Gram-negative and gram-positive bacteria use a variety of enzymatic pathways to degrade mRNAs. Although several recent reviews have outlined these pathways, much less attention has been paid to the regulation of mRNA decay. The functional half-life of a particular mRNA, which affects how much protein is synthesized from it, is determined by a combination of multiple factors. These include, but are not necessarily limited to, () stability elements at either the 5′ or the 3′ terminus, () posttranscriptional modifications, () ribosome density on individual mRNAs, () small regulatory RNA (sRNA) interactions with mRNAs, () regulatory proteins that alter ribonuclease binding affinities, () the presence or absence of endonucleolytic cleavage sites, () control of intracellular ribonuclease levels, and () physical location within the cell. Changes in physiological conditions associated with environmental alterations can significantly alter the impact of these factors in the decay of a particular mRNA.


Article metrics loading...

Loading full text...

Full text loading...


Literature Cited

  1. Amster-Choder O. 1.  2011. The compartmentalized vessel: the bacterial cell as a model for subcellular organization (a tale of two studies). Cell Logist. 1:77–81 [Google Scholar]
  2. Andrade JM, Pobre V, Matos AM, Arraiano CM. 2.  2012. The crucial role of PNPase in the degradation of small RNAs that are not associated with Hfq. RNA 18:844–55 [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, Lasser AB. 4.  1978. A conditional lethal mutant of Escherichia coli which affects the processing of ribosomal RNA. J. Biol. Chem. 253:1738–42 [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. August J, Ortiz PJ, Hurwitz J. 6.  1962. Ribonucleic acid-dependent ribonucleotide incorporation. I. Purification and properties of the enzyme. J. Biol. Chem. 237:3786–93 [Google Scholar]
  7. Babitzke P, Granger L, Olszewski J, Kushner SR. 7.  1993. Analysis of mRNA decay and rRNA processing in Escherichia coli multiple mutants carrying a deletion in RNase III. J. Bacteriol. 175:229–39 [Google Scholar]
  8. Babitzke P, Kushner SR. 8.  1991. The Ams (altered mRNA stability) protein and ribonuclease E are encoded by the same structural gene of Escherichia coli. PNAS 88:1–5 [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, Luisi BF. 10.  2013. Licensing and due process in the turnover of bacterial RNA. RNA Biol. 10:627–35 [Google Scholar]
  11. Bandyra KJ, Sinha D, Syrjanen J, Luisi BF, De Lay NR. 11.  2016. The ribonuclease polynucleotide phosphorylase can interact with small regulatory RNAs in both protective and degradative modes. RNA 22:360–72 [Google Scholar]
  12. Bardwell JCA, Regnier P, Chen S-M, Nakamura Y, Grunberg-Manago M, Court DL. 12.  1989. Autoregulation of RNase III operon by mRNA processing. EMBO J. 8:3401–7 [Google Scholar]
  13. Bechhofer D. 13.  1993. 5′ mRNA stabilizers. Control of Messenger RNA Stability J Belasco, G Brawerman 31–35 San Diego, CA: Academic [Google Scholar]
  14. Bechhofer DH, Oussenko IA, Deikus G, Yao S, Mathy N, Condon C. 14.  2008. Analysis of mRNA decay in Bacillus subtilis. Methods Enzymol. 447:259–76 [Google Scholar]
  15. Bernstein JA, Khodursky AB, Lin P-H, Lin-Chao S, Cohen SN. 15.  2002. Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. PNAS 99:9697–702 [Google Scholar]
  16. Blum E, Carpousis AJ, Higgins CF. 16.  1999. Polyadenylation promotes degradation of 3′-structured RNA by the Escherichia coli mRNA degradosome in vitro. J. Biol. Chem. 274:4009–16 [Google Scholar]
