研究者詳細 - 井原　邦夫

論文 - 井原　邦夫

分割表示 105 件中 41 - 60 件目／全件表示 >>

Complete Genome Sequence of Kosakonia sacchari Strain BO-1, an Endophytic Diazotroph Isolated from a Sweet Potato. 査読有り

Shinjo R, Uesaka K, Ihara K, Loshakova K, Mizuno Y, Yano K, Tanaka A.

Genome Announc. 4 巻 ( 5 ) 頁： e00868-16 2016年9月

A Robust Analytical Pipeline for Genome-Wide Identification of the Genes Regulated by a Transcription Factor: Combinatorial Analysis Performed Using gSELEX-Seq and RNA-Seq. 査読有り

Kojima T, Kunitake E, Ihara K, Kobayashi T, Nakano H.

PLoS One. 11 巻 ( 7 ) 頁： e0159011 2016年7月

Crystal Structure of the 11-cis Isomer of Pharaonis Halorhodopsin: Structural Constraints on Interconversions among Different Isomeric States. 査読有り

Chan SK, Kawaguchi H, Kubo H, Murakami M, Ihara K, Maki K, Kouyama T.

Biochemistry. 55 巻 ( 29 ) 頁： 4092-4104 2016年7月

FliH and FliI ensure efficient energy coupling of flagellar type III protein export in Salmonella. 査読有り

Minamino T, Kinoshita M, Inoue Y, Morimoto YV, Ihara K, Koya S, Hara N, Nishioka N, Kojima S, Homma M, Namba K.

Microbiologyopen 5 巻 ( 3 ) 頁： 424-435 2016年6月

Evolution of Green Plants Accompanied Changes in Light-Harvesting Systems. 査読有り

Kunugi M, Satoh S, Ihara K, Shibata K, Yamagishi Y, Kogame K, Obokata J, Takabayashi A, Tanaka A.

Plant Cell Physiol. 57 巻 ( 6 ) 頁： 1231-1243 2016年6月

Identification of a Cyanobacterial RND-Type Efflux System Involved in Export of Free Fatty Acids. 査読有り

Kato A, Takatani N, Use K, Uesaka K, Ikeda K, Chang Y, Kojima K, Aichi M, Ihara K, Nakahigashi K, Maeda S, Omata T.

Plant Cell Physiol. 56 巻 ( 12 ) 頁： 2467-2477 2015年12月

Structural and functional roles of the N- and C-terminal extended modules in channelrhodopsin-1. 査読有り

Doi S, Mori A, Tsukamoto T, Reissig L, Ihara K, Sudo Y.

Photochem Photobiol Sci. 14 巻 ( 9 ) 頁： 1628-36 2015年9月

Microbial rhodopsins of Halorubrum species isolated from Ejinoor salt lake in Inner Mongolia of China.

Chaoluomeng, Dai G, Kikukawa T, Ihara K, Iwasa T.

Photochem Photobiol Sci. 頁： Epub ahead of print 2015年8月

Probing the Cl--pumping photocycle of pharaonis halorhodopsin: Examinations with bacterioruberin, an intrinsic dye, and membrane potential-induced modulation of the photocycle. 査読有り

Kikukawa T, Kusakabe C, Kokubo A, Tsukamoto T, Kamiya M, Aizawa T, Ihara K, Kamo N, Demura M.

Biochim Biophys Acta. 1847 巻 ( 8 ) 頁： 748-758 2015年8月

A genetic mechanism for female-limited Batesian mimicry in Papilio butterfly. 査読有り

Nishikawa H, Iijima T, Kajitani R, Yamaguchi J, Ando T, Suzuki Y, Sugano S, Fujiyama A, Kosugi S, Hirakawa H, Tabata S, Ozaki K, Morimoto H, Ihara K, Obara M, Hori H, Itoh T, Fujiwara H.

