Flexible comparative genomics of prokaryotic transcriptional regulatory networks
Kılıç, Sefa (University of Maryland Baltimore County)
Sánchez-Osuna, Miquel (Universitat Autònoma de Barcelona)
Collado-Padilla, Antonio (Universitat Autònoma de Barcelona)
Barbé García, Jordi (Universitat Autònoma de Barcelona)
Erill, Ivan (University of Maryland Baltimore County)

Data:	2020
Resum:	Comparative genomics methods enable the reconstruction of bacterial regulatory networks using available experimental data. In spite of their potential for accelerating research into the composition and evolution of bacterial regulons, few comparative genomics suites have been developed for the automated analysis of these regulatory systems. Available solutions typically rely on precomputed databases for operon and ortholog predictions, limiting the scope of analyses to processed complete genomes, and several key issues such as the transfer of experimental information or the integration of regulatory information in a probabilistic setting remain largely unaddressed. Here we introduce CGB, a flexible platform for comparative genomics of prokaryotic regulons. CGB has few external dependencies and enables fully customized analyses of newly available genome data. The platform automates the merging of experimental information and uses a gene-centered, Bayesian framework to generate and integrate easily interpretable results. We demonstrate its flexibility and power by analyzing the evolution of type III secretion system regulation in pathogenic Proteobacteria and by characterizing the SOS regulon of a new bacterial phylum, the Balneolaeota. Our results demonstrate the applicability of the CGB pipeline in multiple settings. CGB's ability to automatically integrate experimental information from multiple sources and use complete and draft genomic data, coupled with its non-reliance on precomputed databases and its easily interpretable display of gene-centered posterior probabilities of regulation provide users with an unprecedented level of flexibility in launching comparative genomics analyses of prokaryotic transcriptional regulatory networks. The analyses of type III secretion and SOS response regulatory networks illustrate instances of convergent and divergent evolution of these regulatory systems, showcasing the power of formal ancestral state reconstruction at inferring the evolutionary history of regulatory networks.
Ajuts:	Ministerio de Economía y Competitividad BIO2016-77011-R
Drets:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Llengua:	Anglès
Document:	Article ; recerca ; Versió publicada
Matèria:	Comparative genomics ; Regulon ; Operon ; Promoter ; Transcription ; Bacteria ; SOS response ; Type III secretion system
Publicat a:	BMC genomics, Vol. 21, Suppl. 5 (December 2020) , art. 466, ISSN 1471-2164

DOI: 10.1186/s12864-020-06838-x
PMID: 33327941

11 p, 2.9 MB

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