1932

Abstract

mRNA degradation is an important mechanism for controlling gene expression in bacterial cells. This process involves the orderly action of a battery of cellular endonucleases and exonucleases, some universal and others present only in certain species. These ribonucleases function with the assistance of ancillary enzymes that covalently modify the 5′ or 3′ end of RNA or unwind base-paired regions. Triggered by initiating events at either the 5′ terminus or an internal site, mRNA decay occurs at diverse rates that are transcript specific and governed by RNA sequence and structure, translating ribosomes, and bound sRNAs or proteins. In response to environmental cues, bacteria are able to orchestrate widespread changes in mRNA lifetimes by modulating the concentration or specific activity of cellular ribonucleases or by unmasking the mRNA-degrading activity of cellular toxins.

Loading

Article metrics loading...

/content/journals/10.1146/annurev-genet-120213-092340
2014-11-23
2024-06-17
Loading full text...

Full text loading...

/deliver/fulltext/genet/48/1/annurev-genet-120213-092340.html?itemId=/content/journals/10.1146/annurev-genet-120213-092340&mimeType=html&fmt=ahah

Literature Cited

  1. Aït-Bara S, Carpousis AJ. 1.  2010. Characterization of the RNA degradosome of Pseudoalteromonas haloplanktis: conservation of the RNase E-RhlB interaction in the gammaproteobacteria. J. Bacteriol. 192:5413–23 [Google Scholar]
  2. Amblar M, Barbas A, Fialho AM, Arraiano CM. 2.  2006. Characterization of the functional domains of Escherichia coli RNase II. J. Mol. Biol. 360:921–33 [Google Scholar]
  3. Apirion D. 3.  1973. Degradation of RNA in Escherichia coli. A hypothesis. Mol. Gen. Genet. 122:313–22 [Google Scholar]
  4. Apirion D. 4.  1978. Isolation, genetic mapping and some characterization of a mutation in Escherichia coli that affects the processing of ribonucleic acid. Genetics 90:659–71 [Google Scholar]
  5. Arnold TE, Yu J, Belasco JG. 5.  1998. mRNA stabilization by the ompA 5′ untranslated region: two protective elements hinder distinct pathways for mRNA degradation. RNA 4:319–30 [Google Scholar]
  6. Awano N, Rajagopal V, Arbing M, Patel S, Hunt J. 6.  et al. 2010. Escherichia coli RNase R has dual activities, helicase and RNase. J. Bacteriol. 192:1344–52 [Google Scholar]
  7. Babitzke P, Kushner SR. 7.  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 [Google Scholar]
  8. Båga M, Göransson M, Normark S, Uhlin BE. 8.  1988. Processed mRNA with differential stability in the regulation of E. coli pilin gene expression. Cell 52:197–206 [Google Scholar]
  9. Baker KE, Mackie GA. 9.  2003. Ectopic RNase E sites promote bypass of 5′-end-dependent mRNA decay in Escherichia coli. Mol. Microbiol. 47:75–88 [Google Scholar]
  10. Bandyra KJ, Said N, Pfeiffer V, Gorna MW, Vogel J, Luisi BF. 10.  2012. The seed region of a small RNA drives the controlled destruction of the target mRNA by the endoribonuclease RNase E. Mol. Cell 47:943–53 [Google Scholar]
  11. Bechhofer DH, Zen KH. 11.  1989. Mechanism of erythromycin-induced ermC mRNA stability in Bacillus subtilis. J. Bacteriol. 171:5803–11 [Google Scholar]
  12. Belasco JG, Nilsson G, von Gabain A, Cohen SN. 12.  1986. The stability of E. coli gene transcripts is dependent on determinants localized to specific mRNA segments. Cell 46:245–51 [Google Scholar]
  13. Bernstein JA, Lin PH, Cohen SN, Lin-Chao S. 13.  2004. Global analysis of Escherichia coli RNA degradosome function using DNA microarrays. Proc. Natl. Acad. Sci. USA 101:2758–63 [Google Scholar]
  14. Blaszczyk J, Gan J, Tropea JE, Court DL, Waugh DS, Ji X. 14.  2004. Noncatalytic assembly of ribonuclease III with double-stranded RNA. Structure 12:457–66 [Google Scholar]
  15. Bouvet P, Belasco JG. 15.  1992. Control of RNase E-mediated RNA degradation by 5′-terminal base pairing in E. coli. Nature 360:488–91 [Google Scholar]
  16. Braun F, Le Derout J, Regnier P. 16.  1998. Ribosomes inhibit an RNase E cleavage which induces the decay of the rpsO mRNA of Escherichia coli. EMBO J. 17:4790–97 [Google Scholar]
