Chapter 4 : Small RNAs Regulate Primary and Secondary Metabolism in Gram-negative Bacteria

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in

Small RNAs Regulate Primary and Secondary Metabolism in Gram-negative Bacteria, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555818883/9781555818869_Chap04-1.gif /docserver/preview/fulltext/10.1128/9781555818883/9781555818869_Chap04-2.gif


A diverse palette of novel small regulatory RNAs (sRNAs) has been identified in bacteria in recent years, and many play important roles in regulating gene expression and adaptation to constantly changing physiological and metabolic needs. To date, more than a hundred sRNAs have been identified and characterized in gram-negative bacteria, with crucial and sometimes global regulatory functions that can easily rival protein regulators. The most studied and widely dispersed class of sRNAs in gram-negative bacteria act post-transcriptionally by base pairing to target mRNAs in order to effect positive or negative regulatory outcomes.

Citation: Bobrovskyy M, Vanderpool C, Richards G. 2015. Small RNAs Regulate Primary and Secondary Metabolism in Gram-negative Bacteria, p 59-94. In Conway T, Cohen P (ed), Metabolism and Bacterial Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MBP-0009-2014
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


Image of Figure 1
Figure 1

Simplified network of sRNAs regulating biofilm formation and motility in . The regulatory network shows a set of sRNAs (in bold) and relevant protein factors (grey boxes) controlling (blue circle), (red circle) and (violet circle) at the transcriptional (dashed lines), translational (solid lines) and protein (dotted lines) levels. Other factors known to regulate , , and were omitted for clarity. Arrows indicate activating interactions, and lines with blunt ends indicate inhibitory interactions.

Citation: Bobrovskyy M, Vanderpool C, Richards G. 2015. Small RNAs Regulate Primary and Secondary Metabolism in Gram-negative Bacteria, p 59-94. In Conway T, Cohen P (ed), Metabolism and Bacterial Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MBP-0009-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 2
Figure 2

Quorum sensing systems of . uses histidine kinases CqsS and LuxPQ to sense autoinducers (AIs) CAI-1 (violet triangle) and AI-2 (orange triangle) respectively. Receptors function as kinases at low cell density (LCD), when concentrations of CAI-1 and AI-2, which are produced by CqsA and LuxS, respectively, are low. This stimulates σ-dependent activation of gene expression through LuxU and LuxO phosphorylation cascade. The Qrr 1-4 sRNAs (red square), facilitated by Hfq, activate , which stimulates expression of , a known activator of the major virulence factors. Additionally Qrr 1-4 repress , which leads to polysaccharide production and biofilm formation. Qrr 1-4 also negatively regulate genes for biogenesis of type VI secretion system (T6SS). In contrast, at high cell density (HCD) receptors sense the presence of AIs and function as phosphatases that stimulate dephosphorylation of LuxU, resulting in cessation of expression. In the absence of Qrr sRNAs, expression increases, which leads to the inhibition of biofilm formation and shut down of virulence factor production, while stimulating T6SS biosynthesis. Lines with arrowheads indicate activating interactions, and lines with blunt ends indicate inhibitory interactions.

Citation: Bobrovskyy M, Vanderpool C, Richards G. 2015. Small RNAs Regulate Primary and Secondary Metabolism in Gram-negative Bacteria, p 59-94. In Conway T, Cohen P (ed), Metabolism and Bacterial Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MBP-0009-2014
Permissions and Reprints Request Permissions
Download as Powerpoint


1. Masse E,, Salvail H,, Desnoyers G,, Arguin M . 2007. Small RNAs controlling iron metabolism. Cur Opin Microbiol 10 : 140 145.[PubMed] [CrossRef]
2. Vanderpool CK,, Gottesman S . 2007. The novel transcription factor SgrR coordinates the response to glucose-phosphate stress. J Bacteriol 189 : 2238 2248.[PubMed] [CrossRef]
3. Altuvia S,, Weinstein-Fischer D,, Zhang A,, Postow L,, Storz G . 1997. A small, stable RNA induced by oxidative stress: role as a pleiotropic regulator and antimutator. Cell 90 : 43 53.[PubMed] [CrossRef]
4. Frohlich KS,, Papenfort K,, Berger AA,, Vogel J . 2012. A conserved RpoS-dependent small RNA controls the synthesis of major porin OmpD. Nucleic Acids Res 40 : 3623 3640.[PubMed] [CrossRef]
5. Boysen A,, Moller-Jensen J,, Kallipolitis B,, Valentin-Hansen P,, Overgaard M . 2010. Translational regulation of gene expression by an anaerobically induced small non-coding RNA in Escherichia coli . J Biol Chem 285 : 10690 10702.[PubMed] [CrossRef]
6. Storz G,, Vogel J,, Wassarman KM . 2011. Regulation by small RNAs in bacteria: expanding frontiers. Mol Cell 43 : 880 891.[PubMed] [CrossRef]
7. Richards GR,, Vanderpool CK . 2011. Molecular call and response: the physiology of bacterial small RNAs. Biochim Biophys Acta 1809 : 525 531.[PubMed] [CrossRef]
8. Hoe CH,, Raabe CA,, Rozhdestvensky TS,, Tang TH . 2013. Bacterial sRNAs: regulation in stress. Int J Med Microbiol 303 : 217 229.[PubMed] [CrossRef]
9. Opdyke JA,, Kang JG,, Storz G . 2004. GadY, a small-RNA regulator of acid response genes in Escherichia coli . J Bacteriol 186 : 6698 6705.[PubMed] [CrossRef]
10. Kawano M,, Aravind L,, Storz G . 2007. An antisense RNA controls synthesis of an SOS-induced toxin evolved from an antitoxin. Mol Microbiol 64 : 738 754.[PubMed] [CrossRef]
11. Toledo-Arana A,, Dussurget O,, Nikitas G,, Sesto N,, Guet-Revillet H,, Balestrino D,, Loh E,, Gripenland J,, Tiensuu T,, Vaitkevicius K,, Barthelemy M,, Vergassola M,, Nahori MA,, Soubigou G,, Regnault B,, Coppee JY,, Lecuit M,, Johansson J,, Cossart P . 2009. The Listeria transcriptional landscape from saprophytism to virulence. Nature 459 : 950 956.[PubMed] [CrossRef]
