Human T-cell leukemia virus type 1 uses a specific tRNAPro isodecoder to prime reverse transcription

Human T-cell leukemia virus type 1 (HTLV-1) is the only oncogenic human retrovirus discovered to date. All retroviruses are believed to use a host cell tRNA to prime reverse transcription (RT). In HTLV-1, the primer-binding site (PBS) in the genomic RNA is complementary to the 3 ' 18 nucleotides (nt) of human tRNA(Pro). The human genome encodes 20 cytoplasmic tRNA(Pro) genes representing seven isodecoders, all of which share the same 3 ' 18 nt sequence but vary elsewhere. Whether all tRNA(Pro) isodecoders are used to prime RT in cells is unknown. A previous study showed that a 3 ' 18 nt tRNA(Pro)-derived fragment (tRF(Pro)) is packaged into HTLV-1 particles and can serve as an RT primer in vitro. The role of this tRNA fragment in the viral life cycle is unclear. In retroviruses, N1-methylation of the tRNA primer at position A58 (m(1)A) is essential for successful plus-strand transfer. Using primer-extension assays performed in chronically HTLV-1-infected cells, we found that A58 of tRNA(Pro) is m(1)A-modified, implying that full-length tRNA(Pro) is capable of facilitating successful plus-strand transfer. Analysis of HTLV-1 RT primer extension products indicated that full-length tRNA(Pro) is likely to be the primer. To determine which tRNA(Pro) isodecoder is used as the RT primer, we sequenced the minus-strand strong-stop RT product containing the intact tRNA primer and established that HTLV-1 primes RT using a specific tRNA(Pro) UGG isodecoder. Further studies are required to understand how this primer is annealed to the highly structured HTLV-1 PBS and to investigate the role of tRF(Pro) in the viral life cycle.