INI1/SMARCB1 Rpt1 domain mimics TAR RNA in binding to integrase to facilitate HIV-1 replication

Updesh Dixit,P Rajesh Kumar,Seetharama A Acharya,Sheeba Mathew,Richard Harris,Mark E Girvin ,Steven C Almo,Xiaolin Wu ,Menachem Spira,David Cowburn,Lucas J Adams,Savita Bhutoria,Minh Anh Nguyen ,Sean M Cahill ,Alasdair C Steven,Xiaoqin Zou,Michael Brenowitz,Rajiv Pathak,Liming Qiu,Ganjam V Kalpana

doi:10.1038/s41467-021-22733-9

Abstract

INI1/SMARCB1 binds to HIV-1 integrase (IN) through its Rpt1 domain and exhibits multifaceted role in HIV-1 replication. Determining the NMR structure of INI1-Rpt1 and modeling its interaction with the IN-C-terminal domain (IN-CTD) reveal that INI1-Rpt1/IN-CTD interface residues overlap with those required for IN/RNA interaction. Mutational analyses validate our model and indicate that the same IN residues are involved in both INI1 and RNA binding. INI1-Rpt1 and TAR RNA compete with each other for IN binding with similar IC50 values. INI1-interaction-defective IN mutant viruses are impaired for incorporation of INI1 into virions and for particle morphogenesis. Computational modeling of IN-CTD/TAR complex indicates that the TAR interface phosphates overlap with negatively charged surface residues of INI1-Rpt1 in three-dimensional space, suggesting that INI1-Rpt1 domain structurally mimics TAR. This possible mimicry between INI1-Rpt1 and TAR explains the mechanism by which INI1/SMARCB1 influences HIV-1 late events and suggests additional strategies to inhibit HIV-1 replication.

Highlights

INI1/SMARCB1 binds to HIV-1 integrase (IN) through its Rpt[1] domain and exhibits multifaceted role in HIV-1 replication
Structural mimicry between INI1-Rpt[1] and TAR RNA explains the multifaceted role of INI1/SMARCB1 during HIV-1 replication in vivo and provides mechanistic insights into INI1–IN interactions
We found that INI1183-304 mutants D225G and T214A were highly defective and D227G mutant was least defective, for binding to IN and IN-C-terminal domain (IN-CTD), consistent with the prediction of the model (Fig. 3b)

Summary

Introduction

INI1/SMARCB1 binds to HIV-1 integrase (IN) through its Rpt[1] domain and exhibits multifaceted role in HIV-1 replication. Computational modeling of IN-CTD/TAR complex indicates that the TAR interface phosphates overlap with negatively charged surface residues of INI1-Rpt[1] in three-dimensional space, suggesting that INI1-Rpt[1] domain structurally mimics TAR This possible mimicry between INI1-Rpt[1] and TAR explains the mechanism by which INI1/SMARCB1 influences HIV-1 late events and suggests additional strategies to inhibit HIV1 replication. We provide the solution structure of the conserved Rpt1+ linker domain (INI1183-265) of INI1 (PDB ID: 6AX5) and molecular docking of the IN-CTD/INI1-Rpt[1] complex These studies indicate that the IN residues at the IN/INI1 interface are the same as those needed for the interaction of IN with the TAR region of the HIV-1 genome[18]. Structural mimicry between INI1-Rpt[1] and TAR RNA explains the multifaceted role of INI1/SMARCB1 during HIV-1 replication in vivo and provides mechanistic insights into INI1–IN interactions

Methods

Results

Conclusion