12. Lee E-J,, Groisman E . 2010. An antisense RNA that governs the expression kinetics of a multifunctional virulence gene. Mol Microbiol 76 : 1020 1033.[PubMed] [CrossRef]
13. Stazic D,, Lindell D,, Steglich C . 2011. Antisense RNA protects mRNA from RNase E degradation by RNA-RNA duplex formation during phage infection. Nucleic Acids Res 39 : 4890 4899.[PubMed] [CrossRef]
14. Wurtzel O,, Sesto N,, Mellin JR,, Karunker I,, Edelheit S,, Becavin C,, Archambaud C,, Cossart P,, Sorek R . 2012. Comparative transcriptomics of pathogenic and non-pathogenic Listeria species. Mol Sys Biol 8 : 583. [PubMed] [CrossRef]
15. Simons R,, Kleckner N . 1983. Translational control of IS10 transposition. Cell 34 : 683 691.[PubMed] [CrossRef]
16. Landt S,, Abeliuk E,, McGrath P,, Lesley J,, McAdams H,, Shapiro L . 2008. Small non-coding RNAs in Caulobacter crescentus . Mol Microbiol 68 : 600 614.[PubMed] [CrossRef]
17. Padalon-Brauch G,, Hershberg R,, Elgrably-Weiss M,, Baruch K,, Rosenshine I,, Margalit H,, Altuvia S . 2008. Small RNAs encoded within genetic islands of Salmonella typhimurium show host-induced expression and role in virulence. Nucleic Acids Res 36 : 1913 1927.[PubMed] [CrossRef]
18. Waters JL,, Salyers AA . 2012. The small RNA RteR inhibits transfer of the Bacteroides conjugative transposon CTnDOT. J Bacteriol 194 : 5228 5236.[PubMed] [CrossRef]
19. Fozo E,, Kawano M,, Fontaine F,, Kaya Y,, Mendieta K,, Jones K,, Ocampo A,, Rudd K,, Storz G . 2008. Repression of small toxic protein synthesis by the Sib and OhsC small RNAs. Mol Microbiol 70 : 1076 1093.[PubMed] [CrossRef]
20. Fozo E,, Makarova K,, Shabalina S,, Yutin N,, Koonin E,, Storz G . 2010. Abundance of type I toxin-antitoxin systems in bacteria: searches for new candidates and discovery of novel families. Nucleic Acids Res 38 : 3743 3759.[PubMed] [CrossRef]
21. Georg J,, Hess W . 2011. cis-antisense RNA, another level of gene regulation in bacteria. Microbiol Mol Biol Rev 75 : 286 300.[PubMed] [CrossRef]
22. Morfeldt E,, Taylor D,, von Gabain A,, Arvidson S . 1995. Activation of alpha-toxin translation in Staphylococcus aureus by the trans-encoded antisense RNA, RNAIII. EMBO J 14 : 4569 4577.[PubMed]
23. Lease RA,, Cusick ME,, Belfort M . 1998. Riboregulation in Escherichia coli: DsrA RNA acts by RNA:RNA interactions at multiple loci. Proc Natl Acad Sci U S A 95 : 12456 12461.[PubMed] [CrossRef]
24. Prevost K,, Salvail H,, Desnoyers G,, Jacques JF,, Phaneuf E,, Masse E . 2007. The small RNA RyhB activates the translation of shiA mRNA encoding a permease of shikimate, a compound involved in siderophore synthesis. Mol Microbiol 64 : 1260 1273.[PubMed] [CrossRef]
25. Sledjeski DD,, Gupta A,, Gottesman S . 1996. The small RNA, DsrA, is essential for the low temperature expression of RpoS during exponential growth in Escherichia coli . EMBO J 15 : 3993 4000.[PubMed]
26. Majdalani N,, Chen S,, Murrow J,, St John K,, Gottesman S . 2001. Regulation of RpoS by a novel small RNA: the characterization of RprA. Mol Microbiol 39 : 1382 1394.[PubMed] [CrossRef]
27. Mandin P,, Gottesman S . 2010. Integrating anaerobic/aerobic sensing and the general stress response through the ArcZ small RNA. EMBO J 29 : 3094 3107.[PubMed] [CrossRef]
28. Brown L,, Elliott T . 1997. Mutations that increase expression of the rpoS gene and decrease its dependence on hfq function in Salmonella typhimurium. J Bacteriol 179 : 656 662.[PubMed]
29. Cunning C,, Brown L,, Elliott T . 1998. Promoter substitution and deletion analysis of upstream region required for rpoS translational regulation. J Bacteriol 180 : 4564 4570.[PubMed]
30. Majdalani N,, Cunning C,, Sledjeski D,, Elliott T,, Gottesman S . 1998. DsrA RNA regulates translation of RpoS message by an anti-antisense mechanism, independent of its action as an antisilencer of transcription. Proc Natl Acad Sci U S A 95 : 12462 12467.[PubMed] [CrossRef]
31. Majdalani N,, Hernandez D,, Gottesman S . 2002. Regulation and mode of action of the second small RNA activator of RpoS translation, RprA. Mol Microbiol 46 : 813 826.[PubMed] [CrossRef]
32. Mackie G . 1998. Ribonuclease E is a 5′-end-dependent endonuclease. Nature 395 : 720 723.[PubMed] [CrossRef]
33. Papenfort K,, Sun Y,, Miyakoshi M,, Vanderpool CK,, Vogel J . 2013. Small RNA-mediated activation of sugar phosphatase mRNA regulates glucose homeostasis. Cell 153 : 426 437.[PubMed] [CrossRef]
34. Frohlich KS,, Papenfort K,, Fekete A,, Vogel J . 2013. A small RNA activates CFA synthase by isoform-specific mRNA stabilization. EMBO J 32 : 2963 2979.[PubMed] [CrossRef]
35. Koonin EV,, Tatusov RL . 1994. Computer analysis of bacterial haloacid dehalogenases defines a large superfamily of hydrolases with diverse specificity. Application of an iterative approach to database search. J Mol Biol 244 : 125 132.[PubMed] [CrossRef]
36. Morita T,, Mochizuki Y,, Aiba H . 2006. Translational repression is sufficient for gene silencing by bacterial small noncoding RNAs in the absence of mRNA destruction. Proc Natl Acad Sci U S A 103 : 4858 4863.[PubMed] [CrossRef]
37. Sharma CM,, Darfeuille F,, Plantinga TH,, Vogel J . 2007. A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome-binding sites. Genes Dev 21 : 2804 2817.[PubMed] [CrossRef]
38. Yang Q,, Figueroa-Bossi N,, Bossi L . 2014. Translation enhancing ACA motifs and their silencing by a bacterial small regulatory RNA. PLoS Genet 10 : e1004026. [PubMed] [CrossRef]
39. Darfeuille F,, Unoson C,, Vogel J,, Wagner EG . 2007. An antisense RNA inhibits translation by competing with standby ribosomes. Mol Cell 26 : 381 392.[PubMed] [CrossRef]
40. Vecerek B,, Moll I,, Blasi U . 2007. Control of Fur synthesis by the non-coding RNA RyhB and iron-responsive decoding. EMBO J 26 : 965 975.[PubMed] [CrossRef]
41. Beyer D,, Skripkin E,, Wadzack J,, Nierhaus KH . 1994. How the ribosome moves along the mRNA during protein synthesis. J Biol Chem 269 : 30713 30717.[PubMed]
42. Huttenhofer A,, Noller HF . 1994. Footprinting mRNA-ribosome complexes with chemical probes. EMBO J 13 : 3892 3901.[PubMed]
