業績リスト
原著論文（研究室学生、*責任著者、#共同筆頭著者） 当研究室では発表論文のOpen accessを推進しています
2022年
68. *Nakabachi A., Inoue H., Hirose Y. High-resolution microbiome analyses of nine Psyllid species of the family Triozidae identified previously unrecognized but
major bacterial populations, including Liberibacter and Wolbachia of supergroup O. Microbes Environ. 37(4):ME22078 (2022) [Open access]
67. Meng L., Xie L., Hirose Y., Nishiuchi T., *Yoshida N. Reduced graphene oxide increases cells with enlarged outer membrane of Citrifermentans bremense and exopolysaccharides secretion. Biosens Bioelectron. 218:114754 (2022) [URL]
66. Tanabe N., Takasu R., Hirose Y., Kamei Y., Kondo M., *Nakabachi A. Diaphorin, a polyketide produced by a bacterial symbiont of the Asian Citrus Psyllid,
inhibits the growth and cell division of Bacillus subtilis but promotes the growth and metabolic activity of Escherichia coli. Microbiol Spectr. 10(4):e0175722. (2022) [Open access]
65. Otsu T., Eki T., *Hirose Y. A hybrid type of chromatic acclimation regulated by the dual green/red photosensory systems in cyanobacteria. Plant Physiol. 29;190(1):779-793. (2022) [URL] [TUT Research]
64. *Kawakami K., Hamaguchi T., Hirose Y., Kosumi D. Miyata M. Kamiya N., *Yonekura K. Core and rod structures of a thermophilic cyanobacterial light-harvesting phycobilisome. Nat Commun. 13(1):3389. (2022) [Open access] [Press release]
63. *Nakane D., *Enomoto G., Bähre H., Hirose Y., Wilde A., Nishizaka T. Thermosynechococcus switches the direction of phototaxis by a c-di-GMP-
dependent process with high spatial resolution. Elife.11:e73405. (2022) [Open access]
62. *Ohtsubo Y., Hirose Y., Nagata Y. Algorisms used for in silico finishing of bacterial genomes based on short-read assemblage implemented in GenoFinisher, AceFileViewer, and ShortReadManager. Biosci Biotechnol Biochem. 86(6):693-703. (2022) [Open access]
61. Murakami T., Takeuchi N., Mori H., Hirose Y., Edwards A., Irvine-Fynn T., Li Z., Ishii S., *Segawa T. Metagenomics reveals global-scale contrasts in nitrogen cycling and cyanobacterial light-harvesting mechanisms in glacier cryoconite. Microbiome. 10(1):50. (2022) [Open access] [Press release]
60. Okuda Y., Miyoshi R., Kamo T., Fujisawa T., Nagae T., Mishima M., Eki T., *Hirose Y., *Unno M. Raman spectroscopy of an atypical C15-E,syn bilin chromophore in cyanobacteriochrome RcaE. J Phys Chem B. 126(4):813-821 (2022) [URL]
59. *Nakabachi A., Inoue H., Hirose Y. Microbiome analyses of 12 psyllid species of the family Psyllidae identified various bacteria including Fukatsuia and Serratia symbiotica, known as secondary symbionts of aphids. BMC Microbiol. 22(1):15 (2022) [Open access]
2021年
58. Hirose Y., *Katayama M. Complete genome sequence of a thin-sheath mutant of the phototropic cyanobacterium Calothrix sp. strain PCC 7716. Microbiol Resour Announc. 10(48):e0094721 (2021) [Open access]
57. Kenmotsu H., Takabayashi E., Takase A., Hirose Y., *Eki T. Use of universal primers for the 18S ribosomal RNA gene and whole soil DNAs to reveal the taxonomic structures of soil nematodes by high-throughput amplicon sequencing. PLoS One. 16(11):e0259842 (2021) [Open access]
