Insights into the Usage of Nucleobase Triplets and Codon Context Pattern in Five Influenza A Virus Subtypes

Deka, Himangshu; Chakraborty, Supriyo

doi:10.4014/jmb.1605.05016

Cited by 11 publications

(8 citation statements)

References 38 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…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: 90%

“…Furthermore, it has also been noted that the viral CUB can be significantly different from the host CUB (8). While this is often attributed to the suppression of CpG codons for evading the host immune system (12), the correlation is not ubiquitously distributed throughout all NSVs. Other requirements for virus growth may place constraints on the evolution of NSVs.…”

mentioning

confidence: 99%

See 1 more Smart Citation

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

Gumpper

Luo

2019

J Virol

View full text Add to dashboard Cite

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.

show abstract

Section: Discussionmentioning

confidence: 90%

mentioning

confidence: 99%

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

Gumpper

Luo

2019

J Virol

View full text Add to dashboard Cite

show abstract

“…6). Deka et al reported three major clusters of influenza A virus genes [14]. A feasible relationship of porcine circovirus 3 to other circoviruses was found with hierarchical clustering among them [18].…”

Section: Discussionmentioning

confidence: 94%

Codon usage pattern and its influencing factors in different genomes of hepadnaviruses

Deb

Uddin²,

Chakraborty

2020

Arch Virol

Self Cite

View full text Add to dashboard Cite

Codon usage bias (CUB) arises from the preference for a codon over codons for the same amino acid. The major factors contributing to CUB are evolutionary forces, compositional properties, gene expression, and protein properties. The present analysis was performed to investigate the compositional properties and the extent of CUB across the genomes of members of the family Hepadnaviridae, as previously no work using bioinformatic tools has been reported. The viral genes were found to be AT rich with low CUB. Analysis of relative synonymous codon usage (RSCU) was used to identify overrepresented and underrepresented codons for each amino acid. Correlation analysis of overall nucleotide composition and its composition at the third codon position suggested that mutation pressure might influence the CUB. A highly significant correlation was observed between GC12 and GC3 (r = 0.910, p < 0.01), indicating that directional mutation affected all three codon positions across the genome. Translational selection (P2) and mutational responsive index (MRI) values of genes suggested that mutation plays a more important role than translational selection in members of the family Hepadnaviridae.Publisher's Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

show abstract

“…Here are the reasons of choosing these subtypes. Even though the number of possible lAVs combinations is huge, given the fact that there are 18 types of HA genes and 11 types of NA genes (till the year of late 2017, from NCBI), it is interesting that very few have been reported to infect humans 23 . Common subtypes, such as H1N1, H1N2, H2N2, H3N2, and H5N1 24–27 , were found to circulate around humans to cause seasonal flu.…”

Section: Methodsmentioning

confidence: 99%

Predicting correct serotypes using machine-learning models based on codon usage patterns of influenza A viruses

Yang¹

2019

Preprint

View full text Add to dashboard Cite

Consistent codon usage patterns across species was supposed to be observed owing to the degeneracy of genetic code and the conservation of the translation machinery. In fact, however, codon usage vary dramatically among organisms, and the choice difference might also affect downstream protein expressions, structures as well as their functions. It is suggested that different codon usage patterns should encrypt distinct characters for a certain type of organism, and as a result, a series of machine-learning models have been constructed, not only for learning the patterns from certain species, but also for predicting the species based on given patterns. Two gene segments of influenza A virus, hemagglutinin (HA; gene 4) and neuraminidase (NA; gene 6), were so essential for the immune response of their hosts, that the serotypes of the viruses are named after their combinations. They thus become the objects of this study, and those proposed models work quite well on the designated tasks.

show abstract

Insights into the Usage of Nucleobase Triplets and Codon Context Pattern in Five Influenza A Virus Subtypes

Cited by 11 publications

References 38 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

Codon usage pattern and its influencing factors in different genomes of hepadnaviruses

Predicting correct serotypes using machine-learning models based on codon usage patterns of influenza A viruses

Contact Info

Product

Resources

About