43. Bouvier M,, Sharma CM,, Mika F,, Nierhaus KH,, Vogel J . 2008. Small RNA binding to 5′ mRNA coding region inhibits translational initiation. Mol Cell 32 : 827 837.[PubMed] [CrossRef]
44. Holmqvist E,, Reimegard J,, Sterk M,, Grantcharova N,, Romling U,, Wagner EG . 2010. Two antisense RNAs target the transcriptional regulator CsgD to inhibit curli synthesis. EMBO J 29 : 1840 1850.[PubMed] [CrossRef]
45. Desnoyers G,, Masse E . 2012. Noncanonical repression of translation initiation through small RNA recruitment of the RNA chaperone Hfq. Genes Devel 26 : 726 739.[PubMed] [CrossRef]
46. Desnoyers G,, Bouchard MP,, Masse E . 2013. New insights into small RNA-dependent translational regulation in prokaryotes. Trends Genet 29 : 92 98.[PubMed] [CrossRef]
47. Sonnleitner E,, Gonzalez N,, Sorger-Domenigg T,, Heeb S,, Richter AS,, Backofen R,, Williams P,, Huttenhofer A,, Haas D,, Blasi U . 2011. The small RNA PhrS stimulates synthesis of the Pseudomonas aeruginosa quinolone signal. Mol Microbiol 80 : 868 885.[PubMed] [CrossRef]
48. Masse E,, Gottesman S . 2002. A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli . Proc Natl Acad Sci U S A 99 : 4620 4625.[PubMed] [CrossRef]
49. Masse E,, Escorcia FE,, Gottesman S . 2003. Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli . Genes Devel 17 : 2374 2383.[PubMed] [CrossRef]
50. Morita T,, Maki K,, Aiba H . 2005. RNase E-based ribonucleoprotein complexes: mechanical basis of mRNA destabilization mediated by bacterial noncoding RNAs. Genes Devel 19 : 2176 2186.[PubMed] [CrossRef]
51. Moller T,, Franch T,, Udesen C,, Gerdes K,, Valentin-Hansen P . 2002. Spot 42 RNA mediates discoordinate expression of the E. coli galactose operon. Genes Devel 16 : 1696 1706.[PubMed] [CrossRef]
52. Pfeiffer V,, Papenfort K,, Lucchini S,, Hinton J,, Vogel Jr . 2009. Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation. Nat Struct Mol Biol 16 : 840 846.[PubMed] [CrossRef]
53. Carpousis AJ,, Luisi BF,, McDowall KJ . 2009. Endonucleolytic initiation of mRNA decay in Escherichia coli . Prog Mol Biol Transl Sci 85 : 91 135.[PubMed] [CrossRef]
54. Viegas SC,, Silva IJ,, Saramago M,, Domingues S,, Arraiano CM . 2011. Regulation of the small regulatory RNA MicA by ribonuclease III: a target-dependent pathway. Nucleic Acids Res 39 : 2918 2930.[PubMed] [CrossRef]
55. Sneppen K,, Dodd I,, Shearwin K,, Palmer A,, Schubert R,, Callen B,, Egan J . 2005. A mathematical model for transcriptional interference by RNA polymerase traffic in Escherichia coli . J Mol Biol 346 : 399 409.[PubMed] [CrossRef]
56. Crampton N,, Bonass W,, Kirkham J,, Rivetti C,, Thomson N . 2006. Collision events between RNA polymerases in convergent transcription studied by atomic force microscopy. Nucleic Acids Res 34 : 5416 5425.[PubMed] [CrossRef]
57. Callen B,, Shearwin K,, Egan J . 2004. Transcriptional interference between convergent promoters caused by elongation over the promoter. Mol Cell 14 : 647 656.[PubMed] [CrossRef]
58. Palmer A,, Ahlgren-Berg A,, Egan J,, Dodd I,, Shearwin K . 2009. Potent transcriptional interference by pausing of RNA polymerases over a downstream promoter. Mol Cell 34 : 545 555.[PubMed] [CrossRef]
59. Andre G,, Even S,, Putzer H,, Burguiere P,, Croux C,, Danchin A,, Martin-Verstraete I,, Soutourina O . 2008. S-box and T-box riboswitches and antisense RNA control a sulfur metabolic operon of Clostridium acetobutylicum . Nucleic Acids Res 36 : 5955 5969.[PubMed] [CrossRef]
60. Stork M,, Di Lorenzo M,, Welch T,, Crosa J . 2007. Transcription termination within the iron transport-biosynthesis operon of Vibrio anguillarum requires an antisense RNA. J Bacteriol 189 : 3479 3488.[PubMed] [CrossRef]
61. Giangrossi M,, Prosseda G,, Tran C,, Brandi A,, Colonna B,, Falconi M . 2010. A novel antisense RNA regulates at transcriptional level the virulence gene icsA of Shigella flexneri . Nucleic Acids Res 38 : 3362 3375.[PubMed] [CrossRef]
62. Wassarman K,, Storz G . 2000. 6S RNA regulates E. coli RNA polymerase activity. Cell 101 : 613 623.[PubMed] [CrossRef]
63. Barrick J,, Sudarsan N,, Weinberg Z,, Ruzzo W,, Breaker R . 2005. 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter. RNA 11 : 774 784.[PubMed] [CrossRef]
64. Trotochaud A,, Wassarman K . 2005. A highly conserved 6S RNA structure is required for regulation of transcription. Nat Struct Mol Biol 12 : 313 319.[PubMed] [CrossRef]
65. Trotochaud A,, Wassarman K . 2004. 6S RNA function enhances long-term cell survival. J Bacteriol 186 : 4978 4985.[PubMed] [CrossRef]
66. Cavanagh AT,, Klocko AD,, Liu X,, Wassarman KM . 2008. Promoter specificity for 6S RNA regulation of transcription is determined by core promoter sequences and competition for region 4.2 of sigma70. Mol Microbiol 67 : 1242 1256.[PubMed] [CrossRef]
67. Klocko AD,, Wassarman KM . 2009. 6S RNA binding to Esigma(70) requires a positively charged surface of sigma(70) region 4.2. Mol Microbiol 73 : 152 164.[PubMed] [CrossRef]
68. Dulebohn D,, Choy J,, Sundermeier T,, Okan N,, Karzai A . 2007. Trans-translation: the tmRNA-mediated surveillance mechanism for ribosome rescue, directed protein degradation, and nonstop mRNA decay. Biochemistry 46 : 4681 4693.[PubMed] [CrossRef]
69. Shpanchenko O,, Golovin A,, Bugaeva E,, Isaksson L,, Dontsova O . 2010. Structural aspects of trans-translation. IUBMB Life 62 : 120 124.[PubMed]
70. Keiler KC,, Waller PR,, Sauer RT . 1996. Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA. Science 271 : 990 993.[PubMed] [CrossRef]
71. Withey JH,, Friedman DI . 2003. A salvage pathway for protein structures: tmRNA and trans-translation. Annu Rev Microbiol 57 : 101 123.[PubMed] [CrossRef]
72. Williams KP,, Bartel DP . 1996. Phylogenetic analysis of tmRNA secondary structure. RNA 2 : 1306 1310.[PubMed]
73. Felden B,, Himeno H,, Muto A,, Atkins JF,, Gesteland RF . 1996. Structural organization of Escherichia coli tmRNA. Biochimie 78 : 979 983.[PubMed] [CrossRef]
