Journal
NUCLEIC ACIDS RESEARCH
Volume 49, Issue 10, Pages 5925-5942Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkab342
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Funding
- National Institutes of Health [R01AI150460, R01GM109980, R35GM136409, R01GM063732, R01GM117059, R35GM134919]
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HIV-1 reverse transcription initiates at the primer binding site (PBS) in the viral genomic RNA (gRNA), where proper folding of the PBS-segment is crucial for loading beneficial host factors. DHX9/RNA helicase A (RHA) enhances the processivity of reverse transcriptase by binding preferentially to the PBS-segment. The three-way junction structure of the PBS-segment, encompassing the primer activation stem (PAS), tRNA-like element (TLE), and tRNA annealing arm, plays a key role in efficient reverse transcription and viral infectivity.
HIV-1 reverse transcription initiates at the primer binding site (PBS) in the viral genomic RNA (gRNA). Although the structure of the PBS-segment undergoes substantial rearrangement upon tRNA(Lys3) annealing, the proper folding of the PBS-segment during gRNA packaging is important as it ensures loading of beneficial host factors. DHX9/RNA helicase A (RHA) is recruited to gRNA to enhance the processivity of reverse transcriptase. Because the molecular details of the interactions have yet to be defined, we solved the solution structure of the PBS-segment preferentially bound by RHA. Evidence is provided that PBS-segment adopts a previously undefined adenosine-rich three-way junction structure encompassing the primer activation stem (PAS), tRNA-like element (TLE) and tRNA annealing arm. Disruption of the PBS-segment three-way junction structure diminished reverse transcription products and led to reduced viral infectivity. Because of the existence of the tRNA annealing arm, the TLE and PAS form a bent helical structure that undergoes shape-dependent recognition by RHA double-stranded RNA binding domain 1 (dsRBD1). Mutagenesis and phylogenetic analyses provide evidence for conservation of the PBS-segment three-way junction structure that is preferentially bound by RHA in support of efficient reverse transcription, the hallmark step of HIV-1 replication.
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