  17. Bouvet P, Belasco JG. 17.  1992. Control of RNase E-mediated RNA degradation by 5′ terminal base pairing in E. coli. Nature 360:488–91 [Google Scholar]
  18. Braun F, Le Derout J, Régnier P. 18.  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]
  19. Briani F, Carzaniga T, Deho G. 19.  2016. Regulation and functions of bacterial PNPase. WIREs RNA 7:241–58 [Google Scholar]
  20. Broude NE. 20.  2011. Analysis of RNA localization and metabolism in single live bacterial cells: achievements and challenges. Mol. Microbiol. 80:1137–47 [Google Scholar]
  21. Callaghan AJ, Marcaida MJ, Stead JA, McDowall KJ, Scott WG, Luisi BF. 21.  2005. Structure of Escherichia coli RNase E catalytic domain and implications for RNA turnover. Nature 437:1187–91 [Google Scholar]
  22. Campos-Guillen J, Bralley P, Jones GH, Bechhofer DH, Olmedo-Alvarez G. 22.  2005. Addition of poly(A) and heteropolymeric 3′ ends in B. subtilis wild-type and polynucleotide phosphorylase-deficient strains. J. Bacteriol. 187:4698–706 [Google Scholar]
  23. Cao G-J, Sarkar N. 23.  1992. Identification of the gene for an Escherichia coli poly(A) polymerase. PNAS 89:10380–84 [Google Scholar]
  24. Carabetta VJ, Silhavy TJ, Cristea IM. 24.  2010. The response regulator SprE (RssB) is required for maintaining poly(A) polymerase I-degradosome association during stationary phase. J. Bacteriol. 192:3713–21 [Google Scholar]
  25. Caron MP, Lafontaine DA, Masse E. 25.  2010. Small RNA-mediated regulation at the level of transcript stability. RNA Biol. 7:140–44 [Google Scholar]
  26. Carpousis AJ, Van Houwe G, Ehretsmann C, Krisch HM. 26.  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]
  27. Carzaniga T, Briani F, Zangrossi S, Merlino G, Marchi P, Deho G. 27.  2009. Autogenous regulation of Escherichia coli polynucleotide phosphorylase expression revisited. J. Bacteriol. 191:1738–48 [Google Scholar]
  28. Casarégola S, Jacq A, Laoudj D, McGurk G, Margarson S. 28.  et al. 1992. Cloning and analysis of the entire Escherichia coli ams gene: ams is identical to hmp1 and encodes a 114 kDa protein that migrates as a 180 kDa protein. J. Mol. Biol. 228:30–40 [Google Scholar]
  29. Chen C, Deutscher MP. 29.  2010. RNase R is a highly unstable protein regulated by growth phase and stress. RNA 16:667–72 [Google Scholar]
  30. Cheng Z-F, Deutscher MP. 30.  2005. An important role for RNase R in mRNA decay. Mol. Cell 17:313–18 [Google Scholar]
  31. Cheng Z-F, Deutscher MP. 31.  2002. Purification and characterization of the Escherichia coli exoribonuclease RNase R: comparison with RNase II. J. Biol. Chem. 277:21624–49 [Google Scholar]
  32. Cheng Z-F, Deutscher MP. 32.  2003. Quality control of ribosomal RNA mediated by polynucleotide phosphorylase and RNase R. PNAS 100:6388–93 [Google Scholar]
  33. Cheng Z-F, Zuo Y, Li Z, Rudd KE, Deutscher MP. 33.  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]
  34. Chevrier-Miller M, Jacques N, Raibaud O, Dreyfus M. 34.  1990. Transcription of single-copy hybrid lacZ genes by T7 RNA polymerase in Escherichia coli: mRNA synthesis and degradation can be uncoupled from translation. Nucleic Acids Res. 18:5787–92 [Google Scholar]
  35. Chung D-H, Min Z, Wang B-C, Kushner SR. 35.  2010. Single amino acid changes in the predicted RNase H domain of E. coli RNase G lead to the complementation of RNase E mutants. RNA 16:1371–85 [Google Scholar]
  36. Clarke JE, Kime L, Romero AD, McDowall KJ. 36.  2014. Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli. Nucleic Acids Res. 42:11733–51 [Google Scholar]
