Synonymous codon usage of the VP2 gene of a very virulent infectious bursal disease virus isolate serial passaged in chicken embryos

Comparative genome-wide analysis of codon usage of different bacterial species infecting Oryza sativa

Oryza sativa is vastly affected by microbial pathogen, causing blight-related diseases, which in turn deplete the growth and productivity of rice. In this study, we analyzed four bacterial rice pathogen genomes and reported on their codon usage that might have greater implication in mutation-related research. Differential codon usage indices, such as codon adaptation index (CAI), codon bias index (CBI), effective number of codons (ENc), relative synonymous codon usage (RSCU), correspondence analysis (COA), and parity plots, were applied on coding sequences of Pseudomonas fuscovaginae, Pseudomonas syringae, Xanthomonas oryzae, and Pseudomonas avenae speices. The RSCU results proposed a high-frequency usage of CUG and CGC that codes for leucine and arginine in all of the species. The CBI and CAI values between the genomes range from 0.17 to 0.3 and from 0.26 to 0.35, respectively, indicating a direct proportionality between these indexes. The mean ENc value of P. avenae coding sequence showed high codon bias compared with other genomes. The axis I variation from COA analysis shows a mean value of 42.28% codon variations in these bacterial species. Correlation studies between axis I and ENc-GC3, along with CAI and CBI, suggested the presence of nucleotide bias and mutational pressure as major forces for codon bias within these species. Hence, certain genes with high CAI-CBI have been correlated for better gene expression. Our study highlights the importance of nucleotide biasness, mutation pressure, and natural selection in shaping protein-coding genes in these four rice-affecting bacteria. This would further help in investigating the evolution of pathogenic gene families, which may direct research toward synthetic genes that could be suppressed or overrepresented based on their codon usage pattern toward pathogenicity.

Analysis of synonymous codon usage in spike protein gene of infectious bronchitis virus

Infectious bronchitis virus (IBV) is responsible for causing respiratory, renal, and urogenital diseases in poultry. IBV infection in poultry leads to high mortality rates in affected flocks and to severe economic losses due to a drop in egg production and a reduced gain in live weight of the broiler birds. IBV-encoded spike protein (S) is the major protective immunogen for the host. Although the functions of the S protein have been well studied, the factors shaping synonymous codon usage bias and nucleotide composition in the S gene have not been reported yet. In the present study, we analyzed the relative synonymous codon usage and effective number of codons (Nc) using the 53 IBV S genes. The major trend in codon usage variation was studied using correspondence analysis. The plot of Nc values against GC3 as well as the correlation between base composition and codon usage bias suggest that mutational pressure rather than natural selection is the main factor that determines the codon usage bias in the S gene. Interestingly, no association of aromaticity, degree of hydrophobicity, and aliphatic index was observed with the codon usage variation in IBV S genes. The study represents a comprehensive analysis of IBV S gene codon usage patterns and provides a basic understanding of the codon usage bias.

Histamine levels in embryonic chicken livers infected with very virulent infectious bursal disease virus

Histamine is an endogenous nitrogenous compound with extensive effects on immunologic cells and involved in many physiological functions. The current aim was to determine histamine levels in embryonic liver and its association with the pathogenicity of a very virulent infectious bursal disease virus (vvIBDV) isolate serially passaged in chicken embryos. A vvIBDV isolate and the passaged viruses were inoculated into SPF embryonated chicken eggs (0.2 ml per egg) via the chorioallantoic membrane. Embryonic livers were collected at 24, 48, 72, 96, and 120 h post-inoculation and histamine contents were quantified by fluorescence spectrophotometry analyses. Results showed that the histamine content in embryonic livers infected with the original vvIBDV isolate and the early passaged viruses significantly increased 48 h post-inoculation, as compared with the adapted IBDV isolate (p<0.01) and controls (p<0.01), with the concentration peaking from 72 h to 96 h. Most of the infected chicken embryos died from 48 h to 96 h post-inoculation. Moreover, the histamine content in dead embryos was markedly increased compared with live embryos (p<0.05), peaking at 72 h post-inoculation (p<0.01). There was an association between histamine content in embryonic livers and an elevation in histidine decarboxylase activity. Taken together, our results suggest that an excess of histamine correlates with inflammatory responses during vvIBDV infection. This study provides an incremental step in the understanding of the pathogenesis of vvIBDV.