Giovanni Franzo1, Claudia Maria Tucciarone2, Matteo Legnardi2, Mattia Cecchinato2. 1. Microbiology and Infectious Diseases, Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell'Università 16 - 35020 Legnaro, Padua, Italy. giovanni.franzo@unipd.it. 2. Microbiology and Infectious Diseases, Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell'Università 16 - 35020 Legnaro, Padua, Italy.
Abstract
BACKGROUND: Infectious bronchitis virus (IBV) is one of the most relevant viruses affecting the poultry industry, and several studies have investigated the factors involved in its biological cycle and evolution. However, very few of those studies focused on the effect of genome composition and the codon bias of different IBV proteins, despite the remarkable increase in available complete genomes. In the present study, all IBV complete genomes were downloaded (n = 383), and several statistics representative of genome composition and codon bias were calculated for each protein-coding sequence, including but not limited to, the nucleotide odds ratio, relative synonymous codon usage and effective number of codons. Additionally, viral codon usage was compared to host codon usage based on a collection of highly expressed genes in IBV target and nontarget tissues. RESULTS: The results obtained demonstrated a significant difference among structural, non-structural and accessory proteins, especially regarding dinucleotide composition, which appears under strong selective forces. In particular, some dinucleotide pairs, such as CpG, a probable target of the host innate immune response, are underrepresented in genes coding for pp1a, pp1ab, S and N. Although genome composition and dinucleotide bias appear to affect codon usage, additional selective forces may act directly on codon bias. Variability in relative synonymous codon usage and effective number of codons was found for different proteins, with structural proteins and polyproteins being more adapted to the codon bias of host target tissues. In contrast, accessory proteins had a more biased codon usage (i.e., lower number of preferred codons), which might contribute to the regulation of their expression level and timing throughout the cell cycle. CONCLUSIONS: The present study confirms the existence of selective forces acting directly on the genome and not only indirectly through phenotype selection. This evidence might help understanding IBV biology and in developing attenuated strains without affecting the protein phenotype and therefore immunogenicity.
BACKGROUND:Infectious bronchitis virus (IBV) is one of the most relevant viruses affecting the poultry industry, and several studies have investigated the factors involved in its biological cycle and evolution. However, very few of those studies focused on the effect of genome composition and the codon bias of different IBV proteins, despite the remarkable increase in available complete genomes. In the present study, all IBV complete genomes were downloaded (n = 383), and several statistics representative of genome composition and codon bias were calculated for each protein-coding sequence, including but not limited to, the nucleotide odds ratio, relative synonymous codon usage and effective number of codons. Additionally, viral codon usage was compared to host codon usage based on a collection of highly expressed genes in IBV target and nontarget tissues. RESULTS: The results obtained demonstrated a significant difference among structural, non-structural and accessory proteins, especially regarding dinucleotide composition, which appears under strong selective forces. In particular, some dinucleotide pairs, such as CpG, a probable target of the host innate immune response, are underrepresented in genes coding for pp1a, pp1ab, S and N. Although genome composition and dinucleotide bias appear to affect codon usage, additional selective forces may act directly on codon bias. Variability in relative synonymous codon usage and effective number of codons was found for different proteins, with structural proteins and polyproteins being more adapted to the codon bias of host target tissues. In contrast, accessory proteins had a more biased codon usage (i.e., lower number of preferred codons), which might contribute to the regulation of their expression level and timing throughout the cell cycle. CONCLUSIONS: The present study confirms the existence of selective forces acting directly on the genome and not only indirectly through phenotype selection. This evidence might help understanding IBV biology and in developing attenuated strains without affecting the protein phenotype and therefore immunogenicity.
Authors: Swaine L Chen; William Lee; Alison K Hottes; Lucy Shapiro; Harley H McAdams Journal: Proc Natl Acad Sci U S A Date: 2004-02-27 Impact factor: 11.205
Authors: Giovanni Franzo; Matteo Legnardi; Claudia Maria Tucciarone; Michele Drigo; Marco Martini; Mattia Cecchinato Journal: Vet Res Date: 2019-11-09 Impact factor: 3.683
Authors: Taha Alqahtani; Rekha Khandia; Nidhi Puranik; Ali M Alqahtani; Kumarappan Chidambaram; Mohammad Amjad Kamal Journal: Front Genet Date: 2022-08-09 Impact factor: 4.772