Human T-cell leukemia virus type 1 uses a specific tRNA^Pro 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 (m¹A) 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 m¹A-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.