Cargando…

Increments and Duplication Events of Enzymes and Transcription Factors Influence Metabolic and Regulatory Diversity in Prokaryotes

In this work, the content of enzymes and DNA-binding transcription factors (TFs) in 794 non-redundant prokaryotic genomes was evaluated. The identification of enzymes was based on annotations deposited in the KEGG database as well as in databases of functional domains (COG and PFAM) and structural d...

Descripción completa

Detalles Bibliográficos
Autores principales: Martínez-Núñez, Mario Alberto, Poot-Hernandez, Augusto Cesar, Rodríguez-Vázquez, Katya, Perez-Rueda, Ernesto
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3726781/
https://www.ncbi.nlm.nih.gov/pubmed/23922780
http://dx.doi.org/10.1371/journal.pone.0069707
_version_ 1782278710367354880
author Martínez-Núñez, Mario Alberto
Poot-Hernandez, Augusto Cesar
Rodríguez-Vázquez, Katya
Perez-Rueda, Ernesto
author_facet Martínez-Núñez, Mario Alberto
Poot-Hernandez, Augusto Cesar
Rodríguez-Vázquez, Katya
Perez-Rueda, Ernesto
author_sort Martínez-Núñez, Mario Alberto
collection PubMed
description In this work, the content of enzymes and DNA-binding transcription factors (TFs) in 794 non-redundant prokaryotic genomes was evaluated. The identification of enzymes was based on annotations deposited in the KEGG database as well as in databases of functional domains (COG and PFAM) and structural domains (Superfamily). For identifications of the TFs, hidden Markov profiles were constructed based on well-known transcriptional regulatory families. From these analyses, we obtained diverse and interesting results, such as the negative rate of incremental changes in the number of detected enzymes with respect to the genome size. On the contrary, for TFs the rate incremented as the complexity of genome increased. This inverse related performance shapes the diversity of metabolic and regulatory networks and impacts the availability of enzymes and TFs. Furthermore, the intersection of the derivatives between enzymes and TFs was identified at 9,659 genes, after this point, the regulatory complexity grows faster than metabolic complexity. In addition, TFs have a low number of duplications, in contrast to the apparent high number of duplications associated with enzymes. Despite the greater number of duplicated enzymes versus TFs, the increment by which duplicates appear is higher in TFs. A lower proportion of enzymes among archaeal genomes (22%) than in the bacterial ones (27%) was also found. This low proportion might be compensated by the interconnection between the metabolic pathways in Archaea. A similar proportion was also found for the archaeal TFs, for which the formation of regulatory complexes has been proposed. Finally, an enrichment of multifunctional enzymes in Bacteria, as a mechanism of ecological adaptation, was detected.
format Online
Article
Text
id pubmed-3726781
institution National Center for Biotechnology Information
language English
publishDate 2013
publisher Public Library of Science
record_format MEDLINE/PubMed
spelling pubmed-37267812013-08-06 Increments and Duplication Events of Enzymes and Transcription Factors Influence Metabolic and Regulatory Diversity in Prokaryotes Martínez-Núñez, Mario Alberto Poot-Hernandez, Augusto Cesar Rodríguez-Vázquez, Katya Perez-Rueda, Ernesto PLoS One Research Article In this work, the content of enzymes and DNA-binding transcription factors (TFs) in 794 non-redundant prokaryotic genomes was evaluated. The identification of enzymes was based on annotations deposited in the KEGG database as well as in databases of functional domains (COG and PFAM) and structural domains (Superfamily). For identifications of the TFs, hidden Markov profiles were constructed based on well-known transcriptional regulatory families. From these analyses, we obtained diverse and interesting results, such as the negative rate of incremental changes in the number of detected enzymes with respect to the genome size. On the contrary, for TFs the rate incremented as the complexity of genome increased. This inverse related performance shapes the diversity of metabolic and regulatory networks and impacts the availability of enzymes and TFs. Furthermore, the intersection of the derivatives between enzymes and TFs was identified at 9,659 genes, after this point, the regulatory complexity grows faster than metabolic complexity. In addition, TFs have a low number of duplications, in contrast to the apparent high number of duplications associated with enzymes. Despite the greater number of duplicated enzymes versus TFs, the increment by which duplicates appear is higher in TFs. A lower proportion of enzymes among archaeal genomes (22%) than in the bacterial ones (27%) was also found. This low proportion might be compensated by the interconnection between the metabolic pathways in Archaea. A similar proportion was also found for the archaeal TFs, for which the formation of regulatory complexes has been proposed. Finally, an enrichment of multifunctional enzymes in Bacteria, as a mechanism of ecological adaptation, was detected. Public Library of Science 2013-07-29 /pmc/articles/PMC3726781/ /pubmed/23922780 http://dx.doi.org/10.1371/journal.pone.0069707 Text en © 2013 Martinez-Nuñez et al http://creativecommons.org/licenses/by/4.0/ 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 properly credited.
spellingShingle Research Article
Martínez-Núñez, Mario Alberto
Poot-Hernandez, Augusto Cesar
Rodríguez-Vázquez, Katya
Perez-Rueda, Ernesto
Increments and Duplication Events of Enzymes and Transcription Factors Influence Metabolic and Regulatory Diversity in Prokaryotes
title Increments and Duplication Events of Enzymes and Transcription Factors Influence Metabolic and Regulatory Diversity in Prokaryotes
title_full Increments and Duplication Events of Enzymes and Transcription Factors Influence Metabolic and Regulatory Diversity in Prokaryotes
title_fullStr Increments and Duplication Events of Enzymes and Transcription Factors Influence Metabolic and Regulatory Diversity in Prokaryotes
title_full_unstemmed Increments and Duplication Events of Enzymes and Transcription Factors Influence Metabolic and Regulatory Diversity in Prokaryotes
title_short Increments and Duplication Events of Enzymes and Transcription Factors Influence Metabolic and Regulatory Diversity in Prokaryotes
title_sort increments and duplication events of enzymes and transcription factors influence metabolic and regulatory diversity in prokaryotes
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3726781/
https://www.ncbi.nlm.nih.gov/pubmed/23922780
http://dx.doi.org/10.1371/journal.pone.0069707
work_keys_str_mv AT martineznunezmarioalberto incrementsandduplicationeventsofenzymesandtranscriptionfactorsinfluencemetabolicandregulatorydiversityinprokaryotes
AT poothernandezaugustocesar incrementsandduplicationeventsofenzymesandtranscriptionfactorsinfluencemetabolicandregulatorydiversityinprokaryotes
AT rodriguezvazquezkatya incrementsandduplicationeventsofenzymesandtranscriptionfactorsinfluencemetabolicandregulatorydiversityinprokaryotes
AT perezruedaernesto incrementsandduplicationeventsofenzymesandtranscriptionfactorsinfluencemetabolicandregulatorydiversityinprokaryotes