The DnaJK chaperone of Bacillus subtilis post-transcriptionally regulates gene expression through the YlxR(RnpM)/RNase P complex

Authors: Mitsuo Ogura, Yu Kanesaki, Hirofumi Yoshikawa, Koki Haga

Source: mBio, Vol 16, Iss 3 (2025)

Subject Terms: chaperone, transcriptome, RNase P, DnaJK, YlxR(RnpM), mRNA metabolism, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2150-7511

Access URL: https://doaj.org/article/f00e3e0108734f3daef66360b8e9eb05

Class II LitR serves as an effector of 'short' LOV-type blue-light photoreceptor in Pseudomonas mendocina

Authors: Takafumi Maruyama, Satoru Sumi, Mitsuru Kobayashi, Teppei Ebuchi, Yu Kanesaki, Hirofumi Yoshikawa, Kenji Ueda, Hideaki Takano

Source: Scientific Reports, Vol 12, Iss 1, Pp 1-16 (2022)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/f09bc6b9083b42b0be9a4216fd268388

RNA-seq analysis identified glucose-responsive genes and YqfO as a global regulator in Bacillus subtilis

Authors: Yu Kanesaki, Mitsuo Ogura

Source: BMC Research Notes, Vol 14, Iss 1, Pp 1-5 (2021)

Subject Terms: RNA-seq, Glucose, Catabolite regulation, Transcriptome, Medicine, Biology (General), QH301-705.5, Science (General), Q1-390

File Description: electronic resource

Relation: https://doaj.org/toc/1756-0500

Access URL: https://doaj.org/article/2e241ecead5f49669c705908a230aa64

The Rubisco small subunits in the green algal genus Chloromonas provide insights into evolutionary loss of the eukaryotic carbon-concentrating organelle, the pyrenoid

Authors: Ryo Matsuzaki, Shigekatsu Suzuki, Haruyo Yamaguchi, Masanobu Kawachi, Yu Kanesaki, Hirofumi Yoshikawa, Toshiyuki Mori, Hisayoshi Nozaki

Source: BMC Ecology and Evolution, Vol 21, Iss 1, Pp 1-14 (2021)

Subject Terms: Chloromonas, Evolution, Green algae, Hydrophobicity of RBCS helices, Pyrenoid, Pyrenoid loss, Ecology, QH540-549.5, QH359-425

File Description: electronic resource

Relation: https://doaj.org/toc/2730-7182

Access URL: https://doaj.org/article/e25176ef30ad4137a0e28fcb6e02a918

Mutations in degP and spoT Genes Mediate Response to Fermentation Stress in Thermally Adapted Strains of Acetic Acid Bacterium Komagataeibacter medellinensis NBRC 3288

Authors: Naoya Kataoka, Minenosuke Matsutani, Nami Matsumoto, Misuzu Oda, Yuki Mizumachi, Kohei Ito, Shuhei Tanaka, Yu Kanesaki, Toshiharu Yakushi, Kazunobu Matsushita

Source: Frontiers in Microbiology, Vol 13 (2022)

Subject Terms: DegP, SpoT, acetic acid fermentation, thermotolerance, experimental evolution, cell length, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fmicb.2022.802010/full; https://doaj.org/toc/1664-302X

Access URL: https://doaj.org/article/76ec59a2dd1c43dab729e16f314338f1

Responses of unicellular predators to cope with the phototoxicity of photosynthetic prey

Authors: Akihiro Uzuka, Yusuke Kobayashi, Ryo Onuma, Shunsuke Hirooka, Yu Kanesaki, Hirofumi Yoshikawa, Takayuki Fujiwara, Shin-ya Miyagishima

Source: Nature Communications, Vol 10, Iss 1, Pp 1-17 (2019)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/d11cfb418907489fb10babc3cf41c340

Bacillus subtilis Nucleoid-Associated Protein YlxR Is Involved in Bimodal Expression of the Fructoselysine Utilization Operon (frlBONMD-yurJ) Promoter

Authors: Mitsuo Ogura, Kazutoshi Shindo, Yu Kanesaki

Source: Frontiers in Microbiology, Vol 11 (2020)

Subject Terms: amino sugar utilization, bimodal expression, autoregulation of ylxR, Bacillus subtilis, bet-hedging strategy, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fmicb.2020.02024/full; https://doaj.org/toc/1664-302X

Access URL: https://doaj.org/article/007cb447317f4d12854d8c84f05ebfe3

Fpr1, a primary target of rapamycin, functions as a transcription factor for ribosomal protein genes cooperatively with Hmo1 in Saccharomyces cerevisiae.

