Overall codon usage pattern of enterovirus 71

R, M; Liu, Hui; Wang, M L; Yao, Tsuneyoshi; Chang, Yu-Kaung; Jia, Qiuhong; Wang, X H; Wei, Yan; Ha, Xiaoqin

doi:10.4238/2014.january.21.1

Cited by 10 publications

(9 citation statements)

References 18 publications

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“…This result suggests that the expression of CYP genes is less affected by the pattern of codon bias. Ma et al (Ma et al, 2014) found similar results in enterovirus.…”

Section: Gene Expression Level Of Cyp Genessupporting

confidence: 87%

Cytochrome P450 genes in coronary artery diseases: Codon usage analysis reveals genomic GC adaptation

Malakar

Halder

Pavlidis

et al. 2016

Gene

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“…This result suggests that the expression of CYP genes is less affected by the pattern of codon bias. Ma et al (Ma et al, 2014) found similar results in enterovirus.…”

Section: Gene Expression Level Of Cyp Genessupporting

confidence: 87%

Cytochrome P450 genes in coronary artery diseases: Codon usage analysis reveals genomic GC adaptation

Malakar

Halder

Pavlidis

et al. 2016

Gene

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“…In NSVs, however, their CUB does not match that of the host cell despite their reliance on host protein translation. This phenomenon has previously been attributed to limiting CpG to evade the host's immune system and to the concept of codon constellation (8,12,(31)(32)(33). More importantly, analyses of codon usages revealed that CUB of NSVs did not result from transitional selection (34)(35)(36).…”

Section: Discussionmentioning

confidence: 89%

“…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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“…The data points follow a curvilinear trend if the synonymous codon usage is only determined by the GC content on the third codon position (Gu et al, 2004). If the synonymous codon usage depends on compositional constraints, the data points occur on or just below the expected curve; however, if the synonymous codon usage is subject to natural selection, the points should be considerably below the expected curve (Wright, 1990;Ma et al, 2014). In this study, all the data points were immediately below the expected curve, suggesting that synonymous codon usage in these 39 HPV genomes was basically influenced by compositional constraints.…”

Section: Discussionmentioning

confidence: 95%

“…The ENC value, which is one of the best overall estimators of absolute synonymous codon usage bias, provides an intuitively meaningful measure of the extent of codon preference in a gene (Wright, 1990;Ma et al, 2014). Compared to the ENC values of other DNA viruses, ENC values of the HPV suggest that the low c codon bias may result from an increase in its replication efficiency in order to adapt to the replication system of the host (Liu et al, 2012).…”

Section: Discussionmentioning

confidence: 99%