A-rich RNA sequences of HIV-1 pol are important for the synthesis of viral cDNA

• Published in: Nucleic acids research Vol. 37; no. 3; pp. 945 - 956
• Main Authors: Keating, Cameron P, Hill, Melissa K, Hawkes, David J, Smyth, Redmond P, Isel, Catherine, Le, Shu-Yun, Palmenberg, Ann C, Marshall, John A, Marquet, Roland, Nabel, Gary J, Mak, Johnson
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.02.2009; Oxford Publishing Limited (England)
• Subjects: Adenine; Adenine - analysis; Base Sequence; Biochemistry, Molecular Biology; Cell Line; Cellular Biology; Codon; Dimerization; DNA, Complementary; DNA, Complementary - biosynthesis; DNA, Viral; DNA, Viral - biosynthesis; Genes, pol; HIV-1; HIV-1 - genetics; HIV-1 - physiology; Human immunodeficiency virus 1; Humans; Life Sciences; Nucleic Acid Conformation; Regulatory Sequences, Ribonucleic Acid; Reverse Transcription; RNA; RNA, Viral; RNA, Viral - chemistry; Viral Proteins; Viral Proteins - metabolism; Virion; Virion - metabolism; Virus Internalization; Virus Replication
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkn1015

The bias of A-rich codons in HIV-1 pol is thought to be a record of hypermutations in viral genomes that lack biological functions. Bioinformatic analysis predicted that A-rich sequences are generally associated with minimal local RNA structures. Using codon modifications to reduce the amount of A-rich sequences within HIV-1 genomes, we have reduced the flexibility of RNA sequences in pol to analyze the functional significance of these A-rich 'structurally poor' RNA elements in HIV-1 pol. Our data showed that codon modification of HIV-1 sequences led to a suppression of virus infectivity by 5-100-fold, and this defect does not correlate with, viral entry, viral protein expression levels, viral protein profiles or virion packaging of genomic RNA. Codon modification of HIV-1 pol correlated with an enhanced dimer stability of the viral RNA genome, which was associated with a reduction of viral cDNA synthesis both during HIV-1 infection and in a cell free reverse transcription assay. Our data provided direct evidence that the HIV-1 A-rich pol sequence is not merely an evolutionary artifact of enzyme-induced hypermutations, and that HIV-1 has adapted to rely on A-rich RNA sequences to support the synthesis of viral cDNA during reverse transcription, highlighting the utility of using 'structurally poor' RNA domains in regulating biological process.