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TitleA multi-dentate, cooperative interaction between endo- and exo-ribonucleases within the bacterial RNA degradosome.
Journal, issue, pagesNucleic Acids Res, Vol. 53, Issue 18, Year 2025
Publish dateSep 23, 2025
AuthorsGiulia Paris / Kai Katsuya-Gaviria / Hannah Clarke / Margaret Johncock / Tom Dendooven / Aleksei Lulla / Ben F Luisi /
PubMed AbstractIn Escherichia coli and numerous other bacteria, two of the principal enzymes mediating messenger RNA decay and RNA processing-RNase E, an endoribonuclease, and polynucleotide phosphorylase (PNPase), ...In Escherichia coli and numerous other bacteria, two of the principal enzymes mediating messenger RNA decay and RNA processing-RNase E, an endoribonuclease, and polynucleotide phosphorylase (PNPase), an exoribonuclease-assemble into a multi-enzyme complex known as the RNA degradosome. While RNase E forms a homotetramer and PNPase a homotrimer, it remains unclear how these two enzymes interact within the RNA degradosome to potentially satisfy all mutual recognition sites. In this study, we used cryo-EM, biochemistry, and biophysical studies to discover and characterize a new binding mode for PNPase encompassing two or more motifs that are necessary and sufficient for strong interaction with RNase E. While a similar interaction is seen in Salmonella enterica, a different recognition mode arose for Pseudomonas aeruginosa, illustrating the evolutionary drive to maintain physical association of the two ribonucleases. The data presented here suggest a model for the quaternary organization of the RNA degradosome of E. coli, where one PNPase trimer interacts with one RNase E protomer. Conformational transitions are predicted to facilitate substrate capture and transfer to catalytic centres. The model suggests how the endo- and exo-ribonucleases might cooperate in cellular RNA turnover and recruitment of regulatory RNA by the degradosome assembly.
External linksNucleic Acids Res / PubMed:41036625 / PubMed Central
MethodsEM (single particle)
Resolution2.4 - 2.52 Å
Structure data

53151

9qh0

EMDB-53151, PDB-9qh0:
Escherichia coli polynucleotide phosphorylase in complex with recognition site of RNase E
Method: EM (single particle) / Resolution: 2.52 Å

53153

9qh3

EMDB-53153, PDB-9qh3:
Pseudomonas aeruginosa polynucleotide phosphorylase in complex with recognition site of RNase E
Method: EM (single particle) / Resolution: 2.4 Å

Chemicals

ChemComp-HOH:
WATER

ChemComp-A:
ADENOSINE-5'-MONOPHOSPHATE

Source
  • escherichia coli (E. coli)
  • Pseudomonas aeruginosa (bacteria)
  • pseudomonas aeruginosa pao1 (bacteria)
KeywordsRNA BINDING PROTEIN / polynucleotide phosphorylase / ribonuclease E / RNA degradosome

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