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TitleBacterial Rps3 counters oxidative and UV stress by recognizing and processing AP-sites on mRNA via a novel mechanism.
Journal, issue, pagesNucleic Acids Res, Vol. 52, Issue 22, Page 13996-14012, Year 2024
Publish dateDec 11, 2024
AuthorsMohammad Afsar / Ankita Shukla / Faiz Ali / Rahul Kumar Maurya / Suman Bharti / Nelam Kumar / Mohammad Sadik / Surabhi Chandra / Huma Rahil / Sanjay Kumar / Imran Ansari / Farheen Jahan / Saman Habib / Tanweer Hussain / Manju Yasoda Krishnan / Ravishankar Ramachandran /
PubMed AbstractLesions and stable secondary structures in mRNA severely impact the translation efficiency, causing ribosome stalling and collisions. Prokaryotic ribosomal proteins Rps3, Rps4 and Rps5, located in ...Lesions and stable secondary structures in mRNA severely impact the translation efficiency, causing ribosome stalling and collisions. Prokaryotic ribosomal proteins Rps3, Rps4 and Rps5, located in the mRNA entry tunnel, form the mRNA helicase center and unwind stable mRNA secondary structures during translation. However, the mechanism underlying the detection of lesions on translating mRNA is unclear. We used Cryo-EM, biochemical assays, and knockdown experiments to investigate the apurinic/apyrimidinic (AP) endoribonuclease activity of bacterial ribosomes on AP-site containing mRNA. Our biochemical assays show that Rps3, specifically the 130RR131 motif, is important for recognizing and performing the AP-endoribonuclease activity. Furthermore, structural analysis revealed cleaved mRNA product in the 30S ribosome entry tunnel. Additionally, knockdown studies in Mycobacterium tuberculosis confirmed the protective role of Rps3 against oxidative and UV stress. Overall, our results show that prokaryotic Rps3 recognizes and processes AP-sites on mRNA via a novel mechanism that is distinct from eukaryotes.
External linksNucleic Acids Res / PubMed:39588766 / PubMed Central
MethodsEM (single particle)
Resolution3.39 - 3.88 Å
Structure data

36854

8k3o

EMDB-36854, PDB-8k3o:
Cryo-EM structure of 30S ribosome with cleaved AP-mRNA bound complex I
Method: EM (single particle) / Resolution: 3.88 Å

EMDB-36860: Cryo-EM structure of 30S ribosome with cleaved AP-mRNA bound complex (Body 1)
Method: EM (single particle) / Resolution: 3.39 Å

EMDB-36868: Cryo-EM structure of 30S ribosome with cleaved AP-mRNA bound complex (Body 2)
Method: EM (single particle) / Resolution: 3.52 Å

36883

8k4e

EMDB-36883, PDB-8k4e:
Cryo-EM structure of 30S ribosome with cleaved AP-mRNA bound complex-II
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-36885: Cryo-EM structure of 30S ribosome with cleaved AP-mRNA bound complex-II (Body 1)
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-36886: Cryo-EM structure of 30S ribosome with cleaved AP-mRNA bound complex-II (Body 2)
Method: EM (single particle) / Resolution: 3.5 Å

Source
  • escherichia coli k-12 (bacteria)
KeywordsRIBOSOME / AP-mRNA / 30S Ribosome

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