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

• Published in: Nature structural & molecular biology Vol. 29; no. 4; pp. 306 - 319
• Main Authors: Ye, Liqing, Gribling-Burrer, Anne-Sophie, Bohn, Patrick, Kibe, Anuja, Börtlein, Charlene, Ambi, Uddhav B., Ahmad, Shazeb, Olguin-Nava, Marco, Smith, Maureen, Caliskan, Neva, von Kleist, Max, Smyth, Redmond P.
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.04.2022; Nature Publishing Group
• Subjects: 45/70; 45/91; 5' Untranslated Regions; 5' Untranslated Regions - genetics; 631/1647/2258; 631/326/596; 631/337/2179; 631/45/500; Binding sites; Biochemistry; Biological Microscopy; Biomedical and Life Sciences; Dimerization; Dimers; Functional analysis; Gene sequencing; Genomes; HIV; HIV-1 - physiology; Human immunodeficiency virus; Humans; Life cycles; Life Sciences; Membrane Biology; Nucleic Acid Conformation; Nucleotides; Packaging; Polyadenylation; Protein Structure; Ribonucleic acid; RNA; RNA, Viral - chemistry; Structure-function relationships; Viral Proteins - metabolism; Virions
• ISSN: 1545-9993; 1545-9985
• DOI: 10.1038/s41594-022-00746-2

RNA dimerization is the noncovalent association of two human immunodeficiency virus-1 (HIV-1) genomes. It is a conserved step in the HIV-1 life cycle and assumed to be a prerequisite for binding to the viral structural protein Pr55 Gag during genome packaging. Here, we developed functional analysis of RNA structure-sequencing (FARS-seq) to comprehensively identify sequences and structures within the HIV-1 5′ untranslated region (UTR) that regulate this critical step. Using FARS-seq, we found nucleotides important for dimerization throughout the HIV-1 5′ UTR and identified distinct structural conformations in monomeric and dimeric RNA. In the dimeric RNA, key functional domains, such as stem-loop 1 (SL1), polyadenylation signal (polyA) and primer binding site (PBS), folded into independent structural motifs. In the monomeric RNA, SL1 was reconfigured into long- and short-range base pairings with polyA and PBS, respectively. We show that these interactions disrupt genome packaging, and additionally show that the PBS–SL1 interaction unexpectedly couples the PBS with dimerization and Pr55 Gag binding. Altogether, our data provide insights into late stages of HIV-1 life cycle and a mechanistic explanation for the link between RNA dimerization and packaging. Comprehensive functional and structural probing of the HIV-1 5′ untranslated region reveals novel interactions that regulate RNA dimerization, Pr55Gag binding and genome packaging into virions.