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Rapid evolution of protein kinase PKR alters sensitivity to viral inhibitors

Nature Structural & Molecular Biology volume 16, pages 63–70 (2009)Cite this article

Abstract

Protein kinase PKR (also known as EIF2AK2) is activated during viral infection and phosphorylates the α subunit of eukaryotic translation initiation factor 2 (eIF2), leading to inhibition of translation and viral replication. We report fast evolution of the PKR kinase domain in vertebrates, coupled with positive selection of specific sites. Substitution of positively selected residues in human PKR with residues found in related species altered sensitivity to PKR inhibitors from different poxviruses. Species-specific differences in sensitivity to poxviral pseudosubstrate inhibitors were identified between human and mouse PKR, and these differences were traced to positively selected residues near the eIF2α binding site. Our findings indicate how an antiviral protein evolved to evade viral inhibition while maintaining its primary function. Moreover, the identified species-specific differences in the susceptibility to viral inhibitors have important implications for studying human infections in nonhuman model systems.

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Figure 1: Accelerated evolution of PKR.
Figure 2: Positively selected sites in the PKR kinase domain.
Figure 3: Altered sensitivity of PKR mutants to poxvirus proteins K3L and E3L.
Figure 4: Positively selected residues (PSRs) in PKR that alter sensitivity to poxvirus inhibitors.
Figure 5: Effects of PKR variants on sensitivity to pseudosubstrate inhibition in HeLa cells.

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Acknowledgements

We are grateful to A. Hinnebusch, M. Yu and L. Tazi for helpful discussion and for careful reading of the manuscript; F. Sicheri, M. Dey, D. McClellan, A. Furano and C. Tellgren-Roth for helpful discussion; C. Samuel (University of California, Santa Barbara) for providing the PKR knockdown cells; and M. Kawagishi-Kobayashi and M. Dey (US National Institute of Child Health and Human Development (NICHD)) for yeast strains. This work was supported by funding from the Intramural Research Program of the US National Institutes of Health, NICHD, to T.E.D.

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Authors and Affiliations

  1. Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, 20892, Maryland, USA

    Stefan Rothenburg, Eun Joo Seo & Thomas E Dever

  2. Laboratory of Viral Diseases, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.,

    James S Gibbs

  3. Department of Biological Sciences, State University of New York at Buffalo, Buffalo, 14260, New York, USA

    Katharina Dittmar

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Correspondence to Stefan Rothenburg.

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Rothenburg, S., Seo, E., Gibbs, J. et al. Rapid evolution of protein kinase PKR alters sensitivity to viral inhibitors. Nat Struct Mol Biol 16, 63–70 (2009). https://doi.org/10.1038/nsmb.1529

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