56. *Hirose Y., Ohtsubo Y., Misawa N., Yonekawa C., Nagao N., Shimura Y., Fujisawa T., Kanesaki Y., Katoh H., Katayama M., Yamaguchi H., Yoshikawa H., Ikeuchi M., Eki T., Nakamura Y., Kawachi M. Genome sequencing of the NIES Cyanobacteria collection with a focus on the heterocyst-forming clade. DNA Res. 28(6): dsab024 (2021) [Open access] [Press release]
55. Hirose Y., *Katayama M. Draft genome sequence of a phototropic cyanobacterium Rivularia sp. IAM M-261. Microbiol Resour Announc. 10(39):e0079021 (2021) [Open access]
54. Inoue M., Hirose Y., Tobe R., Saito S., Aono R., Prakash N. T., *Mihara H. Complete Genome Sequence of Pseudomonas stutzeri Strain F2a, Isolated from Seleniferous Soil. Microbiol Resour Announc. 10(33):e0063121 (2021) [Open access]
53. *Unno M., Hirose Y., Mishima M., Kikukawa T., Fujisawa T., Iwata T., Tamogami J. Spectroscopic approach for exploring structure and function of photoreceptor proteins. Biophys Physicobiol. 18:127-130 (2021) [Open access]
52. *#Harada N., #Hirose Y., Chihong S., Kurita H., Sato M., Onodera J., Murata K., Itoh F. A novel characteristic of a phytoplankton as a potential source of straight-chain alkanes. Sci Rep. 11(1):14190 (2021) [Open access]
51. Nagae T. *Unno M., Koizumi T. Miyanori Y. Fujisawa T. Masui K., Kamo T., Wada K. Eki T., Ito Y., *Hirose Y., *Mishima M. Structural basis of the protochromic green/red photocycle of the chromatic acclimation sensor RcaE. Proc. Natl. Acad. Sci. U.S.A. 118(20):e2024583118 (2021) [Open access] [Press release]
50. Kenmotsu H., Ishikawa M., Nitta T., Hirose Y., *Eki T. Distinct community structures of soil nematodes from three ecologically different sites revealed by high-throughput amplicon sequencing of four 18S ribosomal RNA gene regions. PLoS One. 16(4):e0249571 (2021) [Open access]
49. *Shiozaki T., Itoh F., Hirose Y., Onodera J., Kuwata A., Harada N. A DNA metabarcoding approach for recovering plankton communities from archived samples fixed in formalin. PLoS One. 16(2):e0245936. (2021) [Open access]
48. Shimura Y., Fujisawa T., Hirose Y., Misawa N., Kanesaki Y., Nakamura Y., *Kawachi M. Complete sequence and structure of the genome of the harmful algal bloom-forming cyanobacterium Planktothrix agardhii NIES-204T and detailed analysis of secondary metabolite gene clusters. Harmful Algae 101:101942 (2021) [URL]
47. Kamo T., Eki T., *Hirose Y. Pressurized liquid extraction of a phycocyanobilin chromophore and its reconstitution with a cyanobacteriochrome photosensor for efficient isotopic labeling. Plant Cell Physiol. 62(2):334-347 (2021) [Open access] [Press release] [Eurekalart]
2020年
46. *Hirose Y., Kumsab J., Tobe R., *Mihara H. Complete Genome Sequence of an Acetic Acid Bacterium, Acetobacter aceti JCM20276. Microbiol Resour Announc. 9(42):e00962-20 (2020) [Open access]
45. Kenmotsu H., Uchida K., Hirose Y., *Eki T. Taxonomic profiling of individual nematodes isolated from copse soils using deep amplicon sequencing of four distinct regions of the 18S ribosomal RNA gene. PLoS One 15(10):e0240336. (2020) [Open access]
44. *Shiozaki T., Fujiwara A., Inomura K., Hirose Y., Hashihama F., Harada N. Biological nitrogen fixation detected under Antarctic sea ice. Nature Geoscience 13: 729–732 (2020) [URL]