  17. Bricker AL, Belasco JG. 17.  1999. Importance of a 5′ stem-loop for longevity of papA mRNA in Escherichia coli. J. Bacteriol. 181:3587–90 [Google Scholar]
  18. Britton RA, Wen T, Schaefer L, Pellegrini O, Uicker WC. 18.  et al. 2007. Maturation of the 5′ end of Bacillus subtilis 16S rRNA by the essential ribonuclease YkqC/RNase J1. Mol. Microbiol. 63:127–38 [Google Scholar]
  19. Calin-Jageman I, Nicholson AW. 19.  2003. Mutational analysis of an RNA internal loop as a reactivity epitope for Escherichia coli ribonuclease III substrates. Biochemistry 42:5025–34 [Google Scholar]
  20. Callaghan AJ, Marcaida MJ, Stead JA, McDowall KJ, Scott WG, Luisi BF. 20.  2005. Structure of Escherichia coli RNase E catalytic domain and implications for RNA turnover. Nature 437:1187–91 [Google Scholar]
  21. Cao GJ, Sarkar N. 21.  1992. Identification of the gene for an Escherichia coli poly(A) polymerase. Proc. Natl. Acad. Sci. USA 89:10380–84 [Google Scholar]
  22. Caron MP, Bastet L, Lussier A, Simoneau-Roy M, Masse E, Lafontaine DA. 22.  2012. Dual-acting riboswitch control of translation initiation and mRNA decay. Proc. Natl. Acad. Sci. USA 109:E3444–53 [Google Scholar]
  23. Carpousis AJ, Van Houwe G, Ehretsmann C, Krisch HM. 23.  1994. Copurification of E. coli RNAase E and PNPase: evidence for a specific association between two enzymes important in RNA processing and degradation. Cell 76:889–900 [Google Scholar]
  24. Case CC, Simons EL, Simons RW. 24.  1990. The IS10 transposase mRNA is destabilized during antisense RNA control. EMBO J. 9:1259–66 [Google Scholar]
  25. Celesnik H, Deana A, Belasco JG. 25.  2007. Initiation of RNA decay in Escherichia coli by 5′ pyrophosphate removal. Mol. Cell 27:79–90 [Google Scholar]
  26. Chen LH, Emory SA, Bricker AL, Bouvet P, Belasco JG. 26.  1991. Structure and function of a bacterial mRNA stabilizer: analysis of the 5′ untranslated region of ompA mRNA. J. Bacteriol. 173:4578–86 [Google Scholar]
  27. Chen Z, Itzek A, Malke H, Ferretti JJ, Kreth J. 27.  2013. Multiple roles of RNase Y in Streptococcus pyogenes mRNA processing and degradation. J. Bacteriol. 195:2585–94 [Google Scholar]
  28. Cheng ZF, Deutscher MP. 28.  2002. Purification and characterization of the Escherichia coli exoribonuclease RNase R. Comparison with RNase II. J. Biol. Chem. 277:21624–29 [Google Scholar]
  29. Cheng ZF, Deutscher MP. 29.  2005. An important role for RNase R in mRNA decay. Mol. Cell 17:313–18 [Google Scholar]
  30. Cheng ZF, Zuo Y, Li Z, Rudd KE, Deutscher MP. 30.  1998. The vacB gene required for virulence in Shigella flexneri and Escherichia coli encodes the exoribonuclease RNase R. J. Biol. Chem. 273:14077–80 [Google Scholar]
  31. Collins JA, Irnov I, Baker S, Winkler WC. 31.  2007. Mechanism of mRNA destabilization by the glmS ribozyme. Genes Dev. 21:3356–68 [Google Scholar]
  32. Commichau FM, Rothe FM, Herzberg C, Wagner E, Hellwig D. 32.  et al. 2009. Novel activities of glycolytic enzymes in Bacillus subtilis: interactions with essential proteins involved in mRNA processing. Mol. Cell Proteomics 8:1350–60 [Google Scholar]
  33. Datta AK, Niyogi K. 33.  1975. A novel oligoribonuclease of Escherichia coli. II. Mechanism of action. J. Biol. Chem. 250:7313–19 [Google Scholar]
  34. Deana A, Belasco JG. 34.  2004. The function of RNase G in Escherichia coli is constrained by its amino and carboxyl termini. Mol. Microbiol. 51:1205–17 [Google Scholar]
  35. Deana A, Celesnik H, Belasco JG. 35.  2008. The bacterial enzyme RppH triggers messenger RNA degradation by 5′ pyrophosphate removal. Nature 451:355–58 [Google Scholar]
  36. Deikus G, Condon C, Bechhofer DH. 36.  2008. Role of Bacillus subtilis RNase J1 endonuclease and 5′-exonuclease activities in trp leader RNA turnover. J. Biol. Chem. 283:17158–67 [Google Scholar]
  37. Del Favero M, Mazzantini E, Briani F, Zangrossi S, Tortora P, Dehò G. 37.  2008. Regulation of Escherichia coli polynucleotide phosphorylase by ATP. J. Biol. Chem. 283:27355–59 [Google Scholar]
  38. Deltcheva E, Chylinski K, Sharma CM, Gonzales K, Chao Y. 38.  et al. 2011. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471:602–7 [Google Scholar]
