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Tracing the Repertoire of Promiscuous Enzymes along the Metabolic Pathways in Archaeal Organisms

The metabolic pathways that carry out the biochemical transformations sustaining life depend on the efficiency of their associated enzymes. In recent years, it has become clear that promiscuous enzymes have played an important role in the function and evolution of metabolism. In this work we analyze...

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Autores principales: Martínez-Núñez, Mario Alberto, Rodríguez-Escamilla, Zuemy, Rodríguez-Vázquez, Katya, Pérez-Rueda, Ernesto
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5617955/
https://www.ncbi.nlm.nih.gov/pubmed/28703743
http://dx.doi.org/10.3390/life7030030
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author Martínez-Núñez, Mario Alberto
Rodríguez-Escamilla, Zuemy
Rodríguez-Vázquez, Katya
Pérez-Rueda, Ernesto
author_facet Martínez-Núñez, Mario Alberto
Rodríguez-Escamilla, Zuemy
Rodríguez-Vázquez, Katya
Pérez-Rueda, Ernesto
author_sort Martínez-Núñez, Mario Alberto
collection PubMed
description The metabolic pathways that carry out the biochemical transformations sustaining life depend on the efficiency of their associated enzymes. In recent years, it has become clear that promiscuous enzymes have played an important role in the function and evolution of metabolism. In this work we analyze the repertoire of promiscuous enzymes in 89 non-redundant genomes of the Archaea cellular domain. Promiscuous enzymes are defined as those proteins with two or more different Enzyme Commission (E.C.) numbers, according the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. From this analysis, it was found that the fraction of promiscuous enzymes is lower in Archaea than in Bacteria. A greater diversity of superfamily domains is associated with promiscuous enzymes compared to specialized enzymes, both in Archaea and Bacteria, and there is an enrichment of substrate promiscuity rather than catalytic promiscuity in the archaeal enzymes. Finally, the presence of promiscuous enzymes in the metabolic pathways was found to be heterogeneously distributed at the domain level and in the phyla that make up the Archaea. These analyses increase our understanding of promiscuous enzymes and provide additional clues to the evolution of metabolism in Archaea.
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spelling pubmed-56179552017-09-29 Tracing the Repertoire of Promiscuous Enzymes along the Metabolic Pathways in Archaeal Organisms Martínez-Núñez, Mario Alberto Rodríguez-Escamilla, Zuemy Rodríguez-Vázquez, Katya Pérez-Rueda, Ernesto Life (Basel) Article The metabolic pathways that carry out the biochemical transformations sustaining life depend on the efficiency of their associated enzymes. In recent years, it has become clear that promiscuous enzymes have played an important role in the function and evolution of metabolism. In this work we analyze the repertoire of promiscuous enzymes in 89 non-redundant genomes of the Archaea cellular domain. Promiscuous enzymes are defined as those proteins with two or more different Enzyme Commission (E.C.) numbers, according the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. From this analysis, it was found that the fraction of promiscuous enzymes is lower in Archaea than in Bacteria. A greater diversity of superfamily domains is associated with promiscuous enzymes compared to specialized enzymes, both in Archaea and Bacteria, and there is an enrichment of substrate promiscuity rather than catalytic promiscuity in the archaeal enzymes. Finally, the presence of promiscuous enzymes in the metabolic pathways was found to be heterogeneously distributed at the domain level and in the phyla that make up the Archaea. These analyses increase our understanding of promiscuous enzymes and provide additional clues to the evolution of metabolism in Archaea. MDPI 2017-07-13 /pmc/articles/PMC5617955/ /pubmed/28703743 http://dx.doi.org/10.3390/life7030030 Text en © 2017 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
Martínez-Núñez, Mario Alberto
Rodríguez-Escamilla, Zuemy
Rodríguez-Vázquez, Katya
Pérez-Rueda, Ernesto
Tracing the Repertoire of Promiscuous Enzymes along the Metabolic Pathways in Archaeal Organisms
title Tracing the Repertoire of Promiscuous Enzymes along the Metabolic Pathways in Archaeal Organisms
title_full Tracing the Repertoire of Promiscuous Enzymes along the Metabolic Pathways in Archaeal Organisms
title_fullStr Tracing the Repertoire of Promiscuous Enzymes along the Metabolic Pathways in Archaeal Organisms
title_full_unstemmed Tracing the Repertoire of Promiscuous Enzymes along the Metabolic Pathways in Archaeal Organisms
title_short Tracing the Repertoire of Promiscuous Enzymes along the Metabolic Pathways in Archaeal Organisms
title_sort tracing the repertoire of promiscuous enzymes along the metabolic pathways in archaeal organisms
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5617955/
https://www.ncbi.nlm.nih.gov/pubmed/28703743
http://dx.doi.org/10.3390/life7030030
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