43. *Kawade K., Horiguchi G., Hirose Y., Oikawa A., Hirai M.Y., Saito K., Fujita T., Tsukaya H. Metabolic control of gametophore shoot formation through arginine in the moss Physcomitrium patens. Cell Rep 32(10):108127 (2020) [Open access] [Press release]
42. *Hirose Y., Shiozaki T., Hamano I., Yoshihara S., Tokumoto H., Eki T., Harada N. A specific combination of dual index adaptors decreases the sensitivity of amplicon sequencing with the Illumina platform. DNA Res. 27(4): dsaa017 (2020) [Open access]
41. *Nakabachi A., Piel J., Malenovský I., Hirose Y. Comparative genomics underlines multiple roles of Profftella, an obligate symbiont of Psyllids: providing toxins, vitamins, and carotenoids. Genome Biol Evol. [Open access]
12(11):1975-1987 (2020)
40. Kumsab J., Tobe R., Kurihara T., Hirose Y., Omori T., *Mihara H. Characterization of a novel class of glyoxylate reductase belonging to the β-hydroxyacid dehydrogenase family in Acetobacter aceti. Biosci Biotechnol Biochem. 84(11):2303-2310 (2020) [Open access]
39. Kobayashi T., Murakami T., Hirose Y., *Eki T. Purification and characterization of double-stranded nucleic acid-dependent ATPase activities of tagged dicer-related helicase 1 and its short isoform in Caenorhabditis elegans.Genes (Basel) 11(7):734 (2020) [Open access]
38. Ohbayashi R., Hirooka S., Onuma R., Kanesaki Y., Hirose Y., Kobayashi Y., Fujiwara T., Furusawa C., *Miyagishima S.Y. Evolutionary changes in DnaA-dependent chromosomal replication in cyanobacteria. Front. Microbiol. 11:786 (2020) [Open access]
37. *Hirose Y., Shiozaki T., Otani M., Kudoh S., Imura S., Eki T., Harada N. Investigating algal communities in lacustrine and hydro-terrestrial environments of East Antarctica using deep amplicon sequencing. Microorganisms 8(4):497 (2020). [Open access] [Press release]
36. *Nakabachi A., Malenovský I., Gjonov I., Hirose Y. 16S rRNA sequencing detected Profftella, Liberibacter, Wolbachia, and Diplorickettsia from relatives of the Asian citrus psyllid. Microb. Ecol. 80(2):410-422 (2020) [Open access]
35. *Hiraishi A., Nagao N., Yonekawa C., Umekage S., Kikuchi Y., Eki T., *Hirose Y. Distribution of phototrophic purple nonsulfur bacteria in massive blooms in coastal and wastewater ditch environments. Microorganisms 8(2):150 (2020) [Open access]
2019年
34. *Shiozaki T., Hirose Y., Hamasaki K., Kaneko R., Ishikawa K., Harada N. Eukaryotic phytoplankton contributing to a seasonal bloom and carbon export revealed by tracking sequence variants in the Western North Pacific. Front Microbiol. 26;10:2722 (2019) [Open access]
33. Sato T., Kikukawa T, Miyoshi R, Kajimoto K, Yonekawa C, Fujisawa T, Unno M, Eki T, *Hirose Y. Protochromic absorption changes in the two-Cys photocycle of a blue/orange cyanobacteriochrome. J. Biol. Chem., 294(49):18909-18922 (2019). [Open access]
32. Okazaki S., Sano N., Yamada T., Ishii K., Kojima K., Djedidi S., Artigas Ramírez M.D., Yuan K., Kanekatsu M., Ohkama-Ohtsu N., Hirose Y., Oshima K., Hattori M., *Yokoyama T. Complete Genome Sequence of Plant Growth-Promoting Bacillus pumilus TUAT1. Microbiol. Resour. Announc. 8(21) e00076-19 (2019) [Open access]
