The protein architecture in Bacteria and Archaea identifies a set of promiscuous and ancient domains
Por:
Hernandez-Guerrero, Rafael, Galan-Vasquez, Edgardo, Perez-Rueda, Ernesto
Publicada:
19 dic 2019
Categoría:
Multidisciplinary
Resumen:
In this work, we describe a systematic comparative genomic analysis of
promiscuous domains in genomes of Bacteria and Archaea. A quantitative
measure of domain promiscuity, the weighted domain architecture score
(WDAS), was used and applied to 1317 domains in 1320 genomes of Bacteria
and Archaea. A functional analysis associated with the WDAS per genome
showed that 18 of 50 functional categories were identified as
significantly enriched in the promiscuous domains; in particular,
small-molecule binding domains, transferases domains, DNA binding
domains (transcription factors), and signal transduction domains were
identified as promiscuous. In contrast, non-promiscuous domains were
identified as associated with 6 of 50 functional categories, and the
category Function unknown was enriched. In addition, the WDASs of 52
domains correlated with genome size, i.e., WDAS values decreased as the
genome size increased, suggesting that the number of combinations at
larger domains increases, including domains in the superfamilies Winged
helix-turn-helix and P-loop-containing nucleoside triphosphate
hydrolases. Finally, based on classification of the domains according to
their ancestry, we determined that the set of 52 promiscuous domains are
also ancient and abundant among all the genomes, in contrast to the
non-promiscuous domains. In summary, we consider that the association
between these two classes of protein domains (promiscuous and
non-promiscuous) provides bacterial and archaeal cells with the ability
to respond to diverse environmental challenges.
Filiaciones:
Hernandez-Guerrero, Rafael:
Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Mérida, Yucatán, Mexico
Univ Nacl Autonoma Mexico, Unidad Acad Yucatan, Inst Invest Matemat Aplicadas & Sistemas, Merida, Yucatan, Mexico
Galan-Vasquez, Edgardo:
Departamento de Ingeniería de Sistemas Computacionales y Automatización, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Ciudad Universitaria, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
Univ Nacl Autonoma Mexico, Inst Invest Matemat Aplicadas & Sistemas, Dept Ingn Sistemas Computac & Automatizac, Mexico City, DF, Mexico
Perez-Rueda, Ernesto:
Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Mérida, Yucatán, Mexico
Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
Univ Nacl Autonoma Mexico, Unidad Acad Yucatan, Inst Invest Matemat Aplicadas & Sistemas, Merida, Yucatan, Mexico
Univ Mayor, Fac Ciencias, Ctr Genom & Bioinformat, Santiago, Chile
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