74. Komine Y,, Kitabatake M,, Yokogawa T,, Nishikawa K,, Inokuchi H . 1994. A tRNA-like structure is present in 10Sa RNA, a small stable RNA from Escherichia coli . Proc Natl Acad Sci U S A 91 : 9223 9227.[PubMed] [CrossRef]
75. Karzai AW,, Roche ED,, Sauer RT . 2000. The SsrA-SmpB system for protein tagging, directed degradation and ribosome rescue. Nat Struct Biol 7 : 449 455.[PubMed] [CrossRef]
76. Babitzke P,, Romeo T . 2007. CsrB sRNA family: sequestration of RNA-binding regulatory proteins. Curr Opin Microbiol 10 : 156 163.[PubMed] [CrossRef]
77. Timmermans J,, Van Melderen L . 2010. Post-transcriptional global regulation by CsrA in bacteria. Cell Mol Life Sci 67 : 2897 2908.[PubMed] [CrossRef]
78. Carmichael GG,, Weber K,, Niveleau A,, Wahba AJ . 1975. The host factor required for RNA phage Qbeta RNA replication in vitro. Intracellular location, quantitation, and purification by polyadenylate-cellulose chromatography. J Biol Chem 250 : 3607 3612.[PubMed]
79. Kajitani M,, Kato A,, Wada A,, Inokuchi Y,, Ishihama A . 1994. Regulation of the Escherichia coli hfq gene encoding the host factor for phage Q beta. J Bacteriol 176 : 531 534.[PubMed]
80. Ali Azam T,, Iwata A,, Nishimura A,, Ueda S,, Ishihama A . 1999. Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. J Bacteriol 181 : 6361 6370.[PubMed]
81. Weichenrieder O . 2014. RNA binding by Hfq and ring-forming (L)Sm proteins: A trade-off between optimal sequence readout and RNA backbone conformation. RNA Biol 11( 5) : 537 549.[PubMed] [CrossRef]
82. Franze de Fernandez MT,, Eoyang L,, August JT . 1968. Factor fraction required for the synthesis of bacteriophage Qbeta-RNA. Nature 219 : 588 590.[PubMed] [CrossRef]
83. Franze de Fernandez MT,, Hayward WS,, August JT . 1972. Bacterial proteins required for replication of phage Q ribonucleic acid. Pruification and properties of host factor I, a ribonucleic acid-binding protein. J Biol Chem 247 : 824 831.[PubMed]
84. Tsui HC,, Leung HC,, Winkler ME . 1994. Characterization of broadly pleiotropic phenotypes caused by an hfq insertion mutation in Escherichia coli K-12. Mol Microbiol 13 : 35 49.[PubMed] [CrossRef]
85. Sittka A,, Pfeiffer V,, Tedin K,, Vogel J . 2007. The RNA chaperone Hfq is essential for the virulence of Salmonella typhimurium. Mol Microbiol 63 : 193 217.[PubMed] [CrossRef]
86. Hayashi-Nishino M,, Fukushima A,, Nishino K . 2012. Impact of hfq on the intrinsic drug resistance of Salmonella enterica serovar typhimurium. Front Microbiol 3 : 205. [PubMed] [CrossRef]
87. Sittka A,, Lucchini S,, Papenfort K,, Sharma CM,, Rolle K,, Binnewies TT,, Hinton JC,, Vogel J . 2008. Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq. PLoS Genet 4 : e1000163. [PubMed] [CrossRef]
88. Muffler A,, Traulsen DD,, Fischer D,, Lange R,, Hengge-Aronis R . 1997. The RNA-binding protein HF-I plays a global regulatory role which is largely, but not exclusively, due to its role in expression of the sigmaS subunit of RNA polymerase in Escherichia coli . J Bacteriol 179 : 297 300.[PubMed]
89. Tsui HC,, Feng G,, Winkler ME . 1997. Negative regulation of mutS and mutH repair gene expression by the Hfq and RpoS global regulators of Escherichia coli K-12. J Bacteriol 179 : 7476 7487.[PubMed]
90. Vytvytska O,, Moll I,, Kaberdin VR,, von Gabain A,, Blasi U . 2000. Hfq (HF1) stimulates ompA mRNA decay by interfering with ribosome binding. Genes Dev 14 : 1109 1118.[PubMed]
91. Vecerek B,, Moll I,, Blasi U . 2005. Translational autocontrol of the Escherichia coli hfq RNA chaperone gene. RNA 11 : 976 984.[PubMed] [CrossRef]
92. Salvail H,, Caron MP,, Belanger J,, Masse E . 2013. Antagonistic functions between the RNA chaperone Hfq and an sRNA regulate sensitivity to the antibiotic colicin. EMBO J 32 : 2764 2778.[PubMed] [CrossRef]
93. Sauer E . 2013. Structure and RNA-binding properties of the bacterial LSm protein Hfq. RNA Biol 10 : 610 618.[PubMed] [CrossRef]
94. Panja S,, Woodson SA . 2012. Hexamer to monomer equilibrium of E. coli Hfq in solution and its impact on RNA annealing. J Mol Biol 417 : 406 412.[PubMed] [CrossRef]
95. Link TM,, Valentin-Hansen P,, Brennan RG . 2009. Structure of Escherichia coli Hfq bound to polyriboadenylate RNA. Proc Natl Acad Sci U S A 106 : 19292 19297.[PubMed] [CrossRef]
96. Mikulecky PJ,, Kaw MK,, Brescia CC,, Takach JC,, Sledjeski DD,, Feig AL . 2004. Escherichia coli Hfq has distinct interaction surfaces for DsrA, rpoS and poly(A) RNAs. Nat Struct Mol Biol 11 : 1206 1214.[PubMed] [CrossRef]
97. Zhang A,, Schu DJ,, Tjaden BC,, Storz G,, Gottesman S . 2013. Mutations in Interaction Surfaces Differentially Impact E. coli Hfq Association with Small RNAs and Their mRNA Targets. J Mol Biol 425( 19) : 3678 3697.[PubMed] [CrossRef]
98. Sauer E,, Schmidt S,, Weichenrieder O . 2012. Small RNA binding to the lateral surface of Hfq hexamers and structural rearrangements upon mRNA target recognition. Proc Natl Acad Sci U S A 109 : 9396 9401.[PubMed] [CrossRef]
99. Robinson KE,, Orans J,, Kovach AR,, Link TM,, Brennan RG . 2014. Mapping Hfq-RNA interaction surfaces using tryptophan fluorescence quenching. Nucleic Acids Res 42 : 2736 2749.[PubMed] [CrossRef]
100. Valentin-Hansen P,, Eriksen M,, Udesen C . 2004. The bacterial Sm-like protein Hfq: a key player in RNA transactions. Mol Microbiol 51 : 1525 1533.[PubMed] [CrossRef]
101. Ishikawa H,, Otaka H,, Maki K,, Morita T,, Aiba H . 2012. The functional Hfq-binding module of bacterial sRNAs consists of a double or single hairpin preceded by a U-rich sequence and followed by a 3′ poly(U) tail. RNA 18 : 1062 1074.[PubMed] [CrossRef]
102. Otaka H,, Ishikawa H,, Morita T,, Aiba H . 2011. PolyU tail of rho-independent terminator of bacterial small RNAs is essential for Hfq action. Proc Natl Acad Sci U S A 108( 32) : 13059 13064.[PubMed] [CrossRef]
103. Soper TJ,, Woodson SA . 2008. The rpoS mRNA leader recruits Hfq to facilitate annealing with DsrA sRNA. RNA 14 : 1907 1917.[PubMed] [CrossRef]