  39. Desnoyers G, Bouchard MP, Masse E. 39.  2013. New insights into small RNA-dependent translational regulation in prokaryotes. Trends Genet. 29:92–98 [Google Scholar]
  40. Deutscher MP. 40.  1985. E. coli RNases: making sense of alphabet soup. Cell 40:731–32 [Google Scholar]
  41. Deutscher MP, Marshall GT, Cudny H. 41.  1988. RNase PH: an Escherichia coli phosphate-dependent nuclease distinct from polynucleotide phosphorylase. Proc. Natl. Acad. Sci. USA 85:4710–14 [Google Scholar]
  42. Donovan WP, Kushner SR. 42.  1986. Polynucleotide phosphorylase and ribonuclease II are required for cell viability and mRNA turnover in Escherichia coli K-12. Proc. Natl. Acad. Sci. USA 83:120–24 [Google Scholar]
  43. Dorleans A, Li de la Sierra-Gallay I, Piton J, Zig L, Gilet L. 43.  et al. 2011. Molecular basis for the recognition and cleavage of RNA by the bifunctional 5′-3′ exo/endoribonuclease RNase J. Structure 19:1252–61 [Google Scholar]
  44. Durand S, Gilet L, Bessières P, Nicolas P, Condon C. 44.  2012. Three essential ribonucleases—RNase Y, J1, and III—control the abundance of a majority of Bacillus subtilis mRNAs. PLOS Genet. 8:e1002520 [Google Scholar]
  45. Durand S, Gilet L, Condon C. 45.  2012. The essential function of B. subtilis RNase III is to silence foreign toxin genes. PLOS Genet. 8:e1003181 [Google Scholar]
  46. Durand S, Richard G, Bontems F, Uzan M. 46.  2012. Bacteriophage T4 polynucleotide kinase triggers degradation of mRNAs. Proc. Natl. Acad. Sci. USA 109:7073–78 [Google Scholar]
  47. Dutta T, Deutscher MP. 47.  2009. Catalytic properties of RNase BN/RNase Z from Escherichia coli: RNase BN is both an exo- and endoribonuclease. J. Biol. Chem. 284:15425–31 [Google Scholar]
  48. Emory SA, Bouvet P, Belasco JG. 48.  1992. A 5′-terminal stem-loop structure can stabilize mRNA in Escherichia coli. Genes Dev. 6:135–48 [Google Scholar]
  49. Erce MA, Low JK, March PE, Wilkins MR, Takayama KM. 49.  2009. Identification and functional analysis of RNase E of Vibrio angustum S14 and two-hybrid analysis of its interaction partners. Biochim. Biophys. Acta 1794:1107–14 [Google Scholar]
  50. Even S, Pellegrini O, Zig L, Labas V, Vinh J. 50.  et al. 2005. Ribonucleases J1 and J2: two novel endoribonucleases in B. subtilis with functional homology to E. coli RNase E. Nucleic Acids Res. 33:2141–52 [Google Scholar]
  51. Fang M, Zeisberg WM, Condon C, Ogryzko V, Danchin A, Mechold U. 51.  2009. Degradation of nanoRNA is performed by multiple redundant RNases in Bacillus subtilis. Nucleic Acids Res. 37:5114–25 [Google Scholar]
  52. Figaro S, Durand S, Gilet L, Cayet N, Sachse M, Condon C. 52.  2013. Bacillus subtilis mutants with knockouts of the genes encoding ribonucleases RNase Y and RNase J1 are viable, with major defects in cell morphology, sporulation, and competence. J. Bacteriol. 195:2340–48 [Google Scholar]
  53. Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M. 53.  et al. 2013. STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 41:D808–15 [Google Scholar]
  54. Frazao C, McVey CE, Amblar M, Barbas A, Vonrhein C. 54.  et al. 2006. Unravelling the dynamics of RNA degradation by ribonuclease II and its RNA-bound complex. Nature 443:110–14 [Google Scholar]
  55. Fröhlich KS, Papenfort K, Fekete A, Vogel J. 55.  2013. A small RNA activates CFA synthase by isoform-specific mRNA stabilization. EMBO J. 32:2963–79 [Google Scholar]
  56. Gan J, Tropea JE, Austin BP, Court DL, Waugh DS, Ji X. 56.  2006. Structural insight into the mechanism of double-stranded RNA processing by ribonuclease III. Cell 124:355–66 [Google Scholar]
  57. Gao J, Lee K, Zhao M, Qiu J, Zhan X. 57.  et al. 2006. Differential modulation of E. coli mRNA abundance by inhibitory proteins that alter the composition of the degradosome. Mol. Microbiol. 61:394–406 [Google Scholar]
  58. Ghosh S, Deutscher MP. 58.  1999. Oligoribonuclease is an essential component of the mRNA decay pathway. Proc. Natl. Acad. Sci. USA 96:4372–77 [Google Scholar]
