Advertisement

Current Genetics

, Volume 62, Issue 1, pp 53–57 | Cite as

Using the power of genetic suppressors to probe the essential functions of RNase E

  • Diarmaid Hughes
Review

Abstract

This review describes how, using the power of genetic suppressor analysis, mRNA turnover in bacteria was shown to be an essential function of RNase E. RNase E is an essential multifunctional enzyme in bacteria, involved in the processing of stable RNAs to their mature forms (rRNAs and tRNAs) and in the turnover of most mRNAs. Genetic suppressor analysis was successfully used to address whether mRNA turnover is one of the essential functions of RNase E. Conditional lethal mutations in rne were shown to be suppressible by three different classes of extragenic suppressors, including a class that caused overexpression of RelE. The only known function of RelE is the cleavage of mRNA in the ribosomal A-site. Suppression of the conditional lethal defect in rne by RelE overexpression provides strong genetic evidence that mRNA turnover is one of the essential functions of RNase E. Several hypotheses that could explain why mRNA turnover is essential are discussed. Suppressor analysis is an old-fashioned but very powerful approach that can be usefully applied to address a wide variety of important questions in biology and genetics. In this work suppressor analysis has revealed that mRNA turnover is an essential function of RNase E, a conclusion that raises a host of interesting questions for future research.

Keywords

RelBE RNase R Ribosomal protein S1 rne Genetic suppression Genetic screen Salmonella Escherichia coli 

Notes

Acknowledgments

Research into this project in the Hughes laboratory is supported by Grants from Vetenskapsrådet (Swedish Science Council), SSF (Swedish Strategic Research Foundation), and KAW (The Knut and Alice Wallenberg Foundation, RiboCORE project).

