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Liao Z, Gopalasingam CC, Kameya M, Gerle C, Shigematsu H, Ishii M, Arakawa T, Fushinobu S. Structural insights into thermophilic chaperonin complexes. Structure 2024:S0969-2126(24)00051-0. [PMID: 38492570 DOI: 10.1016/j.str.2024.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/07/2024] [Accepted: 02/20/2024] [Indexed: 03/18/2024]
Abstract
Group I chaperonins are dual heptamer protein complexes that play significant roles in protein homeostasis. The structure and function of the Escherichia coli chaperonin are well characterized. However, the dynamic properties of chaperonins, such as large ATPase-dependent conformational changes by binding of lid-like co-chaperonin GroES, have made structural analyses challenging, and our understanding of these changes during the turnover of chaperonin complex formation is limited. In this study, we used single-particle cryogenic electron microscopy to investigate the structures of GroES-bound chaperonin complexes from the thermophilic hydrogen-oxidizing bacteria Hydrogenophilus thermoluteolus and Hydrogenobacter thermophilus in the presence of ATP and AMP-PNP. We captured the structure of an intermediate state chaperonin complex, designated as an asymmetric football-shaped complex, and performed analyses to decipher the dynamic structural variations. Our structural analyses of inter- and intra-subunit communications revealed a unique mechanism of complex formation through the binding of a second GroES to a bullet-shaped complex.
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Affiliation(s)
- Zengwei Liao
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo City, Tokyo 113-8654, Japan
| | - Chai C Gopalasingam
- Life Science Research Infrastructure Group, RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 1-1-1, Japan
| | - Masafumi Kameya
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo City, Tokyo 113-8654, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo City, Tokyo 113-8654, Japan
| | - Christoph Gerle
- Life Science Research Infrastructure Group, RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 1-1-1, Japan
| | - Hideki Shigematsu
- Structural Biology Division, Japan Synchrotron Radiation Research Institute, SPring-8, Sayo, Hyogo, Japan
| | - Masaharu Ishii
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo City, Tokyo 113-8654, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo City, Tokyo 113-8654, Japan
| | - Takatoshi Arakawa
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba 278-8510, Japan.
| | - Shinya Fushinobu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo City, Tokyo 113-8654, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo City, Tokyo 113-8654, Japan.
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2
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Feng X, Kazama D, Sato K, Kobayashi H. Complete genome sequence of an Achromobacter xylosoxidans strain H1_3_1 isolated from a hybrid biological-inorganic system reactor. Microbiol Resour Announc 2023; 12:e0061223. [PMID: 37889011 PMCID: PMC10652924 DOI: 10.1128/mra.00612-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023] Open
Abstract
We report the complete genome of Achromobacter xylosoxidans strain H1_3_1, which was isolated from a reactor of a hybrid biological-inorganic system. The complete genome comprised 7,071,873 bp, including 6,428 codings, 10 rRNA, and 70 tRNA, with 67.4% G + C content.
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Affiliation(s)
- Xiang Feng
- Department of Systems Innovation, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Daichi Kazama
- Department of Systems Innovation, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Kozo Sato
- Department of Systems Innovation, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
- Frontier Research Center for Energy and Resources (FRCER), Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Hajime Kobayashi
- Department of Systems Innovation, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
- Frontier Research Center for Energy and Resources (FRCER), Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
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3
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Feng X, Kazama D, Sato K, Kobayashi H. Complete genome sequence of Mycolicibacterium mageritense strain H4_3_1 isolated from a hybrid biological-inorganic system reactor. Microbiol Resour Announc 2023; 12:e0023023. [PMID: 37787567 PMCID: PMC10586093 DOI: 10.1128/mra.00230-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/25/2023] [Indexed: 10/04/2023] Open
Abstract
We report the complete genome of Mycolicibacterium mageritense strain H4_3_1, which was isolated from a reactor of a hybrid biological-inorganic system. This genome will provide useful information about hydrogen-oxidizing bacteria as well as mycolicibacteria in non-host environments.
