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Codon usage and codon context bias in Xanthophyllomyces dendrorhous.

Baeza M, Alcaíno J, Barahona S, Sepúlveda D, Cifuentes V - BMC Genomics (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Chile. mbaeza@u.uchile.cl.

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.

No MeSH data available.


Related in: MedlinePlus

Differential display maps of codon context comparison among ORFs with different expression levels. Comparison of the 3′ codon context between groups of ORFs with different expression levels (RPKM: 1–30, 31–70, 71–100, 101–999 and ≥1,000) according to the HV grouping and the Ribosomal (R) ORFs. The upper bar indicates the amino acid codons in the 3′ position, and the left bar indicates the reference amino acid codons for each analysis. The color coding scale is indicated in the figure, where codons with similar residual values are indicated in black and differences are indicated in blue.
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Fig5: Differential display maps of codon context comparison among ORFs with different expression levels. Comparison of the 3′ codon context between groups of ORFs with different expression levels (RPKM: 1–30, 31–70, 71–100, 101–999 and ≥1,000) according to the HV grouping and the Ribosomal (R) ORFs. The upper bar indicates the amino acid codons in the 3′ position, and the left bar indicates the reference amino acid codons for each analysis. The color coding scale is indicated in the figure, where codons with similar residual values are indicated in black and differences are indicated in blue.

Mentions: The 3′ codon context analysis was performed using the Anaconda software [45] and the HV grouping of ORFs. A 3′ codon context bias was observed in all groups, differing according to the expression level (Figure 4). When the 3′ codon context was compared among the groups, a direct relationship between the expression level and differences in the codon context was observed: ORFs with greater differences in expression level showed greater differences in the 3′ codon context, and ORFs with RPKM values of 101–999 and ≥1,000 showed more similarities (Figure 5). The top five preferred and non-preferred codon pairs in each HV group are listed in Table 4. The non-preferred codon pairs CTT-AAG and CCT-AAG appeared in five and four groups, respectively, whereas the preferred codon pairs, TCA-TCC, AAG-AAG and GAA-GAA, appeared in three groups.Figure 4


Codon usage and codon context bias in Xanthophyllomyces dendrorhous.

Baeza M, Alcaíno J, Barahona S, Sepúlveda D, Cifuentes V - BMC Genomics (2015)

Differential display maps of codon context comparison among ORFs with different expression levels. Comparison of the 3′ codon context between groups of ORFs with different expression levels (RPKM: 1–30, 31–70, 71–100, 101–999 and ≥1,000) according to the HV grouping and the Ribosomal (R) ORFs. The upper bar indicates the amino acid codons in the 3′ position, and the left bar indicates the reference amino acid codons for each analysis. The color coding scale is indicated in the figure, where codons with similar residual values are indicated in black and differences are indicated in blue.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4404019&req=5

Fig5: Differential display maps of codon context comparison among ORFs with different expression levels. Comparison of the 3′ codon context between groups of ORFs with different expression levels (RPKM: 1–30, 31–70, 71–100, 101–999 and ≥1,000) according to the HV grouping and the Ribosomal (R) ORFs. The upper bar indicates the amino acid codons in the 3′ position, and the left bar indicates the reference amino acid codons for each analysis. The color coding scale is indicated in the figure, where codons with similar residual values are indicated in black and differences are indicated in blue.
Mentions: The 3′ codon context analysis was performed using the Anaconda software [45] and the HV grouping of ORFs. A 3′ codon context bias was observed in all groups, differing according to the expression level (Figure 4). When the 3′ codon context was compared among the groups, a direct relationship between the expression level and differences in the codon context was observed: ORFs with greater differences in expression level showed greater differences in the 3′ codon context, and ORFs with RPKM values of 101–999 and ≥1,000 showed more similarities (Figure 5). The top five preferred and non-preferred codon pairs in each HV group are listed in Table 4. The non-preferred codon pairs CTT-AAG and CCT-AAG appeared in five and four groups, respectively, whereas the preferred codon pairs, TCA-TCC, AAG-AAG and GAA-GAA, appeared in three groups.Figure 4

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Chile. mbaeza@u.uchile.cl.

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.

No MeSH data available.


Related in: MedlinePlus