研究者基本情報

• 博士（環境科学）, 北海道大学, 2014年03月

• https://researchmap.jp/tomohirowatanabe

• https://orcid.org/0000-0002-5397-2124
• https://jglobal.jst.go.jp/detail?JGLOBAL_ID=202101005787886340
• https://www2.lowtem.hokudai.ac.jp/micro-ecol/member/index.html

• 80731968

• https://orcid.org/0000-0002-5397-2124

• HTR-1086-2023

• 202101005787886340

• 修士課程, 環境科学院
• 博士課程, 環境科学院

研究活動情報

• Desulforhopalus glucosivorans sp. nov., a sulphate-reducing bacterium isolated from brackish lake sediment
  Tomohiro Watanabe; Tatsuya Yabe; Jackson M. Tsuji; Manabu Fukui
  International Journal of Systematic and Evolutionary Microbiology, 2026年04月21日
  研究論文（学術雑誌）
• Anoxygenic phototroph of the Chloroflexota uses a type I reaction centre.
  Jackson M. Tsuji; Nicolette Shaw; Nagashima S; Jason J. Venkiteswaran; Schiff SL; Watanabe T; Fukui M; Hanada S; Tank M; Josh Neufeld
  Nature, 2024年03月13日
  研究論文（学術雑誌）, Scientific exploration of phototrophic bacteria over nearly 200 years has revealed large phylogenetic gaps between known phototrophic groups that limit understanding of how phototrophy evolved and diversified^1,2. Here, through Boreal Shield lake water incubations, we cultivated an anoxygenic phototrophic bacterium from a previously unknown order within the Chloroflexota phylum that represents a highly novel transition form in the evolution of photosynthesis. Unlike all other known phototrophs, this bacterium uses a type I reaction centre (RCI) for light energy conversion yet belongs to the same bacterial phylum as organisms that use a type II reaction centre (RCII) for phototrophy. Using physiological, phylogenomic and environmental metatranscriptomic data, we demonstrate active RCI-utilizing metabolism by the strain alongside usage of chlorosomes³ and bacteriochlorophylls⁴ related to those of RCII-utilizing Chloroflexota members. Despite using different reaction centres, our phylogenomic data provide strong evidence that RCI-utilizing and RCII-utilizing Chloroflexia members inherited phototrophy from a most recent common phototrophic ancestor. The Chloroflexota phylum preserves an evolutionary record of the use of contrasting phototrophic modes among genetically related bacteria, giving new context for exploring the diversification of phototrophy on Earth.
• Desulfoferula mesophilus gen. nov. sp. nov., a mesophilic sulfate-reducing bacterium isolated from a brackish lake sediment
  Tomohiro Watanabe; Tatsuya Yabe; Jackson M. Tsuji; Manabu Fukui
  Archives of Microbiology, 2023年12月
  研究論文（学術雑誌）
• Thiomicrorhabdus immobilis sp. nov., a mesophilic sulfur-oxidizing bacterium isolated from sediment of a brackish lake in northern Japan.
  Hisaya Kojima; Jun Mochizuki; Mamoru Kanda; Tomohiro Watanabe; Manabu Fukui
  Archives of microbiology, 204, 10, 605, 605, 2022年09月07日, ［国際誌］
  英語, 研究論文（学術雑誌）, A novel sulfur-oxidizing bacterium, strain Am19T, was isolated from sediment of a brackish lake. Strain Am19T grew chemolithoautotrophically on inorganic sulfur compounds, and heterotrophic growth was not observed. Cells were rod-shaped with length of 1.1-3.0 μm and diameter of 0.5-0.8 μm. Growth was observed at 5-37 °C with an optimum growth temperature of 30 °C. The pH range for growth was 5.6-8.5 with an optimum pH of 6.6-7.0. Major fatty acids were summed feature 3 (C16: 1ω7c and/or C16: 1ω6c), summed feature 8 (C18: 1ω7c and/or C18: 1ω6c) and C16: 0. The sole respiratory quinone was ubiquinone-8. The complete genome of strain Am19T is composed of a circular chromosome with length of 2.5 Mbp and G + C content of 42.7 mol%. Phylogenetic analysis based on genomic data indicated that strain Am19T belongs to the genus Thiomicrorhabdus but is distinct from any existing species. Analysis of the 16S rRNA gene supported creation of a new species to accommodate strain Am19T. On the basis of genomic and phenotypic characteristics, strain Am19T (= NBRC 114602 T = BCRC 81336 T) is proposed as the type strain of a new species, with name of Thiomicrorhabdus immobilis sp. nov.
