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Gene Review

rne  -  ribonuclease E

Escherichia coli UTI89

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Disease relevance of rne

  • Highly purified RNAase E correctly processed E. coli 5S ribosomal RNA, bacteriophage T4 gene 32 mRNA and E. coli ompA mRNA at sites known to depend on the rne gene for cleavage in vivo [1].
  • The isolation was based on the appearance of a particular RNA precursor molecule upon infection of an rne mutant with a specific bacteriophage T4 deletion strain [2].
  • This notion is supported by our finding that the Synechocystis sp. RNase E homologue does not function as a platform for assembly of E. coli degradosome components [3].
  • Ribonuclease E (RNase E) is a multifunctional endoribonuclease that has been evolutionarily conserved in both Gram-positive and Gram-negative bacteria [4].
  • Previous work has detected an RNase E-like endoribonucleolytic activity in cell extracts obtained from Streptomyces [5].

High impact information on rne

  • Ribonuclease E (RNase E) has a key role in mRNA degradation and the processing of catalytic and structural RNAs in E. coli [6].
  • Initiation of tRNA maturation by RNase E is essential for cell viability in E. coli [7].
  • The description of RNase E now emerging is that of a remarkably complex multidomain protein containing an amino-terminal catalytic domain, a central RNA-binding domain, and carboxy-terminal binding sites for the other major components of the RNA degradosome [8].
  • These results and an analysis of all of the known putative RNase E sites suggest a consensus sequence RAUUW (R = A or G; W = A or U) at the cleavage site [9].
  • We propose that this higher speed unmasks an RNase E cleavage site which is normally shielded by ribosomes soon after its synthesis when the slower E. coli enzyme is used [10].

Chemical compound and disease context of rne

  • A Streptomyces peptide migrating at 70kDa in SDS/polyacrylamide gels binds to RNase E substrates and reacts with three separate anti-RNase E monoclonal antibodies; the endonucleolytic cleavage activity co-purified with the immunoreactive 70 kDa peptide [11].
  • The effects of erythromycin on the formation of ribosomal subunits were examined in wild-type Escherichia coli cells and in an RNase E mutant strain [12].
  • The ptsG mRNA encoding the major glucose transporter is rapidly degraded in an RNase E-dependent manner in response to the accumulation of glucose 6-P or fructose 6-P when the glycolytic pathway is blocked at its early steps in Escherichia coli [13].

Biological context of rne

  • IS10 mRNA stability and steady state levels in Escherichia coli: indirect effects of translation and role of rne function [14].
  • A functional rne gene product is essential for cell viability and for the processing and/or decay of a variety of RNA species, including 9 S RNA, mRNA and RNAI, the antisense RNA regulator of ColE1-type plasmid replication [15].
  • The copy number of plasmid pBR322 in these rne mutants was lower than that in the rne+ isogenic strain [16].
  • However, while restoration of the level of FtsZ to normal in rne null mutant bacteria reverses the filamentation phenotype, it does not restore CFA [17].
  • Physical locations of genes in the rne (ams)-rpmF-plsX-fab region of the Escherichia coli K-12 chromosome [18].

Anatomical context of rne

  • Analysis of interplay between translation mutations and rne function, together with the above observations, suggests that translation stabilizes messages in a general way against rne-dependent endonucleolytic cleavage, and that significant protection may be conferred by one or a few ribosomes [14].
  • These results (i) confirm the central role of DsbC in disulfide bond isomerization in the bacterial periplasm and (ii) suggest a critical role for RNase E in regulating DsbC expression [19].

Associations of rne with chemical compounds

  • In contrast to the S1 domain, an arginine-rich RNA-binding domain in the carboxyl half of RNase E appears to have a more peripheral role in RNase E function, as it is not required for feedback regulation, cell growth or ribonuclease activity [20].
  • The degradation is RNase E dependent and is correlated with the accumulation of either glucose-6-P or fructose-6-P (Kimata et al., 2001, EMBO J 20: 3587-3595; Morita et al., 2003, J Biol Chem 278: 15608-15614) [21].
  • Each of the five surface-exposed aromatic residues and most of the 14 basic residues of this RNase E domain were replaced with alanine to determine their importance for RNase E function [20].
  • The site for endonucleolytic cleavage is located in the intercistronic region between mopP and catA, and contains a potential stem-loop structure and a putative RNase E cleavage site [22].
  • These results indicate that RNase E is required for induction of the glutamate-dependent acid resistance system in a RpoS-independent manner [23].

