Skip to main content
SpringerLink
Log in

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

  • Review
  • Published:
Current Genetics Aims and scope Submit manuscript

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Apirion D, Lassar AB (1978) A conditional lethal mutant of Escherichia coli which affects the processing of ribosomal RNA. J Biol Chem 253:1738–1742

    CAS  PubMed  Google Scholar 

  • 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 16:686–691

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • 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 88:1–5

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • 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 437:1187–1191

    Article  CAS  PubMed  Google Scholar 

  • Carpousis AJ (2007) The RNA degradosome of Escherichia coli: an mRNA-degrading machine assembled on RNase E. Annu Rev Microbiol 61:71–87

    Article  CAS  PubMed  Google Scholar 

  • 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 228:1078–1090

    Article  CAS  PubMed  Google Scholar 

  • Crick FH, Barnett L, Brenner S, Watts-Tobin RJ (1961) General nature of the genetic code for proteins. Nature 192:1227–1232

    Article  CAS  PubMed  Google Scholar 

  • 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 6:149–159

    Article  CAS  PubMed  Google Scholar 

  • 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 15:1055–1066

    Article  CAS  PubMed  Google Scholar 

  • 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 70:1194–1209

    Article  PubMed  Google Scholar 

  • Hammarlof DL, Liljas L, Hughes D (2011) Temperature-sensitive mutants of RNase E in Salmonella enterica. J Bacteriol 193:6639–6650

    Article  PubMed Central  PubMed  Google Scholar 

  • 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

    PubMed Central  Google Scholar 

  • 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 60:265–276

    Article  CAS  PubMed  Google Scholar 

  • 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

    PubMed  Google Scholar 

  • Li Z, Deutscher MP (2002) RNase E plays an essential role in the maturation of Escherichia coli tRNA precursors. RNA 8:97–109

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • 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 96:12406–12411

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Lundberg U, Altman S (1995) Processing of the precursor to the catalytic RNA subunit of RNase P from Escherichia coli. RNA 1:327–334

    PubMed Central  CAS  PubMed  Google Scholar 

  • 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 31:359–365

    Article  CAS  PubMed  Google Scholar 

  • 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 255:349–355

    Article  CAS  PubMed  Google Scholar 

  • 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 5:857–864

    Article  CAS  PubMed  Google Scholar 

  • 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 4:2127–2135

    Article  CAS  PubMed  Google Scholar 

  • Ow MC, Kushner SR (2002) Initiation of tRNA maturation by RNase E is essential for cell viability in E. coli. Genes Dev 16:1102–1115

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • 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 36:5306–5318

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • 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 5:851–855

    Article  CAS  PubMed  Google Scholar 

  • 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 60:193–200

    Article  CAS  PubMed  Google Scholar 

  • 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 35:7651–7664

    Article  PubMed Central  CAS  PubMed  Google Scholar 

Download references

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).

Author information

Authors and Affiliations

  1. Department of Medical Biochemistry and Microbiology, Biomedical Center (Box 582), Uppsala University, Husargatan 3, 75123, Uppsala, Sweden

    Diarmaid Hughes

Authors
  1. Diarmaid Hughes
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Diarmaid Hughes.

Additional information

Communicated by M. Kupiec.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Hughes, D. Using the power of genetic suppressors to probe the essential functions of RNase E. Curr Genet 62, 53–57 (2016). https://doi.org/10.1007/s00294-015-0510-1

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00294-015-0510-1

Keywords

Search

Navigation