. Recent identification of genes and enzymes involved in their biosynthesis now provides exciting opportunities to reconstruct plant natural product pathways in heterologous systems through synthetic biology. The use of plant chassis, although still in infancy, can take advantage of plant cells' inherent capacity to synthesize and store various phytochemicals. Also, large-scale plant biomass production systems, driven by photosynthetic energy production and carbon fixation, could be harnessed for industrial-scale production of natural products. However, little is known about which plants could serve as ideal hosts and how to optimize plant primary metabolism to efficiently provide precursors for the synthesis of desirable downstream natural products or specialized (secondary) metabolites. Although primary metabolism is generally assumed to be conserved, unlike the highly-diversified specialized metabolism, primary metabolic pathways and enzymes can differ between microbes and plants and also among different plants, especially at the interface between primary and specialized metabolisms. This review highlights examples of the diversity in plant primary metabolism and discusses how we can utilize these variations in plant synthetic biology. I propose that understanding the evolutionary, biochemical, genetic, and molecular bases of primary metabolic diversity could provide rational strategies for identifying suitable plant hosts and for further optimizing primary metabolism for sizable production of natural and bio-based products in plants.
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Affiliation(s)
- Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin 53706
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19
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Sharma A, Sharma D, Verma SK. Zinc binding proteome of a phytopathogen Xanthomonas translucens pv. undulosa. ROYAL SOCIETY OPEN SCIENCE 2019; 6:190369. [PMID: 31598288 PMCID: PMC6774946 DOI: 10.1098/rsos.190369] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 08/21/2019] [Indexed: 05/15/2023]
Abstract
Xanthomonas translucens pv. undulosa (Xtu) is a proteobacteria which causes bacterial leaf streak (BLS) or bacterial chaff disease in wheat and barley. The constant competition for zinc (Zn) metal nutrients contributes significantly in plant-pathogen interactions. In this study, we have employed a systematic in silico approach to study the Zn-binding proteins of Xtu. From the whole proteome of Xtu, we have identified approximately 7.9% of proteins having Zn-binding sequence and structural motifs. Further, 115 proteins were found homologous to plant-pathogen interaction database. Among these 115 proteins, 11 were predicted as putative secretory proteins. The functional diversity in Zn-binding proteins was revealed by functional domain, gene ontology and subcellular localization analysis. The roles of Zn-binding proteins were found to be varied in the range from metabolism, proteolysis, protein biosynthesis, transport, cell signalling, protein folding, transcription regulation, DNA repair, response to oxidative stress, RNA processing, antimicrobial resistance, DNA replication and DNA integration. This study provides preliminary information on putative Zn-binding proteins of Xtu which may further help in designing new metal-based antimicrobial agents for controlling BLS and bacterial chaff infections on staple crops.
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20
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Suzuki T, Akiyama N, Yoshida A, Tomita T, Lassak K, Haurat MF, Okada T, Takahashi K, Albers S, Kuzuyama T, Nishiyama M. Biochemical characterization of archaeal homocitrate synthase from
Sulfolobus acidocaldarius. FEBS Lett 2019; 594:126-134. [DOI: 10.1002/1873-3468.13550] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/11/2019] [Accepted: 07/16/2019] [Indexed: 12/30/2022]
Affiliation(s)
| | - Nagisa Akiyama
- Biotechnology Research Center The University of Tokyo Japan
| | - Ayako Yoshida
- Biotechnology Research Center The University of Tokyo Japan
| | - Takeo Tomita
- Biotechnology Research Center The University of Tokyo Japan
- Collaborative Research Institute for Innovative Microbiology The University of Tokyo Japan
| | - Kerstin Lassak
- Molecular Biology of Archaea Institute of Biology University of Freiburg Germany
| | | | - Takuya Okada
- Biotechnology Research Center The University of Tokyo Japan
| | | | - Sonja‐Verena Albers
- Molecular Biology of Archaea Institute of Biology University of Freiburg Germany
| | - Tomohisa Kuzuyama
- Biotechnology Research Center The University of Tokyo Japan
- Collaborative Research Institute for Innovative Microbiology The University of Tokyo Japan
| | - Makoto Nishiyama
- Biotechnology Research Center The University of Tokyo Japan
- Collaborative Research Institute for Innovative Microbiology The University of Tokyo Japan
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21
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Changing substrate specificity and iteration of amino acid chain elongation in glucosinolate biosynthesis through targeted mutagenesis of Arabidopsis methylthioalkylmalate synthase 1. Biosci Rep 2019; 39:BSR20190446. [PMID: 31175145 PMCID: PMC6603273 DOI: 10.1042/bsr20190446] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 05/01/2019] [Accepted: 05/15/2019] [Indexed: 12/19/2022] Open
Abstract
Methylthioalkylmalate synthases catalyse the committing step of amino acid chain elongation in glucosinolate biosynthesis. As such, this group of enzymes plays an important role in determining the glucosinolate composition of Brassicaceae species, including Arabidopsis thaliana. Based on protein structure modelling of MAM1 from A. thaliana and analysis of 57 MAM sequences from Brassicaceae species, we identified four polymorphic residues likely to interact with the 2-oxo acid substrate. Through site-directed mutagenesis, the natural variation in these residues and the effect on product composition were investigated. Fifteen MAM1 variants as well as the native MAM1 and MAM3 from A. thaliana were characterised by heterologous expression of the glucosinolate chain elongation pathway in Escherichia coli. Detected products derived from leucine, methionine or phenylalanine were elongated with up to six methylene groups. Product profile and accumulation were changed in 14 of the variants, demonstrating the relevance of the identified residues. The majority of the single amino acid substitutions decreased the length of methionine-derived products, while approximately half of the substitutions increased the phenylalanine-derived products. Combining two substitutions enabled the MAM1 variant to increase the number of elongation rounds of methionine from three to four. Notably, characterisation of the native MAMs indicated that MAM1 and not MAM3 is responsible for homophenylalanine production. This hypothesis was confirmed by glucosinolate analysis in mam1 and mam3 mutants of A. thaliana.
