Treffer: Codon Usage Bias in Human RNA Viruses and Its Impact on Viral Translation, Fitness, and Evolution.
Title:
Codon Usage Bias in Human RNA Viruses and Its Impact on Viral Translation, Fitness, and Evolution.
Authors:
Ventoso I; Centro de Biología Molecular Severo Ochoa (CSIC-UAM) and Departamento de Biología Molecular, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain.
Source:
Viruses [Viruses] 2025 Sep 06; Vol. 17 (9). Date of Electronic Publication: 2025 Sep 06.
Publication Type:
Journal Article; Review
Language:
English
Journal Info:
Publisher: MDPI Country of Publication: Switzerland NLM ID: 101509722 Publication Model: Electronic Cited Medium: Internet ISSN: 1999-4915 (Electronic) Linking ISSN: 19994915 NLM ISO Abbreviation: Viruses Subsets: MEDLINE
Imprint Name(s):
Original Publication: Basel, Switzerland : MDPI
MeSH Terms:
References:
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Nat Struct Mol Biol. 2013 Feb;20(2):237-43. (PMID: 23262490)
Nat Rev Drug Discov. 2021 Nov;20(11):817-838. (PMID: 34433919)
J Virol. 2014 Sep;88(18):10525-40. (PMID: 24965472)
J Virol. 2012 Sep;86(17):9484-94. (PMID: 22761388)
Int J Mol Sci. 2024 Oct 29;25(21):. (PMID: 39519170)
Nat Rev Microbiol. 2023 Jun;21(6):361-379. (PMID: 37020110)
Virology. 2011 Mar 15;411(2):180-93. (PMID: 21211811)
J Virol. 2019 Aug 28;93(18):. (PMID: 31270226)
J Virol. 2015 Nov;89(21):10762-73. (PMID: 26269186)
Nat Rev Mol Cell Biol. 2018 Jan;19(1):20-30. (PMID: 29018283)
Nat Commun. 2022 Aug 11;13(1):4725. (PMID: 35953468)
Nucleic Acids Res. 2025 Mar 20;53(6):. (PMID: 40193709)
Viruses. 2021 Jun 01;13(6):. (PMID: 34205979)
Virus Res. 2003 Mar;92(1):1-7. (PMID: 12606071)
Annu Rev Biochem. 2021 Jun 20;90:375-401. (PMID: 33441035)
Cell Host Microbe. 2012 Nov 15;12(5):623-32. (PMID: 23159052)
PLoS One. 2013;8(2):e56642. (PMID: 23451064)
J Virol. 2017 Mar 29;91(8):. (PMID: 28148785)
Genome Biol Evol. 2021 Sep 1;13(9):. (PMID: 33988683)
Science. 2020 Sep 4;369(6508):1249-1255. (PMID: 32680882)
Cell Mol Life Sci. 2016 Dec;73(23):4433-4448. (PMID: 27392606)
Annu Rev Virol. 2025 Sep;12(1):223-237. (PMID: 40267166)
Mol Syst Biol. 2024 Oct;20(10):1085-1108. (PMID: 39039212)
Front Microbiol. 2021 Nov 30;12:791750. (PMID: 34917065)
Nat Rev Genet. 2011 Jan;12(1):32-42. (PMID: 21102527)
PLoS One. 2020 Feb 13;15(2):e0228730. (PMID: 32053646)
EMBO J. 2024 Jan;43(2):151-167. (PMID: 38200146)
Front Microbiol. 2021 Jun 30;12:676582. (PMID: 34276608)
Science. 2004 Jul 30;305(5684):645. (PMID: 15286366)
J Virol. 2003 Nov;77(21):11555-62. (PMID: 14557641)
Mol Biol Evol. 2019 Oct 1;36(10):2328-2339. (PMID: 31220870)
Annu Rev Biochem. 2023 Jun 20;92:227-245. (PMID: 37001134)
Annu Rev Genet. 2008;42:287-99. (PMID: 18983258)
Cold Spring Harb Perspect Med. 2018 Oct 1;8(10):. (PMID: 29530949)
Infect Genet Evol. 2011 Dec;11(8):2098-102. (PMID: 21907310)
Viruses. 2024 Jan 30;16(2):. (PMID: 38399981)
Nat Rev Genet. 2024 Jun;25(6):431-448. (PMID: 38297070)
Front Microbiol. 2021 Mar 16;12:606087. (PMID: 33796084)
Virology. 2021 Apr;556:62-72. (PMID: 33545556)
Mol Biol Evol. 2021 Jan 23;38(2):575-588. (PMID: 32986832)
J Mol Biol. 2007 Feb 9;366(1):1-13. (PMID: 17187822)
Genes (Basel). 2021 Apr 19;12(4):. (PMID: 33921764)
Nat Biotechnol. 2010 Jul;28(7):723-6. (PMID: 20543832)
Proc Natl Acad Sci U S A. 2014 Sep 9;111(36):13169-74. (PMID: 25157129)
Nature. 2017 Oct 5;550(7674):124-127. (PMID: 28953888)
Mol Cell. 2007 Dec 14;28(5):860-70. (PMID: 18082610)
Nat Biotechnol. 2024 Jan;42(1):72-86. (PMID: 37024678)
Genes Dev. 2022 Feb 1;36(3-4):108-132. (PMID: 35193946)
J Virol. 2006 Apr;80(7):3259-72. (PMID: 16537593)
Proc Natl Acad Sci U S A. 2013 Jun 4;110(23):9481-6. (PMID: 23690603)
PLoS One. 2009;4(3):e4772. (PMID: 19274090)
PLoS Pathog. 2018 Jan 29;14(1):e1006824. (PMID: 29377940)