• Structures of methanogenic Fdh-Hdr-Fmd complexes give insight into direct electron transfer and electron bifurcation processes
  Tomohiro Watanabe; Olivia Pfeil-Gardiner; Seigo Shima; Bonnie J. Murphy
  Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1863, 148739, 148739, Elsevier {BV}, 2022年09月
  英語, 研究論文（学術雑誌）
• Sulfurimonas aquatica sp. nov., a sulfur-oxidizing bacterium isolated from water of a brackish lake.
  Hisaya Kojima; Yukako Kato; Tomohiro Watanabe; Manabu Fukui
  Archives of microbiology, 204, 9, 559, 559, 2022年08月17日, ［国際誌］
  英語, 研究論文（学術雑誌）, A novel chemolithoautotrophic bacterium, strain H1576T, was isolated from water of a brackish lake. Strain H1576T grew aerobically on inorganic sulfur compounds. Hydrogen gas did not support autotrophic growth, and heterotrophic growth was not observed. Cells were rod shaped, motile, 1.5-2.7 μm in length and 0.6-0.7 μm in width. Growth was observed at 3-22 °C with an optimum growth temperature of 13-15 °C. The pH range for growth was 6.0-7.4 with an optimum pH of 6.6-6.8. Major fatty acids were summed feature 3 (C16: 1ω7c and/or C16: 1ω6c). The complete genome of strain H1576T consists of a circular chromosome and a plasmid, with total length of 2.8 Mbp and G+C content of 46.4 mol%. Phylogenetic analyses indicated that strain H1576T belongs to the genus Sulfurimonas but distinct from representatives of existing species. On the basis of genomic and phenotypic characteristics, a new species named Sulfurimonas aquatica sp. nov. is proposed with the type strain of strain H1576T (= BCRC 81254T = JCM 35004T).
• Dissimilatory microbial sulfur and methane metabolism in the water column of a shallow meromictic lake
  Tomohiro Watanabe; Kyoko Kubo; Yoshiharu Kamei; Hisaya Kojima; Manabu Fukui
  Systematic and Applied Microbiology, 45, 3, 126320, 126320, Elsevier {BV}, 2022年05月, ［国際誌］
  英語, 研究論文（学術雑誌）, Lake Harutori is a brackish meromictic lake with a steep physicochemical gradient in shallow water. Anoxic water below the chemocline has been characterized by high concentrations of sulfide (>10 mM) and methane (>1.5 mM). Previously, we reported that uncultured bacteria in the SEEP-SRB1 group were major sulfate reducers in the lake [21], but knowledge of sulfur oxidation and methane metabolism was scarce. In this current study, the Lake Harutori microbial community structure in the mixolimnion (at depths of 1.5 m and 3.0 m), upper chemocline (3.5 m), and monimolimnion (4.5 m) was further investigated by 16S rRNA gene amplicon sequencing and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH). Reads of type I and II methanotrophs were retrieved mainly from 3.5 m and above. Methanotrophic bacteria detected by CARD-FISH accounted for 3.1% of DAPI-stained cells at 3.5 m. Detection frequencies of reads affiliated with the genera Sulfurimonas and Thiomicrorhabdus, which are known to comprise sulfur oxidizers, were relatively high at 3.5 m. Methanogenic archaeal reads were retrieved from the monimolimnion and they affiliated with the genus Methanosaeta. CARD-FISH counts indicated that the cells of Methanosaeta/Methanosarcina/Methanomicrobiales accounted for up to 0.8% of the DAPI-stained cells in the monimolimnion. On the other hand, many of the reads retrieved primarily from the monimolimnion were affiliated with phylogenetically novel uncultured groups.