Nat Genet. 47 巻 ( 4 ) 頁： 405-409 2015年4月

Loss of cytochrome cM stimulates cyanobacterial heterotrophic growth in the dark 査読有り

Yuto Hiraide, Kenshiro Oshima, Takatomo Fujisawa, Kazuma Uesaka, Yuu Hirose, Ryoma Tsujimoto, Haruki Yamamoto, Shinobu Okamoto, Yasukazu Nakamura, Kazuki Terauchi, Tatsuo Omata, Kunio Ihara, Masahira Hattori, and Yuichi Fujita

Plant and Cell Physiology 2014年11月

記述言語：英語掲載種別：研究論文（学術雑誌）

Although cyanobacteria are photoautotrophs, they have heterotrophic metabolism that enables them to survive in their natural habitat. However, cyanobacterial species that grow heterotrophically in the dark are rare. It remains largely unknown how cyanobacteria regulate heterotrophic activity. The cyanobacterium Leptolyngbya boryana grows heterotrophically with glucose in the dark. A dark-adapted variant dg5 isolated from the wild-type (WT) exhibits enhanced heterotrophic growth in the dark. We sequenced the genomes of dg5 and WT to identify the mutation(s) of dg5. The WT genome consists of a circular chromosome (6,176,364 bp), a circular plasmid pLBA (77,793 bp), and two linear plasmids pLBX (504,942 bp) and pLBY (44,369 bp). Genome comparison revealed three mutation sites. Phenotype analysis of mutants isolated from WT by introducing these mutations individually revealed that the relevant mutation is a single adenine insertion causing a frameshift of cytM encoding cytochrome cM. The respiratory oxygen consumption of the cytM-lacking mutant grown in the dark was significantly higher than that of WT. We isolated a cytM-lacking mutant, ΔcytM, from another cyanobacterium Synechocystis sp. PCC 6803, and ΔcytM grew in the dark with a doubling time of 33 h in contrast to no growth of WT. The respiratory oxygen consumption of ΔcytM grown in the dark was about 2-fold higher than that of wild type. These results suggest a suppressive role(s) of cytochrome cM in regulation of heterotrophic activity.

DOI： 10.1093/pcp/pcu165

Crystal Structure of Cruxrhodopsin-3 from Haloarcula vallismortis. 査読有り

Chan SK, Kitajima-Ihara T, Fujii R, Gotoh T, Murakami M, Ihara K, Kouyama T.

PLoS One 9 巻 ( 9 ) 頁： e108362 2014年9月

記述言語：英語掲載種別：研究論文（学術雑誌）

Cruxrhodopsin-3 (cR3), a retinylidene protein found in the claret membrane of Haloarcula vallismortis, functions as a light-driven proton pump. In this study, the membrane fusion method was applied to crystallize cR3 into a crystal belonging to space group P321. Diffraction data at 2.1 Å resolution show that cR3 forms a trimeric assembly with bacterioruberin bound to the crevice between neighboring subunits. Although the structure of the proton-release pathway is conserved among proton-pumping archaeal rhodopsins, cR3 possesses the following peculiar structural features: 1) The DE loop is long enough to interact with a neighboring subunit, strengthening the trimeric assembly; 2) Three positive charges are distributed at the cytoplasmic end of helix F, affecting the higher order structure of cR3; 3) The cytoplasmic vicinity of retinal is more rigid in cR3 than in bacteriorhodopsin, affecting the early reaction step in the proton-pumping cycle; 4) the cytoplasmic part of helix E is greatly bent, influencing the proton uptake process. Meanwhile, it was observed that the photobleaching of retinal, which scarcely occurred in the membrane state, became significant when the trimeric assembly of cR3 was dissociated into monomers in the presence of an excess amount of detergent. On the basis of these observations, we discuss structural factors affecting the photostabilities of ion-pumping rhodopsins.

DOI： 10.1371/journal.pone.0108362. eCollection 2014.

