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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MDPI AG
2017-07-01
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| author | Mario Alberto Martínez-Núñez Zuemy Rodríguez-Escamilla Katya Rodríguez-Vázquez Ernesto Pérez-Rueda |
| author_facet | Mario Alberto Martínez-Núñez Zuemy Rodríguez-Escamilla Katya Rodríguez-Vázquez Ernesto Pérez-Rueda |
| author_sort | Mario Alberto Martínez-Núñez |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-04-11T12:55:25Z |
| format | Article |
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| institution | Directory Open Access Journal |
| issn | 2075-1729 |
| language | English |
| last_indexed | 2024-04-11T12:55:25Z |
| publishDate | 2017-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Life |
| spelling | doaj.art-8aa03299242b44299eb3b99bcdefad282022-12-22T04:23:05ZengMDPI AGLife2075-17292017-07-01733010.3390/life7030030life7030030Tracing the Repertoire of Promiscuous Enzymes along the Metabolic Pathways in Archaeal OrganismsMario Alberto Martínez-Núñez0Zuemy Rodríguez-Escamilla1Katya Rodríguez-Vázquez2Ernesto Pérez-Rueda3Laboratorio de Estudios Ecogenómicos, Facultad de Ciencias, Unidad Académica de Ciencias y Tecnología de la UNAM en Yucatán, Universidad Nacional Autónoma de México, Carretera Sierra Papacal-Chuburna Km. 5, C.P. 97302, Mérida, Yucatán, MexicoDepartamento de Microbiología, Instituto de Biotecnología, Universidad Nacional, Autónoma de México, C.P. 62210, Cuernavaca, Morelos, MexicoInstituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Ciudad Universitaria, C.P. 04510, Ciudad de México, MexicoDepartamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, C.P. 62210, Cuernavaca, Morelos, MexicoThe 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.https://www.mdpi.com/2075-1729/7/3/30promiscuous enzymesEnzyme Commission numbermetabolismarchaeacomparative genomics |
| spellingShingle | Mario Alberto Martínez-Núñez Zuemy Rodríguez-Escamilla Katya Rodríguez-Vázquez Ernesto Pérez-Rueda Tracing the Repertoire of Promiscuous Enzymes along the Metabolic Pathways in Archaeal Organisms Life promiscuous enzymes Enzyme Commission number metabolism archaea comparative genomics |
| 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 | promiscuous enzymes Enzyme Commission number metabolism archaea comparative genomics |
| url | https://www.mdpi.com/2075-1729/7/3/30 |
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