31. Osoegawa S., Miyoshi R., Watanabe K., Hirose Y., Fujisawa T., Ikeuchi M., *Unno M. Identification of the deprotonated pyrrole nitrogen of the bilin-based photoreceptor by Raman spectroscopy with an advanced computational analysis. J. Phys. Chem. B. 123(15) 3242-3247 (2019) [URL]
30. *Hirose Y., Chihong S., Watanabe M., Yonekawa C., Murata K., Ikeuchi M. and Eki T. Diverse chromatic acclimation processes regulating phycoerythrocyanin and rod-shaped phycobilisome in cyanobacteria. Mol. Plant 12(5) 715-725 (2019) [Open access] [Press release]
2018年
29. *Nonaka L., Yamamoto T., Maruyama F., Hirose Y., Onishi Y., Kobayashi T., Suzuki S., Nomura N., Masuda M. and Yano H. Interplay of a non-conjugative integrative element and a conjugative plasmid in the spread of antibiotic resistance via suicidal plasmid transfer from an aquaculture Vibrio isolate. PLoS One 13(6):e0198613 (2018) [Open access]
28. Komatsu H., Yamamoto J., Suzuki H., Nagao N., Hirose Y., Ohyama T., Umekage S and *Kikuchi Y. Involvement of the response regulator CtrA in the extracellular DNA production of the marine bacterium Rhodovulum sulfidophilum. J. Gen. Appl. Microbiol. 64(3):103-107 (2018) [Open access]
27. Kanesaki Y., Hirose M., Hirose Y., Fujisawa T., Nakamura Y., Watanabe S., Matsunaga S., Uchida H. and *Murakami A. Draft genome sequence of the nitrogen-fixing and hormogonia-inducing cyanobacterium Nostoc cycadae strain WK-1, isolated from the coralloid roots of Cycas revoluta. Genome Announc. 6(7). pii: e00021-18 (2018) [URL]
2017年
26. Hirooka S., Hirose Y., Kanesaki Y., Higuchi S., Fujiwara T., Onuma R., Era A., Ohbayashi R., Uzuka A., Nozaki H., Yoshikawa H. and *Miyagishima S. Y. Acidophilic green algal genome provides insights into adaptation to an acidic environment. Proc. Natl. Acad. Sci. U. S. A. 114(39):E8304-E8313 (2017) [Open access]
25. Ho S. H., Nakanishi A., Kato Y., Yamasaki H., Chang J., Misawa N., Hirose Y., Minagawa J. and *Kondo A. Dynamic metabolic profiling together with transcription analysis reveals salinity-induced starch-to-lipid biosynthesis in alga Chlamydomonas sp. JSC4. Sci Rep. 7:45471 (2017) [Open access]
24. *Hirose Y., Misawa N., Yonekawa C., Nagao N., Watanabe M., Ikeuchi M. and Eki T. Characterization of the genuine type 2 chromatic acclimation in the two Geminocystis cyanobacteria. DNA Res. 24(4):387-396 (2017) [Open access]
23. Shimura Y., Hirose Y., Misawa N., Wakazuki S., Fujisawa T., Nakamura Y. Kanesaki Y., Yamaguchi H. and Kawachi M*. Complete genome sequence of a coastal cyanobacterium, Synechococcus sp. NIES-970. Genome Announc. 5(14): e00139-17 (2017) [Open access]
22. Suzuki H., Sakabe T., Hirose Y., *Eki T. Development and evaluation of yeast-based GFP and luciferase reporter assays for chemical-induced genotoxicity and oxidative damage. Appl. Microbiol. Biotechnol. 101(2): 659-671 (2017) [Open access]
21. Hayashi M., Okada A., Yamamoto K., Okugochi T., Kusaka C., Kudou D., Nemoto M., Inagaki J., Hirose Y., Okajima T., Tamura T., Soda K. and *Inagaki K. Gene cloning, recombinant expression, purification and characterization of l-methionine decarboxylase from Streptomyces sp. 590. J. Biochem. 161(4):389-398 (2017) [Open access]
