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Yang JI, Jung HC, Oh HM, Choi BG, Lee HS, Kang SG. NADP + or CO 2 reduction by frhAGB-encoded hydrogenase through interaction with formate dehydrogenase 3 in the hyperthermophilic archaeon Thermococcus onnurineus NA1. Appl Environ Microbiol 2023; 89:e0147423. [PMID: 37966269 PMCID: PMC10734459 DOI: 10.1128/aem.01474-23] [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: 09/04/2023] [Accepted: 09/23/2023] [Indexed: 11/16/2023] Open
Abstract
IMPORTANCE The strategy using structural homology with the help of structure prediction by AlphaFold was very successful in finding potential targets for the frhAGB-encoded hydrogenase of Thermococcus onnurineus NA1. The finding that the hydrogenase can interact with FdhB to reduce the cofactor NAD(P)+ is significant in that the enzyme can function to supply reducing equivalents, just as F420-reducing hydrogenases in methanogens use coenzyme F420 as an electron carrier. Additionally, it was identified that T. onnurineus NA1 could produce formate from H2 and CO2 by the concerted action of frhAGB-encoded hydrogenase and formate dehydrogenase Fdh3.
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Affiliation(s)
- Ji-in Yang
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
| | - Hae-Chang Jung
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
| | | | - Bo Gyoung Choi
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
| | - Hyun Sook Lee
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
| | - Sung Gyun Kang
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
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2
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Moalic Y, Hartunians J, Dalmasso C, Courtine D, Georges M, Oger P, Shao Z, Jebbar M, Alain K. The Piezo-Hyperthermophilic Archaeon Thermococcus piezophilus Regulates Its Energy Efficiency System to Cope With Large Hydrostatic Pressure Variations. Front Microbiol 2021; 12:730231. [PMID: 34803948 PMCID: PMC8595942 DOI: 10.3389/fmicb.2021.730231] [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: 06/24/2021] [Accepted: 10/13/2021] [Indexed: 11/23/2022] Open
Abstract
Deep-sea ecosystems share a common physical parameter, namely high hydrostatic pressure (HHP). Some of the microorganisms isolated at great depths have a high physiological plasticity to face pressure variations. The adaptive strategies by which deep-sea microorganisms cope with HHP variations remain to be elucidated, especially considering the extent of their biotopes on Earth. Herein, we investigated the gene expression patterns of Thermococcus piezophilus, a piezohyperthermophilic archaeon isolated from the deepest hydrothermal vent known to date, under sub-optimal, optimal and supra-optimal pressures (0.1, 50, and 90 MPa, respectively). At stressful pressures [sub-optimal (0.1 MPa) and supra-optimal (90 MPa) conditions], no classical stress response was observed. Instead, we observed an unexpected transcriptional modulation of more than a hundred gene clusters, under the putative control of the master transcriptional regulator SurR, some of which are described as being involved in energy metabolism. This suggests a fine-tuning effect of HHP on the SurR regulon. Pressure could act on gene regulation, in addition to modulating their expression.
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Affiliation(s)
- Yann Moalic
- Univ Brest, CNRS, Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, UMR 6197, IUEM, Plouzané, France.,IRP 1211 MicrobSea, Sino-French Laboratory of Deep-Sea Microbiology, LM2E, Plouzané, France
| | - Jordan Hartunians
- Univ Brest, CNRS, Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, UMR 6197, IUEM, Plouzané, France.,IRP 1211 MicrobSea, Sino-French Laboratory of Deep-Sea Microbiology, LM2E, Plouzané, France
| | - Cécile Dalmasso
- Univ Brest, CNRS, Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, UMR 6197, IUEM, Plouzané, France.,IRP 1211 MicrobSea, Sino-French Laboratory of Deep-Sea Microbiology, LM2E, Plouzané, France
| | - Damien Courtine
- Univ Brest, CNRS, Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, UMR 6197, IUEM, Plouzané, France.,IRP 1211 MicrobSea, Sino-French Laboratory of Deep-Sea Microbiology, LM2E, Plouzané, France
| | - Myriam Georges
- Univ Brest, CNRS, Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, UMR 6197, IUEM, Plouzané, France.,IRP 1211 MicrobSea, Sino-French Laboratory of Deep-Sea Microbiology, LM2E, Plouzané, France
| | - Philippe Oger
- Université de Lyon, INSA Lyon, CNRS UMR 5240, Villeurbanne, France
| | - Zongze Shao
- IRP 1211 MicrobSea, Sino-French Laboratory of Deep-Sea Microbiology, LM2E, Plouzané, France.,Key Laboratory of Marine Biogenetic Resources, The Third Institute of Oceanography SOA, Xiamen, China