References

  1. Apirion D, Lassar AB (1978) A conditional lethal mutant of Escherichia coli which affects the processing of ribosomal RNA. J Biol Chem 253:1738–1742PubMedGoogle Scholar
  2. Arifuzzaman M, Maeda M, Itoh A, Nishikata K, Takita C, Saito R, Ara T, Nakahigashi K, Huang HC, Hirai A, Tsuzuki K, Nakamura S, Altaf-Ul-Amin M, Oshima T, Baba T, Yamamoto N, Kawamura T, Ioka-Nakamichi T, Kitagawa M, Tomita M, Kanaya S, Wada C, Mori H (2006) Large-scale identification of protein–protein interaction of Escherichia coli K-12. Genome Res 16:686–691PubMedCentralCrossRefPubMedGoogle Scholar
  3. Babitzke P, Kushner SR (1991) The Ams (altered mRNA stability) protein and ribonuclease E are encoded by the same structural gene of Escherichia coli. Proc Natl Acad Sci USA 88:1–5PubMedCentralCrossRefPubMedGoogle Scholar
  4. Callaghan AJ, Marcaida MJ, Stead JA, McDowall KJ, Scott WG, Luisi BF (2005) Structure of Escherichia coli RNase E catalytic domain and implications for RNA turnover. Nature 437:1187–1191CrossRefPubMedGoogle Scholar
  5. Carpousis AJ (2007) The RNA degradosome of Escherichia coli: an mRNA-degrading machine assembled on RNase E. Annu Rev Microbiol 61:71–87CrossRefPubMedGoogle Scholar
  6. Cormack RS, Mackie GA (1992) Structural requirements for the processing of Escherichia coli 5 S ribosomal RNA by RNase E in vitro. J Mol Biol 228:1078–1090CrossRefPubMedGoogle Scholar
  7. Crick FH, Barnett L, Brenner S, Watts-Tobin RJ (1961) General nature of the genetic code for proteins. Nature 192:1227–1232CrossRefPubMedGoogle Scholar
  8. Ehretsmann CP, Carpousis AJ, Krisch HM (1992) Specificity of Escherichia coli endoribonuclease RNase E: in vivo and in vitro analysis of mutants in a bacteriophage T4 mRNA processing site. Genes Dev 6:149–159CrossRefPubMedGoogle Scholar
  9. Ghora BK, Apirion D (1978) Structural analysis and in vitro processing to p5 rRNA of a 9S RNA molecule isolated from an rne mutant of E. coli. Cell 15:1055–1066CrossRefPubMedGoogle Scholar
  10. Hammarlöf DL, Hughes D (2008) Mutants of the RNA-processing enzyme RNase E reverse the extreme slow-growth phenotype caused by a mutant translation factor EF-Tu. Mol Microbiol 70:1194–1209CrossRefPubMedGoogle Scholar
  11. Hammarlof DL, Liljas L, Hughes D (2011) Temperature-sensitive mutants of RNase E in Salmonella enterica. J Bacteriol 193:6639–6650PubMedCentralCrossRefPubMedGoogle Scholar
  12. Hammarlof DL, Bergman JM, Garmendia E, Hughes D (2015) Turnover of mRNAs is one of the essential functions of RNase E. Mol Microbiol. doi: 10.1111/mmi.13100 PubMedCentralGoogle Scholar
  13. Johnson JL, Zuehlke AD, Tenge VR, Langworthy JC (2014) Mutation of essential Hsp90 co-chaperones SGT1 or CNS1 renders yeast hypersensitive to overexpression of other co-chaperones. Curr Genet 60:265–276CrossRefPubMedGoogle Scholar
  14. Kuwada NJ, Traxler B, Wiggins PA (2015) High-throughput cell-cycle imaging opens new doors for discovery. Curr Genet. doi: 10.1007/s00294-015-0493-y PubMedGoogle Scholar
  15. Li Z, Deutscher MP (2002) RNase E plays an essential role in the maturation of Escherichia coli tRNA precursors. RNA 8:97–109PubMedCentralCrossRefPubMedGoogle Scholar
  16. Lin-Chao S, Wei CL, Lin YT (1999) RNase E is required for the maturation of ssrA RNA and normal ssrA RNA peptide-tagging activity. Proc Natl Acad Sci USA 96:12406–12411PubMedCentralCrossRefPubMedGoogle Scholar
  17. Lundberg U, Altman S (1995) Processing of the precursor to the catalytic RNA subunit of RNase P from Escherichia coli. RNA 1:327–334PubMedCentralPubMedGoogle Scholar
  18. Marcaida MJ, DePristo MA, Chandran V, Carpousis AJ, Luisi BF (2006) The RNA degradosome: life in the fast lane of adaptive molecular evolution. Trends Biochem Sci 31:359–365CrossRefPubMedGoogle Scholar
  19. McDowall KJ, Cohen SN (1996) The N-terminal domain of the rne gene product has RNase E activity and is non-overlapping with the arginine-rich RNA-binding site. J Mol Biol 255:349–355CrossRefPubMedGoogle Scholar
  20. Melefors O, von Gabain A (1991) Genetic studies of cleavage-initiated mRNA decay and processing of ribosomal 9S RNA show that the Escherichia coli ams and rne loci are the same. Mol Microbiol 5:857–864CrossRefPubMedGoogle Scholar
  21. Mudd EA, Krisch HM, Higgins CF (1990) RNase E, an endoribonuclease, has a general role in the chemical decay of Escherichia coli mRNA: evidence that rne and ams are the same genetic locus. Mol Microbiol 4:2127–2135CrossRefPubMedGoogle Scholar
  22. Ow MC, Kushner SR (2002) Initiation of tRNA maturation by RNase E is essential for cell viability in E. coli. Genes Dev 16:1102–1115PubMedCentralCrossRefPubMedGoogle Scholar
  23. Perwez T, Hami D, Maples VF, Min Z, Wang BC, Kushner SR (2008) Intragenic suppressors of temperature-sensitive rne mutations lead to the dissociation of RNase E activity on mRNA and tRNA substrates in Escherichia coli. Nucleic Acids Res 36:5306–5318PubMedCentralCrossRefPubMedGoogle Scholar
  24. Taraseviciene L, Miczak A, Apirion D (1991) The gene specifying RNase E (rne) and a gene affecting mRNA stability (ams) are the same gene. Mol Microbiol 5:851–855CrossRefPubMedGoogle Scholar
  25. Veide Vilg J, Dahal S, Ljungdahl T, Grotli M, Tamas MJ (2014) Application of a peptide-based assay to characterize inhibitors targeting protein kinases from yeast. Curr Genet 60:193–200CrossRefPubMedGoogle Scholar
  26. Viegas SC, Pfeiffer V, Sittka A, Silva IJ, Vogel J, Arraiano CM (2007) Characterization of the role of ribonucleases in Salmonella small RNA decay. Nucleic Acids Res 35:7651–7664PubMedCentralCrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  1. 1.Department of Medical Biochemistry and Microbiology, Biomedical Center (Box 582)Uppsala UniversityUppsalaSweden

Personalised recommendations