Use este identificador para citar ou linkar para este item: https://locus.ufv.br//handle/123456789/12674
Tipo: Artigo
Título: Integrated analysis of individual codon contribution to protein biosynthesis reveals a new approach to improving the basis of rational gene design
Autor(es): Villada, Juan C.
Brustolini, Otávio José Bernardes
Silveira, Wendel Batista da
Abstract: Gene codon optimization may be impaired by the misinterpretation of frequency and optimality of codons. Although recent studies have revealed the effects of codon usage bias (CUB) on protein biosynthesis, an integrated perspective of the biological role of individual codons remains unknown. Unlike other previous studies, we show, through an integrated framework that attributes of codons such as frequency, optimality and positional dependency should be combined to unveil individual codon contribution for protein biosynthesis. We designed a codon quantification method for assessing CUB as a function of position within genes with a novel constraint: the relativity of position-dependent codon usage shaped by coding sequence length. Thus, we propose a new way of identifying the enrichment, depletion and non-uniform positional distribution of codons in different regions of yeast genes. We clustered codons that shared attributes of frequency and optimality. The cluster of non-optimal codons with rare occurrence displayed two remarkable characteristics: higher codon decoding time than frequent–non-optimal cluster and enrichment at the 5′-end region, where optimal codons with the highest frequency are depleted. Interestingly, frequent codons with non-optimal adaptation to tRNAs are uniformly distributed in the Saccharomyces cerevisiae genes, suggesting their determinant role as a speed regulator in protein elongation.
Palavras-chave: Codon usage bias
Microbial biotechnology
Position-dependent codon usage
Rational gene design
Yeast genomics
Editor: DNA Research
Tipo de Acesso: Open Access
URI: https://doi.org/10.1093/dnares/dsx014
http://www.locus.ufv.br/handle/123456789/12674
Data do documento: 24-Abr-2017
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