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Evaluation of the Abundance of DNA-Binding Transcription Factors in Prokaryotes

The ability of bacteria and archaea to modulate metabolic process, defensive response, and pathogenic capabilities depend on their repertoire of genes and capacity to regulate the expression of them. Transcription factors (TFs) have fundamental roles in controlling these processes. TFs are proteins...

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Autores principales: Sanchez, Israel, Hernandez-Guerrero, Rafael, Mendez-Monroy, Paul Erick, Martinez-Nuñez, Mario Alberto, Ibarra, Jose Antonio, Pérez-Rueda, Ernesto
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7017128/
https://www.ncbi.nlm.nih.gov/pubmed/31947717
http://dx.doi.org/10.3390/genes11010052
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author Sanchez, Israel
Hernandez-Guerrero, Rafael
Mendez-Monroy, Paul Erick
Martinez-Nuñez, Mario Alberto
Ibarra, Jose Antonio
Pérez-Rueda, Ernesto
author_facet Sanchez, Israel
Hernandez-Guerrero, Rafael
Mendez-Monroy, Paul Erick
Martinez-Nuñez, Mario Alberto
Ibarra, Jose Antonio
Pérez-Rueda, Ernesto
author_sort Sanchez, Israel
collection PubMed
description The ability of bacteria and archaea to modulate metabolic process, defensive response, and pathogenic capabilities depend on their repertoire of genes and capacity to regulate the expression of them. Transcription factors (TFs) have fundamental roles in controlling these processes. TFs are proteins dedicated to favor and/or impede the activity of the RNA polymerase. In prokaryotes these proteins have been grouped into families that can be found in most of the different taxonomic divisions. In this work, the association between the expansion patterns of 111 protein regulatory families was systematically evaluated in 1351 non-redundant prokaryotic genomes. This analysis provides insights into the functional and evolutionary constraints imposed on different classes of regulatory factors in bacterial and archaeal organisms. Based on their distribution, we found a relationship between the contents of some TF families and genome size. For example, nine TF families that represent 43.7% of the complete collection of TFs are closely associated with genome size; i.e., in large genomes, members of these families are also abundant, but when a genome is small, such TF family sizes are decreased. In contrast, almost 102 families (56.3% of the collection) do not exhibit or show only a low correlation with the genome size, suggesting that a large proportion of duplication or gene loss events occur independently of the genome size and that various yet-unexplored questions about the evolution of these TF families remain. In addition, we identified a group of families that have a similar distribution pattern across Bacteria and Archaea, suggesting common functional and probable coevolution processes, and a group of families universally distributed among all the genomes. Finally, a specific association between the TF families and their additional domains was identified, suggesting that the families sense specific signals or make specific protein-protein contacts to achieve the regulatory roles.
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spelling pubmed-70171282020-02-28 Evaluation of the Abundance of DNA-Binding Transcription Factors in Prokaryotes Sanchez, Israel Hernandez-Guerrero, Rafael Mendez-Monroy, Paul Erick Martinez-Nuñez, Mario Alberto Ibarra, Jose Antonio Pérez-Rueda, Ernesto Genes (Basel) Article The ability of bacteria and archaea to modulate metabolic process, defensive response, and pathogenic capabilities depend on their repertoire of genes and capacity to regulate the expression of them. Transcription factors (TFs) have fundamental roles in controlling these processes. TFs are proteins dedicated to favor and/or impede the activity of the RNA polymerase. In prokaryotes these proteins have been grouped into families that can be found in most of the different taxonomic divisions. In this work, the association between the expansion patterns of 111 protein regulatory families was systematically evaluated in 1351 non-redundant prokaryotic genomes. This analysis provides insights into the functional and evolutionary constraints imposed on different classes of regulatory factors in bacterial and archaeal organisms. Based on their distribution, we found a relationship between the contents of some TF families and genome size. For example, nine TF families that represent 43.7% of the complete collection of TFs are closely associated with genome size; i.e., in large genomes, members of these families are also abundant, but when a genome is small, such TF family sizes are decreased. In contrast, almost 102 families (56.3% of the collection) do not exhibit or show only a low correlation with the genome size, suggesting that a large proportion of duplication or gene loss events occur independently of the genome size and that various yet-unexplored questions about the evolution of these TF families remain. In addition, we identified a group of families that have a similar distribution pattern across Bacteria and Archaea, suggesting common functional and probable coevolution processes, and a group of families universally distributed among all the genomes. Finally, a specific association between the TF families and their additional domains was identified, suggesting that the families sense specific signals or make specific protein-protein contacts to achieve the regulatory roles. MDPI 2020-01-03 /pmc/articles/PMC7017128/ /pubmed/31947717 http://dx.doi.org/10.3390/genes11010052 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Sanchez, Israel
Hernandez-Guerrero, Rafael
Mendez-Monroy, Paul Erick
Martinez-Nuñez, Mario Alberto
Ibarra, Jose Antonio
Pérez-Rueda, Ernesto
Evaluation of the Abundance of DNA-Binding Transcription Factors in Prokaryotes
title Evaluation of the Abundance of DNA-Binding Transcription Factors in Prokaryotes
title_full Evaluation of the Abundance of DNA-Binding Transcription Factors in Prokaryotes
title_fullStr Evaluation of the Abundance of DNA-Binding Transcription Factors in Prokaryotes
title_full_unstemmed Evaluation of the Abundance of DNA-Binding Transcription Factors in Prokaryotes
title_short Evaluation of the Abundance of DNA-Binding Transcription Factors in Prokaryotes
title_sort evaluation of the abundance of dna-binding transcription factors in prokaryotes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7017128/
https://www.ncbi.nlm.nih.gov/pubmed/31947717
http://dx.doi.org/10.3390/genes11010052
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