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ORIGINAL RESEARCH article

Front. Bioinform.
Sec. Network Bioinformatics
Volume 4 - 2024 | doi: 10.3389/fbinf.2024.1419274

Rhizobium etli CFN42 and Sinorhizobium meliloti 1021 bioinformatic transcriptional regulatory networks from culture and symbiosis

Provisionally accepted
Hermenegildo Taboada Hermenegildo Taboada 1Alfredo J. Hernández-Alvarez Alfredo J. Hernández-Alvarez 1Juan Miguel Escorcia-Rodríguez Juan Miguel Escorcia-Rodríguez 1Julio A. Freyre-Gonzalez Julio A. Freyre-Gonzalez 1Edgardo Galán-Vásquez Edgardo Galán-Vásquez 2Sergio Encarnacion-Guevara Sergio Encarnacion-Guevara 1*
  • 1 Center for Genomic Sciences, National Autonomous University of Mexico, Cuernavaca, Morelos, Mexico
  • 2 Institute of Applied Mathematics and Systems Research, National Autonomous University of Mexico, Mexico City, México, Mexico

The final, formatted version of the article will be published soon.

    A Rhizobium etli CFN42 proteome-transcriptome mixed data of exponential growth and nitrogenfixing bacteroids, as well as Sinorhizobium meliloti 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 construction of networks was done with the prediction of regulatory networks application of the RhizoBindingSites database (http://rhizobindingsites.ccg.unam.mx/). The deduced free-living Rhizobium etli network contained 1146 genes, including 380 TFs and 12 sigma factors. In addition, the bacteroid R. etli CFN42 network contained 884 genes, 364 TFs, and 12 sigma factors. While the deduced free-living Sinorhizobium meliloti 1021 network contained 643 genes, 259 were TFs and seven sigma factor, and in the bacteroid Sinorhizobium meliloti 1021 network, 357 genes, 210 were TFs and six sigma factors. The Similarity of these deduced condition-dependent networks and the biological E.coli and B. subtilis independent condition networks segregate from the random Erdös-Rényi 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 rpoD in the E. coli K12 network. For rhizobia networks, partitioning the genome in the chromosome, chromids, and plasmids, where essential genes are distributed, and the symbiotic ability is mostly coded in plasmids, may alter the structure of these deduced condition-dependent networks. It provides potential TF gen-target relationship data for constructing regulons, which are basic units of a TRN.

    Keywords: Transcriptional, Regulatory, network, motif, Symbiosis, Rhizobia, etli, Nitrogen-Fixation

    Received: 18 Apr 2024; Accepted: 24 Jul 2024.

    Copyright: © 2024 Taboada, Hernández-Alvarez, Escorcia-Rodríguez, Freyre-Gonzalez, Galán-Vásquez and Encarnacion-Guevara. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Sergio Encarnacion-Guevara, Center for Genomic Sciences, National Autonomous University of Mexico, Cuernavaca, 62210, Morelos, Mexico

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