104. Salim NN,, Faner MA,, Philip JA,, Feig AL . 2012. Requirement of upstream Hfq-binding (ARN)x elements in glmS and the Hfq C-terminal region for GlmS upregulation by sRNAs GlmZ and GlmY. Nucleic Acids Res 40 : 8021 8032.[PubMed] [CrossRef]
105. Salim NN,, Feig AL . 2010. An upstream Hfq binding site in the fhlA mRNA leader region facilitates the OxyS-fhlA interaction. PLoS One 5( 9) : e13028. [PubMed] [CrossRef]
106. Sledjeski DD,, Whitman C,, Zhang A . 2001. Hfq is necessary for regulation by the untranslated RNA DsrA. J Bacteriol 183 : 1997 2005.[PubMed] [CrossRef]
107. Zhang A,, Wassarman KM,, Ortega J,, Steven AC,, Storz G . 2002. The Sm-like Hfq protein increases OxyS RNA interaction with target mRNAs. Molec Cell 9 : 11 22.[PubMed] [CrossRef]
108. Fender A,, Elf J,, Hampel K,, Zimmermann B,, Wagner EG . 2010. RNAs actively cycle on the Sm-like protein Hfq. Genes Develop 24 : 2621 2626.[PubMed] [CrossRef]
109. Hopkins JF,, Panja S,, Woodson SA . 2011. Rapid binding and release of Hfq from ternary complexes during RNA annealing. Nucleic Acids Res 39 : 5193 5202.[PubMed] [CrossRef]
110. Maki K,, Morita T,, Otaka H,, Aiba H . 2010. A minimal base-pairing region of a bacterial small RNA SgrS required for translational repression of ptsG mRNA. Molecular Microbiol 76 : 782 792.[PubMed] [CrossRef]
111. Soper T,, Mandin P,, Majdalani N,, Gottesman S,, Woodson SA . 2010. Positive regulation by small RNAs and the role of Hfq. Proc Natl Acad Sci U S A 107 : 9602 9607.[PubMed] [CrossRef]
112. Adamson DN,, Lim HN . 2011. Essential requirements for robust signaling in Hfq dependent small RNA networks. PLoS Comput Biol 7 : e1002138. [PubMed] [CrossRef]
113. Hussein R,, Lim HN . 2011. Disruption of small RNA signaling caused by competition for Hfq. Proc Natl Acad Sci U S A 108 : 1110 1115.[PubMed] [CrossRef]
114. Moon K,, Gottesman S . 2011. Competition among Hfq-binding small RNAs in Escherichia coli . Mol Microbiol 82 : 1545 1562.[PubMed] [CrossRef]
115. Sukhodolets MV,, Garges S . 2003. Interaction of Escherichia coli RNA polymerase with the ribosomal protein S1 and the Sm-like ATPase Hfq. Biochemistry 42 : 8022 8034.[PubMed] [CrossRef]
116. Rabhi M,, Espeli O,, Schwartz A,, Cayrol B,, Rahmouni AR,, Arluison V,, Boudvillain M . 2011. The Sm-like RNA chaperone Hfq mediates transcription antitermination at Rho-dependent terminators. EMBO J 30 : 2805 2816.[PubMed] [CrossRef]
117. Hajnsdorf E,, Regnier P . 2000. Host factor Hfq of Escherichia coli stimulates elongation of poly(A) tails by poly(A) polymerase I. Proc Natl Acad Sci U S A 97 : 1501 1505.[PubMed] [CrossRef]
118. Ikeda Y,, Yagi M,, Morita T,, Aiba H . 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 : 419 432.[PubMed] [CrossRef]
119. De Lay N,, Gottesman S . 2011. Role of polynucleotide phosphorylase in sRNA function in Escherichia coli . RNA 17 : 1172 1189.[PubMed] [CrossRef]
120. Mohanty BK,, Maples VF,, Kushner SR . 2004. The Sm-like protein Hfq regulates polyadenylation dependent mRNA decay in Escherichia coli . Mol Microbiol 54 : 905 920.[PubMed] [CrossRef]
121. Bandyra KJ,, Luisi BF . 2013. Licensing and due process in the turnover of bacterial RNA. RNA Biol 10 : 627 635.[PubMed] [CrossRef]
122. Belasco JG . 2010. All things must pass: contrasts and commonalities in eukaryotic and bacterial mRNA decay. Nature reviews. Mol Cell Biol 11 : 467 478.[PubMed] [CrossRef]
123. Carpousis AJ . 2007. The RNA degradosome of Escherichia coli: an mRNA-degrading machine assembled on RNase E. Ann Rev Microbiol 61 : 71 87.[PubMed] [CrossRef]
124. Bandyra KJ,, Said N,, Pfeiffer V,, Gorna MW,, Vogel J,, Luisi BF . 2012. The seed region of a small RNA drives the controlled destruction of the target mRNA by the endoribonuclease RNase E. Mol Cell 47 : 943 953.[PubMed] [CrossRef]
125. Jiang X,, Belasco JG . 2004. Catalytic activation of multimeric RNase E and RNase G by 5′-monophosphorylated RNA. Proc Natl Acad Sci U S A 101 : 9211 9216.[PubMed] [CrossRef]
126. Dreyfus M . 2009. Killer and protective ribosomes. Prog Mol Biol Transl Sci 85 : 423 466.[PubMed]
127. Joyce SA,, Dreyfus M . 1998. In the absence of translation, RNase E can bypass 5′ mRNA stabilizers in Escherichia coli . J Mol Biol 282 : 241 254.[PubMed] [CrossRef]
128. Deana A,, Belasco JG . 2005. Lost in translation: the influence of ribosomes on bacterial mRNA decay. Genes Dev 19 : 2526 2533.[PubMed] [CrossRef]
129. Prevost K,, Desnoyers G,, Jacques JF,, Lavoie F,, Masse E . 2011. Small RNA-induced mRNA degradation achieved through both translation block and activated cleavage. Genes Dev 25 : 385 396.[PubMed] [CrossRef]
130. Davies BW,, Walker GC . 2008. A highly conserved protein of unknown function is required by Sinorhizobium meliloti for symbiosis and environmental stress protection. J Bacteriol 190 : 1118 1123.[PubMed] [CrossRef]
131. Vercruysse M,, Kohrer C,, Davies BW,, Arnold MF,, Mekalanos JJ,, RajBhandary UL,, Walker GC . 2014. The Highly Conserved Bacterial RNase YbeY Is Essential in Vibrio cholerae, Playing a Critical Role in Virulence, Stress Regulation, and RNA Processing. PLoS Pathog 10 : e1004175. [PubMed] [CrossRef]
132. Meister G . 2013. Argonaute proteins: functional insights and emerging roles. Nat Rev Genet 14 : 447 459.[PubMed] [CrossRef]
133. Jacob AI,, Kohrer C,, Davies BW,, RajBhandary UL,, Walker GC . 2013. Conserved bacterial RNase YbeY plays key roles in 70S ribosome quality control and 16S rRNA maturation. Mol Cell 49 : 427 438.[PubMed] [CrossRef]
134. Davies BW,, Kohrer C,, Jacob AI,, Simmons LA,, Zhu J,, Aleman LM,, Rajbhandary UL,, Walker GC . 2010. Role of Escherichia coli YbeY, a highly conserved protein, in rRNA processing. Mol Microbiol 78 : 506 518.[PubMed] [CrossRef]
135. Pandey SP,, Minesinger BK,, Kumar J,, Walker GC . 2011. A highly conserved protein of unknown function in Sinorhizobium meliloti affects sRNA regulation similar to Hfq. Nucleic Acids Res 39 : 4691 4708.[PubMed] [CrossRef]
