RNA helical imperfections regulate activation of the protein kinase PKR: Effects of bulge position, size, and geometry

Laurie A. Heinicke, Subba Rao Nallagatla, Chelsea M. Hull, Philip C. Bevilacqua

Research output: Contribution to journalArticle

16 Scopus citations

Abstract

The protein kinase, PKR, is activated by long stretches of double-stranded (ds) RNA. Viruses often make long dsRNA elements with imperfections that still activate PKR. However, due to the complexity of the RNA structure, prediction of whether a given RNA is an activator of PKR is difficult. Herein, we systematically investigated how various RNA secondary structure defects contained within model dsRNA affect PKR activation. We find that bulges increasingly disfavor activation as they are moved toward the center of a duplex and as they are increased in size. Model RNAs designed to conform to cis, trans, or bent global geometries through strategic positioning of one or more bulges decreased activation of PKR relative to perfect dsRNA, although cis-bulged RNAs activated PKR much more potently than trans-bulged RNAs. Activation studies on bulge-containing chimeric duplexes support a model wherein PKR monomers interact adjacently, rather than through-space, for activation on bulged substrates. Last, unusually low ionic strength induced substantial increases in PKR activation in the presence of bulged RNAs suggesting that discrimination against bulges is higher under biological ionic strength conditions. Overall, this study provides a set of rules for understanding how secondary structural defects affect PKR activity.

Original languageEnglish (US)
Pages (from-to)957-966
Number of pages10
JournalRNA
Volume17
Issue number5
DOIs
StatePublished - May 1 2011

All Science Journal Classification (ASJC) codes

  • Molecular Biology

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