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22
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Kumar R, Lee SG, Augustine R, Reichelt M, Vassão DG, Palavalli MH, Allen A, Gershenzon J, Jez JM, Bisht NC. Molecular Basis of the Evolution of Methylthioalkylmalate Synthase and the Diversity of Methionine-Derived Glucosinolates. THE PLANT CELL 2019; 31:1633-1647. [PMID: 31023839 PMCID: PMC6635866 DOI: 10.1105/tpc.19.00046] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 03/29/2019] [Accepted: 04/19/2019] [Indexed: 05/23/2023]
Abstract
The globally cultivated Brassica species possess diverse aliphatic glucosinolates, which are important for plant defense and animal nutrition. The committed step in the side chain elongation of methionine-derived aliphatic glucosinolates is catalyzed by methylthioalkylmalate synthase, which likely evolved from the isopropylmalate synthases of leucine biosynthesis. However, the molecular basis for the evolution of methylthioalkylmalate synthase and its generation of natural product diversity in Brassica is poorly understood. Here, we show that Brassica genomes encode multiple methylthioalkylmalate synthases that have differences in expression profiles and 2-oxo substrate preferences, which account for the diversity of aliphatic glucosinolates across Brassica accessions. Analysis of the 2.1 Å resolution x-ray crystal structure of Brassica juncea methylthioalkylmalate synthase identified key active site residues responsible for controlling the specificity for different 2-oxo substrates and the determinants of side chain length in aliphatic glucosinolates. Overall, these results provide the evolutionary and biochemical foundation for the diversification of glucosinolate profiles across globally cultivated Brassica species, which could be used with ongoing breeding strategies toward the manipulation of beneficial glucosinolate compounds for animal health and plant protection.
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Affiliation(s)
- Roshan Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Soon Goo Lee
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Rehna Augustine
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Micheal Reichelt
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena D-07745, Germany
| | - Daniel G Vassão
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena D-07745, Germany
| | - Manoj H Palavalli
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Aron Allen
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Jonathan Gershenzon
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena D-07745, Germany
| | - Joseph M Jez
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Naveen C Bisht
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
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23
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Abe T, Toyokawa Y, Sugimoto Y, Azuma H, Tsukahara K, Nasuno R, Watanabe D, Tsukahara M, Takagi H. Characterization of a New Saccharomyces cerevisiae Isolated From Hibiscus Flower and Its Mutant With L-Leucine Accumulation for Awamori Brewing. Front Genet 2019; 10:490. [PMID: 31231421 PMCID: PMC6558412 DOI: 10.3389/fgene.2019.00490] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 05/06/2019] [Indexed: 11/13/2022] Open
Abstract
Since flavors of alcoholic beverages produced in fermentation process are affected mainly by yeast metabolism, the isolation and breeding of yeasts have contributed to the alcoholic beverage industry. To produce awamori, a traditional spirit (distilled alcoholic beverage) with unique flavors made from steamed rice in Okinawa, Japan, it is necessary to optimize yeast strains for a diversity of tastes and flavors with established qualities. Two categories of flavors are characteristic of awamori; initial scented fruity flavors and sweet flavors that arise with aging. Here we isolated a novel strain of Saccharomyces cerevisiae from hibiscus flowers in Okinawa, HC02-5-2, that produces high levels of alcohol. The whole-genome information revealed that strain HC02-5-2 is contiguous to wine yeast strains in a phylogenic tree. This strain also exhibited a high productivity of 4-vinyl guaiacol (4-VG), which is a precursor of vanillin known as a key flavor of aged awamori. Although conventional awamori yeast strain 101-18, which possesses the FDC1 pseudogene does not produce 4-VG, strain HC02-5-2, which has the intact PAD1 and FDC1 genes, has an advantage for use in a novel kind of awamori. To increase the contents of initial scented fruity flavors, such as isoamyl alcohol and isoamyl acetate, we attempted to breed strain HC02-5-2 targeting the L-leucine synthetic pathway by conventional mutagenesis. In mutant strain T25 with L-leucine accumulation, we found a hetero allelic mutation in the LEU4 gene encoding the Gly516Ser variant α-isopropylmalate synthase (IPMS). IPMS activity of the Gly516Ser variant was less sensitive to feedback inhibition by L-leucine, leading to intracellular L-leucine accumulation. In a laboratory-scale test, awamori brewed with strain T25 showed higher concentrations of isoamyl alcohol and isoamyl acetate than that brewed with strain HC02-5-2. Such a combinatorial approach to yeast isolation, with whole-genome analysis and metabolism-focused breeding, has the potentials to vary the quality of alcoholic beverages.
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Affiliation(s)
| | - Yoichi Toyokawa
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Yukiko Sugimoto
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | | | | | - Ryo Nasuno
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Daisuke Watanabe
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | | | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
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24
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Wang YY, Xu JZ, Zhang WG. Metabolic engineering of l-leucine production in Escherichia coli and Corynebacterium glutamicum: a review. Crit Rev Biotechnol 2019; 39:633-647. [PMID: 31055970 DOI: 10.1080/07388551.2019.1577214] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
l-Leucine, as an essential branched-chain amino acid for humans and animals, has recently been attracting much attention because of its potential for a fast-growing market demand. The applicability ranges from flavor enhancers, animal feed additives and ingredients in cosmetic to specialty nutrients in pharmaceutical and medical fields. Microbial fermentation is the major method for producing l-leucine by using Escherichia coli and Corynebacterium glutamicum as host bacteria. This review gives an overview of the metabolic pathway of l-leucine (i.e. production, import and export systems) and highlights the main regulatory mechanisms of operons in E. coli and C. glutamicum l-leucine biosynthesis. We summarize here the current trends in metabolic engineering techniques and strategies for manipulating l-leucine producing strains. Finally, future perspectives to construct industrially advantageous strains are considered with respect to recent advances in biology.
