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Cited by 94HIV Research and TreatmentRNA and protein synthesis mechanismsEvolution and Genetic Dynamics

The biased nucleotide composition of the HIV genome: a constant factor in a highly variable virus

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van der Kuyl, Antoinette C, Berkhout, Ben·2012·Retrovirology
DOI 10.1186/1742-4690-9-92PMC PMC3511177
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Abstract

Viruses often deviate from their hosts in the nucleotide composition of their genomes. The RNA genome of the lentivirus family of retroviruses, including human immunodeficiency virus (HIV), contains e.g. an above average percentage of adenine (A) nucleotides, while being extremely poor in cytosine (C). Such a deviant base composition has implications for the amino acids that are encoded by the open reading frames (ORFs), both in the requirement of specific tRNA species and in the preference for amino acids encoded by e.g. A-rich codons. Nucleotide composition does obviously affect the secondary and tertiary structure of the RNA genome and its biological functions, but it does also influence phylogenetic analysis of viral genome sequences, and possibly the activity of the integrated DNA provirus. Over time, the nucleotide composition of the HIV-1 genome is exceptionally conserved, varying by less than 1% per base position per isolate within either group M, N, or O during 1983-2009. This extreme stability of the nucleotide composition may possibly be achieved by negative selection, perhaps conserving semi-stable RNA secondary structure as reverse transcription would be significantly affected for a less A-rich genome where secondary structures are expected to be more stable and thus more difficult to unfold.This review will discuss all aspects of the lentiviral genome composition, both of the RNA and of its derived double-stranded DNA genome, with a focus on HIV-1, the nucleotide composition over time, the effects of artificially humanized codons as well as contributions of immune system pressure on HIV nucleotide bias.

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  • The genomes of HIV-1 and other lentiviruses contain an above-average fraction of A nucleotides.

    “The genomes of HIV-1 and other lentiviruses contain an above-average fraction of A nucleotides (101, 102), which not only affects the rate of viral mRNA translation (103) but also ensures efficient reverse transcription, potentially by maintaining the flexibility of viral RNAs (104).”

    From Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication (2019) · cites this paper as [101]

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Cited by

Sorted by citations

Authors
van der Kuyl, A. C., & Berkhout, B.
Affiliations
Amsterdam UMC Location University of Amsterdam (NL)
ORCID
Berkhout, Ben
Venue
Retrovirology
Publisher
Springer Science and Business Media LLC
Published
2012-11-06
Volume
9
Issue
1
Pages
92-92
ISSN
1742-4690 (ISSN-L)
DOI
10.1186/1742-4690-9-92
PMC
PMC3511177
OpenAlex
W2104401897
Cited by
94
References
2
Citations by year
2026: 3 · 2025: 4 · 2024: 9 · 2023: 7 · 2022: 7 · 2021: 4 · 2020: 6 · 2019: 4 · 2018: 7 · 2017: 9 · 2016: 5 · 2015: 7 · 2014: 8 · 2013: 12 · 2012: 2
FWCI
1.16
Type
journal article
Language
en
Open access
Licence
Locations
  • Retrovirology (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Data Archiving and Networked Services (DANS) (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Pure Amsterdam UMC (submittedVersion)
Funders
Nederlandse Organisatie voor Wetenschappelijk Onderzoek
Topics
  • Life Sciences › Immunology and Microbiology › Virology › HIV Research and Treatment
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
Keywords
HIV-1, nucleotide composition bias, codon usage, RNA secondary structure, reverse transcription, negative selection, immune pressure, HIV-1 provirus, HIV-1 evolution
MeSH terms
Animals, Base Composition, Codon, Genes, Viral, Humans, Immunity, Innate, Nucleic Acid Conformation, RNA, Viral, HIV-1, HIV Infections, Genome, Viral

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