Authors: Koji Kasahara, Risa Nakayama, Yuh Shiwa, Yu Kanesaki, Taichiro Ishige, Hirofumi Yoshikawa, Tetsuro Kokubo

Source: PLoS Genetics, Vol 16, Iss 6, p e1008865 (2020)

Subject Terms: Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1553-7390; https://doaj.org/toc/1553-7404

Access URL: https://doaj.org/article/5edadf1528554ce499d48f255e54a35a

H-NS Family Proteins Drastically Change Their Targets in Response to the Horizontal Transfer of the Catabolic Plasmid pCAR1

Authors: Taisuke Nakamura, Chiho Suzuki-Minakuchi, Hibiki Kawano, Yu Kanesaki, Shinji Kawasaki, Kazunori Okada, Hideaki Nojiri

Source: Frontiers in Microbiology, Vol 11 (2020)

Subject Terms: nucleoid-associated proteins, H-NS, MvaT, Pseudomonas, plasmid, transcriptome, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fmicb.2020.01099/full; https://doaj.org/toc/1664-302X

Access URL: https://doaj.org/article/3c8742c8471e4ae5a185ac2301990d51

Evolutionary Adaptation by Repetitive Long-Term Cultivation with Gradual Increase in Temperature for Acquiring Multi-Stress Tolerance and High Ethanol Productivity in Kluyveromyces marxianus DMKU 3-1042

Authors: Sornsiri Pattanakittivorakul, Tatsuya Tsuzuno, Tomoyuki Kosaka, Masayuki Murata, Yu Kanesaki, Hirofumi Yoshikawa, Savitree Limtong, Mamoru Yamada

Source: Microorganisms, Vol 10, Iss 4, p 798 (2022)

Subject Terms: repetitive long-term cultivation with gradual increases in temperature (RLCGT), K. marxianus DMKU 3-1042, evolutionarily adapted mutants, thermotolerant ethanol-fermenting yeast, multi-stress tolerance, genomic and transcriptomic analyses, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.mdpi.com/2076-2607/10/4/798; https://doaj.org/toc/2076-2607

Access URL: https://doaj.org/article/840aaad176e3415aa7e0c2b866ee20f7

Evolutionary Changes in DnaA-Dependent Chromosomal Replication in Cyanobacteria

Authors: Ryudo Ohbayashi, Shunsuke Hirooka, Ryo Onuma, Yu Kanesaki, Yuu Hirose, Yusuke Kobayashi, Takayuki Fujiwara, Chikara Furusawa, Shin-ya Miyagishima

Source: Frontiers in Microbiology, Vol 11 (2020)

Subject Terms: CDS skew, chromosome replication, cyanobacteria, DnaA, GC skew, polyploidy, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fmicb.2020.00786/full; https://doaj.org/toc/1664-302X

Access URL: https://doaj.org/article/767840270ed54cc4999c62d9f65b1b70

Transcriptome profile of carbon catabolite repression in an efficient l-(+)-lactic acid-producing bacterium Enterococcus mundtii QU25 grown in media with combinations of cellobiose, xylose, and glucose.

Authors: Yuh Shiwa, Haruko Fujiwara, Mao Numaguchi, Mohamed Ali Abdel-Rahman, Keisuke Nabeta, Yu Kanesaki, Yukihiro Tashiro, Takeshi Zendo, Naoto Tanaka, Nobuyuki Fujita, Hirofumi Yoshikawa, Kenji Sonomoto, Mariko Shimizu-Kadota

Source: PLoS ONE, Vol 15, Iss 11, p e0242070 (2020)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/656151ec9003494fb666e1c0a9119595

Identification of Transcription Factors and the Regulatory Genes Involved in Triacylglycerol Accumulation in the Unicellular Red Alga Cyanidioschyzon merolae

Authors: Sota Takahashi, Riho Okubo, Yu Kanesaki, Baifeng Zhou, Kazuhiro Takaya, Satoru Watanabe, Kan Tanaka, Sousuke Imamura

Source: Plants, Vol 10, Iss 5, p 971 (2021)

Subject Terms: algal biofuel, lysophosphatidic acid acyltransferase, red alga, transcription factor, triacylglycerol, Botany, QK1-989

File Description: electronic resource

Relation: https://www.mdpi.com/2223-7747/10/5/971; https://doaj.org/toc/2223-7747

Access URL: https://doaj.org/article/649453b39f45425fb2c3c1ba9f301053

Integration of a Galdieria plasma membrane sugar transporter enables heterotrophic growth of the obligate photoautotrophic red alga Cynanidioschyzon merolae

