HIV-1 Tat interactions with cellular 7SK and viral TAR RNAs identifies dual structural mimicry

Vincent V Pham,Hugues De Rocquigny,W Clay Brown,Janet L Smith,Shamsun Nahar Khan,Victoria M D’Souza,Jennifer L Meagher,Carolina Salguero,Nicolas Humbert

doi:10.1038/s41467-018-06591-6

Abstract

The HIV Tat protein competes with the 7SK:HEXIM interaction to hijack pTEFb from 7SK snRNP and recruit it to the TAR motif on stalled viral transcripts. Here we solve structures of 7SK stemloop-1 and TAR in complex with Tat’s RNA binding domain (RBD) to gain insights into this process. We find that 7SK is peppered with arginine sandwich motifs (ASM)—three classical and one with a pseudo configuration. Despite having similar RBDs, the presence of an additional arginine, R52, confers Tat the ability to remodel the pseudo configuration, required for HEXIM binding, into a classical sandwich, thus displacing HEXIM. Tat also uses R52 to remodel the TAR bulge into an ASM whose structure is identical to that of the remodeled ASM in 7SK. Together, our structures reveal a dual structural mimicry wherein viral Tat and TAR have co-opted structural motifs present in cellular HEXIM and 7SK for productive transcription of its genome.

Highlights

The HIV Tat protein competes with the 7SK:HEXIM interaction to hijack pTEFb from 7SK snRNP and recruit it to the TAR motif on stalled viral transcripts
arginine sandwich motifs (ASM) previously thought to be exclusive to retroviral TAR RNA (HIV-1, HIV-2, and bovine immunodeficiency virus (BIV))[22,29,37]
The structure of the Tat RNA binding domain (RBD):7SK-SL1apical complex shows that the Tat RBD is able to snake through an entire helical turn of the major groove due to the multiple points of arginine intercalations that allow for numerous stacking and hydrogen-bonding interactions

Summary

Introduction

The HIV Tat protein competes with the 7SK:HEXIM interaction to hijack pTEFb from 7SK snRNP and recruit it to the TAR motif on stalled viral transcripts. HIV has evolved the viral Tat protein, whose RBD directly interacts with the 7SK snRNA to displace HEXIM and capture pTEFb13,14. Tat transfers pTEFb as part of a larger super elongation complex to the viral genome[15,16,17] This handover occurs via the interaction of Tat with the stem loop structure, TAR, which forms at the 5’ end of stalled nascent HIV transcripts. While there are no structures detailing how Tat RBD binds TAR, on the basis of biophysical studies, it is clear that the hallmark of this interaction is the formation of an arginine sandwich motif (ASM) when an arginine in Tat’s RBD intercalates into the bulge region of TAR20–25. We provide mechanistic details of how Tat is able to first compete with HEXIM to engage 7SK for pTEFb extraction and subsequently bind TAR to transfer pTEFb

Methods

Results

Conclusion