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Gene Review

rne  -  ribonuclease E

Escherichia coli O157:H7 str. Sakai

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Disease relevance of ECs1462


High impact information on ECs1462

  • Enhanced sequence searches reveal hitherto unidentified S1 domains in RNase E, RNase II, NusA, EMB-5, and other proteins [6].
  • These results show that RNase E has inherent vectorial properties, with its activity depending on the 5' end of its substrates; this can account for the direction of mRNA decay in E. coli, the phenomenon of 'all or none' mRNA decay, and the stabilization provided by 5' stem-loop structures [7].
  • This activity, which leaves a 6-nucleotide adenylate or a 1-nucleotide uridylate remnant on primary transcripts, resides in the amino-terminal region of RNase E and does not require other protein cofactors [8].
  • A mutation that inactivates E. coli RNase E also increases the average lifetime of bulk E. coli mRNA and of many individual messages, suggesting that cleavage by this endonuclease may be the rate-determining step in the degradation of most mRNAs in E. coli [1].
  • The sensitivity of RNase E to 5'-terminal base pairing may explain how determinants near the 5' end can control rates of mRNA decay in bacteria [1].

Chemical compound and disease context of ECs1462


Biological context of ECs1462

  • We report here that RNase E has an unprecedented substrate specificity for an endoribonuclease, as it preferentially cleaves RNAs that have several unpaired nucleotides at the 5' end [1].
  • Autoregulation is mediated in cis by the 361-nucleotide 5' untranslated region (UTR) of rne (RNase E) mRNA [10].
  • Regions for oligomerization were detected in the amino-terminal and central regions of RNase E. Furthermore, polypeptides derived from the highly charged region of RNase E, containing the RhlB binding site, stimulate RhlB activity at least 15-fold, saturating at one polypeptide per RhlB molecule [11].
  • An evolutionarily conserved RNA stem-loop functions as a sensor that directs feedback regulation of RNase E gene expression [10].
  • In fact, recent experiments have suggested that defects in 9S rRNA processing and mRNA decay are not responsible for the lack of cell growth in RNase E mutants [12].

Anatomical context of ECs1462


Associations of ECs1462 with chemical compounds

  • Accumulation of phosphosugars such as glucose-6-phosphate causes a rapid degradation of ptsG mRNA encoding the major glucose transporter IICB(Glc) in an RNase E/degradosome-dependent manner [16].
  • When cells containing the rne plasmid were treated with chloramphenicol, the pre-existing RNase E became less heat labile with time [15].
  • These results indicate that RNase E is required for induction of the glutamate-dependent acid resistance system in a RpoS-independent manner [17].

Physical interactions of ECs1462

  • A single molecule of the RNase E peptide binds asymmetrically in a conserved cleft at the interface of the enolase dimer [18].

Other interactions of ECs1462


Analytical, diagnostic and therapeutic context of ECs1462

  • Here we report the effects of specific sequence changes introduced by site-directed mutagenesis on the location of ribonucleolytic cleavage near the 5' end of pBR322 RNA I in rne-3071 and congenic rne+ E. coli and on cleavage of RNA I by RNase E in vitro [14].
  • 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 [3].
  • Binding sites for RNase E, a component of the RNA degradosome, and RNA were mapped by North-western and Far-western blotting using truncated forms of PAP I [24].
  • Using Northern blot analysis, full-length FinP was found to be stabilized sevenfold in an RNase E-deficient strain [25].