• A enzyme complex of methanogenic electron-bifurcating and CO2-fixing enzymes
  Tomohiro Watanabe
  Bioscience & Industry, 2022年03月10日
  研究論文（学術雑誌）
• Three-megadalton complex of methanogenic electron-bifurcating and CO 2 -fixing enzymes
  Tomohiro Watanabe; Olivia Pfeil-Gardiner; Jörg Kahnt; Jürgen Koch; Seigo Shima; Bonnie J. Murphy
  Science, 373, 6559, 1151, 1156, American Association for the Advancement of Science ({AAAS}), 2021年09月03日
  研究論文（学術雑誌）
• MvhB-type polyferredoxin as an electron-transfer chain in putative redox-enzyme complexes
  Tomohiro Watanabe; Seigo Shima
  Chemistry Letters, The Chemical Society of Japan, 2020年11月18日
  英語, 研究論文（学術雑誌）
• Anoxygenic phototrophicChloroflexotamember uses a Type I reaction center
  JM Tsuji; NA Shaw; S Nagashima; JJ Venkiteswaran; SL Schiff; T Watanabe; M Fukui; S Hanada; M Tank; JD Neufeld
  2020年07月07日
• The Bacterial [Fe]-Hydrogenase Paralog HmdII Uses Tetrahydrofolate Derivatives as Substrates
  Tomohiro Watanabe; Tristan Wagner; Gangfeng Huang; Jörg Kahnt; Kenichi Ataka; Ulrich Ermler; Seigo Shima
  Angewandte Chemie International Edition, 58, 11, 3506, 3510, 2019年03月11日
  英語, 研究論文（学術雑誌）
• Genomes of Neutrophilic Sulfur-Oxidizing Chemolithoautotrophs Representing 9 Proteobacterial Species From 8 Genera
  Tomohiro Watanabe; Hisaya Kojima; Kazuhiro Umezawa; Chiaki Hori; Taichi E. Takasuka; Yukako Kato; Manabu Fukui
  FRONTIERS IN MICROBIOLOGY, 10, 2019年02月
  英語, 研究論文（学術雑誌）
• Diversity of anaerobic arsenite-oxidizing bacteria in low-salt environments analyzed with a newly developed PCR-based method
  Melody Cabrera Ospino; Hisaya Kojima; Tomohiro Watanabe; Tomoya Iwata; Manabu Fukui
  Limnology, 19, 2, 177, 183, 2018年04月
  英語, 研究論文（学術雑誌）
• Dominance of Sulfuritalea species in nitrate-depleted water of a stratified freshwater lake and arsenate respiration ability within the genus
  Tomohiro Watanabe; Aya Miura; Tomoya Iwata; Hisaya Kojima; Manabu Fukui
  Environmental Microbiology Reports, 9, 5, 522, 527, Wiley, 2017年10月, ［国際誌］
  英語, 研究論文（学術雑誌）, Facultative autotrophs of the genus Sulfuritalea within the class Betaproteobacteria have been predicted to be an important bacterial population in stratified freshwater lakes based on previous PCR-based studies. Here, we designed a new probe specific for the genus Sulfuritalea and performed catalysed reporter deposition-fluorescence in situ hybridisation to enumerate cells of Sulfuritalea species throughout the water column in a stratified freshwater lake. The cells stained with the Sulfuritalea-specific probe were detected in all hypoxic water samples collected in different seasons and years. Their abundance ranged from 1.4 × 104 to 2.1 × 105 cells ml-1 , corresponding to 0.5-5.5% of the total DAPI-stained cells and 2.3-15% of the total bacterial cells. A high abundance of Sulfuritalea species was recorded in hypoxic water samples without nitrate, which is the only known anaerobic electron acceptor for Sulfuritalea. Nitrate-independent anaerobic respiration was further investigated using a single cultured representative of this genus, and its growth via arsenate respiration was experimentally demonstrated. In conclusion, Sulfuritalea species were found to be a major component of the planktonic bacterial community in nitrate-depleted hypoxic water, where arsenate respiration is one of the possible energy metabolisms of Sulfuritalea.
