{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T15:46:10Z","timestamp":1753890370578,"version":"3.41.2"},"reference-count":61,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2024,8,28]],"date-time":"2024-08-28T00:00:00Z","timestamp":1724803200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Bioinform."],"abstract":"<jats:p><jats:italic>Rhizobium etli<\/jats:italic> CFN42 proteome\u2013transcriptome mixed data of exponential growth and nitrogen-fixing bacteroids, as well as <jats:italic>Sinorhizobium meliloti<\/jats:italic> 1021 transcriptome data of growth and nitrogen-fixing bacteroids, were integrated into transcriptional regulatory networks (TRNs). The one-step construction network consisted of a matrix-clustering analysis of matrices of the gene profile and all matrices of the transcription factors (TFs) of their genome. The networks were constructed with the prediction of regulatory network application of the RhizoBindingSites database (<jats:ext-link>http:\/\/rhizobindingsites.ccg.unam.mx\/<\/jats:ext-link>). The deduced free-living <jats:italic>Rhizobium etli<\/jats:italic> network contained 1,146 genes, including 380\u00a0TFs and 12 sigma factors. In addition, the bacteroid <jats:italic>R. etli<\/jats:italic> CFN42 network contained 884 genes, where 364 were TFs, and 12 were sigma factors, whereas the deduced free-living <jats:italic>Sinorhizobium meliloti<\/jats:italic> 1021 network contained 643 genes, where 259 were TFs and seven were sigma factors, and the bacteroid <jats:italic>Sinorhizobium meliloti<\/jats:italic> 1021 network contained 357 genes, where 210 were TFs and six were sigma factors. The similarity of these deduced condition-dependent networks and the biological <jats:italic>E. coli<\/jats:italic> and <jats:italic>B. subtilis<\/jats:italic> independent condition networks segregates from the random Erd\u00f6s\u2013R\u00e9nyi networks. Deduced networks showed a low average clustering coefficient. They were not scale-free, showing a gradually diminishing hierarchy of TFs in contrast to the hierarchy role of the sigma factor <jats:italic>rpoD<\/jats:italic> in the <jats:italic>E. coli<\/jats:italic> K12 network. For rhizobia networks, partitioning the genome in the chromosome, chromids, and plasmids, where essential genes are distributed, and the symbiotic ability that is mostly coded in plasmids, may alter the structure of these deduced condition-dependent networks. It provides potential TF gen\u2013target relationship data for constructing regulons, which are the basic units of a TRN.<\/jats:p>","DOI":"10.3389\/fbinf.2024.1419274","type":"journal-article","created":{"date-parts":[[2024,8,28]],"date-time":"2024-08-28T06:01:03Z","timestamp":1724824863000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Rhizobium etli CFN42 and Sinorhizobium meliloti 1021 bioinformatic transcriptional regulatory networks from culture and symbiosis"],"prefix":"10.3389","volume":"4","author":[{"given":"Hermenegildo","family":"Taboada-Castro","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alfredo Jos\u00e9","family":"Hern\u00e1ndez-\u00c1lvarez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Juan Miguel","family":"Escorcia-Rodr\u00edguez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Julio Augusto","family":"Freyre-Gonz\u00e1lez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Edgardo","family":"Gal\u00e1n-V\u00e1squez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sergio","family":"Encarnaci\u00f3n-Guevara","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2024,8,28]]},"reference":[{"key":"B61","doi-asserted-by":"publisher","first-page":"8786","DOI":"10.3390\/S130708786","article-title":"Breadth-first search-based single-phase algorithms for bridge detection in wireless sensor networks","volume":"13","author":"Akram","year":"2013","journal-title":"Sensors"},{"key":"B1","doi-asserted-by":"publisher","first-page":"705","DOI":"10.3390\/ijms18040705","article-title":"Specificity in legume-rhizobia symbioses","volume":"18","author":"Andrews","year":"2017","journal-title":"Int. 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