Skip to main content
SpringerLink
Log in

PpsA-mediated alternative pathway to complement RNase E essentiality in Escherichia coli

  • Original Paper
  • Published:
Archives of Microbiology Aims and scope Submit manuscript

Abstract

Escherichia coli cells require RNase E, encoded by the essential gene rne, to propagate. The growth properties on different carbon sources of E. coli cells undergoing suppression of RNase E production suggested that reduction in RNase E is associated with decreased expression of phosphoenolpyruvate synthetase (PpsA), which converts pyruvate to phosphoenolpyruvate during gluconeogenesis. Western blotting and genetic complementation confirmed the role of RNase E in PpsA expression. Adventitious ppsA overexpression from a multicopy plasmid was sufficient to restore colony formation of ∆rne E. coli on minimal media containing glycerol or succinate as the sole carbon source. Complementation of ∆rne by ppsA overproduction was observed during growth on solid media but was only partial, and bacteria showed slowed cell division and grew as filamentous chains. We found that restoration of colony-forming ability by ppsA complementation occurred independent of the presence of endogenous RNase G or second-site suppressors of RNase E essentiality. Our investigations demonstrate the role of phosphoryl transfer catalyzable by PpsA as a determinant of RNase E essentiality in E. coli.

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
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

References

  • Alifano P, Rivellini F, Piscitelli C, Arraiano CM, Bruni CB, Carlomagno MS (1994) Ribonuclease E provides substrates for ribonuclease P-dependent processing of a polycistronic mRNA. Genes Dev 8:3021–3031

    Article  CAS  PubMed  Google Scholar 

  • Anupama K, Leela JK, Gowrishankar J (2011) Two pathways for RNase E action in Escherichia coli in vivo and bypass of its essentiality in mutants defective for Rho-dependent transcription termination. Mol Microbiol 82:1330–1348

    Article  CAS  PubMed  Google Scholar 

  • Apirion D (1978) Isolation, genetic mapping and some characterization of a mutation in Escherichia coli that affects the processing of ribonuleic acid. Genetics 90:659–671

    CAS  PubMed  PubMed Central  Google Scholar 

  • Apirion D, Ghora BK, Plautz G, Misra TK, Gegenheimer P (1980) Processing of rRNA and tRNA in Escherichia coli: cooperation between processing enzymes. In Transfer RNA: biological aspects. Cold Spring Harbor Laboratory, New York, pp 139–154

  • Baba T et al (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2(2006):0008

    PubMed  Google Scholar 

  • Berman KM, Cohn M (1970) Phosphoenolpyruvate synthetase of Escherichia coli. Purification, some properties, and the role of divalent metal ions. J Biol Chem 245:5309–5318

    CAS  PubMed  Google Scholar 

  • Bernstein JA, Khodursky AB, Lin PH, Lin-Chao S, Cohen SN (2002) Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc Natl Acad Sci USA 99:9697–9702

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Brice CB, Kornberg HL (1967) Location of a gene specifying phosphopyruvate synthase activity on the genome of Escherichia coli, K12. Proc R Soc Lond B Biol Sci 168:281–292

    Article  CAS  PubMed  Google Scholar 

  • Cam K, Rome G, Krisch HM, Bouche JP (1996) RNase E processing of essential cell division genes mRNA in Escherichia coli. Nucleic Acids Res 24:3065–3070

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chao YP, Patnaik R, Roof WD, Young RF, Liao JC (1993) Control of gluconeogenic growth by pps and pck in Escherichia coli. J Bacteriol 175:6939–6944

    CAS  PubMed  PubMed Central  Google Scholar 

  • Cherepanov PP, Wackernagel W (1995) Gene disruption in Escherichia coli: TcR and KmR cassettes with the option of Flp-catalyzed excision of the antibiotic-resistance determinant. Gene 158:9–14

    Article  CAS  PubMed  Google Scholar 

  • Chung DH, Min Z, Wang BC, Kushner SR (2010) Single amino acid changes in the predicted RNase H domain of Escherichia coli RNase G lead to complementation of RNase E deletion mutants. RNA 16:1371–1385

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cohen SN, Chang AC, Boyer HW, Helling RB (1973) Construction of biologically functional bacterial plasmids in vitro. Proc Natl Acad Sci USA 70:3240–3244

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cooper RA, Kornberg HL (1965) Net formation of phosphoenolpyruvate from pyruvate by Escherichia coli. Biochim Biophys Acta 104:618–620

    Article  CAS  PubMed  Google Scholar 

  • Datsenko KA, Wanner BL (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci USA 97:6640–6645

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Deana A, Belasco JG (2004) The function of RNase G in Escherichia coli is constrained by its amino and carboxyl termini. Mol Microbiol 51:1205–1217

    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 

  • Goldblum K, Apririon D (1981) Inactivation of the ribonucleic acid-processing enzyme ribonuclease E blocks cell division. J Bacteriol 146:128–132

