Codon usage roles in human papillomavirus

Abstract

Human papillomavirus (HPV) genomes, similar to other virus genomes, frequently have a G + C content significantly different from their host species. The HPV genomes show a strong codon usage bias to 18 codons, with 14 showing T at the third position amongst degenerately encoded amino acids. The codon usage pattern in HPV genome plays an important role, which regulates low or non-translational expression of the viral capsid genes and results in very weak protein expression of oncogenes in a wide range of mammalian cells. Codon modification has been proved to be a powerful technology to overcome the translational blockage and weak expression of both HPV capsid genes and oncogenes in different expression systems. Furthermore, keratinocytes are the host cells of HPV infection; the codon usage in HPV capsid genes matches available aminoacyl-tRNAs in differentiated keratinocytes to modulate their protein expression. HPV DNA vaccines with codon optimization have been shown to have higher immunogenicity and induce both strong cellular and humoral responses in animal models, which may be a promising form of therapeutic HPV vaccines.

Hepatitis A Virus Adaptation to Cellular Shutoff Is Driven by Dynamic Adjustments of Codon Usage and Results in the Selection of Populations with Altered Capsids

“…The particular codon usage (codon bias) of an organism reflects the evolutionary forces acting within its genome (37,38) and contributes to drastically reducing the actual sequence space. In the virus world, at least four mechanisms underlying such a bias exist: mutational bias or the specific nucleotide composition (39-42); translation selection, or the optimal codon adaptation to the tRNA pool in order to get a highly efficient and accurate translation (43)(44)(45)(46)(47); fine-tuning translation kinetics selection, or the right combination of abundant and rare codons to allow a regulated ribosome traffic rate that temporally separates protein folding events, ensuring "beneficial" and avoiding "unwanted" interactions within the growing peptide (17); and selection for mechanisms to escape the antiviral cell responses (48,49). Except the last, all these mechanisms are shared in all organisms (50), and it is likely that a combination of all of them is the actual evolutionary force shaping the codon usage of HAV.…”

Analysis of factors affecting codon usage bias in human papillomavirus

“…Gene expression of HPV in squamous epithelial cells is linked to the differentiation and function of the epithelial cells (Zheng and Baker, 2006;Zhao and Chen, 2011). The complete nucleotide sequence of the HPV genome was determined in 1985 (Seedorf et al, 1985).…”

“…Although there are several studies on the HPV genome (Zhou et al, 1999;Zhao et al, 2003;Zhao and Chen, 2011), there is dearth of information on synonymous codon usage of HPV and factors that influence it. To obtain better and integrated understanding of synonymous codon usage of HPV, codon usage patterns of 39 HPV genomes were analyzed.…”

Surface modification of tri-calcium phosphate nanoparticles by DOPE and/or anti-E6 antibody to enhance uptake of antisense of E6 mRNA

“…It is the most common cancer in female genital system. Moreover, it is an important malignancy in the world [2]. It has been found that more than 99% of cervical cancers are induced by human papilloma virus (HPV) [3].…”