Transcriptome Analysis of Reaction Wood in Gymnosperms by Next-Generation Sequencing 査読有り

Saori Sato, Masato Yoshida, Hideto Hiraide, Kunio Ihara, Hiroyuki Yamamoto

American Journal of Plant Sciences 5 巻頁： 2785-2798 2014年8月

記述言語：英語掲載種別：研究論文（学術雑誌）

Special xylem tissue called compression wood is formed on the lower side of inclined stems
when gymnosperms grow on a slope. We investigated the molecular mechanism of compression
wood formation. Transcriptome analysis by next-generation sequencing (NGS) was applied to the
xylem of Chamaecyparis obtusa to develop a catalog of general gene expression in differentiating
xylem during compression and normal wood formation. The sequencing output generated
234,924,605 reads and 40,602 contigs (mean size = 529 bp). Based on a sequence similarity
search with known proteins, 54.2% (22,005) of the contigs showed homology with sequences in
the databases. Of these annotated contigs, 19,293 contigs were assigned to Gene Ontology categories.
Differential gene expression between the compression and normal wood libraries was
analyzed by mapping the reads from each library to the assembled contigs. In total, 2875 contigs
were identified as differentially expressed, including 1207 that were up-regulated and 1668 that
were down-regulated in compression wood. We selected 30 genes and compared the transcript
abundance between compression and normal wood by quantitative polymerase chain reaction
analysis to validate the NGS results. We found that 27 of the 30 genes showed the same expression
patterns as the original NGS results.

DOI： 10.4236/ajps.2014.518295

Searching for genomic region of high-fat diet-induced type 2 diabetes in mouse chromosome 2 by analysis of congenic strains. 査読有り

Kobayashi M, Ohno T, Ihara K, Murai A, Kumazawa M, Hoshino H, Iwanaga K, Iwai H, Hamana Y, Ito M, Ohno K, Horio F.

PLoS One 9 巻 ( 5 ) 頁： e96271 2014年5月

Mutation in the a-subunit of F(1)F(O)-ATPase causes an increased motility phenotype through the sodium-driven flagella of Vibrio.

Terashima H, Terauchi T, Ihara K, Nishioka N, Kojima S, Homma M.

J Biochem. 154 巻 ( 2 ) 頁： 177-184 2013年8月

A blue-shifted light-driven proton pump for neural silencing

Sudo Y, Okazaki A, Ono H, Yagasaki J, Sugo S, Kamiya M, Reissig L, Inoue K, Ihara K, Kandori H, Takagi S, Hayashi S.

J Biol Chem. 288 巻 ( 28 ) 頁： 20624-20632 2013年7月

Crystal structure of deltarhodopsin-3 from Haloterrigena thermotolerans

Zhang J, Mizuno K, Murata Y, Koide H, Murakami M, Ihara K, Kouyama T.

Proteins. 81 巻 ( 9 ) 頁： 1585-1592 2013年6月

Exome sequencing of senescence-accelerated mice (SAM) reveals deleterious mutations in degenerative disease-causing genes. 査読有り

Tanisawa K, Mikami E, Fuku N, Honda Y, Honda S, Ohsawa I, Ito M, Endo S, Ihara K, Ohno K, Kishimoto Y, Ishigami A, Maruyama N, Sawabe M, Iseki H, Okazaki Y, Hasegawa-Ishii S, Takei S, Shimada A, Hosokawa M, Mori M, Higuchi K, Takeda T, Higuchi M, Tanaka M.

BMC Genomics 14 巻頁： 248 2013年4月

Large deformation of helix F during the photoreaction cycle of Pharaonis halorhodopsin in complex with azide. 査読有り

Nakanishi T, Kanada S, Murakami M, Ihara K, Kouyama T.

Biophys J. 104 巻 ( 2 ) 頁： 377-385 2013年2月

A Novel dnaJ Family Gene, sflA, Encodes an Inhibitor of Flagellation in Marine Vibrio Species.

Kitaoka M, Nishigaki T, Ihara K, Nishioka N, Kojima S, Homma M.

Journal of Bacteriology 195 巻 ( 4 ) 頁： 816-822 2013年2月

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