The characteristics of synonymous codon usage in the initial and terminal translation regions of encephalomyocarditis virus

Xx, Ma; Yp, Feng; Jl, Liu; Yq, Zhao; Chen, L; Ph, Guo; Jz, Guo; Zr, Ma

doi:10.4149/av_2014_01_86

Cited by 3 publications

(2 citation statements)

References 26 publications

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“…In positive-strand RNA viruses, the faster genome replication and optimal codon usage select viruses with good fitness (27)(28)(29). Since RNA viruses rely on the host cell for protein translation, the CUB of positive-strand RNA viruses is similar to that of the host cell since its genomic RNA is also used as the mRNA for protein translation (30,31). In NSVs, however, their CUB does not match that of the host cell despite their reliance on host protein translation.…”

Section: Discussionmentioning

confidence: 99%

Constraints of Viral RNA Synthesis on Codon Usage of Negative-Strand RNA Virus

Gumpper

Luo

2019

J Virol

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Negative-strand RNA viruses (NSVs) include some of the most pathogenic human viruses known. NSVs completely rely on the host cell for protein translation, but their codon usage bias is often different from that of the host. This discrepancy may have originated from the unique mechanism of NSV RNA synthesis in that the genomic RNA sequestered in the nucleocapsid serves as the template. The stability of the genomic RNA in the nucleocapsid appears to regulate its accessibility to the viral RNA polymerase, thus placing constraints on codon usage to balance viral RNA synthesis. By in situ analyses of vesicular stomatitis virus RNA synthesis, specific activities of viral RNA synthesis were correlated with the genomic RNA sequence. It was found that by simply altering the sequence and not the amino acid that it encoded, a significant reduction, up to an ∼750-fold reduction, in viral RNA transcripts occurred. Through subsequent sequence analysis and thermal shift assays, it was found that the purine/pyrimidine content modulates the overall stability of the polymerase complex, resulting in alteration of the activity of viral RNA synthesis. The codon usage is therefore constrained by the obligation of the NSV genome for viral RNA synthesis. IMPORTANCE Negative-strand RNA viruses (NSVs) include the most pathogenic viruses known. New methods to monitor their evolutionary trends are urgently needed for the development of antivirals and vaccines. The protein translation machinery of the host cell is currently recognized as a main genomic regulator of RNA virus evolution, which works especially well for positive-strand RNA viruses. However, this approach fails for NSVs because it does not consider the unique mechanism of their viral RNA synthesis. For NSVs, the viral RNA-dependent RNA polymerase (vRdRp) must gain access to the genome sequestered in the nucleocapsid. Our work suggests a paradigm shift that the interactions between the RNA genome and the nucleocapsid protein regulate the activity of vRdRp, which selects codon usage.

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Section: Discussionmentioning

confidence: 99%

Constraints of Viral RNA Synthesis on Codon Usage of Negative-Strand RNA Virus

Gumpper

Luo

2019

J Virol

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“…The synonymous codon usage bias, which is caused by the changes of nucleotide usages in the third codon position, often serves as the regulatory of gene expression or modulation of the translation system . Nucleotide, synonymous codon, and amino acid usages have been classical topics for studies of mRNA folding, gene translation, fine‐tuning translation kinetics selection, effects on protein structure, genetic diversity, and evolution . In addition, some reports represent that neighboring nucleotides surrounding a genetic code play roles in the usage of the specific codon from synonymous species .…”

Section: Introductionmentioning

confidence: 99%

Comparative genomic analysis for nucleotide, codon, and amino acid usage patterns of mycoplasmas

Cao

et al. 2018

J Basic Microbiol

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The evolutionary factors in influencing the genetic characteristics of nucleotide, synonymous codon, and amino acid usage of 18 mycoplasma species were analyzed. The nucleotide usage at the 1st and 2nd codon position which determines amino acid composition of proteins has a significant correlation with the total nucleotide composition of gene population of these mycoplasma species, however, the nucleotide usage at the 3rd codon position which affects synonymous codon usage patterns has a slight correlation with either the total nucleotide composition or the nucleotide usage at the 1st and 2nd codon position. Other evolutionary factors join in the evolutionary process of mycoplasma apart from mutation pressure caused by nucleotide usage constraint based on the relationships between effective number of codons/codon adaptation index and nucleotide usage at the 3rd codon position. Although nucleotide usage of gene population in mycoplasma dominates in forming the overall codon usage trends, the relative abundance of codon with nucleotide context and amino acid usage pattern show that translation selection involved in translation accuracy and efficiency play an important role in synonymous codon usage patterns. In addition, synonymous codon usage patterns of gene population have a bigger power to represent genetic diversity among different species than amino acid usage. These results suggest that although the mycoplasmas reduce its genome size during the evolutionary process and shape the form, which is opposite to their hosts, of AT usages at high levels, this kind organism still depends on nucleotide usage at the 1st and 2nd codon positions to control syntheses of the requested proteins for surviving in their hosts and nucleotide usage at the 3rd codon position to develop genetic diversity of different mycoplasma species. This systemic analysis with 18 mycoplasma species may provide useful clues for further in vivo genetic studies on the related species.

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Analyses of nucleotide, codon and amino acids usages between peste des petits ruminants virus and rinderpest virus

Chang

et al. 2017

Gene

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The characteristics of synonymous codon usage in the initial and terminal translation regions of encephalomyocarditis virus

Cited by 3 publications

References 26 publications

Constraints of Viral RNA Synthesis on Codon Usage of Negative-Strand RNA Virus

Constraints of Viral RNA Synthesis on Codon Usage of Negative-Strand RNA Virus

Comparative genomic analysis for nucleotide, codon, and amino acid usage patterns of mycoplasmas

Analyses of nucleotide, codon and amino acids usages between peste des petits ruminants virus and rinderpest virus

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