Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex.

Ursula Schulze-Gahmen,Dina Schneidman-Duhovny,Andrej Sali,Yun Bai,James H Hurley,Ignacia Echeverria,Qiang Zhou,Jennifer A Doudna,Huasong Lu,Goran Stjepanovic

doi:10.7554/elife.15910

Ursula Schulze-Gahmen, Dina Schneidman-Duhovny + Show 8 more

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https://doi.org/10.7554/elife.15910

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Abstract

HIV-1 Tat hijacks the human superelongation complex (SEC) to promote proviral transcription. Here we report the 5.9 Å structure of HIV-1 TAR in complex with HIV-1 Tat and human AFF4, CDK9, and CycT1. The TAR central loop contacts the CycT1 Tat-TAR recognition motif (TRM) and the second Tat Zn2+-binding loop. Hydrogen-deuterium exchange (HDX) shows that AFF4 helix 2 is stabilized in the TAR complex despite not touching the RNA, explaining how it enhances TAR binding to the SEC 50-fold. RNA SHAPE and SAXS data were used to help model the extended (Tat Arginine-Rich Motif) ARM, which enters the TAR major groove between the bulge and the central loop. The structure and functional assays collectively support an integrative structure and a bipartite binding model, wherein the TAR central loop engages the CycT1 TRM and compact core of Tat, while the TAR major groove interacts with the extended Tat ARM.

Highlights

The human immunodeficiency virus-1 (HIV-1) remains one of the world’s leading health threats
The observed peptic peptides of the apo complex covered more than 80% of the trans-activator protein (Tat):AFF4:positive elongation factor b (P-TEFb) sequence (Figure 1—figure supplement 1–3)
Our Hydrogen-deuterium exchange (HDX) data of the apo complex in solution are in good agreement with the crystal structure of Tat:AFF4:P-TEFb (Schulze-Gahmen et al, 2014; Gu et al, 2014) (Figure 1A)

Summary

Introduction

The human immunodeficiency virus-1 (HIV-1) remains one of the world’s leading health threats. In spite of advances in treatment with antiretrovirals (HAART) (Yeni 2006), it has not been possible to eradicate HIV-1 infection. The pool of latent virus is the primary obstacle to eradicating HIV, and the mechanisms by which latency is regulated are of paramount interest. The molecular mechanisms regulating HIV-1 transcription have been studied for three decades, yet renewed interest in eradicating HIV-1 infection has lent new urgency to obtaining a more complete understanding. Proviral transcription is silenced by host epigenetic mechanisms and/or deficiency in key cofactors, and is reactivated at the level of both initiation and elongation (Mbonye and Karn 2014; Zhou et al, 2012; Jonkers and Lis 2015).

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