• The complete genome sequences of sulfur-oxidizing Gammaproteobacteria Sulfurifustis variabilis skN76T and Sulfuricaulis limicola HA5T
  Kazuhiro Umezawa; Tomohiro Watanabe; Aya Miura; Hisaya Kojima; Manabu Fukui
  Standards in Genomic Sciences, 11, 1, 2016年12月
  英語, 研究論文（学術雑誌）
• Identity of major sulfur-cycle prokaryotes in freshwater lake ecosystems revealed by a comprehensive phylogenetic study of the dissimilatory adenylylsulfate reductase
  Tomohiro Watanabe; Hisaya Kojima; Manabu Fukui
  Scientific Reports, 6, 1, 2016年12月
  英語, 研究論文（学術雑誌）
• Thermithiobacillus plumbiphilus sp. nov., a sulfur-oxidizing bacterium isolated from lead sulfide
  Tomohiro Watanabe; Aya Miura; Arisa Shinohara; Hisaya Kojima; Manabu Fukui
  International Journal of Systematic and Evolutionary Microbiology, 66, 5, 1986, 1989, Microbiology Society, 2016年05月01日, ［国際誌］
  英語, 研究論文（学術雑誌）, A novel sulfur oxidizer, strain wk12T, was isolated from an industrially synthesized lead (II) sulfide. The G+C content of the genomic DNA was around 58.5 mol%. The major components in the cellular fatty acid profile were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The strain oxidized lead sulfide, thiosulfate and tetrathionate as electron donors to support autotrophic growth. Cells of strain wk12T were motile, rod-shaped (0.5-1.0 × 0.7-2.2 μm), and Gram-stain-negative. For growth, the temperature range was 5-37 °C, and optimum growth was observed at 28-32 °C. The pH range for growth was 5.8-8.7, with optimum growth at pH 6.4-7.1. Optimum growth of the isolate was observed in medium without NaCl, and no growth was observed in the medium containing 0.5 M or more NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belongs to the class Acidithiobacillia. The closest relative with a validly published name was Thermithiobacillus tepidarius DSM 3134T, with a 16S rRNA gene sequence similarity of 96 %. On the basis of phylogenetic and phenotypic properties, strain wk12T represents a novel species of the genus Thermithiobacillus, for which the name Thermithiobacillus plumbiphilus sp. nov. is proposed. The type strain is wk12T ( = NBRC 111508T = DSM 101799T).
• Sulfuriferula thiophila sp nov., a chemolithoautotrophic sulfur-oxidizing bacterium, and correction of the name Sulfuriferula plumbophilus Watanabe, Kojima and Fukui 2015 to Sulfuriferula plumbiphila corrig.
  Watanabe Tomohiro; Kojima Hisaya; Fukui Manabu
  International journal of systematic and evolutionary microbiology, 66, 5, 2041, 2045, Society for General Microbiology, 2016年05月01日
  英語, 研究論文（学術雑誌）, A novel sulfur-oxidizing bacterium designated strain mst6(T) was isolated from spring water of Masutomi hot spring in Japan. The cells were rod-shaped (1.2-4.0 x 0.5-0.7 mm) and Gram-stain-negative. The G+C content of genomic DNA was around 52.6 mol%. The isolate possessed summed feature 3 (C-16 : 1 omega 7c and/or C-16 : 1 omega 6c), C-16 : 0 and C-12 : 0 as major cellular fatty acids. Strain mst6(T) grew by inorganic carbon fixation and oxidation of inorganic sulfur compounds with oxygen as an electron acceptor. The isolate grew over a temperature range of 5-34 degrees C, a NaCl concentration range of 0-110 mM and a pH range of 4.6-8.1. Optimum growth occurred at 32 degrees C, in the absence of NaCl and at pH 5.9-6.2. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain mst6(T) belongs to the family Sulfuricellaceae in the class Betaproteobacteria. The closest cultured relative was Sulfuriferula multivorans TTNT with a 16S rRNA gene sequence similarity of 97.0 %. On the basis of the data obtained in this study, strain mst6(T) represents a novel species of the genus Sulfuriferula, for which the name Sulfuriferula thiophila sp. nov. is proposed. The type strain is mst6(T) (=NBRC 111150(T) =DSM 101871(T)). In addition, we propose correcting the name Sulfuriferula plumbophilus Watanabe, Kojima and Fukui 2015 to Sulfuriferula plumbiphila corrig. based on Rule 12c, Rule 61 and Appendix 9 of the International Code of Nomenclature of Prokaryotes.
