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

Mario Martínez-Núñez,Ernesto Pérez-Rueda,Katya Rodríguez-Vázquez,Zuemy Rodríguez-Escamilla

doi:10.3390/life7030030

Mario Martínez-Núñez, Ernesto Pérez-Rueda + Show 2 more

Open Access

https://doi.org/10.3390/life7030030

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Journal: Life	Publication Date: Jul 13, 2017
Citations: 5	License type: CC BY 4.0

Affiliation: Universidad Nacional Autónoma de México

Abstract

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.

Highlights

The adaptation of organisms to environment changes depends on the cellular adequacy to abiotic and biotic variables, such as temperature, nutrients availability, salinity, or the interaction with others organisms, which are in constant changes
To compare the enzymatic content found in the archaeal genomes, we analyzed 705 bacterial genomes; where, an average of 757 enzymes and an average genome size of 3265 open reading frames (ORFs) was observed, i.e., the average content of known enzymes in archaeal genomes is 1.5 times lower than that observed in bacterial genomes
Through the analysis of 89 archaeal genomes, we gained insights into how many promiscuous enzymes there are, what the existing diversity of structural domains is, and how promiscuous enzymes are distributed in metabolic pathways of Archaea organisms

Summary

Introduction

The adaptation of organisms to environment changes depends on the cellular adequacy to abiotic and biotic variables, such as temperature, nutrients availability, salinity, or the interaction with others organisms, which are in constant changes. Promiscuous enzymes can be further classified into substrate promiscuous enzymes, i.e., enzymes with relaxed or broad substrate specificity; and catalytic promiscuous enzymes, i.e., enzymes catalyzing distinctly different chemical transformations with different transition states [7,8] In this context, diverse mechanisms that allow enzymatic promiscuity, such as conformational diversity, alternative substrates positions, and different protonation states, among others have been described [9]. Diverse mechanisms that allow enzymatic promiscuity, such as conformational diversity, alternative substrates positions, and different protonation states, among others have been described [9] Together, these functional and evolutionary processes associated with enzymes shape the evolution of metabolic systems [10,11]

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