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Chaturvedi AK, Dym O, Levin Y, Fluhr R. PGR5-LIKE PHOTOSYNTHETIC PHENOTYPE1A redox states alleviate photoinhibition during changes in light intensity. PLANT PHYSIOLOGY 2024; 194:1059-1074. [PMID: 37787609 DOI: 10.1093/plphys/kiad518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 10/04/2023]
Abstract
Plants have evolved photosynthetic regulatory mechanisms to maintain homeostasis in response to light changes during diurnal transitions and those caused by passing clouds or by wind. One such adaptation directs photosynthetic electron flow to a cyclic pathway to alleviate excess energy surges. Here, we assign a function to regulatory cysteines of PGR5-like protein 1A (PGRL1A), a constituent of the PROTON GRADIENT REGULATION5 (PGR5)-dependent cyclic electron flow (CEF) pathway. During step increases from darkness to low light intensity in Arabidopsis (Arabidopsis thaliana), the intermolecular disulfide of the PGRL1A 59-kDa complex was reduced transiently within seconds to the 28-kDa form. In contrast, step increases from darkness to high light stimulated a stable, partially reduced redox state in PGRL1A. Mutations of 2 cysteines in PGRL1A, Cys82 and Cys183, resulted in a constitutively pseudo-reduced state. The mutant displayed higher proton motive force (PMF) and nonphotochemical quenching (NPQ) than the wild type (WT) and showed altered donor and acceptor dynamic flow around PSI. These changes were found to correspond with the redox state of PGRL1A. Continuous light regimes did not affect mutant growth compared to the WT. However, under fluctuating regimes of high light, the mutant showed better growth than the WT. In contrast, in fluctuating regimes of low light, the mutant displayed a growth penalty that can be attributed to constant stimulation of CEF under low light. Treatment with photosynthetic inhibitors indicated that PGRL1A redox state control depends on the penultimate Fd redox state. Our results showed that redox state changes in PGRL1A are crucial to optimize photosynthesis.
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Affiliation(s)
- Amit Kumar Chaturvedi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Orly Dym
- Department of Life Science Core Facilities, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yishai Levin
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Robert Fluhr
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
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2
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Morita Y, Yoshida A, Ye S, Tomita T, Yoshida M, Kosono S, Nishiyama M. Protein-protein interaction-mediated regulation of lysine biosynthesis of Thermus thermophilus through the function-unknown protein LysV. J GEN APPL MICROBIOL 2023; 69:91-101. [PMID: 37357393 DOI: 10.2323/jgam.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
Abstract
Thermus thermophilus biosynthesizes lysine via α-aminoadipate as an intermediate using the amino-group carrier protein, LysW, to transfer the attached α-aminoadipate and its derivatives to biosynthetic enzymes. A gene named lysV, which encodes a hypothetical protein similar to LysW, is present in the lysine biosynthetic gene cluster. Although the knockout of lysV did not affect lysine auxotrophy, lysV homologs are conserved in the lysine biosynthetic gene clusters of microorganisms belonging to the phylum Deinococcus-Thermus, suggesting a functional role for LysV in lysine biosynthesis. Pulldown assays and crosslinking experiments detected interactions between LysV and all of the biosynthetic enzymes requiring LysW for reactions, and the activities of most of all these enzymes were affected by LysV. These results suggest that LysV modulates the lysine biosynthesis through protein-protein interactions.