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Affiliation(s)
- Ying-Yu Wang
- a The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , WuXi , People's Republic of China
| | - Jian-Zhong Xu
- a The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , WuXi , People's Republic of China.,b The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , WuXi , People's Republic of China
| | - Wei-Guo Zhang
- a The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , WuXi , People's Republic of China
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25
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Holt S, Miks MH, de Carvalho BT, Foulquié-Moreno MR, Thevelein JM. The molecular biology of fruity and floral aromas in beer and other alcoholic beverages. FEMS Microbiol Rev 2019; 43:193-222. [PMID: 30445501 PMCID: PMC6524682 DOI: 10.1093/femsre/fuy041] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 11/13/2018] [Indexed: 12/03/2022] Open
Abstract
Aroma compounds provide attractiveness and variety to alcoholic beverages. We discuss the molecular biology of a major subset of beer aroma volatiles, fruity and floral compounds, originating from raw materials (malt and hops), or formed by yeast during fermentation. We introduce aroma perception, describe the most aroma-active, fruity and floral compounds in fruits and their presence and origin in beer. They are classified into categories based on their functional groups and biosynthesis pathways: (1) higher alcohols and esters, (2) polyfunctional thiols, (3) lactones and furanones, and (4) terpenoids. Yeast and hops are the main sources of fruity and flowery aroma compounds in beer. For yeast, the focus is on higher alcohols and esters, and particularly the complex regulation of the alcohol acetyl transferase ATF1 gene. We discuss the release of polyfunctional thiols and monoterpenoids from cysteine- and glutathione-S-conjugated compounds and glucosides, respectively, the primary biological functions of the yeast enzymes involved, their mode of action and mechanisms of regulation that control aroma compound production. Furthermore, we discuss biochemistry and genetics of terpenoid production and formation of non-volatile precursors in Humulus lupulus (hops). Insight in these pathways provides a toolbox for creating innovative products with a diversity of pleasant aromas.
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Affiliation(s)
- Sylvester Holt
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Marta H Miks
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark
- Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Plac Cieszyński 1, 10–726 Olsztyn, Poland
| | - Bruna Trindade de Carvalho
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Maria R Foulquié-Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
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Yoshida A, Yoshida M, Kuzuyama T, Nishiyama M, Kosono S. Protein acetylation on 2-isopropylmalate synthase from Thermus thermophilus HB27. Extremophiles 2019; 23:377-388. [PMID: 30919057 DOI: 10.1007/s00792-019-01090-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/14/2019] [Indexed: 12/23/2022]
Abstract
Protein lysine Nε-acetylation is one of the important factors regulating cellular metabolism. We performed a proteomic analysis to identify acetylated proteins in the extremely thermophilic bacterium, Thermus thermophilus HB27. A total of 335 unique acetylated lysine residues, including many metabolic enzymes and ribosomal proteins, were identified in 208 proteins. Enzymes involved in amino acid metabolism were the most abundant among acetylated metabolic proteins. 2-Isopropylmalate synthase (IPMS), which catalyzes the first step in leucine biosynthesis, was acetylated at four lysine residues. Acetylation-mimicking mutations at Lys332 markedly decreased IPMS activity in vitro, suggesting that Lys332, which is located in subdomain II, plays a regulatory role in IPMS activity. We also investigated the acetylation-deacetylation mechanism of IPMS and revealed that it was acetylated non-enzymatically by acetyl-CoA and deacetylated enzymatically by TT_C0104. The present results suggest that leucine biosynthesis is regulated by post-translational protein modifications, in addition to feedback inhibition/repression, and that metabolic enzymes are regulated by protein acetylation in T. thermophilus.
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Affiliation(s)
- Ayako Yoshida
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Minoru Yoshida
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan.,Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Tomohisa Kuzuyama
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Makoto Nishiyama
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Saori Kosono
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan. .,RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan. .,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
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Distinct mechanisms of substrate selectivity in the DRE-TIM metallolyase superfamily: A role for the LeuA dimer regulatory domain. Arch Biochem Biophys 2019; 664:1-8. [DOI: 10.1016/j.abb.2019.01.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/14/2019] [Accepted: 01/16/2019] [Indexed: 11/20/2022]
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Maeda HA. Evolutionary Diversification of Primary Metabolism and Its Contribution to Plant Chemical Diversity. FRONTIERS IN PLANT SCIENCE 2019; 10:881. [PMID: 31354760 PMCID: PMC6635470 DOI: 10.3389/fpls.2019.00881] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 06/20/2019] [Indexed: 05/05/2023]
Abstract
Plants produce a diverse array of lineage-specific specialized (secondary) metabolites, which are synthesized from primary metabolites. Plant specialized metabolites play crucial roles in plant adaptation as well as in human nutrition and medicine. Unlike well-documented diversification of plant specialized metabolic enzymes, primary metabolism that provides essential compounds for cellular homeostasis is under strong selection pressure and generally assumed to be conserved across the plant kingdom. Yet, some alterations in primary metabolic pathways have been reported in plants. The biosynthetic pathways of certain amino acids and lipids have been altered in specific plant lineages. Also, two alternative pathways exist in plants for synthesizing primary precursors of the two major classes of plant specialized metabolites, terpenoids and phenylpropanoids. Such primary metabolic diversities likely underlie major evolutionary changes in plant metabolism and chemical diversity by acting as enabling or associated traits for the evolution of specialized metabolic pathways.
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29
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Yoshida A, Kosono S, Nishiyama M. Characterization of two 2-isopropylmalate synthase homologs from Thermus thermophilus HB27. Biochem Biophys Res Commun 2018; 501:465-470. [DOI: 10.1016/j.bbrc.2018.05.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 05/02/2018] [Indexed: 10/16/2022]
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Ma B, Shen J, Yindeeyoungyeon W, Ruan Y. A Novel Antibiotic Mechanism of l-Cyclopropylalanine Blocking the Biosynthetic Pathway of Essential Amino Acid l-Leucine. Molecules 2017; 22:molecules22122224. [PMID: 29240717 PMCID: PMC6149818 DOI: 10.3390/molecules22122224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 12/11/2017] [Accepted: 12/12/2017] [Indexed: 12/20/2022] Open
Abstract
The unusual amino acid l-cyclopropylalanine was isolated from the mushroom Amanita virgineoides after detection in an anti-fungal screening test. l-Cyclopropylalanine was found to exhibit broad-spectrum inhibition against fungi and bacteria. The anti-fungal activity was found to be abolished in the presence of the amino acid l-leucine, but not any other amino acids, indicating that l-cyclopropylalanine may block the biosynthesis of the essential amino acid l-leucine, thereby inhibiting fungal and bacteria growth. Further biochemical studies found l-cyclopropylalanine indeed inhibits α-isopropylmalate synthase (α-IMPS), the enzyme that catalyzes the rate-limiting step in the biosynthetic pathway of l-leucine. Inhibition of essential l-leucine synthesis in fungal and bacteria organisms, a pathway absent in host organisms such as humans, may represent a novel antibiotic mechanism to counter the ever-increasing problem of drug resistance to existing antibiotics.
