Human genes with codon usage bias similar to that of the nonstructural protein 1 gene of influenza A viruses are ... View Full Text


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Article Info

DATE

2022-04-08

AUTHORS

Komi Nambou, Manawa Anakpa, Yin Selina Tong

ABSTRACT

Molecular mechanisms of the non-structural protein 1 (NS1) in influenza A-induced pathological changes remain ambiguous. This study explored the pathogenesis of human infection by influenza A viruses (IAVs) through identifying human genes with codon usage bias (CUB) similar to NS1 gene of these viruses based on the relative synonymous codon usage (RSCU). CUB of the IAV subtypes H1N1, H3N2, H3N8, H5N1, H5N2, H5N8, H7N9 and H9N2 was analyzed and the correlation of RSCU values of NS1 sequences with those of the human genes was calculated. The CUB of NS1 was uneven and codons ending with A/U were preferred. The ENC-GC3 and neutrality plots suggested natural selection as the main determinant for CUB. The RCDI, CAI and SiD values showed that the viruses had a high degree of adaptability to human. A total of 2155 human genes showed significant RSCU-based correlation (p < 0.05 and r > 0.5) with NS1 coding sequences and was considered as human genes with CUB similar to NS1 gene of IAV subtypes. Differences and similarities in the subtype-specific human protein–protein interaction (PPI) networks and their functions were recorded among IAVs subtypes, indicating that NS1 of each IAV subtype has a specific pathogenic mechanism. Processes and pathways involved in influenza, transcription, immune response and cell cycle were enriched in human gene sets retrieved based on the CUB of NS1 gene of IAV subtypes. The present work may advance our understanding on the mechanism of NS1 in human infections of IAV subtypes and shed light on the therapeutic options. More... »

PAGES

97-115

References to SciGraph publications

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  • 2020-01-23. Research progress on human infection with avian influenza H7N9 in FRONTIERS OF MEDICINE
  • 2021-02-18. Molecular features similarities between SARS-CoV-2, SARS, MERS and key human genes could favour the viral infections and trigger collateral effects in SCIENTIFIC REPORTS
  • 2019-07-01. Structural basis for influenza virus NS1 protein block of mRNA nuclear export in NATURE MICROBIOLOGY
  • 2011-04-19. The NS1 protein of influenza a virus interacts with heat shock protein Hsp90 in human alveolar basal epithelial cells: Implication for virus-induced apoptosis in VIROLOGY JOURNAL
  • 2014-10-07. Honeysuckle-encoded atypical microRNA2911 directly targets influenza A viruses in CELL RESEARCH
  • 2015-05-06. Non-uniqueness of factors constraint on the codon usage in Bombyx mori in BMC GENOMICS
  • 1986-12. An evolutionary perspective on synonymous codon usage in unicellular organisms in JOURNAL OF MOLECULAR EVOLUTION
  • 2018-05-29. The Evolution of Molecular Compatibility between Bacteriophage ΦX174 and its Host in SCIENTIFIC REPORTS
  • 2017-01-26. Ror2 signaling regulates Golgi structure and transport through IFT20 for tumor invasiveness in SCIENTIFIC REPORTS
  • 2018-11-28. Host and viral determinants of influenza A virus species specificity in NATURE REVIEWS MICROBIOLOGY
  • 2012-05-02. Experimental adaptation of an influenza H5 HA confers respiratory droplet transmission to a reassortant H5 HA/H1N1 virus in ferrets in NATURE
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/s10709-022-00155-9

    DOI

    http://dx.doi.org/10.1007/s10709-022-00155-9

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1146958419

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/35396627


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