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Affiliation(s)
- Yutaro Morita
- Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Ayako Yoshida
- Graduate School of Agricultural and Life Sciences, The University of Tokyo
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo
| | - Siyan Ye
- Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Takeo Tomita
- Graduate School of Agricultural and Life Sciences, The University of Tokyo
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo
| | - Minoru Yoshida
- Graduate School of Agricultural and Life Sciences, The University of Tokyo
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science
| | - Saori Kosono
- Graduate School of Agricultural and Life Sciences, The University of Tokyo
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo
| | - Makoto Nishiyama
- Graduate School of Agricultural and Life Sciences, The University of Tokyo
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo
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3
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Wu Y, Zhang J, Wang B, Zhang Y, Li H, Liu Y, Yin J, He D, Luo H, Gan F, Tang B, Tang XF. Dissecting the Arginine and Lysine Biosynthetic Pathways and Their Relationship in Haloarchaeon Natrinema gari J7-2 via Endogenous CRISPR-Cas System-Based Genome Editing. Microbiol Spectr 2023; 11:e0028823. [PMID: 37347159 PMCID: PMC10433800 DOI: 10.1128/spectrum.00288-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 06/07/2023] [Indexed: 06/23/2023] Open
Abstract
The evolutionary relationship between arginine and lysine biosynthetic pathways has been well established in bacteria and hyperthermophilic archaea but remains largely unknown in haloarchaea. Here, the endogenous CRISPR-Cas system was harnessed to edit arginine and lysine biosynthesis-related genes in the haloarchaeon Natrinema gari J7-2. The ΔargW, ΔargX, ΔargB, and ΔargD mutant strains display an arginine auxotrophic phenotype, while the ΔdapB mutant shows a lysine auxotrophic phenotype, suggesting that strain J7-2 utilizes the ArgW-mediated pathway and the diaminopimelate (DAP) pathway to synthesize arginine and lysine, respectively. Unlike the ArgD in Escherichia coli acting as a bifunctional aminotransferase in both the arginine biosynthesis pathway and the DAP pathway, the ArgD in strain J7-2 participates only in arginine biosynthesis. Meanwhile, in strain J7-2, the function of argB cannot be compensated for by its evolutionary counterpart ask in the DAP pathway. Moreover, strain J7-2 cannot utilize α-aminoadipate (AAA) to synthesize lysine via the ArgW-mediated pathway, in contrast to hyperthermophilic archaea that employ a bifunctional LysW-mediated pathway to synthesize arginine (or ornithine) and lysine from glutamate and AAA, respectively. Additionally, the replacement of a 5-amino-acid signature motif responsible for substrate specificity of strain J7-2 ArgX with that of its hyperthermophilic archaeal homologs cannot endow the ΔdapB mutant with the ability to biosynthesize lysine from AAA. The in vitro analysis shows that strain J7-2 ArgX acts on glutamate rather than AAA. These results suggest that the arginine and lysine biosynthetic pathways of strain J7-2 are highly specialized during evolution. IMPORTANCE Due to their roles in amino acid metabolism and close evolutionary relationship, arginine and lysine biosynthetic pathways represent interesting models for probing functional specialization of metabolic routes. The current knowledge with respect to arginine and lysine biosynthesis is limited for haloarchaea compared to that for bacteria and hyperthermophilic archaea. Our results demonstrate that the haloarchaeon Natrinema gari J7-2 employs the ArgW-mediated pathway and the DAP pathway for arginine and lysine biosynthesis, respectively, and the two pathways are functionally independent of each other; meanwhile, ArgX is a key determinant of substrate specificity of the ArgW-mediated pathway in strain J7-2. This study provides new clues about haloarchaeal amino acid metabolism and confirms the convenience and efficiency of endogenous CRISPR-Cas system-based genome editing in haloarchaea.
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Affiliation(s)
- Yi Wu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jia Zhang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Bingxue Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yanyan Zhang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Huai Li
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yang Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jing Yin
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Dan He
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Hongyi Luo
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Fei Gan
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Wuhan, China
| | - Bing Tang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Wuhan, China
| | - Xiao-Feng Tang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Wuhan, China
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4
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Yu Y, van der Donk WA. Biosynthesis of 3-thia-α-amino acids on a carrier peptide. Proc Natl Acad Sci U S A 2022; 119:e2205285119. [PMID: 35787182 PMCID: PMC9303977 DOI: 10.1073/pnas.2205285119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/23/2022] [Indexed: 11/18/2022] Open
Abstract
A subset of natural products, such as polyketides and nonribosomal peptides, is biosynthesized while tethered to a carrier peptide via a thioester linkage. Recently, we reported that the biosyntheses of 3-thiaglutamate and ammosamide, single amino acid-derived natural products, employ a very different type of carrier peptide to which the biosynthetic intermediates are bound via an amide linkage. During their biosyntheses, a peptide aminoacyl-transfer ribonucleic acid (tRNA) ligase (PEARL) first loads an amino acid to the C terminus of the carrier peptide for subsequent modification by other enzymes. Proteolytic removal of the modified C-terminal amino acid yields the mature product. We termed natural products that are biosynthesized using such pathways pearlins. To investigate the diversity of pearlins, in this study we experimentally characterized another PEARL-encoding biosynthetic gene cluster (BGC) from Tistrella mobilis (tmo). The enzymes encoded in the tmo BGC transformed cysteine into 3-thiahomoleucine both in vitro and in Escherichia coli. During this process, a cobalamin-dependent radical S-adenosylmethionine (SAM) enzyme catalyzes C-isopropylation. This work illustrates that the biosynthesis of amino acid-derived natural products on a carrier peptide is a widespread strategy in nature and expands the spectrum of thiahemiaminal analogs of amino acids that may serve a broader, currently unknown function.