136. Pandey SP,, Winkler JA,, Li H,, Camacho DM,, Collins JJ,, Walker GC . 2014. Central role for RNase YbeY in Hfq-dependent and Hfq-independent small-RNA regulation in bacteria. BMC Genomics 15 : 121. [PubMed] [CrossRef]
137. Englesberg E,, Anderson RL,, Weinberg R,, Lee N,, Hoffee P,, Huttenhauer G,, Boyer H . 1962. L-Arabinose-sensitive, L-ribulose 5-phosphate 4-epimerase-deficient mutants of Escherichia coli . J Bacteriol 84 : 137 146.[PubMed]
138. Horler RS,, Vanderpool CK . 2009. Homologs of the small RNA SgrS are broadly distributed in enteric bacteria but have diverged in size and sequence. Nucleic Acids Res 37 : 5465 5476.[PubMed] [CrossRef]
139. Martinez-Hackert E,, Stock AM . 1997. Structural relationships in the OmpR family of winged-helix transcription factors. J Mol Biol 269 : 301 312.[PubMed] [CrossRef]
140. Tam R,, Saier MH Jr . 1993. Structural, functional, and evolutionary relationships among extracellular solute-binding receptors of bacteria. Microbiol Rev 57 : 320 346.[PubMed]
141. Vanderpool CK,, Gottesman S . 2004. Involvement of a novel transcriptional activator and small RNA in post-transcriptional regulation of the glucose phosphoenolpyruvate phosphotransferase system. Mol Microbiol 54 : 1076 1089.[PubMed] [CrossRef]
142. Kawamoto H,, Koide Y,, Morita T,, Aiba H . 2006. Base-pairing requirement for RNA silencing by a bacterial small RNA and acceleration of duplex formation by Hfq. Mol Microbiol 61 : 1013 1022.[PubMed] [CrossRef]
143. Wadler C,, Vanderpool C . 2007. A dual function for a bacterial small RNA: SgrS performs base pairing-dependent regulation and encodes a functional polypeptide. Proc Natl Acad Sci U S A 104 : 20454 20459.[PubMed] [CrossRef]
144. Rice J,, Vanderpool C . 2011. The small RNA SgrS controls sugar-phosphate accumulation by regulating multiple PTS genes. Nucleic Acids Res 39 : 3806 3819.[PubMed] [CrossRef]
145. Rice JB,, Balasubramanian D,, Vanderpool CK . 2012. Small RNA binding-site multiplicity involved in translational regulation of a polycistronic mRNA. Proc Natl Acad Sci U S A 109 : e2691 e2698.[PubMed] [CrossRef]
146. Richards GR,, Vivas EI,, Andersen AW,, Rivera-Santos D,, Gilmore S,, Suen G,, Goodrich-Blair H . 2009. Isolation and characterization of Xenorhabdus nematophila transposon insertion mutants defective in lipase activity against Tween. J Bacteriol 191 : 5325 5331.[PubMed] [CrossRef]
147. Papenfort K,, Podkaminski D,, Hinton JC,, Vogel J . 2012. The ancestral SgrS RNA discriminates horizontally acquired Salmonella mRNAs through a single G-U wobble pair. Proc Natl Acad Sci U S A 109 : e757 e764.[PubMed] [CrossRef]
148. Jiang X,, Rossanese OW,, Brown NF,, Kujat-Choy S,, Galan JE,, Finlay BB,, Brumell JH . 2004. The related effector proteins SopD and SopD2 from Salmonella enterica serovar Typhimurium contribute to virulence during systemic infection of mice. Mol Microbiol 54 : 1186 1198.[PubMed] [CrossRef]
149. Sun Y,, Vanderpool CK . 2011. Regulation and function of Escherichia coli sugar efflux transporter A (SetA) during glucose-phosphate stress. J Bacteriol 193 : 143 153.[PubMed] [CrossRef]
150. Liu JY,, Miller PF,, Willard J,, Olson ER . 1999. Functional and biochemical characterization of Escherichia coli sugar efflux transporters. J Biol Chem 274 : 22977 22984.[PubMed] [CrossRef]
151. Kim SH,, Schneider BL,, Reitzer L . 2010. Genetics and regulation of the major enzymes of alanine synthesis in Escherichia coli . J Bacteriol 192 : 5304 5311.[PubMed] [CrossRef]
152. Vanderpool CK . 2007. Physiological consequences of small RNA-mediated regulation of glucose-phosphate stress. Curr Opin Microbiol 10 : 146 151.[PubMed] [CrossRef]
153. Richards GR,, Vanderpool CK . 2012. Induction of the Pho regulon suppresses the growth defect of an Escherichia coli sgrS mutant, connecting phosphate metabolism to the glucose-phosphate stress response. J Bacteriol 194 : 2520 2530.[PubMed] [CrossRef]
154. Sun Y,, Vanderpool CK . 2013. Physiological consequences of multiple-target regulation by the small RNA SgrS in Escherichia coli . J Bacteriol 195 : 4804 4815.[PubMed] [CrossRef]
155. Horler R,, Vanderpool C . 2009. Homologs of the small RNA SgrS are broadly distributed in enteric bacteria but have diverged in size and sequence. Nucleic Acids Res 37 : 5465 5476.[PubMed] [CrossRef]
156. Wadler C,, Vanderpool C . 2009. Characterization of homologs of the small RNA SgrS reveals diversity in function. Nucleic Acids Res 37 : 5477 5485.[PubMed] [CrossRef]
157. Balasubramanian D,, Vanderpool CK . 2013. Deciphering the interplay between two independent functions of the small RNA regulator SgrS in Salmonella . J Bacteriol 195 : 4620 4630.[PubMed] [CrossRef]
158. Kimata K,, Tanaka Y,, Inada T,, Aiba H . 2001. Expression of the glucose transporter gene, ptsG, is regulated at the mRNA degradation step in response to glycolytic flux in Escherichia coli . EMBO J 20 : 3587 3595.[PubMed] [CrossRef]
159. Morita T,, El-Kazzaz W,, Tanaka Y,, Inada T,, Aiba H . 2003. Accumulation of glucose 6-phosphate or fructose 6-phosphate is responsible for destabilization of glucose transporter mRNA in Escherichia coli . J Biol Chem 278 : 15608 15614.[PubMed] [CrossRef]
160. Richards GR,, Patel MV,, Lloyd CR,, Vanderpool CK . 2013. Depletion of glycolytic intermediates plays a key role in glucose-phosphate stress in Escherichia coli . J Bacteriol 195 : 4816 4825.[PubMed] [CrossRef]
161. Morita T,, El-Kazzaz W,, Tanaka Y,, Inada T,, Aiba H . 2003. Accumulation of glucose 6-phosphate or fructose 6-phosphate is responsible for destabilization of glucose transporter mRNA in Escherichia coli . J Biol Chem 278 : 15608 15614.[PubMed] [CrossRef]
162. Møller T,, Franch T,, Udesen C,, Gerdes K,, Valentin-Hansen P . 2002. Spot 42 RNA mediates discoordinate expression of the E. coli galactose operon. Genes Develop 16 : 1696 1706.[PubMed] [CrossRef]
163. Adhya S, . 1987. The galactose operon, p 1503 1512. In Neidhardt FC,, Ingraham JL,, Curtiss R (ed), Escherichia coli and Salmonella typhimurium: Cellular and molecular biology. ASM Press, Washington, D.C.
