Identification of Critical Elements in the tRNA Acceptor Stem and TΨC Loop Necessary for Human Immunodeficiency Virus Type 1 Infectivity

A mutant human immunodeficiency virus type 1 (HIV-1) with a primer binding site (PBS) complementary to yeast tRNA(Phe) (psHIV-Phe), which relies on exogenous yeast tRNA(Phe) as reverse transcription primer, was used to investigate elements in the tRNA acceptor stem and TΨC stem-loop required for the tRNA primer selection and use in HIV-1 replication. tRNA(Phe) mutants with two- or four-nucleotide deletions in the 3′ end retained the capacity to complement replication of psHIV-Phe. tRNA(Phe) mutants with an extended 5′ end had reduced capacity for complementation, which could be restored by extension of the 3′ end of these tRNA(Phe) mutants with sequences complementary to the HIV-1 U5 region. Further analysis of mutations in the acceptor stem of tRNA(Phe) suggested that an intact acceptor stem RNA structure is important for complementation. Analysis of single-nucleotide changes in the TΨC stem-loop of tRNA(Phe) revealed an unexpected, essential role of this region for rescue of psHIV-Phe.