2016年
20. Kuramochi K., Uchimura K., Kurata A., Kobayashi T., Hirose Y., Miura T., Kishimoto N., Usami R., *Horikoshi K. A high-molecular-weight, alkaline, and thermostable β-1,4-xylanase of a subseafloor Microcella alkaliphila. Extremophiles 20(4): 471-478 (2016) [Open access]
19. *Hirose Y., Fujisawa T., Ohtsubo Y., Katayama M., Misawa N., Wakazuki S., Shimura Y., Nakamura Y., Kawachi M., Yoshikawa H., Eki T. and Kanesaki Y. Complete genome sequence of cyanobacterium Leptolyngbya sp. NIES-3755. Genome Announc. 4(2): e00090-16 (2016) [Open access]
18. Nishijima S., Suda W., Oshima K., Kim S. W., Hirose Y., Morita H. and *Hattori M. The gut microbiome of healthy Japanese and its microbial and functional uniqueness. DNA Res. 23(2): 125-133 (2016) [Open access]
17. Kurata A., Hirose Y., Misawa N., Wakazuki S., Kishimoto N. and *Kobayashi T. Complete genome sequence of the xylan-degrading subseafloor bacterium Microcella alkaliphila JAM-AC0309. J. Biotechnol. 221: 32-33 (2016) [URL]
16. *Hirose Y., Fujisawa T., Ohtsubo Y., Katayama M., Misawa N., Wakazuki S., Shimura Y., Nakamura Y., Kawachi M., Yoshikawa H., Eki T. and Kanesaki Y. Complete genome sequence of cyanobacterium Fischerella sp. NIES-3754, providing thermoresistant optogenetic tools. J. Biotechnol. 220:45-46 (2016) [URL]
15. *Hirose Y., Fujisawa T., Ohtsubo Y., Katayama M., Misawa N., Wakazuki S., Shimura Y., Nakamura Y., Kawachi M., Yoshikawa H., Eki T. and Kanesaki Y. Complete genome sequence of cyanobacterium Nostoc sp. NIES-3756, a potentially useful strain for phytochrome-based bioengineering. J. Biotechnol. 228:51-52 (2016) [URL]
2015年
14. Shimura Y., Hirose Y., Misawa N., Osana Y., Katoh H., Yamaguchi H. and *Kawachi M. Comparison of the terrestrial cyanobacterium Leptolyngbya sp. NIES-2104 and the freshwater Leptolyngbya boryana PCC 6306 genomes. DNA Res. 22(6): 403-412 (2015) [Open access]
13. Tsukatani Y., Hirose Y., Harada J., Misawa N., Mori K., Inoue K. and *Tamiaki H. Complete genome sequence of the bacteriochlorophyll b-producing photosynthetic bacterium Blastochloris viridis. Genome Announc. 3(5): e01006-15 (2015) [Open access]
12. *Hirose Y., Katayama M., Ohtsubo Y., Misawa N., Iioka E., Suda W., Oshima K., Hanaoka M., Tanaka K., Eki T., Ikeuchi M., Kikuchi Y., Ishida M. and Hattori M. Complete genome sequence of cyanobacterium Geminocystis sp. strain NIES-3708, which performs type II complementary chromatic acclimation. Genome Announc. 3(3): e00357-15 (2015) [Open access]
11. *Hirose Y., Katayama M., Ohtsubo Y., Misawa N., Iioka E., Suda W., Oshima K., Hanaoka M., Tanaka K., Eki T., Ikeuchi M., Kikuchi Y., Ishida M. and Hattori M. Complete genome sequence of cyanobacterium Geminocystis sp. strain NIES-3709, which harbors a phycoerythrin-rich phycobilisome. Genome Announc. 3(2): e00385-15 (2015) [Open access]
10. Nagao N., Hirose Y., Misawa N., Ohtsubo Y., Umekage S. and *Kikuchi Y. Complete genome sequence of Rhodovulum sulfidophilum DSM 2351, an extracellular nucleic acid-producing bacterium. Genome Announc. 3(2): e00388-15 (2015) [Open access]