• Sulfuricaulis limicola gen. nov., sp nov., a sulfur oxidizer isolated from a lake
  Kojima Hisaya; Watanabe Tomohiro; Fukui Manabu
  International journal of systematic and evolutionary microbiology, 66, 1, 266, 270, the International Union of Microbiological Societies, 2016年01月01日
  英語, 研究論文（学術雑誌）, A novel sulfur-oxidizing bacterium, strain HA5(T), was isolated from sediment of a lake in Japan. The cells were rod-shaped (0.3-0.5 x 1.2-6.0 gm) and Gram-stain-negative. The G + C content of the genomic DNA was 63 mol%. The major components in the cellular fatty acid profile were C-16 : 0 and summed feature 3 (C-16 (:) (1)omega 7c and/or C-16 : 1 omega 6c). The strain oxidized thiosulfate, tetrathionate and elemental sulfur as electron donors to support autotrophic growth. Growth was observed at a temperature range of 8-37 degrees C, with optimum growth at 28-32 degrees C. The pH range for growth was pH 6.1-9.2.Optimunn growth of the isolate was observed in medium without NaCI. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain belongs to the family Acidiferrobacteraceae in the class Gammaproteobacteria. The closest relative was Sulfurifustis variabilis skN76(T) with the highest 16S rRNA gene sequence similarity of 93%. On the basis of phylogenetic and phenotypic properties, strain HA5(T) is proposed to represent a novel species of a new genus, Sulfuricaulis limicola gen. nov., sp. nov. The type strain of the type species is HA5(T) (=DSM 100373(T)=NBRC 110752(T)).
• Draft Genome Sequence of Desulfatitalea tepidiphila S28bFT
  Y. Higashioka; H. Kojima; T. Watanabe; M. Fukui
  Genome Announcements, 3, 6, 2015年11月12日
  英語, 研究論文（学術雑誌）
• Sulfurirhabdus autotrophica gen. nov., sp. nov., isolated from a freshwater lake.
  Tomohiro Watanabe
  International journal of systematic and evolutionary microbiology, 66, 1, 113, 117, Microbiology Society, 2015年10月15日
  研究論文（学術雑誌）, A novel sulfur-oxidizing bacterium, designated strain BiS0T, was isolated from a sediment sample collected from a freshwater lake in Japan. The cells were rod-shaped, 1.4-4.6 × 0.4-0.7 μm and Gram-stain-negative. The G+C content of the genomic DNA was around 44 mol%. The isolate possessed summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C10 : 0 3-OH as major cellular fatty acids. Strain BiS0T grew by carbon dioxide fixation and oxidation of inorganic sulfur compounds with oxygen as the electron acceptor. Growth was observed over a temperature range of 0-32 °C (optimum, 15-22 °C), an NaCl concentration range of 0-546.4 mM (optimum 0-66.7 mM) and a pH range of 5.2-8.1 (optimum 6.1-6.3). Phylogenetic analysis, based on 16S rRNA gene sequences, indicated that strain BiS0T belongs to the family Sulfuricellaceae in the class Betaproteobacteria. The closest cultured relatives were Sulfuricella denitrificans skB26T and Sulfuricella sp. T08, with 16S rRNA gene sequence similarities of 96.3 %. On the basis of the data obtained in this study, strain BiS0T represents a novel species of a novel genus, for which the name Sulfurirhabdus autotrophica gen. nov., sp. nov. is proposed. The type strain is BiS0T ( = NBRC 110941T = DSM 100309T).