| | - Mohamed Jebbar
- Univ Brest, CNRS, Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, UMR 6197, IUEM, Plouzané, France.,IRP 1211 MicrobSea, Sino-French Laboratory of Deep-Sea Microbiology, LM2E, Plouzané, France
| | - Karine Alain
- Univ Brest, CNRS, Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, UMR 6197, IUEM, Plouzané, France.,IRP 1211 MicrobSea, Sino-French Laboratory of Deep-Sea Microbiology, LM2E, Plouzané, France
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3
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Direct Electron Transfer between the frhAGB-Encoded Hydrogenase and Thioredoxin Reductase in the Nonmethanogenic Archaeon Thermococcus onnurineus NA1. Appl Environ Microbiol 2020; 86:AEM.02630-19. [PMID: 31924613 DOI: 10.1128/aem.02630-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 12/21/2019] [Indexed: 11/20/2022] Open
Abstract
To date, NAD(P)H, ferredoxin, and coenzyme F420 have been identified as electron donors for thioredoxin reductase (TrxR). In this study, we present a novel electron source for TrxR. In the hyperthermophilic archaeon Thermococcus onnurineus NA1, the frhAGB-encoded hydrogenase, a homolog of the F420-reducing hydrogenase of methanogens, was demonstrated to interact with TrxR in coimmunoprecipitation experiments and in vitro pulldown assays. Electrons derived from H2 oxidation by the frhAGB-encoded hydrogenase were transferred to TrxR and reduced Pdo, a redox partner of TrxR. Interaction and electron transfer were observed between TrxR and the heterodimeric hydrogenase complex (FrhAG) as well as the heterotrimeric complex (FrhAGB). Hydrogen-dependent reduction of TrxR was 7-fold less efficient than when NADPH was the electron donor. This study not only presents a different type of electron donor for TrxR but also reveals new functionality of the frhAGB-encoded hydrogenase utilizing a protein as an electron acceptor.IMPORTANCE This study has importance in that TrxR can use H2 as an electron donor with the aid of the frhAGB-encoded hydrogenase as well as NAD(P)H in T. onnurineus NA1. Further studies are needed to explore the physiological significance of this protein. This study also has importance as a significant step toward understanding the functionality of the frhAGB-encoded hydrogenase in a nonmethanogen; the hydrogenase can transfer electrons derived from oxidation of H2 to a protein target by direct contact without the involvement of an electron carrier, which is distinct from the mechanism of its homologs, F420-reducing hydrogenases of methanogens.
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4
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Lee SH, Kim MS, Kang SG, Lee HS. Biohydrogen production of obligate anaerobic archaeon Thermococcus onnurineus NA1 under oxic conditions via overexpression of frhAGB-encoding hydrogenase genes. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:24. [PMID: 30774712 PMCID: PMC6367845 DOI: 10.1186/s13068-019-1365-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/29/2019] [Indexed: 05/15/2023]
Abstract
BACKGROUND The production of biohydrogen (H2) as a promising future fuel in anaerobic hyperthermophiles has attracted great attention because H2 formation is more thermodynamically feasible at elevated temperatures and fewer undesired side products are produced. However, these microbes require anoxic culture conditions for growth and H2 production, thereby necessitating costly and time-consuming physical or chemical methods to remove molecular oxygen (O2). Therefore, the development of an O2-tolerant strain would be useful for industrial applications. RESULTS In this study, we found that the overexpression of frhAGB-encoding hydrogenase genes in Thermococcus onnurineus NA1, an obligate anaerobic archaeon and robust H2 producer, enhanced O2 tolerance. When the recombinant FO strain was exposed to levels of O2 up to 20% in the headspace of a sealed bottle, it showed significant growth. Whole transcriptome analysis of the FO strain revealed that several genes involved in the stress response such as chaperonin β subunit, universal stress protein, peroxiredoxin, and alkyl hydroperoxide reductase subunit C, were significantly up-regulated. The O2 tolerance of the FO strain enabled it to grow on formate and produce H2 under oxic conditions, where prior O2-removing steps were omitted, such as the addition of reducing agent Na2S, autoclaving, and inert gas purging. CONCLUSIONS Via the overexpression of frhAGB genes, the obligate anaerobic archaeon T. onnurineus NA1 gained the ability to overcome the inhibitory effect of O2. This O2-tolerant property of the strain may provide another advantage to this hyperthermophilic archaeon as a platform for biofuel H2 production.