  37. Claverie-Martin F, Diaz-Torres MR, Yancey SD, Kushner SR. 37.  1991. Analysis of the altered mRNA stability (ams) gene from Escherichia coli: nucleotide sequence, transcriptional analysis, and homology of its product to MRP3, a mitochondrial ribosomal protein from Neurospora crassa. J. Biol. Chem. 266:2843–51 [Google Scholar]
  38. Datta AK, Niyogi K. 38.  1975. A novel oligoribonuclease of Escherichia coli. II. Mechanism of action. J. Biol. Chem. 250:7313–19 [Google Scholar]
  39. Deana A, Celesnik H, Belasco JG. 39.  2008. The bacterial enzyme RppH triggers messenger RNA degradation by 5′ pyrophosphate removal. Nature 451:355–58 [Google Scholar]
  40. Del Campo C, Bartholomaus A, Fedyunin I, Ignatova Z. 40.  2015. Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function. PLOS Genet. 11:e1005613 [Google Scholar]
  41. Desnoyers G, Bouchard MP, Masse E. 41.  2013. New insights into small RNA-dependent translational regulation in prokaryotes. Trends Genet. 29:92–8 [Google Scholar]
  42. Diestra E, Cayrol B, Arluison V, Risco C. 42.  2009. Cellular electron microscopy imaging reveals the localization of the Hfq protein close to the bacterial membrane. PLOS ONE 4:e8301 [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, Bessieres 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, Tomasini A, Braun F, Condon C, Romby P. 46.  2015. sRNA and mRNA turnover in gram-positive bacteria. FEMS Microbiol. Rev. 39:316–30 [Google Scholar]
  47. Emory SA, Bouvet P, Belasco JG. 47.  1992. A 5′-terminal stem-loop structure can stabilize mRNA in Escherichia coli. Genes Develop. 6:135–48 [Google Scholar]
  48. Even S, Pellegrini O, Zig L, Labas V, Vinh J. 48.  et al. 2005. Ribonuclease 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]
  49. Fang M, Zeisberg WM, Condon C, Ogryzko V, Danchin A, Mechold U. 49.  2009. Degradation of nanoRNA is performed by multiple redundant RNases in Bacillus subtilis. Nucleic Acids Res. 37:5114–25 [Google Scholar]
  50. Foley PL, Hsieh P-K, Luciano DJ, Belasco JG. 50.  2015. Specificity and evolutionary conservation of the Escherichia coli RNA pyrophosphohydrolase RppH. J. Biol. Chem. 2909478–86 [Google Scholar]
  51. Franze de Fernandez MT, Eoyang L, August TL. 51.  1968. Factor fraction required for the synthesis of bacteriophage Qβ-RNA. Nature 219:588–90 [Google Scholar]
  52. Gardner PP, Barquist L, Bateman A, Nawrocki EP, Weinberg Z. 52.  2011. RNIE: genome-wide prediction of bacterial intrinsic terminators. Nucleic Acids Res. 39:5845–52 [Google Scholar]
  53. Ghosh S, Deutscher MP. 53.  1999. Oligoribonuclease is an essential component of the mRNA decay pathway. PNAS 96:4372–77 [Google Scholar]
  54. Golding I, Cox EC. 54.  2004. RNA dynamics in live Escherichia coli cells. PNAS 101:11310–15 [Google Scholar]
  55. Goldman SR, Sharp JS, Vvedenskaya IO, Livny J, Dove SL, Nickels BE. 55.  2011. NanoRNAs prime transcription initiation in vivo. Mol. Cell 42:817–25 [Google Scholar]
  56. Gorna MW, Pietras Z, Tsai YC, Callaghan AJ, Hernandez H. 56.  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]
  57. Gottesman S, Storz G. 57.  2011. Bacterial small RNA regulators: versatile roles and rapidly evolving variations. Cold Spring Harb. Perspect. Biol. 3:a003798 [Google Scholar]
  58. Grunberg-Manago M. 58.  1963. Polynucleotide phosphorylase. Prog. Nucl. Acids Res. 1:93–133 [Google Scholar]
  59. Grunberg-Manago M, Ochoa S. 59.  1955. Enzymatic synthesis and breakdown of polynucleotides-polynucleotide phosphorylase. J. Amer. Chem. Soc. 11:3165–6 [Google Scholar]
  60. Grunberg-Manago M, Ortiz PJ, Ochoa S. 60.  1955. Enzymatic synthesis of nucleic acidlike polynucleotides. Science 122:907–10 [Google Scholar]