9. Hiraide Y., Oshima K., Fujisawa T., Uesaka K., Hirose Y., Tsujimoto R., Yamamoto H., Okamoto S., Nakamura Y., Terauchi K., Omata T., Ihara K., Hattori M., *Fujita Y. Loss of cytochrome cM stimulates cyanobacterial heterotrophic growth in the dark. Plant Cell Physiol. 56(2): 334-345 (2015) [Open access]
8. Nagao N., Yamamoto J., Komatsu H., Suzuki H., Hirose Y. Umekage S., Ohyama S. and *Kikuchi Y. The gene transferagent-like particle of the marine phototrophic bacterium Rhodovulum sulfidophilum. Biochem. Biophys. Rep. 4:369-337 (2015) [Open access]
2014年
7. Kurata A., Hirose Y., Misawa N., Hurunaka K., and *Kishimoto N. Draft genome sequence of the ionic liquid-tolerant bacterium Bacillus amyloliquefaciens CMW1. Genome Announc. 2(5): e01051-14 (2014) [Open access]
6. Shiwa Y., Yanase H., Hirose Y., Satomi S., Araya-Kojima T., Watanabe S., Zendo T., Chibazakura T., Shimizu-Kadota M., Yoshikawa H., *Sonomoto K. Complete genome sequence of Enterococcus mundtii QU 25, an efficient L-(+)-lactic acid-producing bacterium. DNA Res. 21(4): 369-377 (2014) [Open access]
2013年
5. Hirose Y., Rockwell N. C., Nishiyama K., Narikawa R., Ukaji Y., Inomata K., *Lagarias J. C. and *Ikeuchi M. Green/red cyanobacteriochromes regulate complementary chromatic acclimation via a protochromic photocycle. Proc. Natl. Acad. Sci. U.S.A. 110: 4974-9 (2013) [Open access] [Press release]
4. Gottlieb S. M., Kim P. W., Rockwell N. C., Hirose Y., Ikeuchi M., Lagarias J. C. and *Larsen D. S. Primary photodynamics of the green/red-absorbing photoswitching regulator of the chromatic adaptation E domain from Fremyella diplosiphon. Biochemistry 53(6): 1029-40 (2013) [URL]
2012年
3. Enomoto G., Hirose Y., Narikawa R. and *Ikeuchi M. Thiol-based photocycle of the blue and teal light-sensing cyanobacteriochrome tlr1999. Biochemistry , 51: 3050-8 (2012) [URL]
2010年
2. Hirose Y., Narikawa R., Katayama M. and *Ikeuchi M. Cyanobacteriochrome CcaS regulates phycoerythrin accumulation in Nostoc punctiforme, a group II chromatic adapter. Proc. Natl. Acad. Sci. U.S.A., 107: 8854-8859 (2010) [Open access]
2008年
1. Hirose Y., Shimada T., Narikawa R., Katayama M. and *Ikeuchi M. Cyanobacteriochrome CcaS is the green light receptor that induces the expression of phycobilisome linker protein. Proc. Natl. Acad. Sci. U.S.A., 105: 9528–33 (2008) [Open access]
著書
3. 広瀬侑「シアノバクテリアの補色応答の制御メカニズムの解明」光合成研究と産業応用最前線（NTS出版），109-117頁，2014年
2. 広瀬侑、池内昌彦「光合成微生物の光合成メカニズムに関与するタンパク質機構の解明」藻類オイル生産技術研究の最前線（NTS出版），165-172頁、2013年
1. 広瀬侑、佐藤桃子、池内昌彦「シアノバクテリア」光合成研究法，67 巻１号，9 -15頁，2009年 [Open access]
総説・解説
7. 広瀬侑「天然の青色発色団フィコシアノビリンの抽出と応用 」アグリバイオ 5(10):849-853, 2021年
6. 広瀬侑「シアノバクテリアの光色順化と多様性と進化」光合成研究，29巻2号、156−170頁，2019年 [Open access]
5. Hirose Y., Ikeuchi M. and Eki T. Diverse molecular processes of chromatic acclimation in the cyanobacteria phylum. Plant Morphol. 29:41-45 (2017)
4. 広瀬侑「シアノバクテリアのゲノム解析とそれを活用した補色応答現象の理解」生物の科学遺伝（NTS出版），71巻2号，98 – 99頁，2017年
3. 広瀬侑、池内昌彦「シアノバクテリアの補色順化における光色感知機構」化学と生物，54巻6号，403 – 407頁，2016年 [Open access]
2. 広瀬侑「シアノバクテリオクロムと補色順化の研究の最近」光合成研究，22巻1号、5−13頁，2012年 [Open access]
1. 広瀬侑「シアノバクテリオクロムCcaS はフィコビリソームのリンカータンパク質（CpcG2）の発現を誘導する緑色光受容体である」光合成研究，１８巻２号，44-50頁，2008年 [Open access]