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Affiliation(s)
- Seong Hyuk Lee
- Korea Institute of Ocean Science and Technology, Busan, 49111 Republic of Korea
| | - Min-Sik Kim
- Biomass and Waste Energy Laboratory, Korea Institute of Energy Research, Daejeon, 34129 Republic of Korea
| | - Sung Gyun Kang
- Korea Institute of Ocean Science and Technology, Busan, 49111 Republic of Korea
- Department of Marine Biotechnology, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Hyun Sook Lee
- Korea Institute of Ocean Science and Technology, Busan, 49111 Republic of Korea
- Department of Marine Biotechnology, Korea University of Science and Technology, Daejeon, Republic of Korea
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5
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St John E, Liu Y, Podar M, Stott MB, Meneghin J, Chen Z, Lagutin K, Mitchell K, Reysenbach AL. A new symbiotic nanoarchaeote (Candidatus Nanoclepta minutus) and its host (Zestosphaera tikiterensis gen. nov., sp. nov.) from a New Zealand hot spring. Syst Appl Microbiol 2018; 42:94-106. [PMID: 30195930 DOI: 10.1016/j.syapm.2018.08.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/08/2018] [Accepted: 08/08/2018] [Indexed: 01/22/2023]
Abstract
Three thermophilic Nanoarchaeota-Crenarchaeota symbiotic systems have been described. We obtained another stable anaerobic enrichment culture at 80°C, pH 6.0 from a New Zealand hot spring. The nanoarchaeote (Ncl-1) and its host (NZ3T) were isolated in co-culture and their genomes assembled. The small (∼200nm) flagellated cocci were often attached to larger cocci. Based on 16S rRNA gene similarity (88.4%) and average amino acid identity (52%), Ncl-1 is closely related to Candidatus Nanopusillus acidilobi. Their genomes both encode for archaeal flagella and partial glycolysis and gluconeogenesis pathways, but lack ATP synthase genes. Like Nanoarchaeum equitans, Ncl-1 has a CRISPR-Cas system. Ncl-1 also relies on its crenarchaeotal host for most of its biosynthetic needs. The host NZ3T was isolated and grows on proteinaceous substrates but not on sugars, alcohols, or fatty acids. NZ3T requires thiosulfate and grows best at 82°C, pH 6.0. NZ3T is most closely related to the Desulfurococcaceae, Ignisphaera aggregans (∼92% 16S rRNA gene sequence similarity, 45% AAI). Based on phylogenetic, physiological and genomic data, Ncl-1 and NZ3T represent novel genera in the Nanoarchaeota and the Desulfurococcaceae, respectively, with the proposed names Candidatus Nanoclepta minutus and Zestosphaera tikiterensis gen. nov., sp. nov., type strain NZ3T (=DSMZ 107634T=OCM 1213T).
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Affiliation(s)
- Emily St John
- Biology Department, Portland State University, Portland, OR 97201, USA
| | - Yitai Liu
- Biology Department, Portland State University, Portland, OR 97201, USA
| | - Mircea Podar
- Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA; Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Jennifer Meneghin
- Biology Department, Portland State University, Portland, OR 97201, USA
| | - Zhiqiang Chen
- Center for Electron Microscopy and Nanofabrication, Portland State University, Portland, OR 97201, USA
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6
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Müller V, Chowdhury NP, Basen M. Electron Bifurcation: A Long-Hidden Energy-Coupling Mechanism. Annu Rev Microbiol 2018; 72:331-353. [PMID: 29924687 DOI: 10.1146/annurev-micro-090816-093440] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A decade ago, a novel mechanism to drive thermodynamically unfavorable redox reactions was discovered that is used in prokaryotes to drive endergonic electron transfer reactions by a direct coupling to an exergonic redox reaction in one soluble enzyme complex. This process is referred to as flavin-based electron bifurcation, or FBEB. An important function of FBEB is that it allows the generation of reduced low-potential ferredoxin (Fdred) from comparably high-potential electron donors such as NADH or molecular hydrogen (H2). Fdred is then the electron donor for anaerobic respiratory chains leading to the synthesis of ATP. In many metabolic scenarios, Fd is reduced by metabolic oxidoreductases and Fdred then drives endergonic metabolic reactions such as H2 production by the reverse, electron confurcation. FBEB is energetically more economical than ATP hydrolysis or reverse electron transport as a driving force for endergonic redox reactions; thus, it does "save" cellular ATP. It is essential for autotrophic growth at the origin of life and also allows for heterotrophic growth on certain low-energy substrates.