  61. Hammarlöf DL, Bergman JM, Garmendia E, Hughes D. 61.  2015. Turnover of mRNAs is one of the essential functions of RNase E. Mol. Microbiol. 98:34–45 [Google Scholar]
  62. Hui MP, Foley PL, Belasco JG. 62.  2014. Messenger RNA degradation in bacterial cells. Annu. Rev. Genet. 48:537–59 [Google Scholar]
  63. Hunt A, Rawlins JP, Thomaides HB, Errington J. 63.  2006. Functional analysis of 11 putative essential genes in Bacillus subtilis. Microbiology 152:2895–907 [Google Scholar]
  64. Ikeda Y, Yagi M, Morita T, Aiba H. 64.  2011. Hfq binding at RhlB-recognition region of RNase E is crucial for the rapid degradation of target mRNAs mediated by sRNAs in Escherichia coli. Mol. Microbiol. 79:419–32 [Google Scholar]
  65. Jain C, Belasco JG. 65.  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 Develop. 9:84–96 [Google Scholar]
  66. Jarrige A-C, Mathy N, Portier C. 66.  2001. PNPase autocontrols its expression by degrading a double-stranded structure in the pnp mRNA leader. EMBO J. 20:6845–55 [Google Scholar]
  67. Jiang X, Belasco JG. 67.  2004. Catalytic activation of multimeric RNase E and RNase G by 5′-monophosphorylated RNA. PNAS 101:9211–16 [Google Scholar]
  68. Joyce SA, Dreyfus M. 68.  1998. In the absence of translation, RNase E can bypass 5′ mRNA stabilizers in Escherichia coli. J. Mol. Biol. 282:241–54 [Google Scholar]
  69. Keiler KC. 69.  2011. RNA localization in bacteria. Curr. Opin. Microbiol. 14:155–59 [Google Scholar]
  70. Khemici V, Carpousis AJ. 70.  2004. The RNA degradosome and poly(A) polymerase of Escherichia coli are required in vivo for the degradation of small mRNA decay intermediates containing REP-stabilizers. Mol. Microbiol. 51:777–90 [Google Scholar]
  71. Khemici V, Poljak L, Luisi BF, Carpousis AJ. 71.  2008. The RNase E of Escherichia coli is a membrane-binding protein. Mol. Microbiol. 70:799–813 [Google Scholar]
  72. Kime L, Clarke JE, Romero AD, Grasby JA, McDowall KJ. 72.  2014. Adjacent single-stranded regions mediate processing of tRNA precursors by RNase E direct entry. Nucleic Acids Res. 42:4577–89 [Google Scholar]
  73. King TC, Sirdeshmukh R, Schlessinger D. 73.  1984. RNase III cleavage is obligate for maturation but not for function of Escherichia coli pre-23S rRNA. PNAS 81:185–88 [Google Scholar]
  74. Kuwano M, Ono M, Endo H, Hori K, Nakamura K. 74.  et al. 1977. Gene affecting longevity of messenger RNA: a mutant of Escherichia coli with altered mRNA stability. Mol. Gen. Genet. 154:279–85 [Google Scholar]
  75. Laalami S, Bessieres P, Rocca A, Zig L, Nicolas P, Putzer H. 75.  2013. Bacillus subtilis RNase Y activity in vivo analysed by tiling microarrays. PLOS ONE 8:e54062 [Google Scholar]
  76. Lalaouna D, Simoneau-Roy M, Lafontaine D, Masse E. 76.  2013. Regulatory RNAs and target mRNA decay in prokaryotes. Biochim. Biophys. Acta 1829:742–47 [Google Scholar]
  77. Lee K, Bernstein JA, Cohen SN. 77.  2002. RNase G complementation of rne null mutation identifies functional interrelationships with RNase E in Escherichia coli. Mol. Microbiol. 43:1445–56 [Google Scholar]
  78. Lee K, Zhan X, Gao J, Feng Y, Meganathan R. 78.  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]
  79. Lehnik-Habrink M, Newman J, Rothe FM, Solovyova AS, Rodrigues C. 79.  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]
  80. Lehnik-Habrink M, Schaffer M, Mader U, Diethmaier C, Herzberg C, Stulke J. 80.  2011. RNA processing in Bacillus subtilis: identification of targets of the essential RNase Y. Mol. Microbiol. 81:1459–73 [Google Scholar]
  81. Li de la Sierra-Gallay I, Zig L, Jamalli A, Putzer H. 81.  2008. Structural insights into the dual activity of RNase J. Nat. Struct. Mol. Biol. 15:206–12 [Google Scholar]