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Affiliation(s)
- Xiang Feng
- Department of Systems Innovation, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | - Daichi Kazama
- Department of Systems Innovation, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | - Kozo Sato
- Department of Systems Innovation, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
- Frontier Research Center for Energy and Resources (FRCER), Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | - Hajime Kobayashi
- Department of Systems Innovation, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
- Frontier Research Center for Energy and Resources (FRCER), Graduate School of Engineering, University of Tokyo, Tokyo, Japan
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4
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Feng X, Kazama D, He S, Nakayama H, Hayashi T, Tokunaga T, Sato K, Kobayashi H. Enrichment of halotolerant hydrogen-oxidizing bacteria and production of high-value-added chemical hydroxyectoine using a hybrid biological-inorganic system. Front Microbiol 2023; 14:1254451. [PMID: 37711693 PMCID: PMC10497747 DOI: 10.3389/fmicb.2023.1254451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 08/15/2023] [Indexed: 09/16/2023] Open
Abstract
Hybrid biological-inorganic (HBI) systems show great promise as CO2 conversion platforms combining CO2 fixation by hydrogen-oxidizing bacteria (HOB) with water splitting. Herein, halotolerant HOB were enriched using an HBI system with a high-ionic-strength medium containing 180 mM phosphate buffer to identify new biocatalysts. The reactors were inoculated with samples from saline environments and applied with a voltage of 2.0 V. Once an increase in biomass was observed with CO2 consumption, an aliquot of the medium was transferred to a new reactor. After two successive subcultures, Achromobacter xylosoxidans strain H1_3_1 and Mycolicibacterium mageritense strain H4_3_1 were isolated from the reactor media. Genome sequencing indicated the presence of genes for aerobic hydrogen-oxidizing chemolithoautotrophy and synthesis of the compatible solute hydroxyectoine in both strains. Furthermore, both strains produced hydroxyectoine in the reactors under the high-ionic-strength condition, suggesting the potential for new HBI systems using halotolerant HOB to produce high-value-added chemicals.
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Affiliation(s)
- Xiang Feng
- Department of Systems Innovation, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Daichi Kazama
- Department of Systems Innovation, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Sijia He
- Department of Systems Innovation, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Hideki Nakayama
- Department of Environmental Science, Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Japan
| | - Takeshi Hayashi
- Department of Regional Studies and Humanities, Faculty of Education and Human Studies, Akita University, Akita, Japan
| | - Tomochika Tokunaga
- Department of Environment Systems, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Kozo Sato
- Department of Systems Innovation, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
- Frontier Research Center for Energy and Resource, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Hajime Kobayashi
- Department of Systems Innovation, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
- Frontier Research Center for Energy and Resource, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
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Miyahara Y, Wang CT, Ishii-Hyakutake M, Tsuge T. Continuous Supply of Non-Combustible Gas Mixture for Safe Autotrophic Culture to Produce Polyhydroxyalkanoate by Hydrogen-Oxidizing Bacteria. Bioengineering (Basel) 2022; 9:bioengineering9100586. [PMID: 36290554 PMCID: PMC9598887 DOI: 10.3390/bioengineering9100586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/15/2022] [Accepted: 10/18/2022] [Indexed: 11/26/2022] Open
Abstract
Polyhydroxyalkanoates (PHAs) are eco-friendly plastics that are thermoplastic and biodegradable in nature. The hydrogen-oxidizing bacterium Ralstonia eutropha can biosynthesize poly[(R)-3-hydroxybutyrate] [P(3HB)], the most common PHA, from carbon dioxide using hydrogen and oxygen as energy sources. In conventional autotrophic cultivation using R. eutropha, a gas mixture containing 75−80 vol% hydrogen is supplied; however, a gas mixture with such a high hydrogen content has a risk of explosion due to gas leakage. In this study, we aimed to develop an efficient cell culture system with a continuous supply of a non-combustible gas mixture (H2: O2: CO2: N2 = 3.8: 7.3: 13.0: 75.9) for safe autotrophic culture to produce P(3HB) by hydrogen-oxidizing bacteria, with a controlled hydrogen concentration under a lower explosive limit concentration. When the gas mixture was continuously supplied to the jar fermentor, the cell growth of R. eutropha H16 significantly improved compared to that in previous studies using flask cultures. Furthermore, an increased gas flow rate and agitation speed enhanced both cell growth and P(3HB) production. Nitrogen source deficiency promoted P(3HB) production, achieving up to 2.94 g/L P(3HB) and 89 wt% P(3HB) content in the cells after 144 h cultivation. R. eutropha NCIMB 11599, recombinant R. eutropha PHB-4, and Azohydromonas lata grew in a low-hydrogen-content gas mixture. R. eutropha H16 and recombinant R. eutropha PHB-4 expressing PHA synthase from Bacillus cereus YB-4 synthesized P(3HB) with a high weight-average molecular weight of 13.5−16.9 × 105. Thus, this autotrophic culture system is highly beneficial for PHA production from carbon dioxide using hydrogen-oxidizing bacteria as the risk of explosion is eliminated.