  59. Goldman SR, Sharp JS, Vvedenskaya IO, Livny J, Dove SL, Nickels BE. 59.  2011. NanoRNAs prime transcription initiation in vivo. Mol. Cell 42:817–25 [Google Scholar]
  60. Górna MW, Pietras Z, Tsai YC, Callaghan AJ, Hernández H. 60.  et al. 2010. The regulatory protein RraA modulates RNA-binding and helicase activities of the E. coli RNA degradosome. RNA 16:553–62 [Google Scholar]
  61. Grunberg-Manago M. 61.  1963. Enzymatic synthesis of nucleic acids. Prog. Biophys. Mol. Biol. 13:175–239 [Google Scholar]
  62. Hajnsdorf E, Braun F, Haugel-Nielsen J, Regnier P. 62.  1995. Polyadenylylation destabilizes the rpsO mRNA of Escherichia coli. Proc. Natl. Acad. Sci. USA 92:3973–77 [Google Scholar]
  63. Hajnsdorf E, Régnier P. 63.  2000. Host factor Hfq of Escherichia coli stimulates elongation of poly(A) tails by poly(A) polymerase I. Proc. Natl. Acad. Sci. USA 97:1501–5 [Google Scholar]
  64. Hajnsdorf E, Steier O, Coscoy L, Teysset L, Regnier P. 64.  1994. Roles of RNase E, RNase II and PNPase in the degradation of the rpsO transcripts of Escherichia coli: stabilizing function of RNase II and evidence for efficient degradation in an ams pnp rnb mutant. EMBO J. 13:3368–77 [Google Scholar]
  65. Hambraeus G, Karhumaa K, Rutberg B. 65.  2002. A 5′ stem-loop and ribosome binding but not translation are important for the stability of Bacillus subtilis aprE leader mRNA. Microbiology 148:1795–803 [Google Scholar]
  66. Hansen MJ, Chen LH, Fejzo ML, Belasco JG. 66.  1994. The ompA 5′ untranslated region impedes a major pathway for mRNA degradation in Escherichia coli. Mol. Microbiol. 12:707–16 [Google Scholar]
  67. Hardwick SW, Chan VS, Broadhurst RW, Luisi BF. 67.  2011. An RNA degradosome assembly in Caulobacter crescentus. Nucleic Acids Res. 39:1449–59 [Google Scholar]
  68. Hayes CS, Sauer RT. 68.  2003. Cleavage of the A site mRNA codon during ribosome pausing provides a mechanism for translational quality control. Mol. Cell 12:903–11 [Google Scholar]
  69. Heck C, Balzer A, Fuhrmann O, Klug G. 69.  2000. Initial events in the degradation of the polycistronic puf mRNA in Rhodobacter capsulatus and consequences for further processing steps. Mol. Microbiol. 35:90–100 [Google Scholar]
  70. Hsieh PK, Richards J, Liu Q, Belasco JG. 70.  2013. Specificity of RppH-dependent RNA degradation in Bacillus subtilis. Proc. Natl. Acad. Sci. USA 110:8864–69 [Google Scholar]
  71. Hurley JM, Cruz JW, Ouyang M, Woychik NA. 71.  2011. Bacterial toxin RelE mediates frequent codon-independent mRNA cleavage from the 5′ end of coding regions in vivo. J. Biol. Chem. 286:14770–78 [Google Scholar]
  72. Jäger S, Fuhrmann O, Heck C, Hebermehl M, Schiltz E. 72.  et al. 2001. An mRNA degrading complex in Rhodobacter capsulatus. Nucleic Acids Res. 29:4581–88 [Google Scholar]
  73. Jain C. 73.  2012. Novel role for RNase PH in the degradation of structured RNA. J. Bacteriol. 194:3883–90 [Google Scholar]
  74. Jain C, Belasco JG. 74.  1995. RNase E autoregulates its synthesis by controlling the degradation rate of its own mRNA in Escherichia coli: unusual sensitivity of the rne transcript to RNase E activity. Genes Dev. 9:84–96 [Google Scholar]
  75. Jarrige AC, Mathy N, Portier C. 75.  2001. PNPase autocontrols its expression by degrading a double-stranded structure in the pnp mRNA leader. EMBO J. 20:6845–55 [Google Scholar]
  76. Jiang X, Diwa A, Belasco JG. 76.  2000. Regions of RNase E important for 5′-end-dependent RNA cleavage and autoregulated synthesis. J. Bacteriol. 182:2468–75 [Google Scholar]
  77. Karzai AW, Roche ED, Sauer RT. 77.  2000. The SsrA-SmpB system for protein tagging, directed degradation and ribosome rescue. Nat. Struct. Biol. 7:449–55 [Google Scholar]
  78. Khemici V, Poljak L, Luisi BF, Carpousis AJ. 78.  2008. The RNase E of Escherichia coli is a membrane-binding protein. Mol. Microbiol. 70:799–813 [Google Scholar]
  79. Khemici V, Poljak L, Toesca I, Carpousis AJ. 79.  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 102:6913–18 [Google Scholar]
  80. Kim KS, Manasherob R, Cohen SN. 80.  2008. YmdB: a stress-responsive ribonuclease-binding regulator of E. coli RNase III activity. Genes Dev. 22:3497–508 [Google Scholar]