  82. Li Z, Deutscher MP. 82.  2002. RNase E plays an essential role in the maturation of Escherichia coli tRNA precursors. RNA 8:97–109 [Google Scholar]
  83. Li Z, Pandit S, Deutscher MP. 83.  1998. Polyadenylation of stable RNA precursors in vivo. PNAS 95:12158–62 [Google Scholar]
  84. Li Z, Pandit S, Deutscher MP. 84.  1999. RNase G (CafA protein) and RNase E are both required for the 5′ maturation of 16S ribosomal RNA. EMBO J. 18:2878–85 [Google Scholar]
  85. Libby EA, Roggiani M, Goulian M. 85.  2012. Membrane protein expression triggers chromosomal locus repositioning in bacteria. PNAS 109:7445–50 [Google Scholar]
  86. Lim B, Sim SH, Sim M, Kim K, Jeon CO. 86.  et al. 2012. RNase III controls the degradation of corA mRNA in Escherichia coli. J. Bacteriol. 194:2214–20 [Google Scholar]
  87. Link TM, Valentin-Hansen P, Brennan RG. 87.  2009. Structure of Escherichia coli Hfq bound to polyriboadenylate RNA. PNAS 106:19292–97 [Google Scholar]
  88. Liu MF, Cescau S, Mechold U, Wang J, Cohen D. 88.  et al. 2012. Identification of a novel nanoRNase in Bartonella. Microbiology 158:886–95 [Google Scholar]
  89. Lu F, Taghbalout A. 89.  2013. Membrane association via an amino-terminal amphipathic helix is required for the cellular organization and function of RNase II. J. Biol. Chem. 288:7241–51 [Google Scholar]
  90. Mackie GA. 90.  2013. RNase E: at the interface of bacterial RNA processing and decay. Nat. Rev. Microbiol. 11:45–57 [Google Scholar]
  91. Marujo PE, Hajnsdorf E, Le Derout J, Andrade R, Arraiano CM, Regnier P. 91.  2000. RNase II removes the oligo(A) tails that destabilize the rpsO mRNA of Escherichia coli. RNA 6:1185–93 [Google Scholar]
  92. Mathy N, Benard L, Pellegrini O, Daou R, Wen T, Condon C. 92.  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]
  93. Matsunaga J, Simons EL, Simons RW. 93.  1996. RNase III autoregulation: structure and function of rncO, the posttranscriptional “operator.”. RNA 2:1228–40 [Google Scholar]
  94. McDowall KJ, Cohen SN. 94.  1996. The N-terminal domain of the rne gene product has RNase E activity and is non-overlapping with the arginine-rich RNA-binding motif. J. Mol. Biol. 255:349–55 [Google Scholar]
  95. Mechold U, Fang G, Ngo S, Ogryzko V, Danchin A. 95.  2007. YtqI from Bacillus subtilis has both oligoribonuclease and pAp-phosphatase activity. Nucleic Acids Res. 35:4552–61 [Google Scholar]
  96. Mildenhall KB, Wiese N, Chung D, Maples VF, Mohanty BK, Kushner SR. 95a.  2016. RNase E-based degradosome modulates polyadenylation of mRNAs after Rho-independent transcription terminators in Escherichia coli. Mol. Microbiol. In press. doi: 10.1111/mmi.13413 [Google Scholar]
  97. Misra TK, Rhee S, Apirion D. 96.  1976. A new endoribonuclease from Escherichia coli. J. Biol. Chem. 251:7669–74 [Google Scholar]
  98. Mohanty BK, Kushner SR. 97.  1999. Analysis of the function of Escherichia coli poly(A) polymerase I in RNA metabolism. Mol. Microbiol. 34:1094–108 [Google Scholar]
  99. Mohanty BK, Kushner SR. 98.  2000. Polynucleotide phosphorylase functions both as a 3′ → 5′ exonuclease and a poly(A) polymerase in Escherichia coli. PNAS 97:11966–71 [Google Scholar]
  100. Mohanty BK, Kushner SR. 99.  2002. Polyadenylation of Escherichia coli transcripts plays an integral role in regulating intracellular levels of polynucleotide phosphorylase and RNase E. Mol. Microbiol. 45:1315–24 [Google Scholar]
  101. Mohanty BK, Kushner SR. 100.  2003. Genomic analysis in Escherichia coli demonstrates differential roles for polynucleotide phosphorylase and RNase II in mRNA abundance and decay. Mol. Microbiol. 50:645–58 [Google Scholar]