• Draft Genome Sequence of Mizugakiibacter sediminis skMP5(T)
  Tomohiro Watanabe; Hisaya Kojima; Manabu Fukui
  MICROBIOLOGY RESOURCE ANNOUNCEMENTS, 3, 5, 2015年09月, ［査読有り］
  英語, 研究論文（学術雑誌）
• Sulfuriferula multivorans gen. nov., sp. nov., isolated from a freshwater lake, reclassification of ‘thiobacillus plumbophilus’ assulfuriferula plumbophilus sp. nov., and description of sulfuricellaceae fam. nov. and sulfuricellales ord. nov
  Tomohiro Watanabe; Hisaya Kojima; Manabu Fukui
  International Journal of Systematic and Evolutionary Microbiology, 65, 5, 1504, 1508, Society for General Microbiology, 2015年06月27日
  英語, 研究論文（学術雑誌）
• Ecophysiology of Thioploca ingrica as revealed by the complete genome sequence supplemented with proteomic evidence
  Hisaya Kojima; Yoshitoshi Ogura; Nozomi Yamamoto; Tomoaki Togashi; Hiroshi Mori; Tomohiro Watanabe; Fumiko Nemoto; Ken Kurokawa; Tetsuya Hayashi; Manabu Fukui
  The ISME Journal, 9, 5, 1166, 1176, 2015年05月
  英語, 研究論文（学術雑誌）
• Draft Genome Sequence of a Sulfur-Oxidizing Autotroph, Sulfuricella sp. Strain T08, Isolated from a Freshwater Lake
  Tomohiro Watanabe; Hisaya Kojima; Manabu Fukui
  MICROBIOLOGY RESOURCE ANNOUNCEMENTS, 3, 3, 2015年05月
  英語, 研究論文（学術雑誌）
• Draft genome sequence of Mizugakiibacter sediminis skMP5T
  Tomohiro Watanabe; Hisaya Kojima; Manabu Fukui
  Genome Announcements, 3, 5, American Society for Microbiology, 2015年
  英語, 研究論文（学術雑誌）
• Complete genomes of freshwater sulfur oxidizers Sulfuricella denitrificans skB26 and Sulfuritalea hydrogenivorans sk43H: genetic insights into the sulfur oxidation pathway of betaproteobacteria.
  Tomohiro Watanabe
  Systematic and applied microbiology, 37, 6, 387, 395, Elsevier BV, 2014年06月24日
  研究論文（学術雑誌）, Despite detailed studies of marine sulfur-oxidizing bacteria, our knowledge concerning their counterparts in freshwater lake ecosystems is limited. Genome sequencing of the freshwater sulfur-oxidizing betaproteobacteria Sulfuricella denitrificans skB26 and Sulfuritalea hydrogenivorans sk43H have been completed. Strain skB26 possessed a circular plasmid of 86.6-kbp in addition to its chromosome, and an approximate 18-kbp region of the plasmid was occupied by an arxA-like operon, encoding a new clade of anaerobic arsenite oxidase. Multilocus sequence analysis showed that strain skB26 could not be assigned to any existing order; thus a novel order, Sulfuricellales, is proposed. The genomes of strains skB26 and sk43H were examined, focusing on the composition and the phylogeny of genes involved in the oxidation of inorganic sulfur compounds. Strains skB26 and sk43H shared a common pathway, which consisted of Sqr, SoxEF, SoxXYZAB, Dsr proteins, AprBA, Sat, and SoeABC. Comparative genomics of betaproteobacterial sulfur oxidizers showed that this pathway was also shared by the freshwater sulfur oxidizers Thiobacillus denitrificans and Sideroxydans lithotrophicus. It also revealed the presence of a conserved gene cluster, which was located immediately upstream of the betaproteobacterial dsr operon.
