• Call for Physical Sciences Papers
  • Sign-up for PNAS eTOC Alerts

Small-angle X-ray scattering-derived structure of the HIV-1 5′ UTR reveals 3D tRNA mimicry

  1. Karin Musier-Forsyth2
  1. Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210

  1. Edited* by Paul Schimmel, The Skaggs Institute for Chemical Biology, La Jolla, CA, and approved January 23, 2014 (received for review October 21, 2013)

Significance

A highly conserved region of the HIV-1 RNA genome is responsible for regulating numerous steps of the retroviral life cycle, including initiation of reverse transcription. A complete understanding of the mechanisms controlling HIV-1 replication requires structural characterization of this RNA; unfortunately, however, its large size and conformational flexibility makes common methods of solving structures, such as X-ray crystallography and NMR, exceedingly difficult. The present study uses a solution technique, small-angle X-ray scattering coupled with computational molecular modeling, to characterize three ∼100-nucleotide RNAs that play central roles in HIV-1 replication. One of these domains mimics the L-shaped fold of tRNA, providing a structural basis for understanding how this genomic RNA coordinates interactions with a tRNA-binding host factor to facilitate initiation of reverse transcription.

Abstract

The most conserved region of the HIV type 1 (HIV-1) genome, the ∼335-nt 5′ UTR, is characterized by functional stem loop domains responsible for regulating the viral life cycle. Despite the indispensable nature of this region of the genome in HIV-1 replication, 3D structures of multihairpin domains of the 5′ UTR remain unknown. Using small-angle X-ray scattering and molecular dynamics simulations, we generated structural models of the transactivation (TAR)/polyadenylation (polyA), primer-binding site (PBS), and Psi-packaging domains. TAR and polyA form extended, coaxially stacked hairpins, consistent with their high stability and contribution to the pausing of reverse transcription. The Psi domain is extended, with each stem loop exposed for interactions with binding partners. The PBS domain adopts a bent conformation resembling the shape of a tRNA in apo and primer-annealed states. These results provide a structural basis for understanding several key molecular mechanisms underlying HIV-1 replication.

Footnotes

  • ↵1C.P.J. and W.A.C. contributed equally to this work.

  • ↵2To whom correspondence should be addressed. E-mail: musier{at}chemistry.ohio-state.edu.

  • Author contributions: C.P.J. and K.M.-F. designed research; C.P.J., W.A.C., and E.D.O. performed research; C.P.J., W.A.C., and E.D.O. analyzed data; and C.P.J., W.A.C., E.D.O., and K.M.-F. wrote the paper.

  • The authors declare no conflict of interest.

  • ↵*This Direct Submission article had a prearranged editor.

  • This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1319658111/-/DCSupplemental.

Online Impact