Abstract:
:VA RNA(I) is a non-coding adenoviral transcript that counteracts the host cell anti-viral defenses such as immune responses mediated via PKR. We investigated potential alternate secondary structure conformations within the PKR-binding domain of VA RNA(I) using site-directed mutagenesis, RNA UV-melting analysis and enzymatic RNA secondary structure probing. The latter data clearly indicated that the wild-type VA RNA(I) apical stem can adopt two different conformations and that it exists as a mixed population of these two structures. In contrast, in two sequence variants we designed to eliminate one of the possible structures, while leaving the other intact, each formed a unique secondary structure. This clarification of the apical stem pairing also suggests a small alteration to the apical stem-loop secondary structure. The relative ability of the two apical stem conformations to bind PKR and inhibit kinase activity was measured by isothermal titration calorimetry and PKR autophosphorylation inhibition assay. We found that the two sequence variants displayed markedly different activities, with one being a significantly poorer binder and inhibitor of PKR. Whether the presence of the VA RNA(I) conformation with reduced PKR inhibitory activity is directly beneficial to the virus in the cell for some other function requires further investigation.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Wahid AM,Coventry VK,Conn GLdoi
10.1093/nar/gkp595subject
Has Abstractpub_date
2009-09-01 00:00:00pages
5830-7issue
17eissn
0305-1048issn
1362-4962pii
gkp595journal_volume
37pub_type
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