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Affiliation(s)
- Bingji Ma
- Department of Traditional Chinese Medicine, Henan Agricultural University, Zhengzhou 450002, China.
| | - Jinwen Shen
- Department of Microbiology, Henan Agricultural University, Zhengzhou 450002, China.
| | - Wandee Yindeeyoungyeon
- National Center for Genetic Engineering and Biotechnology, NSTDA, Pathum Thani 12120, Thailand.
| | - Yuan Ruan
- Department of Traditional Chinese Medicine, Henan Agricultural University, Zhengzhou 450002, China.
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31
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Amorim Franco TM, Blanchard JS. Bacterial Branched-Chain Amino Acid Biosynthesis: Structures, Mechanisms, and Drugability. Biochemistry 2017; 56:5849-5865. [PMID: 28977745 DOI: 10.1021/acs.biochem.7b00849] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The eight enzymes responsible for the biosynthesis of the three branched-chain amino acids (l-isoleucine, l-leucine, and l-valine) were identified decades ago using classical genetic approaches based on amino acid auxotrophy. This review will highlight the recent progress in the determination of the three-dimensional structures of these enzymes, their chemical mechanisms, and insights into their suitability as targets for the development of antibacterial agents. Given the enormous rise in bacterial drug resistance to every major class of antibacterial compound, there is a clear and present need for the identification of new antibacterial compounds with nonoverlapping targets to currently used antibacterials that target cell wall, protein, mRNA, and DNA synthesis.
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Affiliation(s)
- Tathyana M Amorim Franco
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10805, United States
| | - John S Blanchard
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10805, United States
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32
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Xing A, Last RL. A Regulatory Hierarchy of the Arabidopsis Branched-Chain Amino Acid Metabolic Network. THE PLANT CELL 2017; 29:1480-1499. [PMID: 28522547 PMCID: PMC5502462 DOI: 10.1105/tpc.17.00186] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 04/12/2017] [Accepted: 05/11/2017] [Indexed: 05/18/2023]
Abstract
The branched-chain amino acids (BCAAs) Ile, Val, and Leu are essential nutrients that humans and other animals obtain from plants. However, total and relative amounts of plant BCAAs rarely match animal nutritional needs, and improvement requires a better understanding of the mechanistic basis for BCAA homeostasis. We present an in vivo regulatory model of BCAA homeostasis derived from analysis of feedback-resistant Arabidopsis thaliana mutants for the three allosteric committed enzymes in the biosynthetic network: threonine deaminase (also named l-O-methylthreonine resistant 1 [OMR1]), acetohydroxyacid synthase small subunit 2 (AHASS2), and isopropylmalate synthase 1 (IPMS1). In this model, OMR1 exerts primary control on Ile accumulation and functions independently of AHAS and IPMS AHAS and IPMS regulate Val and Leu homeostasis, where AHAS affects total Val+Leu and IPMS controls partitioning between these amino acids. In addition, analysis of feedback-resistant and loss-of-function single and double mutants revealed that each AHAS and IPMS isoenzyme contributes to homeostasis rather than being functionally redundant. The characterized feedback resistance mutations caused increased free BCAA levels in both seedlings and seeds. These results add to our understanding of the basis of in vivo BCAA homeostasis and inform approaches to improve the amount and balance of these essential nutrients in crops.
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Affiliation(s)
- Anqi Xing
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319
| | - Robert L Last
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824-1319
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33
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Pandey P, Lynn AM, Bandyopadhyay P. Identification of inhibitors against α-Isopropylmalate Synthase of Mycobacterium tuberculosis using docking-MM/PBSA hybrid approach. Bioinformation 2017; 13:144-148. [PMID: 28690380 PMCID: PMC5498780 DOI: 10.6026/97320630013144] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 04/21/2017] [Indexed: 12/23/2022] Open
Abstract
α-Isopropylmalate Synthase (α-IPMS) encoded by leuA in Mycobacterium tuberculosis (M.tb) is involved in the leucine biosynthesis pathway and is extremely critical for the synthesis of branched-chain amino acids (leucine, isoleucine and valine). α-IPMS activity is required not only for the proliferation of M.tb but is also indispensable for its survival during the latent phase of infection. It is absent in humans and is widely regarded as one of the validated drug targets against Tuberculosis (TB). Despite its essentiality, any study on designing of potential chemical inhibitors against α-IPMS has not been reported so far. In the present study, in silico identification of putative inhibitors against α-IPMS exploring three chemical databases i.e. NCI, DrugBank and ChEMBL is reported through structurebased drug design and filtering of ligands based on the pharmacophore feature of the actives. In the absence of experimental results of any inhibitor against α-IPMS, a stringent validation of docking results is done by comparing with molecular mechanics/Poisson- Boltzmann surface area (MM/PBSA) calculations by investigating two more proteins for which experimental results are known.