  81. Koga M, Otsuka Y, Lemire S, Yonesaki T. 81.  2011. Escherichia coli rnlA and rnlB compose a novel toxin-antitoxin system. Genetics 187:123–30 [Google Scholar]
  82. Laalami S, Bessières P, Rocca A, Zig L, Nicolas P, Putzer H. 82.  2013. Bacillus subtilis RNase Y activity in vivo analysed by tiling microarrays. PLOS ONE 8:e54062 [Google Scholar]
  83. Lamontagne B, Elela SA. 83.  2004. Evaluation of the RNA determinants for bacterial and yeast RNase III binding and cleavage. J. Biol. Chem. 279:2231–41 [Google Scholar]
  84. Lee K, Bernstein JA, Cohen SN. 84.  2002. RNase G complementation of rne null mutation identifies functional interrelationships with RNase E in Escherichia coli. Mol. Microbiol. 43:1445–56 [Google Scholar]
  85. Lee K, Zhan X, Gao J, Qiu J, Feng Y. 85.  et al. 2003. RraA: a protein inhibitor of RNase E activity that globally modulates RNA abundance in E. coli. Cell 114:623–34 [Google Scholar]
  86. Lehnik-Habrink M, Newman J, Rothe FM, Solovyova AS, Rodrigues C. 86.  et al. 2011. RNase Y in Bacillus subtilis: a natively disordered protein that is the functional equivalent of RNase E from Escherichia coli. J. Bacteriol. 193:5431–41 [Google Scholar]
  87. Lehnik-Habrink M, Pförtner H, Rempeters L, Pietack N, Herzberg C, Stülke J. 87.  2010. The RNA degradosome in Bacillus subtilis: identification of CshA as the major RNA helicase in the multiprotein complex. Mol. Microbiol. 77:958–71 [Google Scholar]
  88. Lehnik-Habrink M, Schaffer M, Mader U, Diethmaier C, Herzberg C, Stulke J. 88.  2011. RNA processing in Bacillus subtilis: identification of targets of the essential RNase Y. Mol. Microbiol. 81:1459–73 [Google Scholar]
  89. Leroy A, Vanzo NF, Sousa S, Dreyfus M, Carpousis AJ. 89.  2002. Function in Escherichia coli of the non-catalytic part of RNase E: role in the degradation of ribosome-free mRNA. Mol. Microbiol. 45:1231–43 [Google Scholar]
  90. Letunic I, Bork P. 90.  2011. Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res. 39:W475–78 [Google Scholar]
  91. Li de la Sierra-Gallay I, Zig L, Jamalli A, Putzer H. 91.  2008. Structural insights into the dual activity of RNase J. Nat. Struct. Mol. Biol. 15:206–12 [Google Scholar]
  92. Li X, Hirano R, Tagami H, Aiba H. 92.  2006. Protein tagging at rare codons is caused by tmRNA action at the 3′ end of nonstop mRNA generated in response to ribosome stalling. RNA 12:248–55 [Google Scholar]
  93. Li Y, Altman S. 93.  2003. A specific endoribonuclease, RNase P, affects gene expression of polycistronic operon mRNAs. Proc. Natl. Acad. Sci. USA 100:13213–18 [Google Scholar]
  94. Liang W, Malhotra A, Deutscher MP. 94.  2011. Acetylation regulates the stability of a bacterial protein: growth stage-dependent modification of RNase R. Mol. Cell 44:160–66 [Google Scholar]
  95. Liou GG, Chang HY, Lin CS, Lin-Chao S. 95.  2002. DEAD box RhlB RNA helicase physically associates with exoribonuclease PNPase to degrade double-stranded RNA independent of the degradosome-assembling region of RNase E. J. Biol. Chem. 277:41157–62 [Google Scholar]
  96. Liu MF, Cescau S, Mechold U, Wang J, Cohen D. 96.  et al. 2012. Identification of a novel nanoRNase in Bartonella. Microbiology 158:886–95 [Google Scholar]
  97. Loomis WP, Koo JT, Cheung TP, Moseley SL. 97.  2001. A tripeptide sequence within the nascent DaaP protein is required for mRNA processing of a fimbrial operon in Escherichia coli. Mol. Microbiol. 39:693–707 [Google Scholar]
  98. Luciano DJ, Hui MP, Deana A, Foley PL, Belasco KJ, Belasco JG. 98.  2012. Differential control of the rate of 5′-end-dependent mRNA degradation in Escherichia coli. J. Bacteriol. 194:6233–39 [Google Scholar]
  99. Mackie GA. 99.  1998. Ribonuclease E is a 5′-end-dependent endonuclease. Nature 395:720–23 [Google Scholar]
  100. Marchand I, Nicholson AW, Dreyfus M. 100.  2001. Bacteriophage T7 protein kinase phosphorylates RNase E and stabilizes mRNAs synthesized by T7 RNA polymerase. Mol. Microbiol. 42:767–76 [Google Scholar]