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Affiliation(s)
- Volker Müller
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, 60438 Frankfurt, Germany;
| | - Nilanjan Pal Chowdhury
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, 60438 Frankfurt, Germany;
| | - Mirko Basen
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, 60438 Frankfurt, Germany;
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7
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Topçuoğlu BD, Meydan C, Orellana R, Holden JF. Formate hydrogenlyase and formate secretion ameliorate H
2
inhibition in the hyperthermophilic archaeon
Thermococcus paralvinellae. Environ Microbiol 2017; 20:949-957. [DOI: 10.1111/1462-2920.14022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 11/06/2017] [Accepted: 11/06/2017] [Indexed: 11/26/2022]
Affiliation(s)
- Begüm D. Topçuoğlu
- Department of MicrobiologyUniversity of MassachusettsAmherst MA 01003 USA
| | - Cem Meydan
- Institute for Computational Biomedicine, Weill Cornell Medical CollegeNew York NY 10021 USA
| | - Roberto Orellana
- Centro de Biotecnología, Universidad Técnica Federico Santa MaríaValparaíso Chile
| | - James F. Holden
- Department of MicrobiologyUniversity of MassachusettsAmherst MA 01003 USA
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8
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Jung HC, Lee SH, Lee SM, An YJ, Lee JH, Lee HS, Kang SG. Adaptive evolution of a hyperthermophilic archaeon pinpoints a formate transporter as a critical factor for the growth enhancement on formate. Sci Rep 2017; 7:6124. [PMID: 28733620 PMCID: PMC5522443 DOI: 10.1038/s41598-017-05424-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 05/30/2017] [Indexed: 11/26/2022] Open
Abstract
Previously, we reported that the hyperthermophilic archaeon Thermococcus onnurineus NA1 could grow on formate and produce H2. Formate conversion to hydrogen was mediated by a formate-hydrogen lyase complex and was indeed a part of chemiosmotic coupling to ATP generation. In this study, we employed an adaptation approach to enhance the cell growth on formate and investigated molecular changes. As serial transfer continued on formate-containing medium at the serum vial, cell growth, H2 production and formate consumption increased remarkably. The 156 times transferred-strain, WTF-156T, was demonstrated to enhance H2 production using formate in a bioreactor. The whole-genome sequencing of the WTF-156T strain revealed eleven mutations. While no mutation was found among the genes encoding formate hydrogen lyase, a point mutation (G154A) was identified in a formate transporter (TON_1573). The TON_1573 (A52T) mutation, when introduced into the parent strain, conferred increase in formate consumption and H2 production. Another adaptive passage, carried out by culturing repeatedly in a bioreactor, resulted in a strain, which has a mutation in TON_1573 (C155A) causing amino acid change, A52E. These results implicate that substitution of A52 residue of a formate transporter might be a critical factor to ensure the increase in formate uptake and cell growth.
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Affiliation(s)
- Hae-Chang Jung
- Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea.,Department of Marine Biotechnology, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Seong Hyuk Lee
- Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea
| | - Sung-Mok Lee
- Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea
| | - Young Jun An
- Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea
| | - Jung-Hyun Lee
- Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea.,Department of Marine Biotechnology, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Hyun Sook Lee
- Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea. .,Department of Marine Biotechnology, Korea University of Science and Technology, Daejeon, Republic of Korea.
| | - Sung Gyun Kang
- Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea. .,Department of Marine Biotechnology, Korea University of Science and Technology, Daejeon, Republic of Korea.
