The effect of the genomic GC content bias of prokaryotic organisms on the secondary structures of their proteins.
Journal
PloS one
ISSN: 1932-6203
Titre abrégé: PLoS One
Pays: United States
ID NLM: 101285081
Informations de publication
Date de publication:
2023
2023
Historique:
received:
26
12
2022
accepted:
17
04
2023
medline:
8
5
2023
pubmed:
4
5
2023
entrez:
4
5
2023
Statut:
epublish
Résumé
One of the main characteristics of prokaryotic genomes is the ratio in which guanine-cytosine bases are used in their DNA sequences. This is known as the genomic GC content and varies widely, from values below 20% to values greater than 74%. It has been demonstrated that the genomic GC content varies in accordance with the phylogenetic distribution of organisms and influences the amino acid composition of their corresponding proteomes. This bias is particularly important for amino acids that are coded by GC content-rich codons such as alanine, glycine, and proline, as well as amino acids that are coded by AT-rich codons, such as lysine, asparagine, and isoleucine. In our study, we extend these results by considering the effect of the genomic GC content on the secondary structure of proteins. On a set of 192 representative prokaryotic genomes and proteome sequences, we identified through a bioinformatic study that the composition of the secondary structures of the proteomes varies in relation to the genomic GC content; random coils increase as the genomic GC content increases, while alpha-helices and beta-sheets present an inverse relationship. In addition, we found that the tendency of an amino acid to form part of a secondary structure of proteins is not ubiquitous, as previously expected, but varies according to the genomic GC content. Finally, we discovered that for some specific groups of orthologous proteins, the GC content of genes biases the composition of secondary structures of the proteins for which they code.
Identifiants
pubmed: 37141209
doi: 10.1371/journal.pone.0285201
pii: PONE-D-22-35366
pmc: PMC10159118
doi:
Substances chimiques
Proteome
0
Amino Acids
0
Codon
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0285201Informations de copyright
Copyright: © 2023 Barceló-Antemate et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
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