164. Beisel CL,, Storz G . 2011. The base-pairing RNA spot 42 participates in a multioutput feedforward loop to help enact catabolite repression in Escherichia coli . Mol Cell 41 : 286 297.[PubMed] [CrossRef]
165. Rice PW,, Dahlberg JE . 1982. A gene between polA and glnA retards growth of Escherichia coli when present in multiple copies: physiological effects of the gene for spot 42 RNA. J Bacteriol 152 : 1196 1210.[PubMed]
166. Polayes DA,, Rice PW,, Garner MM,, Dahlberg JE . 1988. Cyclic AMP-cyclic AMP receptor protein as a repressor of transcription of the spf gene of Escherichia coli . J Bacteriol 170 : 3110 3114.[PubMed]
167. Sahagan B,, Dahlberg JE . 1979. A small, unstable RNA molecule of Escherichia coli: Spot 42 RNA. J Mol Biol 131 : 593 605.[PubMed] [CrossRef]
168. Joseph E,, Danchin A,, Ullmann A . 1981. Regulation of galactose operon expression: glucose effects and role of cyclic adenosine 3′,5′-monophosphate. J Bacteriol 146 : 149 154.[PubMed]
169. Queen C,, Rosenberg M . 1981. Differential translation efficiency explains discoordinate expression of the galactose operon. Cell 25 : 241 249.[PubMed] [CrossRef]
170. Sonnleitner E,, Abdou L,, Haas D . 2009. Small RNA as global regulator of carbon catabolite repression in Pseudomonas aeruginosa . Proc Natl Acad Sci U S A 106 : 21866 21871.[PubMed] [CrossRef]
171. Liu P . 1952. Utilization of carbohydrates by Pseudomonas aeruginosa . J Bacteriol 64 : 773 781.[PubMed]
172. Smyth PF,, Clarke PH . 1975. Catabolite repression of Pseudomonas aeruginosa amidase: The effect of carbon source on amidase synthesis. J Gen Microbiol 90 : 81 90.[PubMed] [CrossRef]
173. Collier DN,, Hager PW,, Phibbs PV . 1996. Catabolite repression control in the pseudomonads. Res Microbiol 147 : 551 561.[PubMed] [CrossRef]
174. Rojo F,, Dinamarca MA, . 2004. Catabolite repression and physiological control, p 365 387. In Ramos JL (ed), Pseudomonas: virulence and gene regulation, vol. 2. Kluwer Academic/Plenum, New York. [CrossRef]
175. MacGregor CH,, Arora SK,, Hager PW,, Dail MB,, Phibbs PVJ . 1996. The nucleotide sequence of the Pseudomonas aeruginosa pyrE-crc-rph region and the purification of the crc gene product. J Bacteriol 178 : 5627 5635.[PubMed]
176. MacGregor CH,, Wolff JA,, Arora SK,, Phibbs PVJ . 1991. Cloning of a catabolite repression control ( crc) gene from Pseudomonas aeruginosa, expression of the gene in Escherichia coli, and identification of the gene product in Pseudomonas aeruginosa . J Bacteriol 173 : 7204 7212.[PubMed]
177. Rojo F . 2010. Carbon catabolite repression in Pseudomonas: optimizing metabolic versatility and interactions with the environment. FEMS Microbiol Rev 34 : 658 684.[PubMed]
178. Moreno R,, Martinez-Gomariz M,, Yuste L,, Gil C,, Rojo F . 2009. The Pseudomonas putida Crc global regulator controls the hierarchical assimilation of amino acids in a complete medium: evidence from proteomic and genomic analyses. Proteomics 9 : 2910 2928.[PubMed] [CrossRef]
179. Moreno R,, Rojo F . 2008. The target for the Pseudomonas putida Crc global regulator in the benzoate degradation pathway is the BenR transcriptional regulator. J Bacteriol 190 : 1539 1545.[PubMed] [CrossRef]
180. Moreno R,, Ruiz-Manzano A,, Yuste L,, Rojo F . 2007. The Pseudomonas putida Crc global regulator is an RNA binding protein that inhibits translation of the AlkS transcriptional regulator. Mol Microbiol 64 : 665 675.[PubMed] [CrossRef]
181. Milojevic T,, Grishkovskaya I,, Sonnleitner E,, Djinovic-Carugo K,, Bläsi U . 2013. The Pseudomonas aeruginosa catabolite repression control protein Crc is devoid of RNA binding activity. PLoS ONE 8 : e64609. [PubMed] [CrossRef]
182. Milojevic T,, Sonnleitner E,, Romeo A,, Djinović-Carugo K,, Bläsi U . 2013. False positive RNA binding activities after Ni-affinity purification from Escherichia coli . RNA Biol 10 : 1066 1069.[PubMed] [CrossRef]
183. Sonnleitner E,, Bläsi U . 2014. Regulation of Hfq by the RNA CrcZ in Pseudomonas aeruginosa carbon catabolite repression. PLoS Genet 10 : e1004440. [PubMed] [CrossRef]
184. Wolff JA,, MacGregor CH,, Eisenberg RC,, Phibbs PV . 1991. Isolation and characterization of catabolite repression control mutants of Pseudomonas aeruginosa PAO. J Bacteriol 173 : 4700 4706.[PubMed]
185. Amador CI,, Canosa I,, Govantes F,, Santero E . 2010. Lack of CbrB in Pseudomonas putida affects not only amino acids metabolism but also different stress responses and biofilm development. Environ Microbiol 12 : 1748 1761.[PubMed] [CrossRef]
186. O’Toole GA,, Gibbs KA,, Hager PW,, Phibbs PVJ,, Kolter R . 2000. The global carbon metabolism regulator Crc is a component of a signal transduction pathway required for biofilm development by Pseudomonas aeruginosa . J Bacteriol 182 : 425 431.[PubMed] [CrossRef]
187. Moreno R,, Fonseca P,, Rojo F . 2012. Two small RNAs, CrcY and CrcZ, act in concert to sequester the Crc global regulator in Pseudomonas putida, modulating catabolite repression. Mol Microbiol 83 : 24 40.[PubMed] [CrossRef]