  102. Mohanty BK, Kushner SR. 101.  2006. The majority of Escherichia coli mRNAs undergo post-transcriptional modification in exponentially growing cells. Nucleic Acids Res. 34:5695–704 [Google Scholar]
  103. Mohanty BK, Kushner SR. 102.  2008. Rho-independent transcription terminators inhibit RNase P processing of the secG leuU and metT tRNA polycistronic transcripts in Escherichia coli. Nucleic Acids Res. 36:364–75 [Google Scholar]
  104. Mohanty BK, Kushner SR. 103.  2010. Bacterial/archaeal/organellar polyadenylation. WIREs RNA 2:256–76 [Google Scholar]
  105. Mohanty BK, Kushner SR. 104.  2010. Processing of the Escherichia coli leuX tRNA transcript, encoding tRNAleu5, requires either the 3′→5′ exoribonuclease polynucleotide phosphorylase or RNase P to remove the Rho-independent transcription terminator. Nucleic Acids Res. 38:597–607 [Google Scholar]
  106. Mohanty BK, Kushner SR. 105.  2013. Deregulation of poly(A) polymerase I in Escherichia coli inhibits protein synthesis and leads to cell death. Nucleic Acids Res. 41:1757–66 [Google Scholar]
  107. Mohanty BK, Maples VF, Kushner SR. 106.  2004. The Sm-like protein Hfq regulates polyadenylation dependent mRNA decay in Escherichia coli. Mol. Microbiol. 54:905–20 [Google Scholar]
  108. Mohanty BK, Maples VF, Kushner SR. 107.  2012. Polyadenylation helps regulate functional tRNA levels in Escherichia coli. Nucleic Acids Res. 40:4589–603 [Google Scholar]
  109. Montero Llopis P, Jackson AF, Sliusarenko O, Surovtsev I, Heinritz J. 108.  et al. 2010. Spatial organization of the flow of genetic information in bacteria. Nature 466:77–81 [Google Scholar]
  110. Nevo-Dinur K, Nussbaum-Shochat A, Ben-Yehuda S, Amster-Choder O. 109.  2011. Translation-independent localization of mRNA in E. coli. Science 331:1081–84 [Google Scholar]
  111. Newbury SF, Smith NH, Higgins CF. 110.  1987. Differential mRNA stability controls relative gene expression within a polycistronic operon. Cell 51:1131–43 [Google Scholar]
  112. Newbury SF, Smith NH, Robinson EC, Hiles ID, Higgins CF. 111.  1987. Stabilization of translationally active mRNA by prokaryotic REP sequences. Cell 48:297–310 [Google Scholar]
  113. Niyogi SK, Datta AK. 112.  1975. A novel oligoribonuclease of Escherichia coli. I. Isolation and properties. J. Biol. Chem. 250:7307–12 [Google Scholar]
  114. Nossal NG, Singer MF. 113.  1968. The processive degradation of individual polynucleotide chains. J. Biol. Chem. 243:913–22 [Google Scholar]
  115. O'Hara EB, Chekanova JA, Ingle CA, Kushner ZR, Peters E, Kushner SR. 114.  1995. Polyadenylylation helps regulate mRNA decay in Escherichia coli. PNAS 92:1807–11 [Google Scholar]
  116. Okada Y, Wachi M, Hirata A, Suzuki K, Nagai K, Matsuhashi M. 115.  1994. Cytoplasmic axial filaments in Escherichia coli cells: possible function in the mechanism of chromosome segregation and cell division. J. Bacteriol. 176:917–22 [Google Scholar]
  117. Ono M, Kuwano M. 116.  1979. A conditional lethal mutation in an Escherichia coli strain with a longer chemical lifetime of mRNA. J. Mol. Biol. 129:343–57 [Google Scholar]
  118. Opdyke JA, Fozo EM, Hemm MR, Storz G. 117.  2011. RNase III participates in GadY-dependent cleavage of the gadX-gadW mRNA. J. Mol. Biol. 406:29–43 [Google Scholar]
  119. Ow MC, Kushner SR. 118.  2002. Initiation of tRNA maturation by RNase E is essential for cell viability in E. coli. Genes Dev. 16:1102–15 [Google Scholar]
  120. Ow MC, Liu Q, Kushner SR. 119.  2000. Analysis of mRNA decay and rRNA processing in Escherichia coli in the absence of RNase E-based degradosome assembly. Mol. Microbiol. 38:854–66 [Google Scholar]