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Affiliation(s)
- Yue Yu
- Department of Chemistry, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- HHMI, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Wilfred A. van der Donk
- Department of Chemistry, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- HHMI, University of Illinois at Urbana–Champaign, Urbana, IL 61801
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5
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Fauziah Ma'ruf I, Sasaki Y, Kerbs A, Nießer J, Sato Y, Taniguchi H, Okano K, Kitani S, Restiawaty E, Akhmaloka, Honda K. Heterologous gene expression and characterization of two serine hydroxymethyltransferases from Thermoplasma acidophilum. Extremophiles 2021; 25:393-402. [PMID: 34196829 DOI: 10.1007/s00792-021-01238-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 06/24/2021] [Indexed: 12/01/2022]
Abstract
Serine hydroxymethyltransferase (SHMT) and threonine aldolase are classified as fold type I pyridoxal-5'-phosphate-dependent enzymes and engaged in glycine biosynthesis from serine and threonine, respectively. The acidothermophilic archaeon Thermoplasma acidophilum possesses two distinct SHMT genes, while there is no gene encoding threonine aldolase in its genome. In the present study, the two SHMT genes (Ta0811 and Ta1509) were heterologously expressed in Escherichia coli and Thermococcus kodakarensis, respectively, and biochemical properties of their products were investigated. Ta1509 protein exhibited dual activities to catalyze tetrahydrofolate (THF)-dependent serine cleavage and THF-independent threonine cleavage, similar to other SHMTs reported to date. In contrast, the Ta0811 protein lacks amino acid residues involved in the THF-binding motif and catalyzes only the THF-independent cleavage of threonine. Kinetic analysis revealed that the threonine-cleavage activity of the Ta0811 protein was 3.5 times higher than the serine-cleavage activity of Ta1509 protein. In addition, mRNA expression of Ta0811 gene in T. acidophilum was approximately 20 times more abundant than that of Ta1509. These observations suggest that retroaldol cleavage of threonine, mediated by the Ta0811 protein, has a major role in glycine biosynthesis in T. acidophilum.
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Affiliation(s)
- Ilma Fauziah Ma'ruf
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Biochemistry Research Group, Faculty of Mathematics and Natural Sciences, Department of Chemistry, Institut Teknologi Bandung, Bandung, 40132, Indonesia
| | - Yuka Sasaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.,International Center for Biotechnology, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Anastasia Kerbs
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, 33617, Bielefeld, Germany
| | - Jochen Nießer
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Institute of Bio and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Julich, Germany
| | - Yu Sato
- International Center for Biotechnology, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hironori Taniguchi
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kenji Okano
- International Center for Biotechnology, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Shigeru Kitani
- International Center for Biotechnology, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Elvi Restiawaty
- Chemical Engineering Process Design and Development Research Group, Faculty of Industrial Technology, Institut Teknologi Bandung, Bandung, 40132, Indonesia
| | - Akhmaloka
- Biochemistry Research Group, Faculty of Mathematics and Natural Sciences, Department of Chemistry, Institut Teknologi Bandung, Bandung, 40132, Indonesia.,Department of Chemistry, Faculty of Science and Computer, Universitas Pertamina, Jakarta, 12220, Indonesia
| | - Kohsuke Honda
- International Center for Biotechnology, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan. .,Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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6
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Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea. Genes (Basel) 2021; 12:genes12070963. [PMID: 34202810 PMCID: PMC8305020 DOI: 10.3390/genes12070963] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/10/2021] [Accepted: 06/15/2021] [Indexed: 12/14/2022] Open
Abstract
Background: Annotation ambiguities and annotation errors are a general challenge in genomics. While a reliable protein function assignment can be obtained by experimental characterization, this is expensive and time-consuming, and the number of such Gold Standard Proteins (GSP) with experimental support remains very low compared to proteins annotated by sequence homology, usually through automated pipelines. Even a GSP may give a misleading assignment when used as a reference: the homolog may be close enough to support isofunctionality, but the substrate of the GSP is absent from the species being annotated. In such cases, the enzymes cannot be isofunctional. Here, we examined a variety of such issues in halophilic archaea (class Halobacteria), with a strong focus on the model haloarchaeon Haloferax volcanii. Results: Annotated proteins of Hfx. volcanii were identified for which public databases tend to assign a function that is probably incorrect. In some cases, an alternative, probably correct, function can be predicted or inferred from the available evidence, but this has not been adopted by public databases because experimental validation is lacking. In other cases, a probably invalid specific function is predicted by homology, and while there is evidence that this assigned function is unlikely, the true function remains elusive. We listed 50 of those cases, each with detailed background information, so that a conclusion about the most likely biological function can be drawn. For reasons of brevity and comprehension, only the key aspects are listed in the main text, with detailed information being provided in a corresponding section of the Supplementary Materials. Conclusions: Compiling, describing and summarizing these open annotation issues and functional predictions will benefit the scientific community in the general effort to improve the evaluation of protein function assignments and more thoroughly detail them. By highlighting the gaps and likely annotation errors currently in the databases, we hope this study will provide a framework for experimentalists to systematically confirm (or disprove) our function predictions or to uncover yet more unexpected functions.
