Alternative tRNA Priming of Human Immunodeficiency Virus Type 1 Reverse Transcription Explains Sequence Variation in the Primer-Binding Site That Has Been Attributed to APOBEC3G Activity

Abstract

It is generally assumed that human immunodeficiency virus type 1 (HIV-1) uses exclusively the cellular tRNA 3Lys molecule as a primer for reverse transcription. We demonstrate that HIV-1 uses not only tRNA 3 Lys but also an alternative tRNA primer. This tRNA was termed tRNA 5 Lys , and the near completion of the human genome project has allowed the identification of four tRNA 5 Lys -encoding genes. Priming with tRNA 5 Lys results in a single nucleotide polymorphism in the viral primer-binding site that is present in multiple natural and laboratory HIV isolates. This sequence variation was recently attributed to APOBEC3G activity. However, our results show that alternative tRNA priming can cause this mutation in the absence of APOBEC3G.

An Extended Stem-Loop 1 Is Necessary for Human Immunodeficiency Virus Type 2 Replication and Affects Genomic RNA Encapsidation

“…Aliquots of supernatants were also harvested at week 26 and processed similarly. Despite the presence of T310 in all of the original plasmid DNAs, all sequences showed a majority of T310C nucleotide changes in the primer-binding site after extended culture (data not shown), which indicates that a tRNA 3 Lys molecule was used as the primer for reverse transcription, rather than tRNA 5 Lys (8). Interestingly, the other nucleotide changes in the 5Ј-untranslated region were located in or close to the mutated pal region.…”

A miRNA-tRNA mix-up: tRNA origin of proposed miRNA

“…We based this on the presence of the identifying point mutation in the PBS of HIV-1 and HIV-2 isolates because this sequence of the viral progeny is in fact copied from the priming tRNA species during reverse transcription. 12,13 We inspected a total of 265 HIV isolates, of which 9 showed the Lys5-specific point mutation (ratio Lys3:Lys5 = 29:1). More recently, deep sequencing of small tRNA fragments in extracts from the SupT1 T-cell line revealed 1966 Lys3 and 53 Lys5 reads, yielding a similar 37:1 ratio (unpublished results).…”

Initiation of HIV Reverse Transcription

“…Incidentally, HIV-1 has been shown to infrequently use tRNA 5a Lys as primer [99]; this tRNA only differs from tRNA 3 Lys by one base-pair in the acceptor stem and has the potential to interacts with both the viral A-rich loop and the PAS sequence.…”