Codon usage and codon context bias in Xanthophyllomyces dendrorhous
Author
dc.contributor.author
Baeza Cancino, Marcelo
Author
dc.contributor.author
Alcaíno Gorman, Jennifer
Author
dc.contributor.author
Barahona‑Crisóstomo, Salvador
Author
dc.contributor.author
Sepúlveda, Dionisia
Author
dc.contributor.author
Cifuentes Guzmán, Víctor
Admission date
dc.date.accessioned
2015-08-19T02:29:24Z
Available date
dc.date.available
2015-08-19T02:29:24Z
Publication date
dc.date.issued
2015
Cita de ítem
dc.identifier.citation
BMC Genomics (2015) 16:293
en_US
Identifier
dc.identifier.other
DOI: 10.1186/s12864-015-1493-5
Identifier
dc.identifier.uri
https://repositorio.uchile.cl/handle/2250/132909
General note
dc.description
Artículo de publicación ISI
en_US
Abstract
dc.description.abstract
Background
Synonymous codons are used differentially in organisms from the three domains of life, a phenomenon referred to as codon usage bias. In addition, codon pair bias, particularly in the 3’ codon context, has also been described in several organisms and is associated with the accuracy and rate of translation. An improved understanding of both types of bias is important for the optimization of heterologous protein expression, particularly in biotechnologically important organisms, such as the yeast Xanthophyllomyces dendrorhous, a promising bioresource for the carotenoid astaxanthin. Using genomic and transcriptomic data, the codon usage and codon context biases of X. dendrorhous open reading frames (ORFs) were analyzed to determine their expression levels, GC% and sequence lengths. X. dendrorhous totiviral ORFs were also included in these analyses.
Results
A total of 1,695 X. dendrorhous ORFs were identified through comparison with sequences in multiple databases, and the intron-exon structures of these sequences were determined. Although there were important expression variations among the ORFs under the studied conditions (different phases of growth and available carbon sources), most of these sequences were highly expressed under at least one of the analyzed conditions. Independent of the culture conditions, the highly expressed genes showed a strong bias in both codon usage and the 3’ context, with a minor association with the GC% and no relationship to the sequence length. The codon usage and codon-pair bias of the totiviral ORFs were highly variable with no similarities to the host ORFs.
Conclusions
There is a direct relation between the level of gene expression and codon usage and 3′ context bias in X. dendrorhous, which is more evident for ORFs that are expressed at the highest levels under the studied conditions. However, there is no direct relation between the totiviral ORF biases and the host ORFs.
en_US
Patrocinador
dc.description.sponsorship
This study was financially supported through FONDECYT grants (nos. 1140504,
1130333 and 11121200).