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9
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Giovannelli D, Sievert SM, Hügler M, Markert S, Becher D, Schweder T, Vetriani C. Insight into the evolution of microbial metabolism from the deep-branching bacterium, Thermovibrio ammonificans. eLife 2017; 6. [PMID: 28436819 PMCID: PMC5441870 DOI: 10.7554/elife.18990] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 04/23/2017] [Indexed: 01/10/2023] Open
Abstract
Anaerobic thermophiles inhabit relic environments that resemble the early Earth. However, the lineage of these modern organisms co-evolved with our planet. Hence, these organisms carry both ancestral and acquired genes and serve as models to reconstruct early metabolism. Based on comparative genomic and proteomic analyses, we identified two distinct groups of genes in Thermovibrio ammonificans: the first codes for enzymes that do not require oxygen and use substrates of geothermal origin; the second appears to be a more recent acquisition, and may reflect adaptations to cope with the rise of oxygen on Earth. We propose that the ancestor of the Aquificae was originally a hydrogen oxidizing, sulfur reducing bacterium that used a hybrid pathway for CO2 fixation. With the gradual rise of oxygen in the atmosphere, more efficient terminal electron acceptors became available and this lineage acquired genes that increased its metabolic flexibility while retaining ancestral metabolic traits. DOI:http://dx.doi.org/10.7554/eLife.18990.001 Life may have arisen on our planet as far back as four billion years ago. Unlike today, the Earth’s atmosphere at the time had no oxygen and an abundance of volcanic emissions including hydrogen, carbon dioxide and sulfur gases. These dramatic differences have led scientists to wonder: how did the ancient microorganisms that inhabited our early planet make a living? And how has microbial life co-evolved with the Earth? One way to answer these questions is to study bacteria that live today in environments that resemble the early Earth. Deep-sea hydrothermal vents are regions of the deep ocean where active volcanic processes recreate primordial conditions. These habitats support microorganisms that are highly adapted to live off hydrogen, carbon dioxide and sulfur gases, and studying these modern-day microorganisms could give insights into the earliest life on Earth. Thermovibrio ammonificans is a bacterium that was obtained from an underwater volcanic system in the East Pacific. Giovannelli et al. have now asked if T. ammonificans might have inherited some of its genetic traits from a long-gone ancestor that also thrived off volcanic gases. The genetic makeup of this microorganism was examined for genes that would help it thrive at a deep-sea hydrothermal vent. Next, Giovannelli et al. compared these genes to related copies in other species of bacteria to reconstruct how the metabolism of T. ammonificans might have changed over time. This approach identified a group of likely ancient genesthat allow a microorganism to use chemicals like hydrogen, carbon dioxide and sulfur to fuel its growth and metabolism. These findings support the hypothesis that an ancestor of T. ammonificans could live off volcanic gases and that the core set of genes involved in those activities had been passed on, through the generations, to this modern-day microorganism. Giovannelli et al. also identified a second group of genes in T. ammonificans that indicate that this bacterium also co-evolved with Earth’s changing conditions, in particular the rise in the concentration of oxygen. The findings of Giovannelli et al. provide insight into how the metabolism of microbes has co-evolved with the Earth’s changing conditions, and will allow others to formulate new hypotheses that can be tested in laboratory experiments. DOI:http://dx.doi.org/10.7554/eLife.18990.002
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Affiliation(s)
- Donato Giovannelli
- Institute of Earth, Ocean and Atmospheric Sciences, Rutgers University, New Brunswick, United States.,Institute of Marine Science, National Research Council of Italy, Ancona, Italy.,Program in Interdisciplinary Studies, Institute for Advanced Studies, Princeton, United States.,Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | - Stefan M Sievert
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, United States
| | | | - Stephanie Markert
- Pharmaceutical Biotechnology, Institute of Pharmacy, Institute of Pharmacy, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Dörte Becher
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Thomas Schweder
- Pharmaceutical Biotechnology, Institute of Pharmacy, Institute of Pharmacy, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Costantino Vetriani
- Institute of Earth, Ocean and Atmospheric Sciences, Rutgers University, New Brunswick, United States.,Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, United States
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10
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Lee SH, Kim MS, Kim YJ, Kim TW, Kang SG, Lee HS. Transcriptomic profiling and its implications for the H 2 production of a non-methanogen deficient in the frhAGB-encoding hydrogenase. Appl Microbiol Biotechnol 2017; 101:5081-5088. [PMID: 28341885 DOI: 10.1007/s00253-017-8234-4] [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: 09/01/2016] [Revised: 03/02/2017] [Accepted: 03/07/2017] [Indexed: 10/19/2022]
Abstract
The F420-reducing hydrogenase of methanogens functions in methanogenesis by providing reduced coenzyme F420 (F420H2) as an electron donor. In non-methanogens, however, their physiological function has not been identified yet. In this study, we constructed an ΔfrhA mutant, whose frhA gene encoding the hydrogenase α subunit was deleted, in the non-methanogenic Thermococcus onnurineus NA1 as a model organism. There was no significant difference in the formate-dependent growth between the mutant and the wild-type strains. Interestingly, the mutation in the frhA gene affected the expression of genes involved in various cellular functions such as H2 oxidation, chemotactic signal transduction, and carbon monoxide (CO) metabolism. Among these genes, the CO oxidation gene cluster, enabling CO-dependent growth and H2 production, showed a 2.8- to 7.0-fold upregulation by microarray-based whole transcriptome expression profiling. The levels of proteins produced by this gene cluster were also significantly increased not only under the formate condition but also under the CO condition. In a controlled bioreactor, where 100% CO was continuously fed, the ΔfrhA mutant exhibited significant increases in cell growth (2.8-fold) and H2 production (3.4-fold). These findings strongly imply that this hydrogenase is functional in non-methanogens and is related to various cellular metabolic processes through an unidentified mechanism. An understanding of the mechanism by which the frhA gene deletion affected the expression of other genes will provide insights that can be applied to the development of strategies for the enhancement of H2 production using CO as a substrate.