    CAS  PubMed  PubMed Central  Google Scholar 

  • Goldie AH, Sanwal BD (1980) Genetic and physiological characterization of Escherichia coli mutants deficient in phosphoenolpyruvate carboxykinase activity. J Bacteriol 141:1115–1121

    CAS  PubMed  PubMed Central  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 98:34–45

    Article  PubMed  Google Scholar 

  • Joyce AR, Reed JL, White A et al (2006) Experimental and computational assessment of conditionally essential genes in Escherichia coli. J Bacteriol 188:8259–8271

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kang KS, Veeder GT, Mirrasoul PJ, Kaneko T, Cottrell IW (1982) Agar-like polysaccharide produced by a pseudomonas species: production and basic properties. Appl Environ Microbiol 43:1086–1091

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kee JM, Oslund RC, Perlman DH, Muir TW (2013) A pan-specific antibody for direct detection of protein histidine phosphorylation. Nat Chem Biol 9:416–421

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Khemici V, Poljak L, Toesca I, Carpousis AJ (2005) Evidence in vivo that the DEAD-box RNA helicase RhlB facilitates the degradation of ribosome-free mRNA by RNase E. Proc Natl Acad Sci USA 102:6913–6918

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lee K, Cohen SN (2003) A Streptomyces coelicolor functional orthologue of Escherichia coli RNase E shows shuffling of catalytic and PNPase-binding domains. Mol Microbiol 48:349–360

    Article  CAS  PubMed  Google Scholar 

  • Lee K, Bernstein JA, Cohen SN (2002) RNase G complementation of rne null mutation identifies functional interrelationships with RNase E in Escherichia coli. Mol Microbiol 43:1445–1456

    Article  CAS  PubMed  Google Scholar 

  • Li Z, Pandit S, Deutscher MP (1999) RNase G (CafA protein) and RNase E are both required for the 5′ maturation of 16S ribosomal RNA. EMBO J 18:2878–2885

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lin-Chao S, Cohen SN (1991) The rate of processing and degradation of antisense RNAI regulates the replication of ColE1-type plasmids in vivo. Cell 65:1233–1242

    Article  CAS  PubMed  Google Scholar 

  • Lopez PJ, Marchand I, Joyce SA, Dreyfus M (1999) The C-terminal half of RNase E, which organizes the Escherichia coli degradosome, participates in mRNA degradation but not rRNA processing in vivo. Mol Microbiol 33:188–199

    Article  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

    CAS  PubMed  PubMed Central  Google Scholar 

  • Mackie GA (2013) RNase E: at the interface of bacterial RNA processing and decay. Nat Rev Microbiol 11:45–57

    Article  CAS  PubMed  Google Scholar 

  • Marr AG (1991) Growth rate of Escherichia coli. Microbiol Rev 55:316–333

    CAS  PubMed  PubMed Central  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 

  • Miczak A, Kaberdin VR, Wei CL, Lin-Chao S (1996) Proteins associated with RNase E in a multicomponent ribonucleolytic complex. Proc Natl Acad Sci USA 93:3865–3869

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Moll I, Afonyushkin T, Vytvytska O, Kaberdin VR, Blasi U (2003) Coincident Hfq binding and RNase E cleavage sites on mRNA and small regulatory RNAs. RNA 9:1308–1314

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Morita T, Kawamoto H, Mizota T, Inada T, Aiba H (2004) Enolase in the RNA degradosome plays a crucial role in the rapid decay of glucose transporter mRNA in the response to phosphosugar stress in Escherichia coli. Mol Microbiol 54:1063–1075

    Article  CAS  PubMed  Google Scholar 

  • Morita T, Maki K, Aiba H (2005) RNase E-based ribonucleoprotein complexes: mechanical basis of mRNA destabilization mediated by bacterial noncoding RNAs. Genes Dev 19:2176–2186

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Narindrasorasak S, Bridger WA (1977) Phosphoenolypyruvate synthetase of Escherichia coli: molecular weight, subunit composition, and identification of phosphohistidine in phosphoenzyme intermediate. J Biol Chem 252:3121–3127

    CAS  PubMed  Google Scholar 

  • Neidhardt FC, Bloch PL, Smith DF (1974) Culture medium for enterobacteria. J Bacteriol 119:736–747

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ono M, Kuwano M (1979) A conditional lethal mutation in an Escherichia coli strain with a longer chemical lifetime of messenger RNA. J Mol Biol 129:343–357

    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  CAS  PubMed  PubMed Central  Google Scholar 

  • Ow MC, Liu Q, Kushner SR (2000) Analysis of mRNA decay and rRNA processing in Escherichia coli in the absence of RNase E-based degradosome assembly. Mol Microbiol 38:854–866

    Article  CAS  PubMed  Google Scholar 

  • Prud’homme-Genereux A, Beran RK, Iost I, Ramey CS, Mackie GA, Simons RW (2004) Physical and functional interactions among RNase E, polynucleotide phosphorylase and the cold-shock protein, CsdA: evidence for a ‘cold shock degradosome’. Mol Microbiol 54:1409–1421