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Affiliation(s)
- Yuki Miyahara
- Correspondence: (Y.M.); (T.T.); Tel.: +81-45-924-5420 (T.T.)
| | | | | | - Takeharu Tsuge
- Correspondence: (Y.M.); (T.T.); Tel.: +81-45-924-5420 (T.T.)
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6
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Claassens NJ, Scarinci G, Fischer A, Flamholz AI, Newell W, Frielingsdorf S, Lenz O, Bar-Even A. Phosphoglycolate salvage in a chemolithoautotroph using the Calvin cycle. Proc Natl Acad Sci U S A 2020; 117:22452-61. [PMID: 32820073 DOI: 10.1073/pnas.2012288117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The Calvin cycle is the most important carbon fixation pathway in the biosphere. However, its carboxylating enzyme Rubisco also accepts oxygen, thus producing 2-phosphoglycolate. Phosphoglycolate salvage pathways were extensively studied in photoautotrophs but remain uncharacterized in chemolithoautotrophs using the Calvin cycle. Here, we study phosphoglycolate salvage in the chemolithoautotrophic model bacterium Cupriavidus necator H16. We demonstrate that this bacterium mainly reassimilates 2-phosphoglycolate via the glycerate pathway. Upon disruption of this pathway, a secondary route, which we term the malate cycle, supports photorespiration by completely oxidizing 2-phosphoglycolate to CO2. While the malate cycle was not previously known to metabolize 2-phosphoglycolate in nature, a bioinformatic analysis suggests that it may support phosphoglycolate salvage in diverse chemoautotrophic bacteria. Carbon fixation via the Calvin cycle is constrained by the side activity of Rubisco with dioxygen, generating 2-phosphoglycolate. The metabolic recycling of phosphoglycolate was extensively studied in photoautotrophic organisms, including plants, algae, and cyanobacteria, where it is referred to as photorespiration. While receiving little attention so far, aerobic chemolithoautotrophic bacteria that operate the Calvin cycle independent of light must also recycle phosphoglycolate. As the term photorespiration is inappropriate for describing phosphoglycolate recycling in these nonphotosynthetic autotrophs, we suggest the more general term “phosphoglycolate salvage.” Here, we study phosphoglycolate salvage in the model chemolithoautotroph Cupriavidus necator H16 (Ralstonia eutropha H16) by characterizing the proxy process of glycolate metabolism, performing comparative transcriptomics of autotrophic growth under low and high CO2 concentrations, and testing autotrophic growth phenotypes of gene deletion strains at ambient CO2. We find that the canonical plant-like C2 cycle does not operate in this bacterium, and instead, the bacterial-like glycerate pathway is the main route for phosphoglycolate salvage. Upon disruption of the glycerate pathway, we find that an oxidative pathway, which we term the malate cycle, supports phosphoglycolate salvage. In this cycle, glyoxylate is condensed with acetyl coenzyme A (acetyl-CoA) to give malate, which undergoes two oxidative decarboxylation steps to regenerate acetyl-CoA. When both pathways are disrupted, autotrophic growth is abolished at ambient CO2. We present bioinformatic data suggesting that the malate cycle may support phosphoglycolate salvage in diverse chemolithoautotrophic bacteria. This study thus demonstrates a so far unknown phosphoglycolate salvage pathway, highlighting important diversity in microbial carbon fixation metabolism.