Front Microbiol. 2019 Mar 05;10:417. (PMID: 30891023)
Mol Cell. 2023 Feb 2;83(3):481-495. (PMID: 36334591)
EMBO Rep. 2023 Sep 6;24(9):e56901. (PMID: 37497756)
Nat Ecol Evol. 2020 Apr;4(4):589-600. (PMID: 32123323)
Cell. 2015 Mar 12;160(6):1111-24. (PMID: 25768907)
Nat Commun. 2022 Mar 22;13(1):1536. (PMID: 35318324)
Microorganisms. 2024 Nov 20;12(11):. (PMID: 39597761)
PLoS Pathog. 2020 Aug 14;16(8):e1008718. (PMID: 32797103)
mBio. 2024 Dec 11;15(12):e0249324. (PMID: 39475243)
Nucleic Acids Res. 2019 Sep 5;47(15):8061-8083. (PMID: 31276592)
Genome Biol Evol. 2021 Sep 1;13(9):. (PMID: 33914886)
Nucleic Acids Res. 2023 Jan 25;51(2):783-795. (PMID: 36610792)
J Virol. 2006 Oct;80(19):9687-96. (PMID: 16973573)
Curr Opin Struct Biol. 2019 Apr;55:138-146. (PMID: 31102979)
Front Microbiol. 2021 Jun 28;12:646300. (PMID: 34262534)
Comput Struct Biotechnol J. 2022 May 17;20:2600-2610. (PMID: 35685354)
J Mol Biol. 1966 Aug;19(2):548-55. (PMID: 5969078)
Sci Rep. 2018 Apr 13;8(1):5960. (PMID: 29654310)
Virol J. 2024 Feb 6;21(1):38. (PMID: 38321453)
Biol Direct. 2008 Sep 16;3:38. (PMID: 18796141)
Science. 2008 Jun 27;320(5884):1784-7. (PMID: 18583614)
Elife. 2014 Dec 09;3:e04531. (PMID: 25490153)
Trends Biotechnol. 2004 Jul;22(7):346-53. (PMID: 15245907)
Nat Struct Mol Biol. 2013 Feb;20(2):237-43. (PMID: 23262490)
Nat Rev Drug Discov. 2021 Nov;20(11):817-838. (PMID: 34433919)
J Virol. 2014 Sep;88(18):10525-40. (PMID: 24965472)
J Virol. 2012 Sep;86(17):9484-94. (PMID: 22761388)
Int J Mol Sci. 2024 Oct 29;25(21):. (PMID: 39519170)
Nat Rev Microbiol. 2023 Jun;21(6):361-379. (PMID: 37020110)
Virology. 2011 Mar 15;411(2):180-93. (PMID: 21211811)
J Virol. 2019 Aug 28;93(18):. (PMID: 31270226)
J Virol. 2015 Nov;89(21):10762-73. (PMID: 26269186)
Nat Rev Mol Cell Biol. 2018 Jan;19(1):20-30. (PMID: 29018283)
Nat Commun. 2022 Aug 11;13(1):4725. (PMID: 35953468)
Nucleic Acids Res. 2025 Mar 20;53(6):. (PMID: 40193709)
Viruses. 2021 Jun 01;13(6):. (PMID: 34205979)
Virus Res. 2003 Mar;92(1):1-7. (PMID: 12606071)
Annu Rev Biochem. 2021 Jun 20;90:375-401. (PMID: 33441035)
Cell Host Microbe. 2012 Nov 15;12(5):623-32. (PMID: 23159052)
PLoS One. 2013;8(2):e56642. (PMID: 23451064)
J Virol. 2017 Mar 29;91(8):. (PMID: 28148785)
Genome Biol Evol. 2021 Sep 1;13(9):. (PMID: 33988683)
Science. 2020 Sep 4;369(6508):1249-1255. (PMID: 32680882)
Cell Mol Life Sci. 2016 Dec;73(23):4433-4448. (PMID: 27392606)
Annu Rev Virol. 2025 Sep;12(1):223-237. (PMID: 40267166)
Contributed Indexing:
Keywords: codon usage bias; human RNA virus; synonymous codons; tRNAs; translation; virus evolution; virus fitness
Substance Nomenclature:
0 (Codon)
Entry Date(s):
Date Created: 20250927 Date Completed: 20250927 Latest Revision: 20250930
Update Code:
20250930
PubMed Central ID:
PMC12474380
DOI:
10.3390/v17091218
PMID:
41012646
Database:
MEDLINE
Weitere Informationen
Synonymous codon usage (codon bias) greatly influences not only translation but also mRNA stability. In vertebrates, highly expressed genes preferentially use codons with an optimal tRNA adaptation index (tAI) that mostly end in C or G. Surprisingly, the codon usage of viruses infecting humans often deviates from optimality, showing an enrichment in A/U-ending codons, which are generally associated with slow decoding and reduced mRNA stability. This observation is particularly evident in RNA viruses causing respiratory illnesses in humans. This review analyzes the mutational and selective forces that shape nucleotide composition and codon usage drift in human RNA viruses, as well as their impact on translation, viral fitness, and evolution. It also describes how some viruses overcome suboptimal codon usage to outcompete host mRNA for translation. Finally, the roles of viral tropism and host adaptation in codon usage bias of prototypical viruses are discussed.