RNA conformational propensities determine cellular activity

• Published in: Nature (London) Vol. 617; no. 7962; pp. 835 - 841
• Main Authors: Ken, Megan L., Roy, Rohit, Geng, Ainan, Ganser, Laura R., Manghrani, Akanksha, Cullen, Bryan R., Schulze-Gahmen, Ursula, Herschlag, Daniel, Al-Hashimi, Hashim M.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 25.05.2023; Nature Publishing Group
• Subjects: 13/106; 13/109; 14/35; 140/131; 631/45/500; 631/45/535/878/1263; 631/57/2272/951; 82/29; 82/6; 96/33; Affinity; Binding; Biological activity; Biomolecules; Genomes; HIV; HIV Long Terminal Repeat - genetics; HIV-1 - genetics; HIV-1 - metabolism; Human immunodeficiency virus; Humanities and Social Sciences; multidisciplinary; Nucleic Acid Conformation; Nucleic acids; Peptides; Protein structure; Proteins; Ribonucleic acid; RNA; RNA, Viral - chemistry; RNA, Viral - genetics; RNA, Viral - metabolism; Science; Science (multidisciplinary); tat Gene Products, Human Immunodeficiency Virus - chemistry; tat Gene Products, Human Immunodeficiency Virus - metabolism; Tat protein; Transcriptional Activation
• ISSN: 0028-0836; 1476-4687; 1476-4687
• DOI: 10.1038/s41586-023-06080-x

Cellular processes are the product of interactions between biomolecules, which associate to form biologically active complexes 1 . These interactions are mediated by intermolecular contacts, which if disrupted, lead to alterations in cell physiology. Nevertheless, the formation of intermolecular contacts nearly universally requires changes in the conformations of the interacting biomolecules. As a result, binding affinity and cellular activity crucially depend both on the strength of the contacts and on the inherent propensities to form binding-competent conformational states 2 , 3 . Thus, conformational penalties are ubiquitous in biology and must be known in order to quantitatively model binding energetics for protein and nucleic acid interactions 4 , 5 . However, conceptual and technological limitations have hindered our ability to dissect and quantitatively measure how conformational propensities affect cellular activity. Here we systematically altered and determined the propensities for forming the protein-bound conformation of HIV-1 TAR RNA. These propensities quantitatively predicted the binding affinities of TAR to the RNA-binding region of the Tat protein and predicted the extent of HIV-1 Tat-dependent transactivation in cells. Our results establish the role of ensemble-based conformational propensities in cellular activity and reveal an example of a cellular process driven by an exceptionally rare and short-lived RNA conformational state. Systematic alteration of HIV-1 TAR RNA and quantitative determination of its propensity to bind to the Tat protein establish a key role role for a rare and short-lived RNA state in Tat-dependent transactivation in cells.