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7
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Amino group carrier protein, a new platform in primary and secondary metabolite biosynthesis. N Biotechnol 2018. [DOI: 10.1016/j.nbt.2018.05.1206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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8
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Fujita S, Cho SH, Yoshida A, Hasebe F, Tomita T, Kuzuyama T, Nishiyama M. Crystal structure of LysK, an enzyme catalyzing the last step of lysine biosynthesis in Thermus thermophilus, in complex with lysine: Insight into the mechanism for recognition of the amino-group carrier protein, LysW. Biochem Biophys Res Commun 2017; 491:409-415. [PMID: 28720495 DOI: 10.1016/j.bbrc.2017.07.088] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 07/14/2017] [Indexed: 11/24/2022]
Abstract
LysK is an M20 peptidase family enzyme that hydrolyzes the isopeptide bond between the carrier protein LysW and lysine in order to release lysine, which is the last step of lysine biosynthesis in Thermus thermophilus. In the present study, we determined the crystal structure of LysK in complex with lysine at a resolution of 2.4 Å. The α-amino group of the bound lysine was oriented toward the catalytic center, which was composed of the residues coordinating divalent metal ions for the hydrolysis of the isopeptide bond. An 11 Å-long path was observed from the active site binding lysine to the protein surface, which may be responsible for recognizing the C-terminal extension domain of LysW with the conserved EDWGE sequence. A positively-charged surface region was detected around the exit of the path, similar to other lysine biosynthetic enzymes using LysW as the carrier protein. Mutational studies of the surface residues provided a plausible model for the electrostatic interaction with LysW.
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Affiliation(s)
- Satomi Fujita
- Biotechnology Research Center, The University of Tokyo, Japan
| | - Su-Hee Cho
- Biotechnology Research Center, The University of Tokyo, Japan
| | - Ayako Yoshida
- Biotechnology Research Center, The University of Tokyo, Japan
| | - Fumihito Hasebe
- Biotechnology Research Center, The University of Tokyo, Japan
| | - Takeo Tomita
- Biotechnology Research Center, The University of Tokyo, Japan
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9
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Ogasawara Y, Dairi T. Biosynthesis of Oligopeptides Using ATP-Grasp Enzymes. Chemistry 2017; 23:10714-10724. [PMID: 28488371 DOI: 10.1002/chem.201700674] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Indexed: 11/08/2022]
Abstract
Peptides are biologically occurring oligomers of amino acids linked by amide bonds and are indispensable for all living organisms. Many bioactive peptides are used as antibiotics, antivirus agents, insecticides, pheromones, and food preservatives. Nature employs several different strategies to form amide bonds. ATP-grasp enzymes that catalyze amide bond formation (ATP-dependent carboxylate-amine ligases) utilize a strategy of activating carboxylic acid as an acylphosphate intermediate to form amide bonds and are involved in many different biological processes in both primary and secondary metabolisms. The recent discovery of several new ATP-dependent carboxylate-amine ligases has expanded the diversity of this group of enzymes and showed their usefulness for generating oligopeptides. In this review, an overview of findings on amide bond formation catalyzed by ATP-grasp enzymes in the past decade is presented.
