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Nucleic acids research
Dec 11, 2024;52 (22): 13996-14012.

Bacterial Rps3 counters oxidative and UV stress by recognizing and processing AP-sites on mRNA via a novel mechanism.

Mohammad 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
Author Information
  1. Mohammad Afsar: Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow-226031, India.
  2. Ankita Shukla: Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow-226031, India.
  3. Faiz Ali: Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow-226031, India.
  4. Rahul Kumar Maurya: Molecular Microbiology and Immunology Division, CSIR-Central Drug Research Institute, Lucknow-226031, India.
  5. Suman Bharti: Molecular Microbiology and Immunology Division, CSIR-Central Drug Research Institute, Lucknow-226031, India.
  6. Nelam Kumar: Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow-226031, India.
  7. Mohammad Sadik: Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow-226031, India.
  8. Surabhi Chandra: Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore-560012, India.
  9. Huma Rahil: Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore-560012, India.
  10. Sanjay Kumar: Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow-226031, India.
  11. Imran Ansari: Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow-226031, India.
  12. Farheen Jahan: Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow-226031, India.
  13. Saman Habib: Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow-226031, India.
  14. Tanweer Hussain: Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore-560012, India. ORCID
  15. Manju Yasoda Krishnan: Molecular Microbiology and Immunology Division, CSIR-Central Drug Research Institute, Lucknow-226031, India.
  16. Ravishankar Ramachandran: Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow-226031, India. ORCID
PMID: 39588766 DOI: 10.1093/nar/gkae1130

Abstract

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.

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Grants

  1. GAP0292/Department of Science and Technology
  2. CII7032/Council of Scientific and Industrial Research
  3. GAP0384/Department of Biotechnology

MeSH Term

Ribosomal Proteins
RNA, Messenger
Oxidative Stress
Mycobacterium tuberculosis
Bacterial Proteins
Ultraviolet Rays
Escherichia coli
Cryoelectron Microscopy
Ribosomes
Protein Biosynthesis
Endoribonucleases

Chemicals

Ribosomal Proteins
RNA, Messenger
Bacterial Proteins
Endoribonucleases
Journal Article
Article has an altmetric score of 4

Word Cloud

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