  1. Control of RNase E-mediated RNA degradation by 5'-terminal base pairing in E. coli. Bouvet, P., Belasco, J.G. Nature (1992) [Pubmed]
  2. 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]
  3. 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]
  4. Bacteriophage T7 protein kinase phosphorylates RNase E and stabilizes mRNAs synthesized by T7 RNA polymerase. Marchand, I., Nicholson, A.W., Dreyfus, M. Mol. Microbiol. (2001) [Pubmed]
  5. Polynucleotide phosphorylase, RNase II and RNase E play different roles in the in vivo modulation of polyadenylation in Escherichia coli. Mohanty, B.K., Kushner, S.R. Mol. Microbiol. (2000) [Pubmed]
  6. The solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold. Bycroft, M., Hubbard, T.J., Proctor, M., Freund, S.M., Murzin, A.G. Cell (1997) [Pubmed]
  7. Ribonuclease E is a 5'-end-dependent endonuclease. Mackie, G.A. Nature (1998) [Pubmed]
  8. Poly(A)- and poly(U)-specific RNA 3' tail shortening by E. coli ribonuclease E. Huang, H., Liao, J., Cohen, S.N. Nature (1998) [Pubmed]
  9. Catalytic activation of multimeric RNase E and RNase G by 5'-monophosphorylated RNA. Jiang, X., Belasco, J.G. Proc. Natl. Acad. Sci. U.S.A. (2004) [Pubmed]
  10. An evolutionarily conserved RNA stem-loop functions as a sensor that directs feedback regulation of RNase E gene expression. Diwa, A., Bricker, A.L., Jain, C., Belasco, J.G. Genes Dev. (2000) [Pubmed]
  11. 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]
  12. 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]
  13. Ribosomes inhibit an RNase E cleavage which induces the decay of the rpsO mRNA of Escherichia coli. Braun, F., Le Derout, J., Régnier, P. EMBO J. (1998) [Pubmed]
  14. Effects of nucleotide sequence on the specificity of rne-dependent and RNase E-mediated cleavages of RNA I encoded by the pBR322 plasmid. Lin-Chao, S., Wong, T.T., McDowall, K.J., Cohen, S.N. J. Biol. Chem. (1994) [Pubmed]
  15. The rne gene and ribonuclease E. Miczak, A., Apirion, D. Biochimie (1993) [Pubmed]
  16. Implication of membrane localization of target mRNA in the action of a small RNA: mechanism of post-transcriptional regulation of glucose transporter in Escherichia coli. Kawamoto, H., Morita, T., Shimizu, A., Inada, T., Aiba, H. Genes Dev. (2005) [Pubmed]
  17. 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]
  18. Recognition of enolase in the Escherichia coli RNA degradosome. Chandran, V., Luisi, B.F. J. Mol. Biol. (2006) [Pubmed]
  19. micF RNA is a substrate for RNase E. Schmidt, M., Delihas, N. FEMS Microbiol. Lett. (1995) [Pubmed]
  20. The rpsO mRNA of Escherichia coli is polyadenylated at multiple sites resulting from endonucleolytic processing and exonucleolytic degradation. Haugel-Nielsen, J., Hajnsdorf, E., Regnier, P. EMBO J. (1996) [Pubmed]
  21. Evidence in vivo that the DEAD-box RNA helicase RhlB facilitates the degradation of ribosome-free mRNA by RNase E. Khemici, V., Poljak, L., Toesca, I., Carpousis, A.J. Proc. Natl. Acad. Sci. U.S.A. (2005) [Pubmed]
  22. The catalytic domain of RNase E shows inherent 3' to 5' directionality in cleavage site selection. Feng, Y., Vickers, T.A., Cohen, S.N. Proc. Natl. Acad. Sci. U.S.A. (2002) [Pubmed]
  23. Escherichia coli poly(A)-binding proteins that interact with components of degradosomes or impede RNA decay mediated by polynucleotide phosphorylase and RNase E. Feng, Y., Huang, H., Liao, J., Cohen, S.N. J. Biol. Chem. (2001) [Pubmed]
  24. Poly(A) polymerase I of Escherichia coli: characterization of the catalytic domain, an RNA binding site and regions for the interaction with proteins involved in mRNA degradation. Raynal, L.C., Carpousis, A.J. Mol. Microbiol. (1999) [Pubmed]
  25. Degradation of FinP antisense RNA from F-like plasmids: the RNA-binding protein, FinO, protects FinP from ribonuclease E. Jerome, L.J., van Biesen, T., Frost, L.S. J. Mol. Biol. (1999) [Pubmed]
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