Abundance, diversity and domain architecture variability in prokaryotic DNA-binding transcription factors

Ernesto Perez-Rueda, Rafael Hernandez-Guerrero, Mario Alberto Martinez-Nuñez, Dagoberto Armenta-Medina, Israel Sanchez, J. Antonio Ibarra

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

© 2018 Perez-Rueda et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Gene regulation at the transcriptional level is a central process in all organisms, and DNAbinding transcription factors, known as TFs, play a fundamental role. This class of proteins usually binds at specific DNA sequences, activating or repressing gene expression. In general, TFs are composed of two domains: The DNA-binding domain (DBD) and an extra domain, which in this work we have named 'companion domain' (CD). This latter could be involved in one or more functions such as ligand binding, protein-protein interactions or even with enzymatic activity. In contrast to DBDs, which have been widely characterized both experimentally and bioinformatically, information on the abundance, distribution, variability and possible role of the CDs is scarce. Here, we investigated these issues associated with the domain architectures of TFs in prokaryotic genomes. To this end, 19 families of TFs in 761 non-redundant bacterial and archaeal genomes were evaluated. In this regard we found four main groups based on the abundance and distribution in the analyzed genomes: I) LysR and TetR/AcrR; ii) AraC/XylS, SinR, and others; iii) Lrp, Fis, ArsR, and others; and iv) a group that included only two families, ArgR and BirA. Based on a classification of the organisms according to the life-styles, a major abundance of regulatory families in free-living organisms, in contrast with pathogenic, extremophilic or intracellular organisms, was identified. Finally, the protein architecture diversity associated to the 19 families considering a weight score for domain promiscuity evidenced which regulatory families were characterized by either a large diversity of CDs, here named as 'promiscuous' families given the elevated number of variable domains found in those TFs, or a low diversity of CDs. Altogether this information helped us to understand the diversity and distribution of the 19 Prokaryotes TF families. Moreover, initial steps were taken to comprehend the variability of the extra domain in those TFs, which eventually might assist in evolutionary and functional studies.
Original languageAmerican English
JournalPLoS ONE
DOIs
StatePublished - 1 Apr 2018

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Transcription Factors
transcription factors
Genes
Gene expression
DNA
organisms
genome
Proteins
DNA sequences
DNA-binding domains
Carrier Proteins
protein-protein interactions
prokaryotic cells
Archaeal Genome
Ligands
lifestyle
binding proteins
Genome
proteins
Bacterial Genomes

Cite this

Perez-Rueda, Ernesto ; Hernandez-Guerrero, Rafael ; Martinez-Nuñez, Mario Alberto ; Armenta-Medina, Dagoberto ; Sanchez, Israel ; Ibarra, J. Antonio. / Abundance, diversity and domain architecture variability in prokaryotic DNA-binding transcription factors. In: PLoS ONE. 2018.
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Abundance, diversity and domain architecture variability in prokaryotic DNA-binding transcription factors. / Perez-Rueda, Ernesto; Hernandez-Guerrero, Rafael; Martinez-Nuñez, Mario Alberto; Armenta-Medina, Dagoberto; Sanchez, Israel; Ibarra, J. Antonio.

In: PLoS ONE, 01.04.2018.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Abundance, diversity and domain architecture variability in prokaryotic DNA-binding transcription factors

AU - Perez-Rueda, Ernesto

AU - Hernandez-Guerrero, Rafael

AU - Martinez-Nuñez, Mario Alberto

AU - Armenta-Medina, Dagoberto

AU - Sanchez, Israel

AU - Ibarra, J. Antonio

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N2 - © 2018 Perez-Rueda et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Gene regulation at the transcriptional level is a central process in all organisms, and DNAbinding transcription factors, known as TFs, play a fundamental role. This class of proteins usually binds at specific DNA sequences, activating or repressing gene expression. In general, TFs are composed of two domains: The DNA-binding domain (DBD) and an extra domain, which in this work we have named 'companion domain' (CD). This latter could be involved in one or more functions such as ligand binding, protein-protein interactions or even with enzymatic activity. In contrast to DBDs, which have been widely characterized both experimentally and bioinformatically, information on the abundance, distribution, variability and possible role of the CDs is scarce. Here, we investigated these issues associated with the domain architectures of TFs in prokaryotic genomes. To this end, 19 families of TFs in 761 non-redundant bacterial and archaeal genomes were evaluated. In this regard we found four main groups based on the abundance and distribution in the analyzed genomes: I) LysR and TetR/AcrR; ii) AraC/XylS, SinR, and others; iii) Lrp, Fis, ArsR, and others; and iv) a group that included only two families, ArgR and BirA. Based on a classification of the organisms according to the life-styles, a major abundance of regulatory families in free-living organisms, in contrast with pathogenic, extremophilic or intracellular organisms, was identified. Finally, the protein architecture diversity associated to the 19 families considering a weight score for domain promiscuity evidenced which regulatory families were characterized by either a large diversity of CDs, here named as 'promiscuous' families given the elevated number of variable domains found in those TFs, or a low diversity of CDs. Altogether this information helped us to understand the diversity and distribution of the 19 Prokaryotes TF families. Moreover, initial steps were taken to comprehend the variability of the extra domain in those TFs, which eventually might assist in evolutionary and functional studies.

AB - © 2018 Perez-Rueda et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Gene regulation at the transcriptional level is a central process in all organisms, and DNAbinding transcription factors, known as TFs, play a fundamental role. This class of proteins usually binds at specific DNA sequences, activating or repressing gene expression. In general, TFs are composed of two domains: The DNA-binding domain (DBD) and an extra domain, which in this work we have named 'companion domain' (CD). This latter could be involved in one or more functions such as ligand binding, protein-protein interactions or even with enzymatic activity. In contrast to DBDs, which have been widely characterized both experimentally and bioinformatically, information on the abundance, distribution, variability and possible role of the CDs is scarce. Here, we investigated these issues associated with the domain architectures of TFs in prokaryotic genomes. To this end, 19 families of TFs in 761 non-redundant bacterial and archaeal genomes were evaluated. In this regard we found four main groups based on the abundance and distribution in the analyzed genomes: I) LysR and TetR/AcrR; ii) AraC/XylS, SinR, and others; iii) Lrp, Fis, ArsR, and others; and iv) a group that included only two families, ArgR and BirA. Based on a classification of the organisms according to the life-styles, a major abundance of regulatory families in free-living organisms, in contrast with pathogenic, extremophilic or intracellular organisms, was identified. Finally, the protein architecture diversity associated to the 19 families considering a weight score for domain promiscuity evidenced which regulatory families were characterized by either a large diversity of CDs, here named as 'promiscuous' families given the elevated number of variable domains found in those TFs, or a low diversity of CDs. Altogether this information helped us to understand the diversity and distribution of the 19 Prokaryotes TF families. Moreover, initial steps were taken to comprehend the variability of the extra domain in those TFs, which eventually might assist in evolutionary and functional studies.

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