Short- and long-range interactions in the HIV-1 5' UTR regulate genome dimerization and packaging

Area of Science:

• Molecular Biology
• Virology
• Structural Biology

Background:

• RNA dimerization, the association of two human immunodeficiency virus-1 (HIV-1) genomes, is a vital step in the viral life cycle.
• This dimerization is believed to be essential for the packaging of the viral genome, mediated by the structural protein Pr55^Gag.

Purpose of the Study:

• To comprehensively identify sequences and structures within the HIV-1 5' untranslated region (UTR) that regulate RNA dimerization.
• To elucidate the structural differences between monomeric and dimeric HIV-1 RNA and their functional implications.

Main Methods:

• Development and application of functional analysis of RNA structure-sequencing (FARS-seq) to map regulatory elements.
• Comparative structural analysis of monomeric and dimeric HIV-1 RNA using FARS-seq data.

Main Results:

• Identification of key nucleotides across the HIV-1 5' UTR critical for RNA dimerization.
• Distinct structural conformations were observed in monomeric versus dimeric RNA.
• In dimeric RNA, functional domains (SL1, polyA, PBS) formed independent motifs, whereas in monomeric RNA, SL1 interacted with polyA and PBS, disrupting genome packaging.

Conclusions:

• The study reveals a novel interaction between the primer binding site (PBS) and stem-loop 1 (SL1) in monomeric HIV-1 RNA.
• This PBS-SL1 interaction links RNA dimerization with Pr55^Gag binding and genome packaging.
• Provides mechanistic insights into late-stage HIV-1 replication, specifically RNA dimerization and packaging.