Deciphering the functional diversity of DNA-binding transcription factors in bacteria and archaea organisms
Cargando...
Archivos
Fecha
2020-08
Profesor/a Guía
Facultad/escuela
Idioma
en
Título de la revista
ISSN de la revista
Título del volumen
Editor
Public Library of Science
Nombre de Curso
Licencia CC
Atribution 4.0 International (CC BY 4.0)
Licencia CC
https://creativecommons.org/licenses/by/4.0/deed.es
Resumen
DNA-binding Transcription Factors (TFs) play a central role in regulation of gene expression
in prokaryotic organisms, and similarities at the sequence level have been reported. These
proteins are predicted with different abundances as a consequence of genome size, where
small organisms contain a low proportion of TFs and large genomes contain a high proportion
of TFs. In this work, we analyzed a collection of 668 experimentally validated TFs across 30
different species from diverse taxonomical classes, including Escherichia coli K-12, Bacillus
subtilis 168, Corynebacterium glutamicum, and Streptomyces coelicolor, among others. This
collection of TFs, together with 111 hidden Markov model profiles associated with DNA-bind ing TFs collected from diverse databases such as PFAM and DBD, was used to identify the
repertoire of proteins putatively devoted to gene regulation in 1321 representative genomes
of Archaea and Bacteria. The predicted regulatory proteins were posteriorly analyzed in
terms of their genomic context, allowing the prediction of functions for TFs and their neighbor
genes, such as genes involved in virulence, enzymatic functions, phosphorylation mecha nisms, and antibiotic resistance. The functional analysis associated with PFAM groups
showed diverse functional categories were significantly enriched in the collection of TFs and
the proteins encoded by the neighbor genes, in particular, small-molecule binding and amino
acid transmembrane transporter activities associated with the LysR family and proteins
devoted to cellular aromatic compound metabolic processes or responses to drugs, stress,
or abiotic stimuli in the MarR family. We consider that with the increasing data derived from
new technologies, novel TFs can be identified and help improve the predictions for this class
of proteins in complete genomes. The complete collection of experimentally characterized
and predicted TFs is available at http://web.pcyt.unam.mx/EntrafDB/.
Notas
Indexación: Scopus.
Palabras clave
Bacterial Genomics, Protein Domains, Gene Regulation, Gene Expression, DNA-binding Proteins, Metabolic Processes, Cell Binding, Genomics
Citación
PLoS ONEO. Volume 15, Issue 8 August 2020. August 2020. Article number e0237135
DOI
DOI: 10.1371/journal.pone.0237135