  101. Marincola G, Schafer T, Behler J, Bernhardt J, Ohlsen K. 101.  et al. 2012. RNase Y of Staphylococcus aureus and its role in the activation of virulence genes. Mol. Microbiol. 85:817–32 [Google Scholar]
  102. Massé E, Escorcia FE, Gottesman S. 102.  2003. Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli. Genes Dev. 17:2374–83 [Google Scholar]
  103. Mathy N, Benard L, Pellegrini O, Daou R, Wen T, Condon C. 103.  2007. 5′-to-3′ exoribonuclease activity in bacteria: role of RNase J1 in rRNA maturation and 5′ stability of mRNA. Cell 129:681–92 [Google Scholar]
  104. Mathy N, Hebert A, Mervelet P, Benard L, Dorleans A. 104.  et al. 2010. Bacillus subtilis ribonucleases J1 and J2 form a complex with altered enzyme behaviour. Mol. Microbiol. 75:489–98 [Google Scholar]
  105. Matos RG, Barbas A, Gomez-Puertas P, Arraiano CM. 105.  2011. Swapping the domains of exoribonucleases RNase II and RNase R: conferring upon RNase II the ability to degrade dsRNA. Proteins 79:1853–67 [Google Scholar]
  106. Matsunaga J, Simons EL, Simons RW. 106.  1996. RNase III autoregulation: structure and function of rncO, the posttranscriptional “operator.”. RNA 2:1228–40 [Google Scholar]
  107. McCullen CA, Benhammou JN, Majdalani N, Gottesman S. 107.  2010. Mechanism of positive regulation by DsrA and RprA small noncoding RNAs: pairing increases translation and protects rpoS mRNA from degradation. J. Bacteriol. 192:5559–71 [Google Scholar]
  108. McDowall KJ, Cohen SN. 108.  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. 255:349–55 [Google Scholar]
  109. McDowall KJ, Hernandez RG, Lin-Chao S, Cohen SN. 109.  1993. The ams-1 and rne-3071 temperature-sensitive mutations in the ams gene are in close proximity to each other and cause substitutions within a domain that resembles a product of the Escherichia coli mre locus. J. Bacteriol. 175:4245–49 [Google Scholar]
  110. McDowall KJ, Lin-Chao S, Cohen SN. 110.  1994. A+U content rather than a particular nucleotide order determines the specificity of RNase E cleavage. J. Biol. Chem. 269:10790–96 [Google Scholar]
  111. Mechold U, Fang G, Ngo S, Ogryzko V, Danchin A. 111.  2007. YtqI from Bacillus subtilis has both oligoribonuclease and pAp-phosphatase activity. Nucleic Acids Res. 35:4552–61 [Google Scholar]
  112. Melefors O, von Gabain A. 112.  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. 5:857–64 [Google Scholar]
  113. Meng W, Nicholson AW. 113.  2008. Heterodimer-based analysis of subunit and domain contributions to double-stranded RNA processing by Escherichia coli RNase III in vitro. Biochem. J. 410:39–48 [Google Scholar]
  114. Mohanty BK, Kushner SR. 114.  2000. Polynucleotide phosphorylase functions both as a 3′→5′ exonuclease and a poly(A) polymerase in Escherichia coli. Proc. Natl. Acad. Sci. USA 97:11966–71 [Google Scholar]
  115. Moller T, Franch T, Hojrup P, Keene DR, Bachinger HP. 115.  et al. 2002. Hfq: a bacterial Sm-like protein that mediates RNA-RNA interaction. Mol. Cell 9:23–30 [Google Scholar]
  116. Morita T, Kawamoto H, Mizota T, Inada T, Aiba H. 116.  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. 54:1063–75 [Google Scholar]
  117. Morita T, Maki K, Aiba H. 117.  2005. RNase E-based ribonucleoprotein complexes: mechanical basis of mRNA destabilization mediated by bacterial noncoding RNAs. Genes Dev. 19:2176–86 [Google Scholar]
  118. Mott JE, Galloway JL, Platt T. 118.  1985. Maturation of Escherichia coli tryptophan operon mRNA: evidence for 3′ exonucleolytic processing after rho-dependent termination. EMBO J. 4:1887–91 [Google Scholar]
  119. Mudd EA, Krisch HM, Higgins CF. 119.  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. 4:2127–35 [Google Scholar]
  120. Newbury SF, Smith NH, Higgins CF. 120.  1987. Differential mRNA stability controls relative gene expression within a polycistronic operon. Cell 51:1131–43 [Google Scholar]
  121. Newbury SF, Smith NH, Robinson EC, Hiles ID, Higgins CF. 121.  1987. Stabilization of translationally active mRNA by prokaryotic REP sequences. Cell 48:297–310 [Google Scholar]
  122. Nilsson G, Belasco JG, Cohen SN, von Gabain A. 122.  1987. Effect of premature termination of translation on mRNA stability depends on the site of ribosome release. Proc. Natl. Acad. Sci. USA 84:4890–94 [Google Scholar]
