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Cited by 130RNA and protein synthesis mechanismsHIV Research and TreatmentEvolution and Genetic Dynamics

HIV-1 modulates the tRNA pool to improve translation efficiency

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van Weringh, Anna, Ragonnet-Cronin, Manon, Pranckeviciene, Erinija, Pavon-Eternod, Mariana, Kleiman, Lawrence, Xia, Xuhua·2011·Molecular Biology and Evolution
DOI 10.1093/molbev/msr005PMC PMC3098512
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Abstract

Despite its poorly adapted codon usage, HIV-1 replicates and is expressed extremely well in human host cells. HIV-1 has recently been shown to package non-lysyl transfer RNAs (tRNAs) in addition to the tRNALys needed for priming reverse transcription and integration of the HIV-1 genome. By comparing the codon usage of HIV-1 genes with that of its human host, we found that tRNAs decoding codons that are highly used by HIV-1 but avoided by its host are overrepresented in HIV-1 virions. In particular, tRNAs decoding A-ending codons, required for the expression of HIV's A-rich genome, are highly enriched. Because the affinity of Gag-Pol for all tRNAs is nonspecific, HIV packaging is most likely passive and reflects the tRNA pool at the time of viral particle formation. Codon usage of HIV-1 early genes is similar to that of highly expressed host genes, but codon usage of HIV-1 late genes was better adapted to the selectively enriched tRNA pool, suggesting that alterations in the tRNA pool are induced late in viral infection. If HIV-1 genes are adapting to an altered tRNA pool, codon adaptation of HIV-1 may be better than previously thought.

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  • HTLV-1 does not exhibit differences in codon adaptation between early and late genes.

    “However, HTLV-1 does not exhibit differences in codon adaptation between early and late genes (99).”

    From Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication (2019) · cites this paper as [99]

  • HIV-1 early genes (tat, rev, nef) adapt to host codon usage better than late genes (gag, pol, env, vif, vpu, vpr), which contain a higher portion of rare codons.

    “HIV-1 early genes (tat, rev, and nef) adapt to the host codon usage better than late genes (gag, pol, env, vif, vpu, and vpr), which contain a higher portion of rare codons (99).”

    From Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication (2019) · cites this paper as [99]

  • HIV-1 uses the host cell translational machinery to translate viral mRNAs but is poorly adapted to the codon usage of host cells.

    “Although HIV-1 uses the host cell translational machinery to translate viral mRNAs, it is poorly adapted to the codon usage of host cells (99).”

    From Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication (2019) · cites this paper as [99]

  • There is a high frequency of A-ending codons in the protein-coding region of the HIV-1 genome, and these codons are under-represented in the host cell genome.

    “In particular, there is a high frequency of A-ending codons in the protein-coding region of the HIV-1 genome, and these codons are under-represented in the host cell genome (99).”

    From Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication (2019) · cites this paper as [99]

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Authors
van Weringh, A., Ragonnet-Cronin, M., Pranckeviciene, E., Pavon-Eternod, M., Kleiman, L., & Xia, X.
Affiliations
  • Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
  • University of Chicago (US)
  • Jewish General Hospital (CA)
  • University of Ottawa (CA)
Corresponding author
Xia, Xuhua
ORCID
Xia, Xuhua
Venue
Molecular Biology and Evolution
Publisher
Oxford University Press (OUP)
Published
2011-01-07
Volume
28
Issue
6
Pages
1827-1834
ISSN
  • 0737-4038 (ISSN-L)
  • 1537-1719
DOI
10.1093/molbev/msr005
PMC
PMC3098512
OpenAlex
W2117312105
Cited by
130
References
3
Citations by year
2026: 6 · 2025: 10 · 2024: 10 · 2023: 11 · 2022: 3 · 2021: 9 · 2020: 10 · 2019: 11 · 2018: 11 · 2017: 6 · 2016: 11 · 2015: 5 · 2014: 6 · 2013: 4 · 2012: 12
FWCI
3.51
Type
journal article
Language
en
Open access
Licence
Locations
  • Molecular Biology and Evolution (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • uO Research (University of Ottawa) (submittedVersion, public-domain)
  • Vytautas Magnus University (submittedVersion)
Funders
Biotechnology and Biological Sciences Research Council (1098048)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Immunology and Microbiology › Virology › HIV Research and Treatment
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
Keywords
HIV-1, tRNA pool, codon usage, translation efficiency, Gag-Pol, viral adaptation, late gene expression, viral particle formation
MeSH terms
Adaptation, Biological, Codon, Humans, RNA, Transfer, Protein Biosynthesis, HIV-1, HIV Infections, Gene Expression Regulation, Viral, Virus Assembly

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