• Identification of major planktonic sulfur oxidizers in stratified freshwater lake
  Hisaya Kojima; Tomohiro Watanabe; Tomoya Iwata; Manabu Fukui
  PLoS ONE, 9, 4, Public Library of Science, 2014年04月02日
  英語, 研究論文（学術雑誌）
• Diversity of sulfur-cycle prokaryotes in freshwater lake sediments investigated using aprA as the functional marker gene
  Tomohiro Watanabe; Hisaya Kojima; Yoshinori Takano; Manabu Fukui
  Systematic and Applied Microbiology, 36, 6, 436, 443, 2013年09月
  英語, 研究論文（学術雑誌）
• Draft Genome Sequence of a Psychrotolerant Sulfur-Oxidizing Bacterium, Sulfuricella denitrificans skB26, and Proteomic Insights into Cold Adaptation
  Tomohiro Watanabe; Hisaya Kojima; Manabu Fukui
  Applied and Environmental Microbiology, 78, 18, 6545, 6549, 2012年09月15日
  英語, 研究論文（学術雑誌）

• Genus Sulfuricella
  Tomohiro Watanabe; Hisaya Kojima, Bergey's manual of Systematics of Archaea and Bacteria, 2019年07月, ［査読有り］, ［招待有り］, ［筆頭著者］
• Hydrogenotrophic methanogenesis
  Wagner, T; Watanabe, T; Shima, S, Biogenesis of hydrocarbons. Handbook of hydrocarbon and lipid microbiology, 1, 29, 2018年
• P14-11 新目Sulfuricella目に属する新たな淡水性硫黄酸化細菌の分離と特徴付け(ポスター発表)
  渡邉 友浩; 小島 久弥; 福井 学, 日本微生物生態学会講演要旨集, 2014, 152, 152, 2014年
  日本微生物生態学会, 日本語
• OA-001 淡水湖沼の硫黄酸化細菌群集における主要構成種の特定とゲノム解析(水圏生態系,口頭発表)
  渡邉 友浩; 小島 久弥; 福井 学, 日本微生物生態学会講演要旨集, 29, 81, 81, 2013年
  日本微生物生態学会, 日本語

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  2023年04月01日 - 2027年03月31日
  渡邉 友浩
  本研究計画の目標は、一部の硫黄酸化菌が合成する機能未知のヘテロジスルフィド還元酵素が亜硫酸生成反応を触媒するとの仮説を、生化学と構造生物学によって検証することである。2023年度は、硫黄酸化菌から精製したヘテロジスルフィド還元酵素複合体の立体構造をクライオ電子顕微鏡で解析した。この結果、本酵素複合体には計画当初には予想していなかった小さなタンパク質が結合していることが判明した。質量分析とAIによる構造予測を組み合わせることで、この小さなタンパク質がサイズ11 kDaの機能未知タンパク質であることを解明した。そのアミノ酸配列の解析結果から、これは硫黄輸送タンパク質の一種だと考えられる。ヘテロジスルフィド還元酵素の酵素反応には複数種類の硫黄輸送タンパク質が関与すると考えているが、今回の様にヘテロジスルフィド還元酵素と硫黄輸送タンパク質が結合した複合体の構造は世界的にも初めてのものである。また、ヘテロジスルフィド還元酵素の活性部位の１つに非キュバン［4Fe-4S］クラスターが結合する可能性を見出した。通常、非キュバン［4Fe-4S］クラスターを結合するタンパク質にはCCGモチーフと呼ばれる配列特徴が保存されているが、今回見出した非キュバン［4Fe-4S］クラスターを配位する領域には、CCGモチーフと大きく異なる配列特徴がみられる。この発見に関しては別実験による精査が必要であるが、少なくとも、その触媒反応は既知のものとは異なると考えられる。
