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TitleSelective 8-oxo-rG stalling occurs in the catalytic core of polynucleotide phosphorylase (PNPase) during degradation.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 121, Issue 46, Page e2317865121, Year 2024
Publish dateNov 12, 2024
AuthorsLucas G Miller / Wantae Kim / Shawn Schowe / Kathleen Taylor / Runhua Han / Vashita Jain / Raeyeon Park / Mark Sherman / Janssen Fang / Haydee Ramirez / Andrew Ellington / Phanourios Tamamis / Marino J E Resendiz / Y Jessie Zhang / Lydia Contreras /
PubMed AbstractRNA oxidation, predominantly through the accumulation of 8-oxo-7,8-dihydroguanosine (8-oxo-rG), represents an important biomarker for cellular oxidative stress. Polynucleotide phosphorylase (PNPase) ...RNA oxidation, predominantly through the accumulation of 8-oxo-7,8-dihydroguanosine (8-oxo-rG), represents an important biomarker for cellular oxidative stress. Polynucleotide phosphorylase (PNPase) is a 3'-5' exoribonuclease that has been shown to preferentially recognize 8-oxo-rG-containing RNA and protect cells from oxidative stress. However, the impact of 8-oxo-rG on PNPase-mediated RNA degradation has not been studied. Here, we show that the presence of 8-oxo-rG in RNA leads to catalytic stalling of PNPase through in vitro RNA degradation experiments and electrophoretic analysis. We also link this stalling to the active site of the enzyme through resolution of single-particle cryo-EM structures for PNPase in complex with singly or doubly oxidized RNA oligonucleotides. Following identification of Arg399 as a key residue in recognition of both single and sequential 8-oxo-rG nucleotides, we perform follow-up in vitro analysis to confirm the importance of this residue in 8-oxo-rG-specific PNPase stalling. Finally, we investigate the effects of mutations to active site residues implicated in 8-oxo-rG binding through cell growth experiments under HO-induced oxidative stress. Specifically, Arg399 mutations show significant effects on cell growth under oxidative stress. Overall, we demonstrate that 8-oxo-rG-specific stalling of PNPase is relevant to bacterial survival under oxidative stress and speculate that this enzyme might associate with other cellular factors to mediate this stress.
External linksProc Natl Acad Sci U S A / PubMed:39495922 / PubMed Central
MethodsEM (single particle)
Resolution3.15 - 3.3 Å
Structure data

43092

8vah

EMDB-43092, PDB-8vah:
E.coli PNPase in complex with single 8-oxoG RNA
Method: EM (single particle) / Resolution: 3.15 Å

43093

8vak

EMDB-43093, PDB-8vak:
E.coli PNPase in complex with double 8-oxoG RNA
Method: EM (single particle) / Resolution: 3.3 Å

Chemicals

ChemComp-MG:
Unknown entry

Source
  • escherichia coli (E. coli)
KeywordsRNA BINDING PROTEIN / PNPase / oxidized RNA / Phosphorolysis / 8-oxo G

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