title: The A-rich RNA sequences of HIV-1 pol are important for the synthesis of viral cDNA.
abstract: 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.
authors.affiliation: Centre for Virology, Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, Australia.
authors.forename: Cameron P
authors.initials: CP
authors.lastname: Keating
authors.forename: Melissa K
authors.initials: MK
authors.lastname: Hill
authors.forename: David J
authors.initials: DJ
authors.lastname: Hawkes
authors.forename: Redmond P
authors.initials: RP
authors.lastname: Smyth
authors.forename: Catherine
authors.initials: C
authors.lastname: Isel
authors.forename: Shu-Yun
authors.initials: SY
authors.lastname: Le
authors.forename: Ann C
authors.initials: AC
authors.lastname: Palmenberg
authors.forename: John A
authors.initials: JA
authors.lastname: Marshall
authors.forename: Roland
authors.initials: R
authors.lastname: Marquet
authors.forename: Gary J
authors.initials: GJ
authors.lastname: Nabel
authors.forename: Johnson
authors.initials: J
authors.lastname: Mak
mesh_terms: D000225:Adenine / Q000032:analysis; D001483:Base Sequence; D002460:Cell Line; D003062:Codon; D018076:DNA, Complementary / Q000096:biosynthesis*; D004279:DNA, Viral / Q000096:biosynthesis*; D019281:Dimerization; D015751:Genes, pol; D015497:HIV-1 / Q000235:genetics* / Q000502:physiology; D006801:Humans; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000737:chemistry*; D038621:Regulatory Sequences, Ribonucleic Acid; D048348:Reverse Transcription; D014764:Viral Proteins / Q000378:metabolism; D014771:Virion / Q000378:metabolism; D053586:Virus Internalization; D014779:Virus Replication
chemical_list: D003062:Codon; D018076:DNA, Complementary; D004279:DNA, Viral; D012367:RNA, Viral; D038621:Regulatory Sequences, Ribonucleic Acid; D014764:Viral Proteins; D000225:Adenine