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Promiscuous Domains in Eukaryotes and HAT Proteins in FUNGI Have Followed Different Evolutionary Paths

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Abstract

Diverse studies have shown that the content of genes present in sequenced genomes does not seem to correlate with the complexity of the organisms. However, various studies have shown that organism complexity and the size of the proteome has, indeed, a significant correlation. This characteristic allows us to postulate that some molecular mechanisms have permitted a greater functional diversity to some proteins to increase their participation in developing organisms with higher complexity. Among those mechanisms, the domain promiscuity, defined as the ability of the domains to organize in combination with other distinct domains, is of great importance for the evolution of organisms. Previous works have analyzed the degree of domain promiscuity of the proteomes showing how it seems to have paralleled the evolution of eukaryotic organisms. The latter has motivated the present study, where we analyzed the domain promiscuity in a collection of 84 eukaryotic proteomes representative of all the taxonomy groups of the tree of life. Using a grammar definition approach, we determined the architecture of 1,223,227 proteins, conformed by 2,296,371 domains, which established 839,184 bigram types. The phylogenetic reconstructions based on differences in the content of information from measures of proteome promiscuity confirm that the evolution of the promiscuity of domains in eukaryotic organisms resembles the evolutionary history of the species. However, a close analysis of the PHD and RING domains, the most promiscuous domains found in fungi and functional components of chromatin remodeling enzymes and important expression regulators, suggests an evolution according to their function.

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Acknowledgements

JMG is grateful to the "Consejo Nacional de Ciencia y Tecnología" (CONACYT) and PIFI/BEIFI-IPN for the scholarships. AMT is fellow of SNI-CONACYT. To the memory of Ph. D. Juan Manuel González Prieto.

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  1. Laboratorio de Biotecnología Vegetal, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Boulevard del Maestro S/N esq. Elías Piña, Col. Narciso Mendoza, 88710, Reynosa, Tamaulipas, Mexico

    Jazmín Murcia-Garzón

  2. Laboratorio de Biotecnología y Bioinformática Genómica, Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. de Carpio y Plan de Ayala s/n, Col. Santo Tomás, 11340, Mexico City, Mexico

    Alfonso Méndez-Tenorio

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  1. Jazmín Murcia-Garzón
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Correspondence to Alfonso Méndez-Tenorio.

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Murcia-Garzón, J., Méndez-Tenorio, A. Promiscuous Domains in Eukaryotes and HAT Proteins in FUNGI Have Followed Different Evolutionary Paths. J Mol Evol 90, 124–138 (2022). https://doi.org/10.1007/s00239-021-10046-w

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