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Affiliation(s)
- Yasushi Ogasawara
- Division of Applied Chemistry, Graduate School of Engineering, Hokkaido University, Sapporo, Hokkaido, 060-8628, Japan
| | - Tohru Dairi
- Division of Applied Chemistry, Graduate School of Engineering, Hokkaido University, Sapporo, Hokkaido, 060-8628, Japan
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10
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Amino-group carrier-protein-mediated secondary metabolite biosynthesis in Streptomyces. Nat Chem Biol 2016; 12:967-972. [DOI: 10.1038/nchembio.2181] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 07/27/2016] [Indexed: 11/08/2022]
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11
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Yoshida A, Tomita T, Atomi H, Kuzuyama T, Nishiyama M. Lysine Biosynthesis of Thermococcus kodakarensis with the Capacity to Function as an Ornithine Biosynthetic System. J Biol Chem 2016; 291:21630-21643. [PMID: 27566549 DOI: 10.1074/jbc.m116.743021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Revised: 08/24/2016] [Indexed: 11/06/2022] Open
Abstract
We recently discovered a biosynthetic system using a novel amino group carrier protein called LysW for lysine biosynthesis via α-aminoadipate (AAA), and revealed that this system is also utilized in the biosynthesis of arginine by Sulfolobus In the present study, we focused on the biosynthesis of lysine and ornithine in the hyperthermophilic archaeon Thermococcus kodakarensis, and showed that their biosynthesis is accomplished by a single set of metabolic enzymes. We also determined the crystal structure of the LysX family protein from T. kodakarensis, which catalyzes the conjugation of LysW with either AAA or glutamate, in a complex with LysW-γ-AAA. This crystal structure is the first example to show how LysX recognizes AAA as a substrate and provides a structural basis for the bifunctionality of the LysX family protein from T. kodakarensis Based on comparisons with other LysX family proteins, we propose a mechanism for substrate recognition and its relationship with molecular evolution among LysX family proteins, which have different substrate specificities.
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Affiliation(s)
- Ayako Yoshida
- From the Biotechnology Research Center, University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657
| | - Takeo Tomita
- From the Biotechnology Research Center, University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657
| | - Haruyuki Atomi
- the Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, and.,the Japan Science and Technology Agency, CREST, 7, Gobancho, Chiyoda-ku, Tokyo 102-0076 Japan
| | - Tomohisa Kuzuyama
- From the Biotechnology Research Center, University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657
| | - Makoto Nishiyama
- From the Biotechnology Research Center, University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657,
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12
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Shimizu T, Tomita T, Kuzuyama T, Nishiyama M. Crystal Structure of the LysY·LysW Complex from Thermus thermophilus. J Biol Chem 2016; 291:9948-59. [PMID: 26966182 DOI: 10.1074/jbc.m115.707034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Indexed: 11/06/2022] Open
Abstract
Several bacteria and archaea utilize the amino group-carrier protein, LysW, for lysine biosynthesis, in which an isopeptide bond is formed between the C-terminal Glu of LysW and an amino group of α-aminoadipate (AAA). The resulting LysW-γ-AAA is phosphorylated by LysZ to form LysW-γ-AAA phosphate, which is subsequently reduced to LysW-γ-aminoadipic semialdehyde (LysW-γ-AASA) through a reaction catalyzed by LysY. In this study, we determined the crystal structures of LysY from Thermus thermophilus HB27 (TtLysY) complexed with TtLysW-γ-AASA and TtLysW-γ-AAA, respectively. In both structures, the globular domain of TtLysW was recognized by positively charged residues on helix α9 and the β11-α10 loop of TtLysY through conformational changes. A mutational analysis confirmed that the interactions observed between TtLysY and TtLysW are important for the function of TtLysY. The extended LysW recognition loop and conserved arginine residue were identified as signatures to discriminate LysY from ArgC, which is involved in arginine biosynthesis. Combined with the previously determined TtLysZ·TtLysW complex structure, TtLysW may simultaneously bind TtLysZ and TtLysY. These structural insights suggest the formation of a TtLysWZY ternary complex, in which the flexible C-terminal extension of TtLysW promotes the efficient transfer of the labile intermediate from the active site of TtLysZ to that of TtLysY during the sequential reactions catalyzed by TtLysZY.
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Affiliation(s)
- Tetsu Shimizu
- From the Biotechnology Research Center, University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takeo Tomita
- From the Biotechnology Research Center, University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tomohisa Kuzuyama
- From the Biotechnology Research Center, University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Makoto Nishiyama
- From the Biotechnology Research Center, University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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