An RNA degradation machine sculpted by Ro autoantigen and noncoding RNA

Area of Science:

• Bacteriology
• Molecular Biology
• RNA Biology

Background:

• Many bacteria possess a Ro autoantigen ortholog that binds Y RNAs.
• In Deinococcus radiodurans, the Ro ortholog Rsr is involved in rRNA processing and decay.
• The precise mechanism of Rsr and Y RNA function remained unclear.

Purpose of the Study:

• To elucidate the mechanism of Ro ortholog Rsr and Y RNA in bacterial RNA processing.
• To characterize the ribonucleoprotein complex formed by Rsr, Y RNA, and PNPase.
• To investigate the role of ncRNA in altering enzyme substrate specificity.

Main Methods:

• Single-particle electron microscopy to determine complex structure.
• Atomic model docking into electron microscopy reconstructions.
• Biochemical assays to assess RNA degradation activity.

Main Results:

• Rsr and polynucleotide phosphorylase (PNPase) form an RNA degradation machine scaffolded by Y RNA.
• Rsr facilitates the channeling of single-stranded RNA into the PNPase active site.
• Rsr and Y RNA enable PNPase to degrade structured RNAs effectively.
• A similar complex involving a Ro ortholog, ncRNA, and PNPase was observed in Salmonella Typhimurium.

Conclusions:

• Identified a novel bacterial ribonucleoprotein machine for RNA degradation.
• Demonstrated that ncRNA can modify enzyme substrate specificity by tethering protein cofactors.
• Revealed a conserved mechanism for RNA processing and degradation across bacterial species.