{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T10:13:02Z","timestamp":1775556782374,"version":"3.50.1"},"reference-count":33,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2025,2,5]],"date-time":"2025-02-05T00:00:00Z","timestamp":1738713600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Grant-in-Aid for Scientific Research","award":["21H05271"],"award-info":[{"award-number":["21H05271"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>To elucidate the mechanism of large-scale transcriptional changes dependent on sulfide in Escherichia coli, a large-scale RNA-sequencing analysis was performed on wild-type and sulfide-responsive transcription factor YgaV deletion mutants grown under three conditions: aerobic, semi-aerobic, and semi-aerobic with sulfide. The resulting dataset from these six conditions was subjected to principal component analysis, which categorized the data into five principal components. Estimation of the typical gene expression regulatory mechanisms in each category suggested the presence of mechanisms that are dependent on sulfide but independent of YgaV, as well as those that depend on YgaV but not on sulfide. In YgaV-dependent transcriptional regulation, YgaV was found to function as both a repressor and an activator. These results support the previous hypothesis that YgaV acts as a global regulator responsible for redox homeostasis.<\/jats:p>","DOI":"10.3390\/microorganisms13020344","type":"journal-article","created":{"date-parts":[[2025,2,5]],"date-time":"2025-02-05T07:44:59Z","timestamp":1738741499000},"page":"344","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Sulfide-Responsive Transcription Control in Escherichia coli"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0530-181X","authenticated-orcid":false,"given":"Koichi","family":"Hori","sequence":"first","affiliation":[{"name":"School of Life Science & Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rajalakshmi","family":"Balasubramanian","sequence":"additional","affiliation":[{"name":"School of Life Science & Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shinji","family":"Masuda","sequence":"additional","affiliation":[{"name":"School of Life Science & Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan"},{"name":"School of Life Science & Technology, Institute of Science Tokyo, Yokohama 226-8501, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,2,5]]},"reference":[{"key":"ref_1","first-page":"57","article-title":"Comparison of fermentation reactions in different regions of the human colon","volume":"72","author":"Macfarlane","year":"1992","journal-title":"J. Appl. Bacteriol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"13582","DOI":"10.1073\/pnas.1312524110","article-title":"Metabolic niche of a prominent sulfate-reducing human gut bacterium","volume":"110","author":"Rey","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"13150","DOI":"10.1074\/jbc.REV120.011304","article-title":"H2S and reactive sulfur signaling at the host-bacterial pathogen interface","volume":"295","author":"Walsh","year":"2020","journal-title":"J. Biol. Chem."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"2241","DOI":"10.1007\/s10620-017-4689-5","article-title":"Sulfurcycling and the intestinal microbiome","volume":"62","author":"Barton","year":"2017","journal-title":"Dig. Dis. Sci."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"986","DOI":"10.1126\/science.1209855","article-title":"H2S: A universal defense against antibiotics in bacteria","volume":"334","author":"Shatalin","year":"2011","journal-title":"Science"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"6022","DOI":"10.1073\/pnas.1703576114","article-title":"Mechanism of H2S-mediated protection against oxidative stress in Escherichia coli","volume":"114","author":"Mironov","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1128\/mBio.01254-20","article-title":"The response of acinetobacter baumannii to hydrogen sulfide reveals two independent persulfide-sensing systems and a connection to biofilm regulation","volume":"11","author":"Walsh","year":"2020","journal-title":"MBio"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Pis Diez, C.M., Antelo, G.T., Dalia, T.N., Dalia, A.B., Giedroc, D.P., and Capdevila, D.A. (2023). Increased intracellular persulfide levels attenuate HlyU-mediated hemolysin transcriptional activation in Vibrio cholerae. J. Biol. Chem., 299.","DOI":"10.1101\/2023.03.13.532278"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Balasubramanian, R., Hori, K., Shimizu, T., Kasamatsu, S., Okamura, K., Tanaka, K., Ihara, H., and Masuda, S. (2022). The sulfide-responsive SqrR\/BigR homologous regulator YgaV of Escherichia coli controls expression of anaerobic respiratory genes and antibiotic tolerance. Antioxidants, 11.","DOI":"10.3390\/antiox11122359"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1038","DOI":"10.1111\/mmi.14593","article-title":"Sulfane Sulfur is an intrinsic signal activating MexR-regulated antibiotic resistance in Pseudomonas aeruginosa","volume":"114","author":"Xuan","year":"2020","journal-title":"Mol. Microbiol."