    Article  PubMed  Google Scholar 

  • Py B, Higgins CF, Krisch HM, Carpousis AJ (1996) A DEAD-box RNA helicase in the Escherichia coli RNA degradosome. Nature 381:169–172

    Article  CAS  PubMed  Google Scholar 

  • Ray A, Apirion D (1980) Cloning the gene for ribonuclease E, an RNA processing enzyme. Gene 12:87–94

    Article  CAS  PubMed  Google Scholar 

  • Ray BK, Apirion D (1981) Transfer RNA precursors are accumulated in Escherichia coli in the absence of RNase E. Eur J Biochem 114:517–524

    Article  CAS  PubMed  Google Scholar 

  • Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual, 3rd edn. CSHL Press, Cold Spring Harbor

    Google Scholar 

  • Sauer U, Eikmanns BJ (2005) The PEP–pyruvate–oxaloacetate node as the switch point for carbon flux distribution in bacteria. FEMS Microbiol Rev 29:765–794

    Article  CAS  PubMed  Google Scholar 

  • Schein A, Sheffy-Levin S, Glaser F, Schuster G (2008) The RNase E/G-type endoribonuclease of higher plants is located in the chloroplast and cleaves RNA similarly to the E. coli enzyme. RNA 14:1057–1068

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shungu D, Valiant M, Tutlane V et al (1983) GELRITE as an agar substitute in bacteriological media. Appl Environ Microbiol 46:840–845

    CAS  PubMed  PubMed Central  Google Scholar 

  • Singh D, Chang SJ, Lin PH, Averina OV, Kaberdin VR, Lin-Chao S (2009) Regulation of ribonuclease E activity by the L4 ribosomal protein of Escherichia coli. Proc Natl Acad Sci USA 106:864–869

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Spring TG, Wold F (1971) The purification and characterization of Escherichia coli enolase. J Biol Chem 246:6797–6802

    CAS  PubMed  Google Scholar 

  • Stead MB, Marshburn S, Mohanty BK et al (2010) Analysis of Escherichia coli RNase E and RNase III activity in vivo using tiling microarrays. Nucleic Acids Res 39:3188–3203

    Article  PubMed  PubMed Central  Google Scholar 

  • Tamura M, Lee K, Miller CA et al (2006) RNase E maintenance of proper FtsZ/FtsA ratio required for nonfilamentous growth of Escherichia coli cells but not for colony-forming ability. J Bacteriol 188:5145–5152

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tamura M, Kers JA, Cohen SN (2012) Second-site suppression of RNase E essentiality by mutation of the deaD RNA helicase in Escherichia coli. J Bacteriol 194:1919–1926

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tamura M, Moore CJ, Cohen SN (2013) Nutrient dependence of RNase E essentiality in Escherichia coli. J Bacteriol 195:1133–1141

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vanderpool CK, Gottesman S (2005) Noncoding RNAs at the membrane. Nat Struct Mol Biol 12:285–286

    Article  CAS  PubMed  Google Scholar 

  • Wachi M, Umitsuki G, Nagai K (1997) Functional relationship between Escherichia coli RNase E and the CafA protein. Mol Gen Genet 253:515–519

    Article  CAS  PubMed  Google Scholar 

  • Wachi M, Umitsuki G, Shimizu M, Takada A, Nagai K (1999) Escherichia coli cafA gene encodes a novel RNase, designated as RNase G, involved in processing of the 5′ end of 16S rRNA. Biochem Biophys Res Commun 259:483–488

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

We thank Kei Kitahara for helpful suggestions on plasmid construction and Teppei Morita for critical review of the manuscript. We also thank Hisako Suzuki for her support. This study was supported by MHLW Grant 11050201 and AMED Grant 48650201 to AK and by Grant AI08619 to SNC.

Author contributions

M. T., H. F., and A. K. designed research; M. T. and N. H. performed research. All authors analyzed data, and M. T. and S. N. C. wrote the article.

Author information

Authors and Affiliations

  1. Department of Quality Assurance and Radiological Protection, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan

    Masaru Tamura, Naoko Honda, Hirofumi Fujimoto & Atsushi Kato

  2. Departments of Genetics and Medicine, School of Medicine, Stanford University, Stanford, CA, USA

    Stanley N. Cohen

Authors
  1. Masaru Tamura
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Naoko Honda
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Hirofumi Fujimoto
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Stanley N. Cohen
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Atsushi Kato
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Masaru Tamura.

Additional information

Communicated by Djamel Drider.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PDF 4288 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Tamura, M., Honda, N., Fujimoto, H. et al. PpsA-mediated alternative pathway to complement RNase E essentiality in Escherichia coli . Arch Microbiol 198, 409–421 (2016). https://doi.org/10.1007/s00203-016-1201-0

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00203-016-1201-0

Keywords

Search

Navigation