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Functional Conservation of RNase III-like Enzymes: Studies on a Vibrio vulnificus Ortholog of Escherichia coli RNase III

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Abstract

Bacterial ribonuclease III (RNase III) belongs to the RNase III enzyme family, which plays a pivotal role in controlling mRNA stability and RNA processing in both prokaryotes and eukaryotes. In the Vibrio vulnificus genome, one open reading frame encodes a protein homologous to E. coli RNase III, designated Vv-RNase III, which has 77.9 % amino acid identity to E. coli RNase III. Here, we report that Vv-RNase III has the same cleavage specificity as E. coli RNase III in vivo and in vitro. Expressing Vv-RNase III in E. coli cells deleted for the RNase III gene (rnc) restored normal rRNA processing and, consequently, growth rates of these cells comparable to wild-type cells. In vitro cleavage assays further showed that Vv-RNase III has the same cleavage activity and specificity as E. coli RNase III on RNase III-targeted sequences of corA and mltD mRNA. Our findings suggest that RNase III-like proteins have conserved cleavage specificity across bacterial species.

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References

  1. Amarasinghe AK, Calin-Jageman I, Harmouch A, Sun W, Nicholson AW (2001) Escherichia coli ribonuclease III: affinity purification of hexahistidine-tagged enzyme and assays for substrate binding and cleavage. Methods Enzymol 342:143–158

    Article  CAS  PubMed  Google Scholar 

  2. Arraiano CM, Andrade JM, Domingues S, Guinote IB, Malecki M, Matos RG, Moreira RN, Pobre V, Reis FP, Saramago M, Silva IJ, Viegas SC (2010) The critical role of RNA processing and degradation in the control of gene expression. FEMS Microbiol Rev 34:883–923

    CAS  PubMed  Google Scholar 

  3. Babitzke P, Granger L, Olszewski J, Kushner SR (1993) Analysis of mRNA decay and rRNA processing in Escherichia coli multiple mutants carrying a deletion in RNase III. J Bacteriol 175:229–239

    CAS  PubMed Central  PubMed  Google Scholar 

  4. Belasco JG (2010) All things must pass: contrasts and commonalities in eukaryotic and bacterial mRNA decay. Nat Rev Mol Cell Biol 11:467–478

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  5. Blaszczyk J, Gan J, Tropea JE, Court DL, Waugh DS, Ji X (2004) Noncatalytic assembly of ribonuclease III with double-stranded RNA. Structure 12:457–466

    Article  CAS  PubMed  Google Scholar 

  6. Chevalier C, Huntzinger E, Fechter P, Boisset S, Vandenesch F, Romby P, Geissmann T (2008) Staphylococcus aureus endoribonuclease III purification and properties. Methods Enzymol 447:309–327

    Article  CAS  PubMed  Google Scholar 

  7. Condon C (2007) Maturation and degradation of RNA in bacteria. Curr Opin Microbiol 10:271–278

    Article  CAS  PubMed  Google Scholar 

  8. Conrad C, Rauhut R (2002) Ribonuclease III: new sense from nuisance. Int J Biochem Cell Biol 34:116–129

    Article  CAS  PubMed  Google Scholar 

  9. Conrad C, Schmitt JG, Evguenieva-Hackenberg E, Klug G (2002) One functional subunit is sufficient for catalytic activity and substrate specificity of Escherichia coli endoribonuclease III artificial heterodimers. FEBS Lett 518:93–96

    Article  CAS  PubMed  Google Scholar 

  10. Court D (1993) RNA processing and degradation by RNase III. In: Belasco JG, Braverman G (eds) Control of messenger RNA stability. Academic Press, San Diego

