Transcription Factors Exhibit Differential Conservation in Bacteria with Reduced Genomes

PloS One
Edgardo Galán-VásquezAgustino Martínez-Antonio

Abstract

The description of transcriptional regulatory networks has been pivotal in the understanding of operating principles under which organisms respond and adapt to varying conditions. While the study of the topology and dynamics of these networks has been the subject of considerable work, the investigation of the evolution of their topology, as a result of the adaptation of organisms to different environmental conditions, has received little attention. In this work, we study the evolution of transcriptional regulatory networks in bacteria from a genome reduction perspective, which manifests itself as the loss of genes at different degrees. We used the transcriptional regulatory network of Escherichia coli as a reference to compare 113 smaller, phylogenetically-related γ-proteobacteria, including 19 genomes of symbionts. We found that the type of regulatory action exerted by transcription factors, as genomes get progressively smaller, correlates well with their degree of conservation, with dual regulators being more conserved than repressors and activators in conditions of extreme reduction. In addition, we found that the preponderant conservation of dual regulators might be due to their role as both global regulators and nucleoid-a...Continue Reading

References

Dec 1, 1977·Proceedings of the National Academy of Sciences of the United States of America·M A Savageau
Jan 1, 1985·Annual Review of Genetics·W S ReznikoffC A Gross
Jan 1, 1984·Annual Review of Genetics·S Gottesman
Apr 2, 1996·Proceedings of the National Academy of Sciences of the United States of America·N A Moran
Mar 29, 2000·Nucleic Acids Research·E Pérez-Rueda, J Collado-Vides
Apr 3, 2003·Nature Reviews. Genetics·Mark Holder, Paul O Lewis
Sep 6, 2003·Trends in Genetics : TIG·Erik van Nimwegen
Oct 24, 2003·Current Opinion in Microbiology·Agustino Martínez-Antonio, Julio Collado-Vides
Feb 19, 2004·Nature Reviews. Genetics·Harley H McAdamsAdam P Arkin
Apr 27, 2004·Nature Genetics·Sarah A Teichmann, M Madan Babu
Oct 29, 2005·Journal of Cell Science·Réka Albert
Nov 29, 2005·Trends in Microbiology·Agustino Martínez-AntonioJulio Collado-Vides
Mar 15, 2006·Journal of Molecular Biology·M Madan BabuL Aravind
Jul 15, 2006·Nucleic Acids Research·Irma Lozada-ChávezJulio Collado-Vides
Mar 21, 2007·Proceedings of the National Academy of Sciences of the United States of America·M Cosentino LagomarsinoH Isambert
May 19, 2007·Nature Reviews. Genetics·Uri Alon
Sep 12, 2007·PLoS Computational Biology·Morgan N PriceAdam P Arkin
Nov 23, 2007·Genome Research·Nacho Molina, Erik van Nimwegen
Nov 29, 2007·Bioinformatics·Gabriel Moreno-Hagelsieb, Kristen Latimer
Jan 10, 2009·Nature Protocols·Da Wei HuangRichard A Lempicki
Apr 22, 2009·Methods in Molecular Biology·M Madan BabuL Aravind
Dec 22, 2009·Molecular BioSystems·Gipsi Lima-Mendez, Jacques van Helden
Feb 9, 2010·Nature Reviews. Microbiology·Shane C Dillon, Charles J Dorman
May 20, 2011·Current Opinion in Biotechnology·Matthew Scott, Terence Hwa
Nov 9, 2011·Nature Reviews. Microbiology·John P McCutcheon, Nancy A Moran
Dec 7, 2011·Nature Reviews. Genetics·Patricia J Wittkopp, Gizem Kalay
Feb 24, 2012·Systematic Biology·Fredrik RonquistJohn P Huelsenbeck
Jan 1, 2011·Microbial Informatics and Experimentation·Edgardo Galán-VásquezAgustino Martínez-Antonio
Nov 13, 2012·Nucleic Acids Research·Ingrid M KeselerPeter D Karp
Jan 18, 2013·BMC Genomics·Paul F BrayIsidore Rigoutsos
Apr 18, 2013·Molecular Systems Biology·Luca GerosaUwe Sauer
Jun 19, 2013·PloS One·Yalbi Itzel Balderas-MartínezJulio Collado-Vides
Jul 6, 2014·Annual Review of Microbiology·Nancy A Moran, Gordon M Bennett
Aug 1, 2015·Proceedings of the National Academy of Sciences of the United States of America·Mathew StracyAchillefs N Kapanidis

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Citations

Aug 5, 2017·Microbiology·Nancy Rivera-GómezErnesto Perez-Rueda
Oct 30, 2020·International Journal of Molecular Sciences·Kristi Moncja, Michael W Van Dyke
Jun 8, 2021·Frontiers in Microbiology·Cinthia V Soberanes-GutiérrezEdgardo Galán-Vásquez
Aug 1, 2019·ACS Synthetic Biology·Lummy Maria Oliveira MonteiroRafael Silva-Rocha

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