Role of RNA structural plasticity in modulating HIV-1 genome packaging and translation

• 成果类型: Article
• 署名作者: Yasin, Saif; Lesko, Sydney L.; Kharytonchyk, Siarhei; Brown, Joshua D.; Chaudry, Issac; Geleta, Samuel A.; Tadzong, Ndeh F.; Zheng, Mei Y.; Patel, Heer B.; Kengni, Gabriel; Neubert, Emma; Quiambao, Jeanelle Mae C.; Becker, Ghazal; Ghinger, Frances Grace; Thapa, Sreeyasha; Williams, A'Lyssa; Radov, Michelle H.; Boehlert, Kellie X.; Hollmann, Nele M.; Singh, Karndeep; Bruce, James W.; Marchant, Jan; Sherer, Nathan M.; Telesnitsky, Alice; Summers, Michael F.
• 署名单位: University System of Maryland; University of Maryland Baltimore County; University of Wisconsin System; University of Wisconsin Madison; University of Wisconsin System; University of Wisconsin Madison; University of Michigan System; University of Michigan; University System of Maryland; University of Maryland Baltimore County; Howard Hughes Medical Institute; University System of Maryland; University of Maryland Baltimore County
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-11598
• DOI: 10.1073/pnas.2407400121
• 发表日期: 2024-08-13
• 关键词: hairpin structure; general-method; nmr detection; region; dimerization; polyadenylation; sequence; prediction; subtypes; platform

摘要

HIV-1 transcript function is controlled in part by twinned transcriptional start site usage, where 5 ' capped RNAs beginning with a single guanosine (1G) are preferentially packaged into progeny virions as genomic RNA (gRNA) whereas those beginning with three sequential guanosines (3G) are retained in cells as mRNAs. In 3G transcripts, one of the additional guanosines base pairs with a cytosine located within a conserved 5 ' polyA element, resulting in formation of an extended 5 ' polyA structure as opposed to the hairpin structure formed in 1G RNAs. To understand how this remodeling influences overall transcript function, we applied in vitro biophysical studies with in-cell genome packaging and competitive translation assays to native and 5 ' polyA mutant transcripts generated with promoters that differentially produce 1G or 3G RNAs. We identified mutations that stabilize the 5 ' polyA hairpin structure in 3G RNAs, which promote RNA dimerization and Gag binding without sequestering the 5 ' cap. None of these 3G transcripts were competitively packaged, confirming that cap exposure is a dominant negative determinant of viral genome packaging. For all RNAs examined, conformations that favored 5 ' cap exposure were both poorly packaged and more efficiently translated than those that favored 5 ' cap sequestration. We propose that structural plasticity of 5 ' polyA and other conserved RNA elements place the 5 ' leader on a thermodynamic tipping point for low-energetic (similar to 3 kcal/mol) control of global transcript structure and function.