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Affiliation(s)
- Preeti Pandey
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, INDIA 110067
| | - Andrew M. Lynn
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, INDIA 110067
| | - Pradipta Bandyopadhyay
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, INDIA 110067
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34
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Huang Q, Liang L, Wu W, Wu S, Huang J. Metabolic engineering of Corynebacterium glutamicum to enhance L-leucine production. ACTA ACUST UNITED AC 2017. [DOI: 10.5897/ajb2017.15911] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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35
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Kumar G, Johnson JL, Frantom PA. Improving Functional Annotation in the DRE-TIM Metallolyase Superfamily through Identification of Active Site Fingerprints. Biochemistry 2016; 55:1863-72. [PMID: 26935545 DOI: 10.1021/acs.biochem.5b01193] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Within the DRE-TIM metallolyase superfamily, members of the Claisen-like condensation (CC-like) subgroup catalyze C-C bond-forming reactions between various α-ketoacids and acetyl-coenzyme A. These reactions are important in the metabolic pathways of many bacterial pathogens and serve as engineering scaffolds for the production of long-chain alcohol biofuels. To improve functional annotation and identify sequences that might use novel substrates in the CC-like subgroup, a combination of structural modeling and multiple-sequence alignments identified active site residues on the third, fourth, and fifth β-strands of the TIM-barrel catalytic domain that are differentially conserved within the substrate-diverse enzyme families. Using α-isopropylmalate synthase and citramalate synthase from Methanococcus jannaschii (MjIPMS and MjCMS), site-directed mutagenesis was used to test the role of each identified position in substrate selectivity. Kinetic data suggest that residues at the β3-5 and β4-7 positions play a significant role in the selection of α-ketoisovalerate over pyruvate in MjIPMS. However, complementary substitutions in MjCMS fail to alter substrate specificity, suggesting residues in these positions do not contribute to substrate selectivity in this enzyme. Analysis of the kinetic data with respect to a protein similarity network for the CC-like subgroup suggests that evolutionarily distinct forms of IPMS utilize residues at the β3-5 and β4-7 positions to affect substrate selectivity while the different versions of CMS use unique architectures. Importantly, mapping the identities of residues at the β3-5 and β4-7 positions onto the protein similarity network allows for rapid annotation of probable IPMS enzymes as well as several outlier sequences that may represent novel functions in the subgroup.
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Affiliation(s)
- Garima Kumar
- Department of Chemistry, The University of Alabama , 250 Hackberry Lane, Tuscaloosa, Alabama 35487, United States
| | - Jordyn L Johnson
- Department of Chemistry, The University of Alabama , 250 Hackberry Lane, Tuscaloosa, Alabama 35487, United States
| | - Patrick A Frantom
- Department of Chemistry, The University of Alabama , 250 Hackberry Lane, Tuscaloosa, Alabama 35487, United States
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36
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Bashiri G, Rehan AM, Sreebhavan S, Baker HM, Baker EN, Squire CJ. Elongation of the Poly-γ-glutamate Tail of F420 Requires Both Domains of the F420:γ-Glutamyl Ligase (FbiB) of Mycobacterium tuberculosis. J Biol Chem 2016; 291:6882-94. [PMID: 26861878 DOI: 10.1074/jbc.m115.689026] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Indexed: 01/21/2023] Open
Abstract
Cofactor F420is an electron carrier with a major role in the oxidoreductive reactions ofMycobacterium tuberculosis, the causative agent of tuberculosis. A γ-glutamyl ligase catalyzes the final steps of the F420biosynthesis pathway by successive additions ofl-glutamate residues to F420-0, producing a poly-γ-glutamate tail. The enzyme responsible for this reaction in archaea (CofE) comprises a single domain and produces F420-2 as the major species. The homologousM. tuberculosisenzyme, FbiB, is a two-domain protein and produces F420with predominantly 5-7l-glutamate residues in the poly-γ-glutamate tail. The N-terminal domain of FbiB is homologous to CofE with an annotated γ-glutamyl ligase activity, whereas the C-terminal domain has sequence similarity to an FMN-dependent family of nitroreductase enzymes. Here we demonstrate that full-length FbiB adds multiplel-glutamate residues to F420-0in vitroto produce F420-5 after 24 h; communication between the two domains is critical for full γ-glutamyl ligase activity. We also present crystal structures of the C-terminal domain of FbiB in apo-, F420-0-, and FMN-bound states, displaying distinct sites for F420-0 and FMN ligands that partially overlap. Finally, we discuss the features of a full-length structural model produced by small angle x-ray scattering and its implications for the role of N- and C-terminal domains in catalysis.
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Affiliation(s)
- Ghader Bashiri
- From the Structural Biology Laboratory, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, and
| | - Aisyah M Rehan
- From the Structural Biology Laboratory, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, and
| | - Sreevalsan Sreebhavan
- the Faculty of Medical and Health Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Heather M Baker
- From the Structural Biology Laboratory, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, and
| | - Edward N Baker
- From the Structural Biology Laboratory, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, and
| | - Christopher J Squire
- From the Structural Biology Laboratory, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, and
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37
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Ning J, Moghe GD, Leong B, Kim J, Ofner I, Wang Z, Adams C, Jones AD, Zamir D, Last RL. A Feedback-Insensitive Isopropylmalate Synthase Affects Acylsugar Composition in Cultivated and Wild Tomato. PLANT PHYSIOLOGY 2015; 169:1821-35. [PMID: 25986128 PMCID: PMC4634047 DOI: 10.1104/pp.15.00474] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 05/15/2015] [Indexed: 05/05/2023]
Abstract
Acylsugars are insecticidal specialized metabolites produced in the glandular trichomes of plants in the Solanaceae family. In the tomato clade of the Solanum genus, acylsugars consist of aliphatic acids of different chain lengths esterified to sucrose, or less frequently to glucose. Through liquid chromatography-mass spectrometry screening of introgression lines, we previously identified a region of chromosome 8 in the Solanum pennellii LA0716 genome (IL8-1/8-1-1) that causes the cultivated tomato Solanum lycopersicum to shift from producing acylsucroses with abundant 3-methylbutanoic acid acyl chains derived from leucine metabolism to 2-methylpropanoic acid acyl chains derived from valine metabolism. We describe multiple lines of evidence implicating a trichome-expressed gene from this region as playing a role in this shift. S. lycopersicum M82 SlIPMS3 (Solyc08g014230) encodes a functional end product inhibition-insensitive version of the committing enzyme of leucine biosynthesis, isopropylmalate synthase, missing the carboxyl-terminal 160 amino acids. In contrast, the S. pennellii LA0716 IPMS3 allele found in IL8-1/8-1-1 encodes a nonfunctional truncated IPMS protein. M82 transformed with an SlIPMS3 RNA interference construct exhibited an acylsugar profile similar to that of IL8-1-1, whereas the expression of SlIPMS3 in IL8-1-1 partially restored the M82 acylsugar phenotype. These IPMS3 alleles are polymorphic in 14 S. pennellii accessions spread throughout the geographical range of occurrence for this species and are associated with acylsugars containing varying amounts of 2-methylpropanoic acid and 3-methylbutanoic acid acyl chains.