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Affiliation(s)
- Seong Hyuk Lee
- Korea Institute of Ocean Science and Technology, Ansan, 15627, Republic of Korea
| | - Min-Sik Kim
- Korea Institute of Ocean Science and Technology, Ansan, 15627, Republic of Korea.,Biomass and Waste Energy Laboratory, Korea Institute of Energy Research, Daejeon, 34129, Republic of Korea
| | - Yun Jae Kim
- Korea Institute of Ocean Science and Technology, Ansan, 15627, Republic of Korea.,Department of Marine Biotechnology, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Tae Wan Kim
- Korea Institute of Ocean Science and Technology, Ansan, 15627, Republic of Korea.,Department of Marine Biotechnology, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Sung Gyun Kang
- Korea Institute of Ocean Science and Technology, Ansan, 15627, Republic of Korea. .,Department of Marine Biotechnology, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea.
| | - Hyun Sook Lee
- Korea Institute of Ocean Science and Technology, Ansan, 15627, Republic of Korea. .,Department of Marine Biotechnology, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea.
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11
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Physiology, Biochemistry, and Applications of F420- and Fo-Dependent Redox Reactions. Microbiol Mol Biol Rev 2016; 80:451-93. [PMID: 27122598 DOI: 10.1128/mmbr.00070-15] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
5-Deazaflavin cofactors enhance the metabolic flexibility of microorganisms by catalyzing a wide range of challenging enzymatic redox reactions. While structurally similar to riboflavin, 5-deazaflavins have distinctive and biologically useful electrochemical and photochemical properties as a result of the substitution of N-5 of the isoalloxazine ring for a carbon. 8-Hydroxy-5-deazaflavin (Fo) appears to be used for a single function: as a light-harvesting chromophore for DNA photolyases across the three domains of life. In contrast, its oligoglutamyl derivative F420 is a taxonomically restricted but functionally versatile cofactor that facilitates many low-potential two-electron redox reactions. It serves as an essential catabolic cofactor in methanogenic, sulfate-reducing, and likely methanotrophic archaea. It also transforms a wide range of exogenous substrates and endogenous metabolites in aerobic actinobacteria, for example mycobacteria and streptomycetes. In this review, we discuss the physiological roles of F420 in microorganisms and the biochemistry of the various oxidoreductases that mediate these roles. Particular focus is placed on the central roles of F420 in methanogenic archaea in processes such as substrate oxidation, C1 pathways, respiration, and oxygen detoxification. We also describe how two F420-dependent oxidoreductase superfamilies mediate many environmentally and medically important reactions in bacteria, including biosynthesis of tetracycline and pyrrolobenzodiazepine antibiotics by streptomycetes, activation of the prodrugs pretomanid and delamanid by Mycobacterium tuberculosis, and degradation of environmental contaminants such as picrate, aflatoxin, and malachite green. The biosynthesis pathways of Fo and F420 are also detailed. We conclude by considering opportunities to exploit deazaflavin-dependent processes in tuberculosis treatment, methane mitigation, bioremediation, and industrial biocatalysis.
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Complete Genome Sequence of the Hyperthermophilic and Piezophilic Archaeon Thermococcus barophilus Ch5, Capable of Growth at the Expense of Hydrogenogenesis from Carbon Monoxide and Formate. GENOME ANNOUNCEMENTS 2016; 4:4/1/e01534-15. [PMID: 26769929 PMCID: PMC4714111 DOI: 10.1128/genomea.01534-15] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report here the complete sequence and fully manually curated annotation of the genome of strain Ch5, a new member of the piezophilic hyperthermophilic species Thermococcus barophilus.
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