PKR Senses Nuclear and Mitochondrial Signals by Interacting with Endogenous Double-Stranded RNAs

Area of Science:

• Cellular Biology
• Molecular Biology
• Immunology

Background:

• Protein kinase RNA-activated (PKR) is known to induce immune responses by sensing viral double-stranded RNAs (dsRNAs).
• Emerging evidence indicates that PKR can also be activated by endogenously expressed dsRNAs, suggesting roles beyond antiviral immunity.

Purpose of the Study:

• To investigate the endogenous RNA molecules that interact with and activate PKR.
• To elucidate the role of mitochondrial RNAs (mtRNAs) in PKR activation and cellular signaling.
• To understand the regulatory mechanisms controlling PKR activity in the absence of viral infection.

Main Methods:

• Formaldehyde-mediated crosslinking and immunoprecipitation sequencing (CLIP-seq) to identify PKR-interacting RNAs.
• Analysis of RNA secondary structures and origins, particularly focusing on mitochondrial transcripts.
• Investigation of PKR and eIF2α phosphorylation in response to mtRNAs and PKR phosphatase activity.

Main Results:

• Various noncoding RNAs were found to interact with PKR.
• Mitochondrial RNAs (mtRNAs) constitute the majority of the PKR-interacting RNA repertoire.
• Bidirectionally transcribed mtRNAs form intermolecular dsRNAs that activate PKR and eIF2α phosphorylation, impacting cell signaling and translation.
• PKR phosphatases counteract mtRNA-induced PKR activation; their disruption leads to apoptosis even in uninfected cells.

Conclusions:

• PKR is dynamically regulated in the absence of viral infection.
• Mitochondrial RNAs serve as endogenous activators of PKR, linking mitochondrial status to cellular signaling.
• PKR acts as a sensor for both nuclear and mitochondrial signaling cues, regulating cellular metabolism and potentially contributing to disease pathogenesis.