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Affiliation(s)
- Jing Ning
- Department of Biochemistry and Molecular Biology (J.N., G.D.M., B.L., Z.W., A.D.J., R.L.L.), Department of Plant Biology (J.K., R.L.L.), and Department of Chemistry (A.D.J.), Michigan State University, East Lansing, Michigan 48824;Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel (I.O., D.Z.); andDepartment of Biochemistry, St. Mary's College of Maryland, St. Mary's City, Maryland 20686 (C.A.)
| | - Gaurav D Moghe
- Department of Biochemistry and Molecular Biology (J.N., G.D.M., B.L., Z.W., A.D.J., R.L.L.), Department of Plant Biology (J.K., R.L.L.), and Department of Chemistry (A.D.J.), Michigan State University, East Lansing, Michigan 48824;Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel (I.O., D.Z.); andDepartment of Biochemistry, St. Mary's College of Maryland, St. Mary's City, Maryland 20686 (C.A.)
| | - Bryan Leong
- Department of Biochemistry and Molecular Biology (J.N., G.D.M., B.L., Z.W., A.D.J., R.L.L.), Department of Plant Biology (J.K., R.L.L.), and Department of Chemistry (A.D.J.), Michigan State University, East Lansing, Michigan 48824;Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel (I.O., D.Z.); andDepartment of Biochemistry, St. Mary's College of Maryland, St. Mary's City, Maryland 20686 (C.A.)
| | - Jeongwoon Kim
- Department of Biochemistry and Molecular Biology (J.N., G.D.M., B.L., Z.W., A.D.J., R.L.L.), Department of Plant Biology (J.K., R.L.L.), and Department of Chemistry (A.D.J.), Michigan State University, East Lansing, Michigan 48824;Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel (I.O., D.Z.); andDepartment of Biochemistry, St. Mary's College of Maryland, St. Mary's City, Maryland 20686 (C.A.)
| | - Itai Ofner
- Department of Biochemistry and Molecular Biology (J.N., G.D.M., B.L., Z.W., A.D.J., R.L.L.), Department of Plant Biology (J.K., R.L.L.), and Department of Chemistry (A.D.J.), Michigan State University, East Lansing, Michigan 48824;Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel (I.O., D.Z.); andDepartment of Biochemistry, St. Mary's College of Maryland, St. Mary's City, Maryland 20686 (C.A.)
| | - Zhenzhen Wang
- Department of Biochemistry and Molecular Biology (J.N., G.D.M., B.L., Z.W., A.D.J., R.L.L.), Department of Plant Biology (J.K., R.L.L.), and Department of Chemistry (A.D.J.), Michigan State University, East Lansing, Michigan 48824;Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel (I.O., D.Z.); andDepartment of Biochemistry, St. Mary's College of Maryland, St. Mary's City, Maryland 20686 (C.A.)
| | - Christopher Adams
- Department of Biochemistry and Molecular Biology (J.N., G.D.M., B.L., Z.W., A.D.J., R.L.L.), Department of Plant Biology (J.K., R.L.L.), and Department of Chemistry (A.D.J.), Michigan State University, East Lansing, Michigan 48824;Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel (I.O., D.Z.); andDepartment of Biochemistry, St. Mary's College of Maryland, St. Mary's City, Maryland 20686 (C.A.)
| | - A Daniel Jones
- Department of Biochemistry and Molecular Biology (J.N., G.D.M., B.L., Z.W., A.D.J., R.L.L.), Department of Plant Biology (J.K., R.L.L.), and Department of Chemistry (A.D.J.), Michigan State University, East Lansing, Michigan 48824;Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel (I.O., D.Z.); andDepartment of Biochemistry, St. Mary's College of Maryland, St. Mary's City, Maryland 20686 (C.A.)
| | - Dani Zamir
- Department of Biochemistry and Molecular Biology (J.N., G.D.M., B.L., Z.W., A.D.J., R.L.L.), Department of Plant Biology (J.K., R.L.L.), and Department of Chemistry (A.D.J.), Michigan State University, East Lansing, Michigan 48824;Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel (I.O., D.Z.); andDepartment of Biochemistry, St. Mary's College of Maryland, St. Mary's City, Maryland 20686 (C.A.)
| | - Robert L Last
- Department of Biochemistry and Molecular Biology (J.N., G.D.M., B.L., Z.W., A.D.J., R.L.L.), Department of Plant Biology (J.K., R.L.L.), and Department of Chemistry (A.D.J.), Michigan State University, East Lansing, Michigan 48824;Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel (I.O., D.Z.); andDepartment of Biochemistry, St. Mary's College of Maryland, St. Mary's City, Maryland 20686 (C.A.)
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Isolation and characterization of awamori yeast mutants with l-leucine accumulation that overproduce isoamyl alcohol. J Biosci Bioeng 2015; 119:140-7. [DOI: 10.1016/j.jbiosc.2014.06.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 06/09/2014] [Accepted: 06/27/2014] [Indexed: 11/19/2022]
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Akasaka N, Ishii Y, Hidese R, Sakoda H, Fujiwara S. Enhanced production of branched-chain amino acids by Gluconacetobacter europaeus with a specific regional deletion in a leucine responsive regulator. J Biosci Bioeng 2014; 118:607-15. [DOI: 10.1016/j.jbiosc.2014.05.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 05/21/2014] [Accepted: 05/29/2014] [Indexed: 10/25/2022]
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40
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Zhang Z, Wu J, Lin W, Wang J, Yan H, Zhao W, Ma J, Ding J, Zhang P, Zhao GP. Subdomain II of α-isopropylmalate synthase is essential for activity: inferring a mechanism of feedback inhibition. J Biol Chem 2014; 289:27966-78. [PMID: 25128527 DOI: 10.1074/jbc.m114.559716] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The committed step of leucine biosynthesis, converting acetyl-CoA and α-ketoisovalerate into α-isopropylmalate, is catalyzed by α-isopropylmalate synthase (IPMS), an allosteric enzyme subjected to feedback inhibition by the end product L-leucine. We characterized the short form IPMS from Leptospira biflexa (LbIPMS2), which exhibits a catalytic activity comparable with that of the long form IPMS (LbIPMS1) and has a similar N-terminal domain followed by subdomain I and subdomain II but lacks the whole C-terminal regulatory domain. We found that partial deletion of the regulatory domain of LbIPMS1 resulted in a loss of about 50% of the catalytic activity; however, when the regulatory domain was deleted up to Arg-385, producing a protein that is almost equivalent to the intact LbIPMS2, about 90% of the activity was maintained. Moreover, in LbIPMS2 or LbIPMS1, further deletion of several residues from the C terminus of subdomain II significantly impaired or completely abolished the catalytic activity, respectively. These results define a complete and independently functional catalytic module of IPMS consisting of both the N-terminal domain and the two subdomains. Structural comparison of LbIPMS2 and the Mycobacterium tuberculosis IPMS revealed two different conformations of subdomain II that likely represent two substrate-binding states related to cooperative catalysis. The biochemical and structural analyses together with the previously published hydrogen-deuterium exchange data led us to propose a conformation transition mechanism for feedback inhibition mediated by subdomains I and II that might associated with alteration of the binding affinity toward acetyl-CoA.