  一方で、酵素反応を生化学実験によって検出するために、2023年度は酵素反応基質の調整および酵素反応を検出するための質量分析実験とゲルシフトアッセイを確立した。なお、酵素反応基質はリポ酸を結合したリポ酸結合タンパク質とスルファン硫黄を結合した硫黄リレータンパク質だと予想している。
  日本学術振興会, 基盤研究(B), 北海道大学, 23K25979
• COを合成するタンパク質超複合体の精製
  科学研究費助成事業
  2023年04月01日 - 2025年03月31日
  渡邉 友浩
  本研究の目標は、硫黄不均化菌のゲノムからその存在が示唆された「二酸化炭素を一酸化炭素に還元する超複合体」の存在を検証することである。2023年度の計画は、本計画最大のボトルネックである硫黄不均化菌の大量培養である。増殖能力に優れた新種の硫黄不均化菌を用いて、培養実験を実施した。計画当初、硫黄不均化反応が生じる硫化水素をファーメンター装置を使って気化あるいは、透析膜に封入した３価鉄によって除去することを提案した。しかし、計画の遂行過程で、新種の硫黄不均化菌が硝酸を使った呼吸によって強く増殖することを新たに発見した。さらに詳細な培養条件の検討により、元素状硫黄の酸化と硝酸の還元によって最も強く増殖することを見出した。また、培養に最適な温度、pH、塩分を決定することで、増殖速度を向上することができた。次いで、最適な培養条件において、硫黄酸化硝酸還元による培養スケールアップを試みた。10 mlから段階的に培地容量を大きくすることで、最終的に1リットルの培地において良好な増殖を確認することができた。そして、1リットルの培養液から1グラム近くの細胞を回収することができた。
  日本学術振興会, 学術変革領域研究(A), 北海道大学, 23H04644
• 祖先的な亜硫酸生成反応の起源に迫る酵素の探索
  科学研究費助成事業
  2021年04月01日 - 2024年03月31日
  渡邉 友浩
  太古代地球における生命のエネルギー代謝のひとつには、亜硫酸の酸化還元反応が関与していたと考えられている。この反応を触媒する酵素は生命進化を研究する上で重要である。本研究では、硫黄化合物を酸化してエネルギーを獲得する微生物（硫黄酸化菌）の一部が、今まで知られていなかった酵素を使って亜硫酸合成反応を触媒する可能性を検証している。情報生物学と生化学の知見を総合すると、未知酵素の触媒反応にはリポ酸の誘導体が関与すると考えられる。このため、リポ酸を利用して硫黄化合物からエネルギーを獲得する硫黄酸化菌を実験材料に用いた。対象の硫黄酸化菌を、複数の硫黄化合物あるいは水素ガスをエネルギー源とする条件で培養し、それぞれの条件で発現する遺伝子を同定した（トランスクリプトーム解析）。この結果、硫黄化合物をエネルギー源とする際に、リポ酸の誘導体を生じる酵素の遺伝子発現量が有意に増加することを見出した。この遺伝子と一緒に発現量が変化する遺伝子の中に、亜硫酸を合成する未知酵素遺伝子が含まれると考えられる。現在、各遺伝子の配列特徴を詳細に解析している。これと同時に、硫黄酸化菌を大量に培養するための実験系を確立した。今後、大量培養で得られた細胞から細胞粗酵素液を調整して、未知酵素が触媒すると考えられる酵素反応の検証実験を行う。この際、リポ酸結合タンパク質が反応基質の１つとして関与すると考えられる。このため、硫黄酸化菌由来のリポ酸結合タンパク質を大腸菌で合成し、これをアフィニティークロマトグラフィー等で精製した。
  日本学術振興会, 若手研究, 北海道大学, 21K14025
• 未知の電子バイフリケーション反応の検証ー新たな遺伝子資源の開拓ー
  科学研究費助成事業
  2020年09月11日 - 2022年03月31日
  渡邉 友浩
  ヘテロジスルフィド還元酵素が触媒する電子分岐反応は、電子対の一方の電子を高エネルギー状態にする。これは、持続可能な社会の技術基盤として応用できる可能性が指摘されている。本研究では、硫黄酸化菌が合成する機能未知のヘテロジスルフィド還元酵素（sHdr）を研究した。遺伝子発現解析の結果、sHdrは硫黄化合物からのエネルギー合成に関与することが示唆された。sHdrを合成する硫黄酸化菌を大量培養することに成功した。細胞粗酵素液を各種クロマトグラフィーで分画した。紫外可視吸収スペクトル、SDS-PAGE、Native-PAGEによってsHdrの精製条件を検討し、得られた画分の質量分析を進めている。
  日本学術振興会, 研究活動スタート支援, 北海道大学, 20K22559