  123. Nou X, Kadner RJ. 123.  1998. Coupled changes in translation and transcription during cobalamin-dependent regulation of btuB expression in Escherichia coli. J. Bacteriol. 180:6719–28 [Google Scholar]
  124. Nurmohamed S, Vincent HA, Titman CM, Chandran V, Pears MR. 124.  et al. 2011. Polynucleotide phosphorylase activity may be modulated by metabolites in Escherichia coli. J. Biol. Chem. 286:14315–23 [Google Scholar]
  125. O'Hara EB, Chekanova JA, Ingle CA, Kushner ZR, Peters E, Kushner SR. 125.  1995. Polyadenylylation helps regulate mRNA decay in Escherichia coli. Proc. Natl. Acad. Sci. USA 92:1807–11 [Google Scholar]
  126. Ono M, Kuwano M. 126.  1979. A conditional lethal mutation in an Escherichia coli strain with a longer chemical lifetime of messenger RNA. J. Mol. Biol. 129:343–57 [Google Scholar]
  127. Otsuka Y, Yonesaki T. 127.  2012. Dmd of bacteriophage T4 functions as an antitoxin against Escherichia coli LsoA and RnlA toxins. Mol. Microbiol. 83:669–81 [Google Scholar]
  128. Papenfort K, Sun Y, Miyakoshi M, Vanderpool CK, Vogel J. 128.  2013. Small RNA–mediated activation of sugar phosphatase mRNA regulates glucose homeostasis. Cell 153:426–37 [Google Scholar]
  129. Pertzev AV, Nicholson AW. 129.  2006. Characterization of RNA sequence determinants and antideterminants of processing reactivity for a minimal substrate of Escherichia coli ribonuclease III. Nucleic Acids Res. 34:3708–21 [Google Scholar]
  130. Perwez T, Kushner SR. 130.  2006. RNase Z in Escherichia coli plays a significant role in mRNA decay. Mol. Microbiol. 60:723–37 [Google Scholar]
  131. Pfeiffer V, Papenfort K, Lucchini S, Hinton JC, Vogel J. 131.  2009. Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation. Nat. Struct. Mol. Biol. 16:840–46 [Google Scholar]
  132. Py B, Higgins CF, Krisch HM, Carpousis AJ. 132.  1996. A DEAD-box RNA helicase in the Escherichia coli RNA degradosome. Nature 381:169–72 [Google Scholar]
  133. Ramirez-Peña E, Treviño J, Liu Z, Perez N, Sumby P. 133.  2010. The group A Streptococcus small regulatory RNA FasX enhances streptokinase activity by increasing the stability of the ska mRNA transcript. Mol. Microbiol. 78:1332–47 [Google Scholar]
  134. Richards J, Liu Q, Pellegrini O, Celesnik H, Yao S. 134.  et al. 2011. An RNA pyrophosphohydrolase triggers 5′-exonucleolytic degradation of mRNA in Bacillus subtilis. Mol. Cell 43:940–49 [Google Scholar]
  135. Richards J, Luciano DJ, Belasco JG. 135.  2012. Influence of translation on RppH-dependent mRNA degradation in Escherichia coli. Mol. Microbiol. 86:1063–72 [Google Scholar]
  136. Richards J, Mehta P, Karzai AW. 136.  2006. RNase R degrades non-stop mRNAs selectively in an SmpB-tmRNA-dependent manner. Mol. Microbiol. 62:1700–12 [Google Scholar]
  137. Robertson HD. 137.  1982. Escherichia coli ribonuclease III cleavage sites. Cell 30:669–72 [Google Scholar]
  138. Robertson HD, Webster RE, Zinder ND. 138.  1968. Purification and properties of ribonuclease III from Escherichia coli. J. Biol. Chem. 243:82–91 [Google Scholar]
  139. Roux CM, DeMuth JP, Dunman PM. 139.  2011. Characterization of components of the Staphylococcus aureus mRNA degradosome holoenzyme-like complex. J. Bacteriol. 193:5520–26 [Google Scholar]
  140. Sandler P, Weisblum B. 140.  1989. Erythromycin-induced ribosome stall in the ermA leader: a barricade to 5′-to-3′ nucleolytic cleavage of the ermA transcript. J. Bacteriol. 171:6680–88 [Google Scholar]
  141. Shahbabian K, Jamalli A, Zig L, Putzer H. 141.  2009. RNase Y, a novel endoribonuclease, initiates riboswitch turnover in Bacillus subtilis. EMBO J. 28:3523–33 [Google Scholar]
  142. Sharp JS, Bechhofer DH. 142.  2003. Effect of translational signals on mRNA decay in Bacillus subtilis. J. Bacteriol. 185:5372–79 [Google Scholar]
  143. Sharp JS, Bechhofer DH. 143.  2005. Effect of 5′-proximal elements on decay of a model mRNA in Bacillus subtilis. Mol. Microbiol. 57:484–95 [Google Scholar]