  121. Ow MC, Perwez T, Kushner SR. 120.  2003. RNase G of Escherichia coli exhibits only limited functional overlap with its essential homologue, RNase E. Mol. Microbiol. 49:607–22 [Google Scholar]
  122. Perwez T, Hami D, Maples VF, Min Z, Wang BC, Kushner SR. 121.  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. 36:5306–18 [Google Scholar]
  123. Perwez T, Kushner SR. 122.  2006. RNase Z in Escherichia coli plays a significant role in mRNA decay. Mol. Microbiol. 60:723–37 [Google Scholar]
  124. Pobre V, Arraiano CM. 123.  2015. Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli. BMC Genomics 16:72 [Google Scholar]
  125. Py B, Higgins CF, Krisch HM, Carpousis AJ. 124.  1996. A DEAD-box RNA helicase in the Escherichia coli RNA degradosome. Nature 381:169–72 [Google Scholar]
  126. Regnier P, Grunberg-Manago M. 125.  1989. Cleavage by RNase III in the transcripts of the metY-nus-infB operon of Escherichia coli releases the tRNA and initiates the decay of the downstream mRNA. J. Mol. Biol. 210:293–302 [Google Scholar]
  127. Richards J, Belasco JG. 126.  2016. Distinct requirements for 5′-monophosphate-assisted RNA cleavage by Escherichia coli RNase E and RNase G. J. Biol. Chem. 2915038–48 [Google Scholar]
  128. Richards J, Liu Q, Pellegrini O, Celesnik H, Yao S. 127.  et al. 2011. An RNA pyrophosphohydrolase triggers 5′-exonucleolytic degradation of mRNA in Bacillus subtilis. Mol. Cell 43:940–49 [Google Scholar]
  129. Robertson HD, Webster RE, Zinder ND. 128.  1967. A nuclease specific for double-stranded RNA. Virology 12:718–19 [Google Scholar]
  130. Romby P, Charpentier E. 129.  2010. An overview of RNAs with regulatory functions in gram-positive bacteria. Cell Mol. Life Sci. 67:217–37 [Google Scholar]
  131. Russell JH, Keiler KC. 130.  2009. Subcellular localization of a bacterial regulatory RNA. PNAS 106:16405–9 [Google Scholar]
  132. Schuck A, Diwa A, Belasco JG. 131.  2009. RNase E autoregulates its synthesis in Escherichia coli by binding directly to a stem-loop in the rne 5′ untranslated region. Mol. Microbiol. 72:470–78 [Google Scholar]
  133. Schumacher MA, Pearson RF, Moller T, Valentin-Hansen P, Brennan RG. 132.  2002. Structures of the pleiotropic translational regulator Hfq and an Hfq-RNA complex: a bacterial Sm-like protein. EMBO J. 21:3546–56 [Google Scholar]
  134. Shahbabian K, Jamalli A, Zig L, Putzer H. 133.  2009. RNase Y, a novel endoribonuclease, initiates riboswitch turnover in Bacillus subtilis. EMBO J. 28:3523–33 [Google Scholar]
  135. Shulman RG, Brown TR, Ugurbil K, Ogawa S, Cohen SM. Hollander JA. 134. , den 1979. Cellular applications of 31P and 13C nuclear magnetic resonance. Science 205:160–66 [Google Scholar]
  136. Silva IJ, Saramago M, Dressaire C, Domingues S, Viegas SC, Arraiano CM. 135.  2011. Importance and key events of prokaryotic RNA decay: the ultimate fate of an RNA molecule. WIREs RNA 2:818–36 [Google Scholar]
  137. Sohlberg B, Huang J, Cohen SN. 136.  2003. The Streptomyces coelicolor polynucleotide phosphorylase homologue, and not the putative poly(A) polymerase, can polyadenylate RNA. J. Bacteriol. 185:7273–78 [Google Scholar]
  138. Spickler C, Mackie GA. 137.  2000. Action of RNase II and polynucleotide phosphorylase against RNAs containing stem-loops of defined structure. J. Bacteriol. 182:2422–27 [Google Scholar]
  139. Spickler C, Stronge V, Mackie GA. 138.  2001. Preferential cleavage of degradative intermediates of rpsT mRNA by the Escherichia coli RNA degradosome. J. Bacteriol. 183:1106–9 [Google Scholar]
