Emergence of compensatory mutations reveals the importance of electrostatic interactions between HIV-1 integrase and genomic RNA

Shema Mugisha, C., Dinh, T., Kumar, A., Tenneti, K., Eschbach, J. E., Davis, K., Gifford, R. , Kvaratskhelia, M. and Kutluay, S. B. (2022) Emergence of compensatory mutations reveals the importance of electrostatic interactions between HIV-1 integrase and genomic RNA. mBio, 13(5), e0043122. (doi: 10.1128/mbio.00431-22) (PMID:35975921) (PMCID:PMC9601147)

Abstract

HIV-1 integrase (IN) has a noncatalytic function in virion maturation through its binding to the viral RNA genome (gRNA). Class II IN substitutions inhibit IN-gRNA binding and result in the formation of virions with aberrant morphologies marked by mislocalization of the gRNA between the capsid lattice and the lipid envelope. These viruses are noninfectious due to a block at an early reverse transcription stage in target cells. HIV-1 IN utilizes basic residues within its C-terminal domain (CTD) to bind to the gRNA; however, the molecular nature of how these residues mediate gRNA binding and whether other regions of IN are involved remain unknown. To address this, we have isolated compensatory substitutions in the background of a class II IN mutant virus bearing R269A/K273A substitutions within the IN-CTD. We found that the nearby D256N and D270N compensatory substitutions restored the ability of IN to bind gRNA and led to the formation of mature infectious virions. Reinstating the local positive charge of the IN-CTD through individual D256R, D256K, D278R, and D279R substitutions was sufficient to specifically restore IN-gRNA binding and reverse transcription for the IN R269A/K273A as well as the IN R262A/R263A class II mutants. Structural modeling suggested that compensatory substitutions in the D256 residue created an additional interaction interface for gRNA binding, whereas other substitutions acted locally within the unstructured C-terminal tail of IN. Taken together, our findings highlight the essential role of CTD in gRNA binding and reveal the importance of pliable electrostatic interactions between the IN-CTD and the gRNA.

• Item Type: Articles
• Additional Information: This work was supported by NIH grants AI150497 (S.B.K.), AI1508470 (U54 Center for HIV RNA Studies, S.B.K., R.G.), and R01 AI143649 (M.K.), and by a Milton Schlesinger Student Fellowship (C.S.M.).
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Gifford, Dr Robert
• Authors: Shema Mugisha, C., Dinh, T., Kumar, A., Tenneti, K., Eschbach, J. E., Davis, K., Gifford, R., Kvaratskhelia, M., and Kutluay, S. B.
• College/School: College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research
• Journal Name: mBio
• Publisher: American Society for Microbiology
• ISSN: 2150-7511
• ISSN (Online): 2150-7511
• Published Online: 17 August 2022
• Copyright Holders: Copyright © 2022 Shema Mugisha et al.
• First Published: First published in mBio 13(5): e0043122
• Publisher Policy: Reproduced under a Creative Commons License