Nucleoside modifications modulate activation of the protein kinase PKR in an RNA structure-specific manner

Nallagatla, Subba Rao; Bevilacqua, Philip C.

doi:10.1261/rna.1007408

Cited by 123 publications

(135 citation statements)

References 44 publications

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“…Upon RNA binding, the kinase PKR inhibits translation by phosphorylating the translation initiation factor eIF-2α. In vitro experiments have shown that PKR activation is abrogated if m 6 A or ψ is present in the RNA (1,82). m 6 A has no effect and ψ has only a moderate effect on RNA-binding affinity to PKR, suggesting that reduced activation of PKR by these modified RNAs may be due primarily to effects at the level of RNA secondary structure.…”

Section: Stability and Degradationmentioning

confidence: 99%

Genome-Wide Analysis of RNA Secondary Structure

Bevilacqua¹,

Ritchey²,

et al. 2016

Annu. Rev. Genet.

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194

157

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Single-stranded RNA molecules fold into extraordinarily complicated secondary and tertiary structures as a result of intramolecular base pairing. In vivo, these RNA structures are not static. Instead, they are remodeled in response to changes in the prevailing physicochemical environment of the cell and as a result of intermolecular base pairing and interactions with RNAbinding proteins. Remarkable technical advances now allow us to probe RNA secondary structure at single-nucleotide resolution and genome-wide, both in vitro and in vivo. These data sets provide new glimpses into the RNA universe. Analyses of RNA structuromes in HIV, yeast, Arabidopsis, and mammalian cells and tissues have revealed regulatory effects of RNA structure on messenger RNA (mRNA) polyadenylation, splicing, translation, and turnover. Application of new methods for genome-wide identification of mRNA modifications, particularly methylation and pseudouridylation, has shown that the RNA "epitranscriptome" both influences and is influenced by RNA structure. In this review, we describe newly developed genome-wide RNA structure-probing methods and synthesize the information emerging from their application.

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Section: Stability and Degradationmentioning

confidence: 99%

Genome-Wide Analysis of RNA Secondary Structure

Bevilacqua¹,

Ritchey²,

et al. 2016

Annu. Rev. Genet.

Self Cite

194

157

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“…[24][25][26][27][28] or activation of RNA-dependent protein kinase (PKR; refs. [29][30][31][32][33]. Alternatively, aptamer binding may modify some signaling pathways in MDSCs affecting their survival.…”

Section: Il4ra Mediates a Prosurvival Signaling In Mdscsmentioning

confidence: 99%

Aptamer-Mediated Blockade of IL4Rα Triggers Apoptosis of MDSCs and Limits Tumor Progression

et al. 2012

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In addition to promoting tumor progression and metastasis by enhancing angiogenesis and invasion, myeloidderived suppressor cells (MDSC) and tumor-associated macrophage (TAM) also inhibit antitumor T-cell functions and limit the efficacy of immunotherapeutic interventions. Despite the importance of these leukocyte populations, a simple method for their specific depletion has not been developed. In this study, we generated an RNA aptamer that blocks the murine or human IL-4 receptor-a (IL4Ra or CD124) that is critical for MDSC suppression function. In tumor-bearing mice, this anti-IL4Ra aptamer preferentially targeted MDSCs and TAM and unexpectedly promoted their elimination, an effect that was associated with an increased number of tumorinfiltrating T cells and a reduction in tumor growth. Mechanistic investigations of aptamer-triggered apoptosis in MDSCs confirmed the importance of IL4Ra-STAT6 pathway activation in MDSC survival. Our findings define a straightforward strategy to deplete MDSCs and TAMs in vivo, and they strengthen the concept that IL4Ra signaling is pivotal for MDSC survival. More broadly, these findings suggest therapeutic strategies based on IL4Ra signaling blockades to arrest an important cellular mechanism of tumoral immune escape mediated by MDSCs and TAM in cancer. Cancer Res; 72(6); 1373-83. Ó2012 AACR.

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“…In addition to a minimum length requirement (∼16 bp), specific structural (bulges, loops, etc.) and nucleotide modifications (i.e., 5 ′ -phosphorylation state) have been observed to be accommodated by PKR and, in some cases, significantly affect both the affinity for and activation of PKR (Bevilacqua and Cech 1996;Kim et al 2006;McKenna et al 2006;Puthenveetil et al 2006;Nallagatla et al 2007;Nallagatla and Bevilacqua 2008). As there is scant structural information about imperfectly duplexed RNA in complex with PKR, a detailed understanding of how PKR accommodates these deviations remains an unanswered question.…”

Section: Introductionmentioning

confidence: 99%

Recognition of viral RNA stem–loops by the tandem double-stranded RNA binding domains of PKR

Dzananovic

Patel

Deo

et al. 2013

RNA

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In humans, the double-stranded RNA (dsRNA)-activated protein kinase (PKR) is expressed in late stages of the innate immune response to viral infection by the interferon pathway. PKR consists of tandem dsRNA binding motifs (dsRBMs) connected via a flexible linker to a Ser/Thr kinase domain. Upon interaction with viral dsRNA, PKR is converted into a catalytically active enzyme capable of phosphorylating a number of target proteins that often results in host cell translational repression. A number of high-resolution structural studies involving individual dsRBMs from proteins other than PKR have highlighted the key features required for interaction with perfectly duplexed RNA substrates. However, viral dsRNA molecules are highly structured and often contain deviations from perfect A-form RNA helices. By use of small-angle X-ray scattering (SAXS), we present solution conformations of the tandem dsRBMs of PKR in complex with two imperfectly base-paired viral dsRNA stemloops; HIV-1 TAR and adenovirus VA I -AS. Both individual components and complexes were purified by size exclusion chromatography and characterized by dynamic light scattering at multiple concentrations to ensure monodispersity. SAXS ab initio solution conformations of the individual components and RNA-protein complexes were determined and highlight the potential of PKR to interact with both stem and loop regions of the RNA. Excellent agreement between experimental and model-based hydrodynamic parameter determination heightens our confidence in the obtained models. Taken together, these data support and provide a framework for the existing biochemical data regarding the tolerance of imperfectly base-paired viral dsRNA by PKR.

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Nucleoside modifications modulate activation of the protein kinase PKR in an RNA structure-specific manner

Cited by 123 publications

References 44 publications

Genome-Wide Analysis of RNA Secondary Structure

Genome-Wide Analysis of RNA Secondary Structure

Aptamer-Mediated Blockade of IL4Rα Triggers Apoptosis of MDSCs and Limits Tumor Progression

Recognition of viral RNA stem–loops by the tandem double-stranded RNA binding domains of PKR

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