Genome polarity of RNA viruses reflects the different evolutionary pressures shaping codon usage

doi:10.1007/s00705-018-3930-7

. 2018 Oct;163(10):2883-2888.

doi: 10.1007/s00705-018-3930-7. Epub 2018 Jul 9.

Genome polarity of RNA viruses reflects the different evolutionary pressures shaping codon usage

Supinya Phakaratsakul¹, Thanyaporn Sirihongthong¹, Chompunuch Boonarkart¹, Ornpreya Suptawiwat², Prasert Auewarakul³

Affiliations

¹ Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
² Research and International Relations Division, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok, Thailand.
³ Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand. prasert.aue@mahidol.ac.th.

PMID: 29987380
DOI: 10.1007/s00705-018-3930-7

Genome polarity of RNA viruses reflects the different evolutionary pressures shaping codon usage

Supinya Phakaratsakul et al. Arch Virol. 2018 Oct.

. 2018 Oct;163(10):2883-2888.

doi: 10.1007/s00705-018-3930-7. Epub 2018 Jul 9.

Authors

Supinya Phakaratsakul¹, Thanyaporn Sirihongthong¹, Chompunuch Boonarkart¹, Ornpreya Suptawiwat², Prasert Auewarakul³

Affiliations

¹ Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
² Research and International Relations Division, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok, Thailand.
³ Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand. prasert.aue@mahidol.ac.th.

PMID: 29987380
DOI: 10.1007/s00705-018-3930-7

Abstract

RNA viruses are classified by their genome polarity and replication strategies. Nucleotide composition and codon usage differ among virus groups, for instance positive-sense RNA (+ssRNA) viruses have higher GC-content than the other RNA virus groups. Codon usage of +ssRNA viruses is closer to humans showing significantly higher codon adaptation index (CAI) than those of negative-sense RNA (-ssRNA), double stranded RNA (dsRNA) and retroviruses. Ambisense viruses have high CAI comparable to that of +ssRNA virus despite their lower GC content, whereas dsRNA viruses have the lowest CAI. This may provide a benefit for +ssRNA viruses as their genomes are used as mRNA. However, analyses for influence of nucleotide composition on codon usage did not show a difference between +ssRNA and -ssRNA viruses. This suggests that genome composition and hence mutational pressure remain the major pressure causing the differences in codon usage among RNA viruses with different genome types.

PubMed Disclaimer

Cited by

Human Schlafen 11 inhibits influenza A virus production.
Jitobaom K, Sirihongthong T, Boonarkart C, Phakaratsakul S, Suptawiwat O, Auewarakul P. Jitobaom K, et al. Virus Res. 2023 Sep;334:199162. doi: 10.1016/j.virusres.2023.199162. Epub 2023 Jun 26. Virus Res. 2023. PMID: 37356582 Free PMC article.
Codon usage similarity between viral and some host genes suggests a codon-specific translational regulation.
Jitobaom K, Phakaratsakul S, Sirihongthong T, Chotewutmontri S, Suriyaphol P, Suptawiwat O, Auewarakul P. Jitobaom K, et al. Heliyon. 2020 May;6(5):e03915. doi: 10.1016/j.heliyon.2020.e03915. Epub 2020 May 8. Heliyon. 2020. PMID: 32395662 Free PMC article.
Host nutritional status affects alphavirus virulence, transmission, and evolution.
Weger-Lucarelli J, Carrau L, Levi LI, Rezelj V, Vallet T, Blanc H, Boussier J, Megrian D, Coutermarsh-Ott S, LeRoith T, Vignuzzi M. Weger-Lucarelli J, et al. PLoS Pathog. 2019 Nov 11;15(11):e1008089. doi: 10.1371/journal.ppat.1008089. eCollection 2019 Nov. PLoS Pathog. 2019. PMID: 31710653 Free PMC article.
A Codon-Pair Bias Associated With Network Interactions in Influenza A, B, and C Genomes.
Plant EP, Ye Z. Plant EP, et al. Front Genet. 2021 Jul 6;12:699141. doi: 10.3389/fgene.2021.699141. eCollection 2021. Front Genet. 2021. PMID: 34295355 Free PMC article.
Crystal structure and biochemical activity of the macrodomain from rubella virus p150.
Stoll GA, Nikolopoulos N, Zhai H, Zhang L, Douse CH, Modis Y. Stoll GA, et al. J Virol. 2024 Feb 20;98(2):e0177723. doi: 10.1128/jvi.01777-23. Epub 2024 Jan 30. J Virol. 2024. PMID: 38289106 Free PMC article.

MeSH terms

Actions
Actions
Actions
Actions
Actions
Actions

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

Genome polarity of RNA viruses reflects the different evolutionary pressures shaping codon usage

Affiliations

Genome polarity of RNA viruses reflects the different evolutionary pressures shaping codon usage

Authors

Affiliations

Abstract

Similar articles

Cited by

MeSH terms

Substances

Grants and funding

LinkOut - more resources

Full Text Sources

Other Literature Sources

Miscellaneous