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Dumolin C, Peeters C, Ehsani E, Tahon G, De Canck E, Cnockaert M, Boon N, Vandamme P. Achromobacter veterisilvae sp. nov., from a mixed hydrogen-oxidizing bacteria enrichment reactor for microbial protein production. Int J Syst Evol Microbiol 2020; 70:530-536. [PMID: 31613739 DOI: 10.1099/ijsem.0.003786] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Strain LMG 30378T was isolated from a hydrogen-oxidizing bacteria enrichment reactor inoculated with forest soil. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that this strain belonged to the genus Achromobacter. Multilocus sequence analysis combined with sequence analysis of a 765 bp nrd A gene fragment both showed Achromobacter agilis LMG 3411T and Achromobacter denitrificans LMG 1231T to be the closest-related neighbours to strain LMG 30378T. Genome sequence analysis revealed a draft genome of 6.81 Mb with a G+C content of 67.2 mol%. In silico DNA-DNA hybridization with A. denitrificans LMG 1231T and A. agilis LMG 3411T showed 42.7 and 42.5% similarity, respectively, confirming that strain LMG 30378T represented a novel Achromobacter species. Phenotypic and metabolic characterization revealed acid phosphatase activity and the absence of phosphoamidase activity as distinctive features. The draft genome composes all necessary metabolic components to fix carbon dioxide and to oxidize molecular hydrogen, suggesting that strain LMG 30378T is a key organism in the enrichment reactor. Together, these data demonstrate that strain LMG 30378T represents a novel species of the genus Achromobacter, for which the name Achromobacter veterisilvae sp. nov. is proposed. The type strain is LMG 30378T (=CCUG 71558T).
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Affiliation(s)
- Charles Dumolin
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Elham Ehsani
- Center for Microbial Ecology and Technology (CMET), Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Guillaume Tahon
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium.,Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Evelien De Canck
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Margo Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Peter Vandamme
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium.,Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
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Nishihara A, Matsuura K, Tank M, McGlynn SE, Thiel V, Haruta S. Nitrogenase Activity in Thermophilic Chemolithoautotrophic Bacteria in the Phylum Aquificae Isolated under Nitrogen-Fixing Conditions from Nakabusa Hot Springs. Microbes Environ 2018; 33:394-401. [PMID: 30473565 PMCID: PMC6307999 DOI: 10.1264/jsme2.me18041] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The phylum Aquificae comprises chemolithoautotrophic thermophilic to hyperthermophilic bacteria, in which the nitrogenase reductase gene (nifH) has been reported. However, nitrogen-fixing activity has not yet been demonstrated in members of this deeply branching bacterial phylum. We isolated two thermophilic diazotrophic strains from chemosynthetic microbial communities in slightly alkaline hot springs (≥70°C) in Nakabusa, Nagano Prefecture, Japan. A phylogenetic analysis based on 16S rRNA genes identified these strains as members of the genus Hydrogenobacter within Aquificae. Their NifH sequences showed 96.5 and 97.4% amino acid sequence identities to that from Hydrogenobacter thermophilus TK-6. Nitrogenase activity, measured by acetylene reduction, was confirmed in both strains at 70°C. These novel strains grew under semi-aerobic conditions by using CO2 as the sole carbon source and N2 as the sole nitrogen source in media containing hydrogen and/or thiosulfate. To the best of our knowledge, this is the first demonstration of active nitrogen fixation in thermophilic bacteria at 70°C and in the phylum Aquificae.
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Affiliation(s)
- Arisa Nishihara
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Katsumi Matsuura
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Marcus Tank
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Shawn E McGlynn
- Department of Biological Sciences, Tokyo Metropolitan University.,Earth-Life Science Institute, Tokyo Institute of Technology.,Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource Science.,Blue Marble Space Institute of Science
| | - Vera Thiel
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University
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