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Species based synonymous codon usage in fusion protein gene of Newcastle disease virus.

Kumar CS, Kumar S - PLoS ONE (2014)

Bottom Line: Aromaticity, GC3s, and aliphatic index were not found responsible for species based synonymous codon usage bias in F gene of NDV.The phylogenetic analysis of isolates was found in corroboration with the relatedness of species based on codon usage bias.The relationship between the host species and the NDV isolates from the host does not represent a significant correlation in our study.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati, Assam, India.

ABSTRACT
Newcastle disease is highly pathogenic to poultry and many other avian species. However, the Newcastle disease virus (NDV) has also been reported from many non-avian species. The NDV fusion protein (F) is a major determinant of its pathogenicity and virulence. The functionalities of F gene have been explored for the development of vaccine and diagnostics against NDV. Although the F protein is well studied but the codon usage and its nucleotide composition from NDV isolated from different species have not yet been explored. In present study, we have analyzed the factors responsible for the determination of codon usage in NDV isolated from four major avian host species. The F gene of NDV is analyzed for its base composition and its correlation with the bias in codon usage. Our result showed that random mutational pressure is responsible for codon usage bias in F protein of NDV isolates. Aromaticity, GC3s, and aliphatic index were not found responsible for species based synonymous codon usage bias in F gene of NDV. Moreover, the low amount of codon usage bias and expression level was further confirmed by a low CAI value. The phylogenetic analysis of isolates was found in corroboration with the relatedness of species based on codon usage bias. The relationship between the host species and the NDV isolates from the host does not represent a significant correlation in our study. The present study provides a basic understanding of the mechanism involved in codon usage among species.

No MeSH data available.


Related in: MedlinePlus

Nc of codons used plotted against the GC3s.The continuous curve as seen in the plot represents the relationship between GC3s and the Nc in the absence of selection. All the values lie below the expected curve. The curve represents the expected codon usage if GC compositional constraints alone account for codon usage bias.
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pone-0114754-g002: Nc of codons used plotted against the GC3s.The continuous curve as seen in the plot represents the relationship between GC3s and the Nc in the absence of selection. All the values lie below the expected curve. The curve represents the expected codon usage if GC compositional constraints alone account for codon usage bias.

Mentions: The Nc value is plotted against the corresponding GC3s. The genes having their codon selection constrained to GC composition are supposed to lie on the continuous curve which represents a random codon usage. If the gene lies below the curve it represents mutational bias and translational selection. All the points were found to lie just below the curve (Figure 2). Furthermore, a significant positive correlation between the values of GC3s and Nc was observed. There was almost no difference between the CAI values for all the isolates. The average CAI was found to be 0.174 (p <0.05), which is apparently low as CAI ranges from 0 to 1. Principal component analysis using Pearson correlation was performed to evaluate the relationship between the first two axes of PCA, GRAVY, aromaticity, GC3s and aliphatic index (Table 4). The GRAVY, aromaticity, GC3s were found to have no correlation with both axes. To represent the variation in position of each codon a scatter plot for the optimal codon usage is plotted between the PC1 and PC2 (Figure 3). The PC1 accounts for 89.10% and PC2 accounts for 7.45% of the total variation. Thus the first axis accounts for the major impact on total variation in synonymous codon usage as compared to an appreciable impact by the second axis. The correlation between the isolates from four species is represented in the plot of isolates against the PC1 and PC2 (Figure 4).


Species based synonymous codon usage in fusion protein gene of Newcastle disease virus.

Kumar CS, Kumar S - PLoS ONE (2014)

Nc of codons used plotted against the GC3s.The continuous curve as seen in the plot represents the relationship between GC3s and the Nc in the absence of selection. All the values lie below the expected curve. The curve represents the expected codon usage if GC compositional constraints alone account for codon usage bias.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4257736&req=5

pone-0114754-g002: Nc of codons used plotted against the GC3s.The continuous curve as seen in the plot represents the relationship between GC3s and the Nc in the absence of selection. All the values lie below the expected curve. The curve represents the expected codon usage if GC compositional constraints alone account for codon usage bias.
Mentions: The Nc value is plotted against the corresponding GC3s. The genes having their codon selection constrained to GC composition are supposed to lie on the continuous curve which represents a random codon usage. If the gene lies below the curve it represents mutational bias and translational selection. All the points were found to lie just below the curve (Figure 2). Furthermore, a significant positive correlation between the values of GC3s and Nc was observed. There was almost no difference between the CAI values for all the isolates. The average CAI was found to be 0.174 (p <0.05), which is apparently low as CAI ranges from 0 to 1. Principal component analysis using Pearson correlation was performed to evaluate the relationship between the first two axes of PCA, GRAVY, aromaticity, GC3s and aliphatic index (Table 4). The GRAVY, aromaticity, GC3s were found to have no correlation with both axes. To represent the variation in position of each codon a scatter plot for the optimal codon usage is plotted between the PC1 and PC2 (Figure 3). The PC1 accounts for 89.10% and PC2 accounts for 7.45% of the total variation. Thus the first axis accounts for the major impact on total variation in synonymous codon usage as compared to an appreciable impact by the second axis. The correlation between the isolates from four species is represented in the plot of isolates against the PC1 and PC2 (Figure 4).

Bottom Line: Aromaticity, GC3s, and aliphatic index were not found responsible for species based synonymous codon usage bias in F gene of NDV.The phylogenetic analysis of isolates was found in corroboration with the relatedness of species based on codon usage bias.The relationship between the host species and the NDV isolates from the host does not represent a significant correlation in our study.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati, Assam, India.

ABSTRACT
Newcastle disease is highly pathogenic to poultry and many other avian species. However, the Newcastle disease virus (NDV) has also been reported from many non-avian species. The NDV fusion protein (F) is a major determinant of its pathogenicity and virulence. The functionalities of F gene have been explored for the development of vaccine and diagnostics against NDV. Although the F protein is well studied but the codon usage and its nucleotide composition from NDV isolated from different species have not yet been explored. In present study, we have analyzed the factors responsible for the determination of codon usage in NDV isolated from four major avian host species. The F gene of NDV is analyzed for its base composition and its correlation with the bias in codon usage. Our result showed that random mutational pressure is responsible for codon usage bias in F protein of NDV isolates. Aromaticity, GC3s, and aliphatic index were not found responsible for species based synonymous codon usage bias in F gene of NDV. Moreover, the low amount of codon usage bias and expression level was further confirmed by a low CAI value. The phylogenetic analysis of isolates was found in corroboration with the relatedness of species based on codon usage bias. The relationship between the host species and the NDV isolates from the host does not represent a significant correlation in our study. The present study provides a basic understanding of the mechanism involved in codon usage among species.

No MeSH data available.


Related in: MedlinePlus