  140. Stead MB, Marshburn S, Mohanty BK, Mitra J, Pena Castillo L. 139.  et al. 2010. Analysis of E. coli RNase E and RNase III activity in vivo using tiling microarrays. Nucleic Acids Res. 39:3188–203 [Google Scholar]
  141. Storz G, Altuvia S, Wassarman KM. 140.  2005. An abundance of RNA regulators. Annu. Rev. Biochem. 74:199–217 [Google Scholar]
  142. Storz G, Vogel J, Wassarman KM. 141.  2011. Regulation by small RNAs in bacteria: expanding frontiers. Mol. Cell 43:880–91 [Google Scholar]
  143. Strahl H, Turlan C, Khalid S, Bond PJ, Kebalo JM. 142.  et al. 2015. Membrane recognition and dynamics of the RNA degradosome. PLOS Genet. 11:e1004961 [Google Scholar]
  144. Taghbalout A, Rothfield L. 143.  2008. New insights into the cellular organization of the RNA processing and degradation machinery of Escherichia coli. Mol. Microbiol. 70:780–82 [Google Scholar]
  145. Tock MR, Walsh AP, Carroll G, McDowall KJ. 144.  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]
  146. Valencia-Burton M, McCullough RM, Cantor CR, Broude NE. 145.  2007. RNA visualization in live bacterial cells using fluorescent protein complementation. Nat. Methods 4:421–27 [Google Scholar]
  147. Valencia-Burton M, Shah A, Sutin J, Borogovac A, McCullough RM. 146.  et al. 2009. Spatiotemporal patterns and transcription kinetics of induced RNA in single bacterial cells. PNAS 106:16399–404 [Google Scholar]
  148. Vanzo NF, Li YS, Py B, Blum E, Higgins CF. 147.  et al. 1998. Ribonuclease E organizes the protein interactions in the Escherichia coli RNA degradosome. Genes Dev. 12:2770–81 [Google Scholar]
  149. Vincent HA, Deutscher MP. 148.  2006. Substrate recognition and catalysis by the exoribonuclease RNase R. J. Biol. Chem. 281:29769–75 [Google Scholar]
  150. Vogel J, Argaman L, Wagner EG, Altuvia S. 149.  2004. The small RNA IstR inhibits synthesis of an SOS-induced toxic peptide. Curr. Biol. 14:2271–76 [Google Scholar]
  151. Vogel J, Luisi BF. 150.  2011. Hfq and its constellation of RNA. Nat. Rev. Microbiol. 9:578–89 [Google Scholar]
  152. Wachi M, Umitsuki G, Nagai K. 151.  1997. Functional relationship between Escherichia coli RNase E and the CafA protein. Mol. Gen. Genet. 253:515–19 [Google Scholar]
  153. Wachi M, Umitsuki G, Shimizu M, Takada A, Nagai K. 152.  1999. Escherichia coli cafA gene encodes a novel RNase, designated as RNase G, involved in processing of the 59 end of 16S rRNA. Biochem. Biophys. Res. Commun. 289:1301–6 [Google Scholar]
  154. Waters LS, Storz G. 153.  2009. Regulatory RNAs in bacteria. Cell 136:615–28 [Google Scholar]
  155. Weill L, Belloc E, Bava FA, Mendez R. 154.  2012. Translational control by changes in poly(A) tail length: recycling mRNAs. Nat. Struct. Mol. Biol. 19:577–85 [Google Scholar]
  156. Yehudai-Resheff S, Hirsh M, Schuster G. 155.  2001. Polynucleotide phosphorylase functions as both an exonuclease and a poly(A) polymerase in spinach chloroplasts. Mol. Cell. Biol. 21:5408–16 [Google Scholar]
  157. Yehudai-Resheff S, Schuster G. 156.  2000. Characterization of the E. coli poly(A) polymerase: nucleotide specificity, RNA-binding affinities and RNA structure dependence. Nucleic Acids Res. 28:1139–44 [Google Scholar]
  158. Zilhao R, Cairrao R, Régnier P, Arraiano CM. 157.  1996. PNPase modulates RNase II expression in Escherichia coli: implications for mRNA decay and cell metabolism. Mol. Microbiol. 20:1033–42 [Google Scholar]
  159. Zuo Y, Vincent HA, Zhang J, Wang Y, Deutscher MP, Malhotra A. 158.  2006. Structural basis for processivity and single-strand specificity of RNase II. Mol. Cell 24:149–56 [Google Scholar]

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