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Li, J., T\u00f6rkel, K., Koch, J., Tanabe, T.S., Hsu, H.Y., and Dahl, C. (2023). In the Alphaproteobacterium Hyphomicrobium denitrificans SoxR Serves a Sulfane Sulfur-Responsive Repressor of Sulfur Oxidation. Antioxidants, 12.","DOI":"10.20944\/preprints202307.0868.v1"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1016\/j.chom.2024.01.004","article-title":"Anaerobic respiration of host-derived methionine sulfoxide protects intracellular Salmonella from the phagocyte NADPH oxidase","volume":"32","author":"Kim","year":"2024","journal-title":"Cell Host Microbe"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Ye, J., Salti, T., Zanditenas, E., Trebicz-Geffen, M., Benhar, M., and Ankri, S. (2024). Impact of Reactive Sulfur Species on Entamoeba histolytica: Modulating Viability, Motility, and Biofilm Degradation Capacity. Antioxidants, 13.","DOI":"10.3390\/antiox13020245"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1002\/mlf2.12109","article-title":"MarR family proteins sense sulfane sulfur in bacteria","volume":"3","author":"Xuan","year":"2024","journal-title":"mLife"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1111\/mmi.13725","article-title":"FisR activates \u03c354-dependent transcription of sulfide-oxidizing genes in Cupriavidus pinatubonensis JMP134","volume":"105","author":"Li","year":"2017","journal-title":"Mol. Microbiol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1343","DOI":"10.1111\/mmi.12835","article-title":"The CsoR-like sulfurtransferase repressor (CstR) is a persulfide sensor in Staphylococcus aureus","volume":"94","author":"Luebke","year":"2014","journal-title":"Mol. Microbiol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"2355","DOI":"10.1073\/pnas.1614133114","article-title":"Sulfide-responsive transcriptional repressor SqrR functions as a master regulator of sulfide-dependent photosynthesis","volume":"114","author":"Shimizu","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Giedroc, D.P., Antelo, G.T., Fakhoury, J.N., and Capdevila, D.A. (2023). Sensing and regulation of reactive sulfur species (RSS) in bacteria. Curr. Opin. Chem. Biol., 76.","DOI":"10.1016\/j.cbpa.2023.102358"},{"key":"ref_19","first-page":"125","article-title":"Persulphide-responsive transcriptional regulation and metabolism in bacteria","volume":"167","author":"Shimizu","year":"2020","journal-title":"J. Biochem."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Shimizu, T., Aritoshi, T., Beatty, J.T., and Masuda, T. (2022). Persulfide-Responsive Transcription Factor SqrR Regulates Gene Transfer and Biofilm Formation via the Metabolic Modulation of Cyclic di-GMP in Rhodobacter capsulatus. Microorganisms, 10.","DOI":"10.3390\/microorganisms10050908"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1038\/s41589-020-00671-9","article-title":"Structural basis for persulfide-sensing specificity in a transcriptional regulator","volume":"17","author":"Capdevila","year":"2020","journal-title":"Nat. Chem. Biol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"pgad048","DOI":"10.1093\/pnasnexus\/pgad048","article-title":"Polysulfide metabolizing enzymes influence SqrR-mediated sulfide-induced transcription by impacting intracellular polysulfide dynamics","volume":"2","author":"Shimizu","year":"2023","journal-title":"PNAS Nexus"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Shimizu, T., Hashimoto, M., and Masuda, T. (2023). Thioredoxin-2 Regulates SqrR-Mediated Polysulfide-Responsive Transcription via Reduction of a Polysulfide Link in SqrR. Antioxidants, 12.","DOI":"10.3390\/antiox12030699"},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Nonoyama, S., Maeno, S., Gotoh, Y., Sugimoto, R., Tanaka, K., Hayashi, T., and Masuda, S. (2024). Increased intracellular H2S levels enhance iron uptake in Escherichia coli. mBio, 15.","DOI":"10.1128\/mbio.01991-24"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1093\/pcp\/pcaa144","article-title":"Repressor Activity of SqrR, a Master Regulator of Persulfide-Responsive Genes, Is Regulated by Heme Coordination","volume":"62","author":"Shimizu","year":"2021","journal-title":"Plant Cell Physiol."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., Datsenko, K.A., Tomita, M., Wanner, B.L., and Mori, H. (2006). Construction of Escherichia coli k-12 in-frame, single-gene knockout mutants: The Keio collection. Mol. Syst. Biol., 2.","DOI":"10.1038\/msb4100050"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Yamamoto, N., Nakahigashi, K., Nakamichi, T., Yoshino, M., Takai, Y., Touda, Y., Furubayashi, A., Kinjyo, S., Dose, H., and Hasegawa, M. (2009). Update on the Keio collection of Escherichia coli single-gene deletion mutants. Mol. Syst. Biol., 5.","DOI":"10.1038\/msb.2009.92"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1038\/s41587-019-0201-4","article-title":"Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype","volume":"37","author":"Kim","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Sun, J., Nishiyama, T., Shimizu, K., and Kadota, K. (2013). TCC: An R package for comparing tag count data with robust normalization strategies. BMC Bioinform., 14.","DOI":"10.1186\/1471-2105-14-219"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"W182","DOI":"10.1093\/nar\/gkm321","article-title":"KAAS: An automatic genome annotation and pathway reconstruction server","volume":"35","author":"Moriya","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1002\/pro.3711","article-title":"KEGG Mapper for inferring cellular functions from protein sequences","volume":"29","author":"Kanehisa","year":"2020","journal-title":"Protein Sci."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.mib.2014.06.017","article-title":"Bacterial gasotransmitters: An innate defense against antibiotics","volume":"21","author":"Luhachack","year":"2014","journal-title":"Curr. Opin. Microbiol."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Hou, N., Yan, Z., Fan, K., Li, H., Zhao, R., Xia, Y., Xun, L., and Liu, H. (2019). OxyR senses sulfane sulfur and activates the genes for its removal in Escherichia coli. Redox Biol., 26.","DOI":"10.1016\/j.redox.2019.101293"}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/13\/2\/344\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T16:27:18Z","timestamp":1760027238000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/13\/2\/344"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,2,5]]},"references-count":33,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2025,2]]}},"alternative-id":["microorganisms13020344"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms13020344","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,2,5]]}}}