A novel combined RNA-protein interaction analysis distinguishes HIV-1 Gag protein binding sites from structural change in the viral RNA leader.

Sci Rep 2015 Oct 9;5:14369. Epub 2015 Oct 9.

Box 157, Cambridge University Dept. of Medicine, Addenbrooke's Hospital, Hills Rd, Cambridge CB2 0QQ.

RNA-protein interactions govern many viral and host cell processes. Conventional 'footprinting' to examine RNA-protein complex formation often cannot distinguish between sites of RNA-protein interaction and sites of RNA structural remodelling. We have developed a novel technique combining photo crosslinking with RNA 2' hydroxyl reactivity ('SHAPE') that achieves rapid and hitherto unachievable resolution of both RNA structural changes and the sites of protein interaction within an RNA-protein complex. 'XL-SHAPE' was validated using well-characterized viral RNA-protein interactions: HIV-1 Tat/TAR and bacteriophage MS2 RNA/Coat Binding Protein. It was then used to map HIV-1 Gag protein interactions on 2D and 3D models of the viral RNA leader. Distinct Gag binding sites were identified on exposed RNA surfaces corresponding to regions identified by mutagenesis as important for genome packaging. This widely applicable technique has revealed a first view of the stoichiometry and structure of the initial complex formed when HIV captures its genome.

Download full-text PDF

Source
http://dx.doi.org/10.1038/srep14369DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4598872PMC
October 2015
17 Reads

Publication Analysis

Top Keywords

rna structural
8
rna-protein complex
8
binding sites
8
gag protein
8
hiv-1 gag
8
rna-protein interaction
8
rna-protein interactions
8
rna leader
8
viral rna
8
rna-protein
6
rna
6
sites
5
technique combining
4
resolution rna
4
unachievable resolution
4
combining photo
4
technique revealed
4
structural changes
4
revealed view
4
interaction rna-protein
4

References

(Supplied by CrossRef)

JD Stephenson et al.
Structure 2013

A Peselis et al.
Biochim Biophys Acta 2014

BM Wohrl et al.
J Biol Chem 1993

M Costa et al.
Methods Mol Biol 2014

J Kenyon et al.
Biochem Soc Trans 2014

M Kuzembayeva et al.
Virology 2014

OA Nikolaitchik et al.
PLoS Pathog 2013

AM Lever et al.
Adv Pharmacol 2007

V D’Souza et al.
Nat Rev Microbiol 2005

N Jouvenet et al.
Nature 2008

Similar Publications