Authors: Takayuki Fujiwara, Shunsuke Hirooka, Mizuna Mukai, Ryudo Ohbayashi, Yu kanesaki, Satoru Watanabe, Shin‐ya Miyagishima

Source: Plant Direct, Vol 3, Iss 4, Pp n/a-n/a (2019)

Subject Terms: Cyanidioschyzon merolae, Galdieria sulphuraria, heterotroph, mixotroph, plasma membrane sugar transporter, Botany, QK1-989

File Description: electronic resource

Relation: https://doaj.org/toc/2475-4455

Access URL: https://doaj.org/article/18d9f1614a6c4b79b21aa97e4c946371

Coordination of Polyploid Chromosome Replication with Cell Size and Growth in a Cyanobacterium

Authors: Ryudo Ohbayashi, Ai Nakamachi, Tetsuhiro S. Hatakeyama, Satoru Watanabe, Yu Kanesaki, Taku Chibazakura, Hirofumi Yoshikawa, Shin-ya Miyagishima

Source: mBio, Vol 10, Iss 2 (2019)

Subject Terms: DNA replication, DnaA, polyploidy, RpoC, cyanobacteria, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2150-7511

Access URL: https://doaj.org/article/3a209cca49224ceabb18d4e0daee2e1c

Complete Genome Sequence of 3-Chlorobenzoate-Degrading Bacterium Cupriavidus necator NH9 and Reclassification of the Strains of the Genera Cupriavidus and Ralstonia Based on Phylogenetic and Whole-Genome Sequence Analyses

Authors: Ryota Moriuchi, Hideo Dohra, Yu Kanesaki, Naoto Ogawa

Source: Frontiers in Microbiology, Vol 10 (2019)

Subject Terms: aromatic degradation, Cupriavidus, Ralstonia, reclassification, ANI (average nucleotide identity), TNA (tetra-nucleotide analysis), Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fmicb.2019.00133/full; https://doaj.org/toc/1664-302X

Access URL: https://doaj.org/article/f2a8b369f0e245a4a0235e9bed19673b

Correction: Capacity for survival in global warming: Adaptation of mesophiles to the temperature upper limit.

Authors: Tomoyuki Kosaka, Yasuyuki Nakajima, Ayana Ishii, Maiko Yamashita, Saki Yoshida, Masayuki Murata, Kunpei Kato, Yuki Shiromaru, Shun Kato, Yu Kanesaki, Hirofumi Yoshikawa, Minenosuke Matsutani, Pornthap Thanonkeo, Mamoru Yamada

Source: PLoS ONE, Vol 14, Iss 6, p e0218985 (2019)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/5339e07fce724e4485616400ea5aaade

Newly Identified Nucleoid-Associated-Like Protein YlxR Regulates Metabolic Gene Expression in Bacillus subtilis

Authors: Mitsuo Ogura, Yu Kanesaki

Source: mSphere, Vol 3, Iss 5 (2018)

Subject Terms: RNA-Seq, metabolic genes, nucleoid, transcription regulation, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2379-5042

Access URL: https://doaj.org/article/f6ba38507fd6407eb6344b806d29bc22

Sulfur-Containing Carotenoids from A Marine Coral Symbiont Erythrobacter flavus Strain KJ5

Authors: Edi Setiyono, Heriyanto, Delianis Pringgenies, Yuzo Shioi, Yu Kanesaki, Koichiro Awai, Tatas Hardo Panintingjati Brotosudarmo

Source: Marine Drugs, Vol 17, Iss 6, p 349 (2019)

Subject Terms: carotenoids, caloxanthin sulfate, nostoxanthin sulfate, zeaxanthin sulfate, Erythrobacter flavus strain KJ5, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.mdpi.com/1660-3397/17/6/349; https://doaj.org/toc/1660-3397

Access URL: https://doaj.org/article/326e7a4ad63749e2a798d4bc17e8f9d3

Genetic Analysis of Collective Motility of Paenibacillus sp. NAIST15-1.

Authors: Kazuo Kobayashi, Yu Kanesaki, Hirofumi Yoshikawa

Source: PLoS Genetics, Vol 12, Iss 10, p e1006387 (2016)

Subject Terms: Genetics, QH426-470

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC5072692?pdf=render; https://doaj.org/toc/1553-7390; https://doaj.org/toc/1553-7404

Access URL: https://doaj.org/article/af919d5cf87547daa21a3344f1c5b9bf