title: The lifestyle of prokaryotic organisms influences the repertoire of promiscuous enzymes.
abstract: The metabolism of microbial organisms and its diversity are partly the result of an adaptation process to the characteristics of the environments that they inhabit. In this work, we analyze the influence of lifestyle on the content of promiscuous enzymes in 761 nonredundant bacterial and archaeal genomes. Promiscuous enzymes were defined as those proteins whose catalytic activities are defined by two or more different Enzyme Commission (E.C.) numbers. The genomes analyzed were categorized into four lifestyles for their exhaustive comparisons: free-living, extremophiles, pathogens, and intracellular. From these analyses we found that free-living organisms have larger genomes and an enrichment of promiscuous enzymes. In contrast, intracellular organisms showed smaller genomes and the lesser proportion of promiscuous enzymes. On the basis of our data, we show that the proportion of promiscuous enzymes in an organism is mainly influenced by the lifestyle, where fluctuating environments promote its emergence. Finally, we evidenced that duplication processes occur preferentially in metabolism of free-living and extremophiles species.
authors.affiliation: Departamento de Ingeniería de Sistemas Computacionales y Automatización, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de Mexico, Ciudad Universitaria, México, D.F., México.|Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.
authors.forename: Mario Alberto
authors.initials: MA
authors.lastname: Martínez-Núñez
authors.affiliation: Departamento de Ingeniería de Sistemas Computacionales y Automatización, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de Mexico, Ciudad Universitaria, México, D.F., México.
authors.forename: Katya
authors.initials: K
authors.lastname: Rodríguez-Vázquez
authors.affiliation: Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.|Unidad Multidisciplinaria de Docencia e Investigación, Sisal Facultad de Ciencias, Sisal, Yucatán, UNAM, México.
authors.forename: Ernesto
authors.initials: E
authors.lastname: Pérez-Rueda
mesh_terms: D019843:Archaeal Proteins / Q000235:genetics / Q000378:metabolism; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D017753:Ecosystem; D004783:Environmental Microbiology; D004798:Enzymes / Q000235:genetics* / Q000378:metabolism; D020440:Gene Duplication; D020745:Genome, Archaeal / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics*; D023281:Genomics / Q000379:methods*
chemical_list: D019843:Archaeal Proteins; D001426:Bacterial Proteins; D004798:Enzymes
keywords: archaea; bacteria; comparative genomics; duplicated enzymes; metabolism