Straightening of bulged RNA by the double-stranded RNA-binding domain from the protein kinase PKR

Zheng, Xiaofeng; Bevilacqua, Philip C.

doi:10.1073/pnas.011355798

Cited by 29 publications

(51 citation statements)

References 40 publications

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“…Straightening, diagrammed in this panel, is supported by independent studies (Zheng and Bevilacqua 2000). Weaker activation of PKR by this RNA as compared to perfect dsRNA, as observed in Figure 4, may be due in part to the thermodynamic penalty for binding to bent RNAs (Zheng and Bevilacqua 2000), although further biophysical studies are needed to confirm this. Panel C presents a model for PKR dimerization and activation by cis 2-chi RNAs, which is also quite similar to panel A involving PKR dimerization.…”

Section: Discussionsupporting

confidence: 55%

“…Panel C presents a model for PKR dimerization and activation by cis 2-chi RNAs, which is also quite similar to panel A involving PKR dimerization. The weakest activation by this RNA, as observed in Figure 4, can be understood by the double penalty of PKR having to bind to bent RNA and having to contend with an RNA-DNA hybrid, for which PKR has poor affinity (Bevilacqua and Cech 1996;Zheng and Bevilacqua 2000). PKR having to contend with this RNA-DNA hybrid region rejects through-space interaction of PKR monomers.…”

Section: Discussionmentioning

confidence: 99%

“…Activators of PKR include viral dsRNA replication intermediates from both DNA and RNA viruses, nonviral RNA aptamers, and a pseudoknot IFN-g mRNA promoter (Jacquemont and Roizman 1975;Katze et al 1987;Maran and Mathews 1988;Bevilacqua et al 1998;Zheng and Bevilacqua 2004;Garcia et al 2006). PKR interacts with these RNAs in a nonsequence specific fashion, and is regulated by RNAs containing helical defects, such as bulges, internal loops, stem-loops, multistem junctions, and even more complex tertiary interactions, such as pseudoknots and kissing hairpins (Zheng and Bevilacqua 2000;Ben-Asouli et al 2002;Cohen-Chalamish et al 2009;Heinicke et al 2009). Due to the diversity of these RNA structural defects, it has been difficult to predict whether a given RNA structure will activate PKR.…”

Section: Introductionmentioning

confidence: 99%

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

Heinicke

Nallagatla

Hull

et al. 2011

RNA

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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.

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Section: Discussionsupporting

confidence: 55%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Heinicke

Nallagatla

Hull

et al. 2011

RNA

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“…The crystal structure of a related complex between dsRNA and a dsRBM from a Xenopus RNA-binding protein indicated that the protein binds to one face of a largely undistorted dsRNA helix, with no wrapping around it (Ryter and Schultz 1998). In addition, experiments from our lab showed that the dsRBD binds to RNAs containing bulge defects by straightening of the helix (Zheng and Bevilacqua 2000). Thus, one possibility is that the dsRBD binds to a face of the aptamer without imperfections, extruding any defects away from the binding interface and thereby straightening the helix.…”

Section: Discussionmentioning

confidence: 88%

“…Experiments were similar to previously described (Bevilacqua and Cech 1996;Zheng and Bevilacqua 2000), using excess protein and trace amounts (nM) of radiolabeled RNA, p*RNA. Gel shifts were in the presence of 0.1 mg/mL tRNA competitor.…”

Section: Binding Assaysmentioning

confidence: 99%

Activation of the protein kinase PKR by short double-stranded RNAs with single-stranded tails

Zheng¹,

Bevilacqua²

2004

RNA

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102

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The human RNA-activated protein kinase PKR is an interferon-induced protein that is part of the innate immune response and inhibits viral replication. The action of PKR involves RNA-dependent autophosphorylation leading to inhibition of translation. PKR has an N-terminal dsRNA-binding domain that can interact non-sequence specifically with long (>33 bp) stretches of dsRNA leading to activation. In addition, certain viral and cellular RNAs containing non-Watson-Crick structures and multiple, shorter dsRNA sections can regulate PKR. In an effort to identify novel binders and possible activators of PKR, we carried out selections on a partially structured dsRNA library using truncated and full-length versions of PKR. A library with 10 11 sequences was constructed and aptamers that bound to His 6 -tagged proteins were isolated. Characterization revealed a novel minimal RNA motif for activation of PKR with the following unified structural characteristics: a hairpin with a nonconserved imperfect 16-bp dsRNA stem flanked by 10-15-nt single-stranded tails, herein termed a "ss-dsRNA motif." Boundary experiments revealed that the single-stranded tails flanking the dsRNA core provide the critical determinant for activation. The ss-dsRNA motif occurs in a variety of cellular and viral RNAs, suggesting possible novel functions for PKR in nature.

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RNA recognition by PKR during DNA virus infection

Zhang,

Karijolich

2024

Journal of Medical Virology

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Protein kinase R (PKR) is a double‐stranded RNA (dsRNA) binding protein that plays a crucial role in innate immunity during viral infection and can restrict both DNA and RNA viruses. The potency of its antiviral function is further reflected by the large number of viral‐encoded PKR antagonists. However, much about the regulation of dsRNA accumulation and PKR activation during viral infection remains unknown. Since DNA viruses do not have an RNA genome or RNA replication intermediates like RNA viruses do, PKR‐mediated dsRNA detection in the context of DNA virus infection is particularly intriguing. Here, we review the current state of knowledge regarding the regulation of PKR activation and its antagonism during infection with DNA viruses.

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Straightening of bulged RNA by the double-stranded RNA-binding domain from the protein kinase PKR

Cited by 29 publications

References 40 publications

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

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

Activation of the protein kinase PKR by short double-stranded RNAs with single-stranded tails

RNA recognition by PKR during DNA virus infection

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