    Google Scholar 

  11. Deutscher MP (2009) Maturation and degradation of ribosomal RNA in bacteria. Prog Mol Biol Transl Sci 85:369–391

    Article  CAS  PubMed  Google Scholar 

  12. Drider D, Condon C (2004) The continuing story of endoribonuclease III. J Mol Microbiol Biotechnol 8:195–200

    Article  PubMed  Google Scholar 

  13. Dunn JJ (1982) Ribonuclease III. In: Boyer P (ed) The enzymes, 3rd edn. Academic Press, New York

    Google Scholar 

  14. Gan J, Shaw G, Tropea JE, Waugh DS, Court DL, Ji X (2008) A stepwise model for double-stranded RNA processing by ribonuclease III. Mol Microbiol 67:143–154

    Article  CAS  PubMed  Google Scholar 

  15. Gao Y, Gong Y, Xu X (2013) RNase III-dependent down-regulation of ftsH by an artificial internal sense RNA in Anabaena sp. PCC 7120. FEMS Microbiol Lett 344:130–137

    Google Scholar 

  16. Kim K, Sim SH, Jeon CO, Lee Y, Lee K (2011) Base substitutions at scissile bond sites are sufficient to alter RNA-binding and cleavage activity of RNase III. FEMS Microbiol Lett 315:30–37

    Article  CAS  PubMed  Google Scholar 

  17. Kime L, Jourdan SS, McDowall KJ (2008) Identifying and characterizing substrates of the RNase E/G family of enzymes. Methods Enzymol 447:215–241

    Article  CAS  PubMed  Google Scholar 

  18. Li HL, Chelladurai BS, Zhang K, Nicholson AW (1993) Ribonuclease III cleavage of a bacteriophage T7 processing signal. Divalent cation specificity, and specific anion effects. Nucleic Acids Res 21:1919–1925

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  19. Lim B, Sim SH, Sim M, Kim K, Jeon CO, Lee Y, Ha NC, Lee K (2012) RNase III controls the degradation of corA mRNA in Escherichia coli. J Bacteriol 194:2214–2220

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  20. Lim B, Ahn SM, Sim M, Bae J, Lee K (2013) RNase III controls degradation of mltD mRNA in Escherichia coli. Curr Microbiol (in press)

  21. Meng W, Nicholson AW (2008) Heterodimer-based analysis of subunit and domain contributions to double-stranded RNA processing by Escherichia coli RNase III in vitro. Biochem J 410:39–48

    Article  CAS  PubMed  Google Scholar 

  22. Nicholson AW (1999) Function, mechanism and regulation of bacterial ribonucleases. FEMS Microbiol Rev 23:371–390

    Article  CAS  PubMed  Google Scholar 

  23. Nicholson AW (2003) The ribonuclease III superfamily: forms and functions in RNA maturation, decay, and gene silencing. In: Hannon G (ed) RNAi: a guide to gene silencing. Cold Spring Harbor, New York

    Google Scholar 

  24. Olmedo G, Guzman P (2008) Mini-III, a fourth class of RNase III catalyses maturation of the Bacillus subtilis 23S ribosomal RNA. Mol Microbiol 68:1073–1076

    Article  CAS  PubMed  Google Scholar 

  25. Park JH, Cho YJ, Chun J, Seok YJ, Lee JK, Kim KS, Lee KH, Park SJ, Choi SH (2011) Complete genome sequence of Vibrio vulnificus MO6-24/O. J Bacteriol 193:2062–2063

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  26. Redko Y, Bechhofer DH, Condon C (2008) Mini-III, an unusual member of the RNase III family of enzymes, catalyses 23S ribosomal RNA maturation in B. subtilis. Mol Microbiol 68:1096–1106

    Article  CAS  PubMed  Google Scholar 

  27. Resch A, Afonyushkin T, Lombo TB, McDowall KJ, Blasi U, Kaberdin VR (2008) Translational activation by the noncoding RNA DsrA involves alternative RNase III processing in the rpoS 5′-leader. RNA 14:454–459

    Article  CAS  PubMed  Google Scholar 

  28. Robertson HD (1982) Escherichia coli ribonuclease III cleavage sites. Cell 30:669–672

    Article  CAS  PubMed  Google Scholar 

  29. Robertson HD, Webster RE, Zinder ND (1968) Purification and properties of ribonuclease III from Escherichia coli. J Biol Chem 243:82–91