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Affiliation(s)
- Zilong Zhang
- From the Chinese Academy of Sciences Key Laboratory of Synthetic Biology and Shanghai International Travel Healthcare Center, Shanghai Entry-Exit Inspection and Quarantine Bureau, Shanghai 200335, China
| | - Jian Wu
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Wei Lin
- From the Chinese Academy of Sciences Key Laboratory of Synthetic Biology and
| | - Jin Wang
- From the Chinese Academy of Sciences Key Laboratory of Synthetic Biology and
| | - Han Yan
- From the Chinese Academy of Sciences Key Laboratory of Synthetic Biology and
| | - Wei Zhao
- Key Laboratory of Medical Molecular Virology affiliated to the Ministries of Education and Health, Shanghai Medical College, and Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jun Ma
- From the Chinese Academy of Sciences Key Laboratory of Synthetic Biology and
| | - Jianping Ding
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China,
| | - Peng Zhang
- From the Chinese Academy of Sciences Key Laboratory of Synthetic Biology and National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China,
| | - Guo-Ping Zhao
- From the Chinese Academy of Sciences Key Laboratory of Synthetic Biology and Key Laboratory of Medical Molecular Virology affiliated to the Ministries of Education and Health, Shanghai Medical College, and Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China, Shanghai-Ministry of Science and Technology Key Laboratory for Health and Disease Genomics, Chinese National Human Genome Center, Shanghai 201203, China, Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong Special Administrative Region 999077, China, and
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41
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Kumar G, Frantom PA. Evolutionarily Distinct Versions of the Multidomain Enzyme α-Isopropylmalate Synthase Share Discrete Mechanisms of V-Type Allosteric Regulation. Biochemistry 2014; 53:4847-56. [DOI: 10.1021/bi500702u] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Garima Kumar
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Patrick A. Frantom
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
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42
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Rodriguez GM, Neyrolles O. Metallobiology of Tuberculosis. Microbiol Spectr 2014; 2:10.1128/microbiolspec.MGM2-0012-2013. [PMID: 26103977 PMCID: PMC5180607 DOI: 10.1128/microbiolspec.mgm2-0012-2013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Indexed: 11/20/2022] Open
Abstract
Transition metals are essential constituents of all living organisms, playing crucial structural and catalytic parts in many enzymes and transcription factors. However, transition metals can also be toxic when present in excess. Their uptake and efflux rates must therefore be carefully controlled by biological systems. In this chapter, we summarize the current knowledge about uptake and efflux systems in Mycobacterium tuberculosis for mainly three of these metals, namely iron, zinc, and copper. We also propose questions for future research in the field of metallobiology of host-pathogen interactions in tuberculosis.
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Affiliation(s)
- G. Marcela Rodriguez
- Public Health Research Institute Center & Department of Medicine, University of Medicine and Dentistry of New Jersey, Newark, NJ 07103
| | - Olivier Neyrolles
- Centre National de la Recherche Scientifique & Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
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43
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Oba T, Nomiyama S, Hirakawa H, Tashiro K, Kuhara S. Asp578 in LEU4p Is One of the Key Residues for Leucine Feedback Inhibition Release in Sake Yeast. Biosci Biotechnol Biochem 2014; 69:1270-3. [PMID: 16041129 DOI: 10.1271/bbb.69.1270] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We identified a new mutation, Asp578Tyr, in alpha-isopropylmalate synthase (a LEU4 gene product) that releases leucine feedback inhibition and causes hyperproduction of isoamyl alcohol (i-AmOH) in sake yeast. Spontaneous sake yeast mutants that express resistance to 5,5,5-trifluoro-DL-leucine (TFL) were isolated, and a mutant strain, TFL20, was characterized at the genetic and biochemical levels. An enzyme assay for alpha-isopropylmalate synthase showed that strain TFL20 was released from feedback inhibition by L-leucine. Furthermore, DNA sequencing of the LEU4 gene for a haploid of the mutant TFL20 revealed that aspartic acid in position 578 changes to tyrosine. A comparison of the three-dimensional structures of wild-type LEU4p and mutant LEU4D578Yp by the homology modeling method showed that Asp578 is important for leucine feedback inhibition. We conclude that the mutation from Asp to Tyr in 578 is a novel change causing release from leucine feedback inhibition.
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Affiliation(s)
- Takahiro Oba
- Biotechnology and Food Research Institute, Fukuoka Industrial Technology Center, Aikawa-machi 1465-5, Kurume, Fukuoka 839-0861.