  144. Sim SH, Yeom JH, Shin C, Song WS, Shin E. 144.  et al. 2010. Escherichia coli ribonuclease III activity is downregulated by osmotic stress: consequences for the degradation of bdm mRNA in biofilm formation. Mol. Microbiol. 75:413–25 [Google Scholar]
  145. Spickler C, Mackie GA. 145.  2000. Action of RNase II and polynucleotide phosphorylase against RNAs containing stem-loops of defined structure. J. Bacteriol. 182:2422–27 [Google Scholar]
  146. Stead MB, Marshburn S, Mohanty BK, Mitra J, Pena Castillo L. 146.  et al. 2011. Analysis of Escherichia coli RNase E and RNase III activity in vivo using tiling microarrays. Nucleic Acids Res. 39:3188–203 [Google Scholar]
  147. Stern MJ, Ames GF, Smith NH, Robinson EC, Higgins CF. 147.  1984. Repetitive extragenic palindromic sequences: a major component of the bacterial genome. Cell 37:1015–26 [Google Scholar]
  148. Stickney LM, Hankins JS, Miao X, Mackie GA. 148.  2005. Function of the conserved S1 and KH domains in polynucleotide phosphorylase. J. Bacteriol. 187:7214–21 [Google Scholar]
  149. Storz G, Vogel J, Wassarman KM. 149.  2011. Regulation by small RNAs in bacteria: expanding frontiers. Mol. Cell 43:880–91 [Google Scholar]
  150. Symmons MF, Jones GH, Luisi BF. 150.  2000. A duplicated fold is the structural basis for polynucleotide phosphorylase catalytic activity, processivity, and regulation. Structure 8:1215–26 [Google Scholar]
  151. Taraseviciene L, Miczak A, Apirion D. 151.  1991. The gene specifying RNase E (rne) and a gene affecting mRNA stability (ams) are the same gene. Mol. Microbiol. 5:851–55 [Google Scholar]
  152. Tock MR, Walsh AP, Carroll G, McDowall KJ. 152.  2000. The CafA protein required for the 5′-maturation of 16 S rRNA is a 5′-end-dependent ribonuclease that has context-dependent broad sequence specificity. J. Biol. Chem. 275:8726–32 [Google Scholar]
  153. Vanzo NF, Li YS, Py B, Blum E, Higgins CF. 153.  et al. 1998. Ribonuclease E organizes the protein interactions in the Escherichia coli RNA degradosome. Genes Dev. 12:2770–81 [Google Scholar]
  154. Vincent HA, Deutscher MP. 154.  2009. The roles of individual domains of RNase R in substrate binding and exoribonuclease activity. The nuclease domain is sufficient for digestion of structured RNA. J. Biol. Chem. 284:486–94 [Google Scholar]
  155. von Gabain A, Belasco JG, Schottel JL, Chang AC, Cohen SN. 155.  1983. Decay of mRNA in Escherichia coli: investigation of the fate of specific segments of transcripts. Proc. Natl. Acad. Sci. USA 80:653–57 [Google Scholar]
  156. Xu F, Cohen SN. 156.  1995. RNA degradation in Escherichia coli regulated by 3′ adenylation and 5′ phosphorylation. Nature 374:180–83 [Google Scholar]
  157. Xu F, Lin-Chao S, Cohen SN. 157.  1993. The Escherichia coli pcnB gene promotes adenylylation of antisense RNAI of ColE1-type plasmids in vivo and degradation of RNAI decay intermediates. Proc. Natl. Acad. Sci. USA 90:6756–60 [Google Scholar]
  158. Yamaguchi Y, Park JH, Inouye M. 158.  2011. Toxin-antitoxin systems in bacteria and archaea. Annu. Rev. Genet. 45:61–79 [Google Scholar]
  159. Yao S, Bechhofer DH. 159.  2010. Initiation of decay of Bacillus subtilis rpsO mRNA by endoribonuclease RNase Y. J. Bacteriol. 192:3279–86 [Google Scholar]
  160. Yao S, Sharp JS, Bechhofer DH. 160.  2009. Bacillus subtilis RNase J1 endonuclease and 5′ exonuclease activities in the turnover of ΔermC mRNA. RNA 15:2331–39 [Google Scholar]
  161. Yarchuk O, Jacques N, Guillerez J, Dreyfus M. 161.  1992. Interdependence of translation, transcription and mRNA degradation in the lacZ gene. J. Mol. Biol. 226:581–96 [Google Scholar]
  162. Zhang K, Nicholson AW. 162.  1997. Regulation of ribonuclease III processing by double-helical sequence antideterminants. Proc. Natl. Acad. Sci. USA 94:13437–41 [Google Scholar]
  163. Zuo Y, Deutscher MP. 163.  2001. Exoribonuclease superfamilies: structural analysis and phylogenetic distribution. Nucleic Acids Res. 29:1017–26 [Google Scholar]
/content/journals/10.1146/annurev-genet-120213-092340
Loading
/content/journals/10.1146/annurev-genet-120213-092340
Loading

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error