    CAS  PubMed  Google Scholar 

  30. Rochat T, Bouloc P, Repoila F (2013) Gene expression control by selective RNA processing and stabilization in bacteria. FEMS Microbiol Lett 344:104–113

    Article  CAS  PubMed  Google Scholar 

  31. Sedmak JJ, Grossberg SE (1977) A rapid, sensitive, and versatile assay for protein using Coomassie brilliant blue G250. Anal Biochem 79:544–552

    Article  CAS  PubMed  Google Scholar 

  32. Silva IJ, Saramago M, Dressaire C, Domingues S, Viegas SC, Arraiano CM (2011) Importance and key events of prokaryotic RNA decay: the ultimate fate of an RNA molecule. Wiley Interdiscip Rev RNA 2:818–836

    Article  CAS  PubMed  Google Scholar 

  33. Sim SH, Yeom JH, Shin C, Song WS, Shin E, Kim HM, Cha CJ, Han SH, Ha NC, Kim SW, Hahn Y, Bae J, Lee K (2010) Escherichia coli ribonuclease III activity is downregulated by osmotic stress: consequences for the degradation of bdm mRNA in biofilm formation. Mol Microbiol 75:413–425

    Article  CAS  PubMed  Google Scholar 

  34. Studier FW (1975) Genetic mapping of a mutation that causes ribonucleases III deficiency in Escherichia coli. J Bacteriol 124:307–316

    CAS  PubMed Central  PubMed  Google Scholar 

  35. Sun W, Jun E, Nicholson AW (2001) Intrinsic double-stranded-RNA processing activity of Escherichia coli ribonuclease III lacking the dsRNA-binding domain. Biochemistry 40:14976–14984

    Article  CAS  PubMed  Google Scholar 

  36. Wright AC, Morris JG Jr, Maneval DR Jr, Richardson K, Kaper JB (1985) Cloning of the cytotoxin-hemolysin gene of Vibrio vulnificus. Infect Immun 50:922–924

    CAS  PubMed Central  PubMed  Google Scholar 

  37. Xiao J, Feehery CE, Tzertzinis G, Maina CV (2009) E. coli RNase III(E38A) generates discrete-sized products from long dsRNA. RNA 15:984–991

    Article  CAS  PubMed  Google Scholar 

  38. Yeom JH, Lee K (2006) RraA rescues Escherichia coli cells over-producing RNase E from growth arrest by modulating the ribonucleolytic activity. Biochem Biophys Res Commun 345:1372–1376

    Article  CAS  PubMed  Google Scholar 

  39. Zhang H, Kolb FA, Jaskiewicz L, Westhof E, Filipowicz W (2004) Single processing center models for human Dicer and bacterial RNase III. Cell 118:57–68

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

This work was supported by NRF Grants (2011-0028553 and 2013R1A1A2006953) funded by the Ministry of Education, Science, and Technology, Republic of Korea and the Next-Generation BioGreen 21 Program (SSAC, Grant#: PJ009025), Rural Development Administration, Republic of Korea.

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Authors and Affiliations

  1. Department of Life Science, Chung-Ang University, 84 Heuksok-Ro, Dongjak-Gu, Seoul, 156-756, Republic of Korea

    Minho Lee, Sangmi Ahn, Boram Lim, Dong-Ho Lee & Kangseok Lee

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  1. Minho Lee
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  2. Sangmi Ahn
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  3. Boram Lim
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  4. Dong-Ho Lee
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  5. Kangseok Lee
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Correspondence to Kangseok Lee.

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Minho Lee and Sangmi Ahn contributed equally to this work.

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Lee, M., Ahn, S., Lim, B. et al. Functional Conservation of RNase III-like Enzymes: Studies on a Vibrio vulnificus Ortholog of Escherichia coli RNase III. Curr Microbiol 68, 413–418 (2014). https://doi.org/10.1007/s00284-013-0492-5

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  • DOI: https://doi.org/10.1007/s00284-013-0492-5

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