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Casey AK, Hicks MA, Johnson JL, Babbitt PC, Frantom PA. Mechanistic and bioinformatic investigation of a conserved active site helix in α-isopropylmalate synthase from Mycobacterium tuberculosis, a member of the DRE-TIM metallolyase superfamily. Biochemistry 2014; 53:2915-25. [PMID: 24720347 PMCID: PMC4025573 DOI: 10.1021/bi500246z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The characterization of functionally diverse enzyme superfamilies provides the opportunity to identify evolutionarily conserved catalytic strategies, as well as amino acid substitutions responsible for the evolution of new functions or specificities. Isopropylmalate synthase (IPMS) belongs to the DRE-TIM metallolyase superfamily. Members of this superfamily share common active site elements, including a conserved active site helix and an HXH divalent metal binding motif, associated with stabilization of a common enolate anion intermediate. These common elements are overlaid by variations in active site architecture resulting in the evolution of a diverse set of reactions that include condensation, lyase/aldolase, and carboxyl transfer activities. Here, using IPMS, an integrated biochemical and bioinformatics approach has been utilized to investigate the catalytic role of residues on an active site helix that is conserved across the superfamily. The construction of a sequence similarity network for the DRE-TIM metallolyase superfamily allows for the biochemical results obtained with IPMS variants to be compared across superfamily members and within other condensation-catalyzing enzymes related to IPMS. A comparison of our results with previous biochemical data indicates an active site arginine residue (R80 in IPMS) is strictly required for activity across the superfamily, suggesting that it plays a key role in catalysis, most likely through enolate stabilization. In contrast, differential results obtained from substitution of the C-terminal residue of the helix (Q84 in IPMS) suggest that this residue plays a role in reaction specificity within the superfamily.
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Affiliation(s)
- Ashley K Casey
- Department of Chemistry, The University of Alabama , 250 Hackberry Lane, Tuscaloosa, Alabama 35406, United States
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45
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Modifying the determinants of α-ketoacid substrate selectivity inmycobacterium tuberculosisα-isopropylmalate synthase. FEBS Lett 2014; 588:1603-7. [DOI: 10.1016/j.febslet.2014.02.053] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 02/22/2014] [Accepted: 02/24/2014] [Indexed: 11/21/2022]
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46
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Vogt M, Haas S, Klaffl S, Polen T, Eggeling L, van Ooyen J, Bott M. Pushing product formation to its limit: Metabolic engineering of Corynebacterium glutamicum for l-leucine overproduction. Metab Eng 2014; 22:40-52. [DOI: 10.1016/j.ymben.2013.12.001] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Revised: 10/31/2013] [Accepted: 12/03/2013] [Indexed: 11/29/2022]
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47
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Emerging computational approaches for the study of protein allostery. Arch Biochem Biophys 2013; 538:6-15. [DOI: 10.1016/j.abb.2013.07.025] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 07/23/2013] [Accepted: 07/30/2013] [Indexed: 12/12/2022]
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Casey AK, Schwalm EL, Hays BN, Frantom PA. V-type allosteric inhibition is described by a shift in the rate-determining step for α-isopropylmalate synthase from Mycobacterium tuberculosis. Biochemistry 2013; 52:6737-9. [PMID: 24033269 DOI: 10.1021/bi401186v] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The kinetic parameters affected by allosteric mechanisms contain collections of rate constants that vary based on differences in the relative rates of individual steps in the reaction. Thus, it may not be useful to compare enzymes with similar allosteric mechanisms unless the point of regulation has been identified. Rapid reaction kinetics and kinetic isotope effects provide a detailed description of V-type feedback allosteric inhibition in α-isopropylmalate synthase from Mycobacterium tuberculosis, an evolutionarily conserved model allosteric system. Results are consistent with a shift in the rate-determining step from product release to the hydrolytic step in catalysis in the presence of the effector.
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Affiliation(s)
- Ashley K Casey
- Department of Chemistry, The University of Alabama , Tuscaloosa, Alabama 35487, United States
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49
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Marcheschi RJ, Gronenberg LS, Liao JC. Protein engineering for metabolic engineering: current and next-generation tools. Biotechnol J 2013; 8:545-55. [PMID: 23589443 DOI: 10.1002/biot.201200371] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 03/07/2013] [Accepted: 03/20/2013] [Indexed: 11/10/2022]
Abstract
Protein engineering in the context of metabolic engineering is increasingly important to the field of industrial biotechnology. As the demand for biologically produced food, fuels, chemicals, food additives, and pharmaceuticals continues to grow, the ability to design and modify proteins to accomplish new functions will be required to meet the high productivity demands for the metabolism of engineered organisms. We review advances in selecting, modeling, and engineering proteins to improve or alter their activity. Some of the methods have only recently been developed for general use and are just beginning to find greater application in the metabolic engineering community. We also discuss methods of generating random and targeted diversity in proteins to generate mutant libraries for analysis. Recent uses of these techniques to alter cofactor use; produce non-natural amino acids, alcohols, and carboxylic acids; and alter organism phenotypes are presented and discussed as examples of the successful engineering of proteins for metabolic engineering purposes.
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Affiliation(s)
- Ryan J Marcheschi
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA, USA
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50
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Amino-acid substitutions at the domain interface affect substrate and allosteric inhibitor binding in α-isopropylmalate synthase from Mycobacterium tuberculosis. Biochem Biophys Res Commun 2013; 433:249-54. [PMID: 23500460 DOI: 10.1016/j.bbrc.2013.02.092] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 02/27/2013] [Indexed: 11/22/2022]
Abstract
α-Isopropylmalate synthase (α-IPMS) is a multi-domain protein catalysing the condensation of α-ketoisovalerate (α-KIV) and acetyl coenzyme A (AcCoA) to form α-isopropylmalate. This reaction is the first committed step in the leucine biosynthetic pathway in bacteria and plants, and α-IPMS is allosterically regulated by this amino acid. Existing crystal structures of α-IPMS from Mycobacterium tuberculosis (MtuIPMS) indicate that this enzyme has a strikingly different domain arrangement in each monomer of the homodimeric protein. This asymmetry results in two distinct interfaces between the N-terminal catalytic domains and the C-terminal regulatory domains in the dimer. In this study, residues Arg97 and Asp444 across one of these unequal domain interfaces were substituted to evaluate the importance of protein asymmetry and salt bridge formation between this pair of residues. Analysis of solution-phase structures of wild-type and variant MtuIPMS indicates that substitutions of these residues have little effect on overall protein conformation, a result also observed for addition of the feedback inhibitor leucine to the wild-type enzyme. All variants had increased catalytic efficiency relative to wild-type MtuIPMS, and those with an Asp444 substitution displayed increased affinity for the substrate AcCoA. All variants also showed reduced sensitivity to leucine and altered biphasic reaction kinetics when compared with those of the wild-type enzyme. It is proposed that substituting residues at the asymmetric domain interface increases flexibility in the protein, particularly affecting the AcCoA binding site and the response to leucine, without penalty on catalysis.
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