Enzymatic interactions of rne

  • Both enzymes are able to cleave the B.subtilis thrS leader at a site that can also be cleaved by E.coli RNase E. We have previously shown that cleavage at this site increases the stability of the downstream messenger [24].

Other interactions of rne

  • As expected, purified degradosomes, a multi-protein complex containing, among others, RNase E, PNPase, and RhlB, generate an authentic 147-residue RNase E cleavage product from the rpsT mRNA in vitro [25].
  • Immunoaffinity purification of the Escherichia coli rne gene product. Evidence that the rne gene encodes the processing endoribonuclease RNase E [26].
  • The role of enolase within the RNase E-based degradosome in RNA decay has been totally mysterious [13].

Analytical, diagnostic and therapeutic context of rne

  • X-ray crystallography and biochemical studies have concluded that the Escherichia coli RNase E protein functions as a homotetramer formed by Zn linkage of dimers within a region extending from amino acid residues 416 through 529 of the 116-kDa protein [4].
  • The Western blot analysis performed using a rabbit antiserum raised against a truncated 110-kDa protein fragment of RNase E (containing two-thirds of the sequence from the N terminus) revealed that the 180-kDa polypeptide is the only protein recognized by the antibodies in a wild type whole cell extract of E. coli [26].


  1. Copurification of E. coli RNAase E and PNPase: evidence for a specific association between two enzymes important in RNA processing and degradation. Carpousis, A.J., Van Houwe, G., Ehretsmann, C., Krisch, H.M. Cell (1994) [Pubmed]
  2. RNA processing: new mutants that affect endonucleolytic processing of RNA. Miczak, A., Ford, J., Marian, M., Apirion, D. Biochem. Biophys. Res. Commun. (1983) [Pubmed]
  3. The endoribonucleolytic N-terminal half of Escherichia coli RNase E is evolutionarily conserved in Synechocystis sp. and other bacteria but not the C-terminal half, which is sufficient for degradosome assembly. Kaberdin, V.R., Miczak, A., Jakobsen, J.S., Lin-Chao, S., McDowall, K.J., von Gabain, A. Proc. Natl. Acad. Sci. U.S.A. (1998) [Pubmed]
  4. Retention of core catalytic functions by a conserved minimal ribonuclease e Peptide that lacks the domain required for tetramer formation. Caruthers, J.M., Feng, Y., McKay, D.B., Cohen, S.N. J. Biol. Chem. (2006) [Pubmed]
  5. A Streptomyces coelicolor functional orthologue of Escherichia coli RNase E shows shuffling of catalytic and PNPase-binding domains. Lee, K., Cohen, S.N. Mol. Microbiol. (2003) [Pubmed]
  6. RraA. a protein inhibitor of RNase E activity that globally modulates RNA abundance in E. coli. Lee, K., Zhan, X., Gao, J., Qiu, J., Feng, Y., Meganathan, R., Cohen, S.N., Georgiou, G. Cell (2003) [Pubmed]
  7. Initiation of tRNA maturation by RNase E is essential for cell viability in E. coli. Ow, M.C., Kushner, S.R. Genes Dev. (2002) [Pubmed]
  8. Ribonuclease E organizes the protein interactions in the Escherichia coli RNA degradosome. Vanzo, N.F., Li, Y.S., Py, B., Blum, E., Higgins, C.F., Raynal, L.C., Krisch, H.M., Carpousis, A.J. Genes Dev. (1998) [Pubmed]
  9. Specificity of Escherichia coli endoribonuclease RNase E: in vivo and in vitro analysis of mutants in a bacteriophage T4 mRNA processing site. Ehretsmann, C.P., Carpousis, A.J., Krisch, H.M. Genes Dev. (1992) [Pubmed]
  10. The stability of Escherichia coli lacZ mRNA depends upon the simultaneity of its synthesis and translation. Iost, I., Dreyfus, M. EMBO J. (1995) [Pubmed]
  11. A developmentally regulated Streptomyces endoribonuclease resembles ribonuclease E of Escherichia coli. Hagège, J.M., Cohen, S.N. Mol. Microbiol. (1997) [Pubmed]
  12. Erythromycin inhibition of 50S ribosomal subunit formation in Escherichia coli cells. Usary, J., Champney, W.S. Mol. Microbiol. (2001) [Pubmed]
  13. 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. Morita, T., Kawamoto, H., Mizota, T., Inada, T., Aiba, H. Mol. Microbiol. (2004) [Pubmed]
  14. IS10 mRNA stability and steady state levels in Escherichia coli: indirect effects of translation and role of rne function. Jain, C., Kleckner, N. Mol. Microbiol. (1993) [Pubmed]
  15. The N-terminal domain of the rne gene product has RNase E activity and is non-overlapping with the arginine-rich RNA-binding site. McDowall, K.J., Cohen, S.N. J. Mol. Biol. (1996) [Pubmed]
  16. RNase E polypeptides lacking a carboxyl-terminal half suppress a mukB mutation in Escherichia coli. Kido, M., Yamanaka, K., Mitani, T., Niki, H., Ogura, T., Hiraga, S. J. Bacteriol. (1996) [Pubmed]
  17. RNase E maintenance of proper FtsZ/FtsA ratio required for nonfilamentous growth of Escherichia coli cells but not for colony-forming ability. Tamura, M., Lee, K., Miller, C.A., Moore, C.J., Shirako, Y., Kobayashi, M., Cohen, S.N. J. Bacteriol. (2006) [Pubmed]
  18. Physical locations of genes in the rne (ams)-rpmF-plsX-fab region of the Escherichia coli K-12 chromosome. Oh, W., Larson, T.J. J. Bacteriol. (1992) [Pubmed]
  19. Genetic analysis of disulfide isomerization in Escherichia coli: expression of DsbC is modulated by RNase E-dependent mRNA processing. Zhan, X., Gao, J., Jain, C., Cieslewicz, M.J., Swartz, J.R., Georgiou, G. J. Bacteriol. (2004) [Pubmed]
  20. Two distinct regions on the surface of an RNA-binding domain are crucial for RNase E function. Diwa, A.A., Jiang, X., Schapira, M., Belasco, J.G. Mol. Microbiol. (2002) [Pubmed]
  21. Metabolic block at early stages of the glycolytic pathway activates the Rcs phosphorelay system via increased synthesis of dTDP-glucose in Escherichia coli. El-Kazzaz, W., Morita, T., Tagami, H., Inada, T., Aiba, H. Mol. Microbiol. (2004) [Pubmed]
  22. The Acinetobacter calcoaceticus NCIB8250 mop operon mRNA is differentially degraded, resulting in a higher level of the 3' CatA-encoding segment than of the 5' phenolhydroxylase-encoding portion. Schirmer, F., Hillen, W. Mol. Gen. Genet. (1998) [Pubmed]
  23. RNase E Is Required for Induction of the Glutamate-Dependent Acid Resistance System in Escherichia coli. Takada, A., Umitsuki, G., Nagai, K., Wachi, M. Biosci. Biotechnol. Biochem. (2007) [Pubmed]
  24. Ribonucleases J1 and J2: two novel endoribonucleases in B.subtilis with functional homology to E.coli RNase E. Even, S., Pellegrini, O., Zig, L., Labas, V., Vinh, J., Bréchemmier-Baey, D., Putzer, H. Nucleic Acids Res. (2005) [Pubmed]
  25. Reconstitution of the degradation of the mRNA for ribosomal protein S20 with purified enzymes. Coburn, G.A., Mackie, G.A. J. Mol. Biol. (1998) [Pubmed]
  26. Immunoaffinity purification of the Escherichia coli rne gene product. Evidence that the rne gene encodes the processing endoribonuclease RNase E. Taraseviciene, L., Naureckiene, S., Uhlin, B.E. J. Biol. Chem. (1994) [Pubmed]
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