188. Filiatrault MJ,, Stodghill PV,, Wilson J,, Butcher BG,, Chen H , al e . 2013. CrcZ and CrcX regulate carbon source utilization in Pseudomonas syringae pathovar tomato strain DC3000. RNA Biol 10 : 245 255.[PubMed] [CrossRef]
189. Joanny G,, Le Derout J,, Brechemier-Baey D,, Labas V,, Vinh J,, Régnier P,, Hajnsdorf E . 2007. Polyadenylation of a functional mRNA controls gene expression in Escherichia coli . Nucleic Acids Res 35 : 2494 2502.[PubMed] [CrossRef]
190. Kalamorz F,, Reichenbach B,, Marz W,, Rak B,, Gorke B . 2007. Feedback control of glucosamine-6-phosphate synthase GlmS expression depends on the small RNA GlmZ and involves the novel protein YhbJ in Escherichia coli . Mol Microbiol 65 : 1518 1533.[PubMed] [CrossRef]
191. Reichenbach B,, Maes A,, Kalamorz F,, Hajnsdorf E,, Gorke B . 2008. The small RNA GlmY acts upstream of the sRNA GlmZ in the activation of glmS expression and is subject to regulation by polyadenylation in Escherichia coli . Nucleic Acids Res. 36 : 2570 2580.[PubMed] [CrossRef]
192. Urban JH,, Papenfort K,, Thomsen J,, Schmitz RA,, Vogel J . 2007. A conserved small RNA promotes discoordinate expression of the glmUS operon mRNA to activate GlmS synthesis. Journal Mol Biol 373 : 521 528.[PubMed] [CrossRef]
193. Urban JH,, Vogel J . 2008. Two seemingly homologous noncoding RNAs act hierarchically to activate glmS mRNA translation. PLoS Biol 6 : e64. [PubMed] [CrossRef]
194. Göpel Y,, Papenfort K,, Reichenbach B,, Vogel J,, Görke B . 2013. Targeted decay of a regulatory small RNA by an adaptor protein for RNase E and counteraction by an anti-adaptor RNA. Genes Devel 27 : 552 564.[PubMed] [CrossRef]
195. Urbanowski ML,, Stauffer LT,, Stauffer GV . 2000. The gcvB gene encodes a small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli . Mol Microbiol 37 : 856 868.[PubMed] [CrossRef]
196. Pulvermacher SC,, Stauffer LT,, Stauffer GV . 2008. The role of the small regulatory RNA GcvB in GcvB/mRNA posttranscriptional regulation of oppA and dppA in Escherichia coli . FEMS Microbiol Lett 281 : 42 50.[PubMed] [CrossRef]
197. Pulvermacher SC,, Stauffer LT,, Stauffer GV . 2009. Role of the sRNA GcvB in regulation of cycA in Escherichia coli . Microbiology 155 : 106 114.[PubMed] [CrossRef]
198. Stauffer LT,, Stauffer GV . 2012. The Escherichia coli GcvB sRNA uses genetic redundancy to control cycA expression. ISRN Microbiol 2012. [PubMed] [CrossRef]
199. Sharma C,, Darfeuille F,, Plantinga T,, Vogel J . 2007. A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome-binding sites. Genes Devel 21 : 2804 2817.[PubMed] [CrossRef]
200. McArthur SD,, Pulvermacher SC,, Stauffer GV . 2006. The Yersinia pestis gcvB gene encodes two small regulatory RNA molecules. BMC Microbiol 6 : 52. [PubMed] [CrossRef]
201. Silveira AC,, Robertson KL,, Lin B,, Wang Z,, Vora GJ,, Vasconcelos AT,, Thompson FL . 2010. Identification of non-coding RNAs in environmental vibrios. Microbiology 156 : 2452 2458.[PubMed] [CrossRef]
202. Sharma CM,, Papenfort K,, Pernitzsch SR,, Mollenkopf HJ,, Hinton JC,, Vogel J . 2011. Pervasive post-transcriptional control of genes involved in amino acid metabolism by the Hfq-dependent GcvB small RNA. Mol Microbiol 81( 5) : 1144 1165.[PubMed] [CrossRef]
203. Wassarman KM,, Repoila F,, Rosenow C,, Storz G,, Gottesman S . 2001. Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev 15 : 1637 1651.[PubMed] [CrossRef]
204. Gerstle K,, Klätschke K,, Hahn U,, Piganeau N . 2012. The small RNA RybA regulates key-genes in the biosynthesis of aromatic amino acids under peroxide stress in E. coli . RNA Biol 9 : 458 468.[PubMed] [CrossRef]
205. Schilling D,, Findeiss S,, Richter AS,, Taylor JA,, Gerischer U . 2010. The small RNA Aar in Acinetobacter baylyi: a putative regulator of amino acid metabolism. Arch Microbiol 192 : 691 702.[PubMed] [CrossRef]
206. Andrews SC,, Robinson AK,, Rodriguez-Quinones F . 2003. Bacterial iron homeostasis. FEMS Microbiol Rev 27 : 215 237.[PubMed] [CrossRef]
207. Schaible UE,, Kaufmann SH . 2004. Iron and microbial infection. Nat Rev Microbiol 2 : 946 953.[PubMed] [CrossRef]
208. Masse E,, Vanderpool CK,, Gottesman S . 2005. Effect of RyhB small RNA on global iron use in Escherichia coli . J Bacteriol 187 : 6962 6971.[PubMed] [CrossRef]
209. Geissmann,, Touati D . 2004. Hfq, a new chaperoning role: binding to messanger RNA determines access for small RNA regulator. EMBO J 23 : 396 405.[PubMed] [CrossRef]
210. Vecerek B,, Moll I,, Afonyushkin T,, Kaberdin V,, Blasi U . 2003. Interaction of the RNA chaperone Hfq with mRNAs: direct and indirect roles of Hfq in iron metabolism of Escherichia coli . Molec Microbiol 50 : 897 909.[PubMed] [CrossRef]
211. Hantke K . 1981. Regulation of ferric iron transport in Escherichia coli K12: isolation of a constitutive mutant. Mol Gen Genet 182 : 288 292.[PubMed] [CrossRef]
212. Salvail H,, Lanthier-Bourbonnais P,, Sobota JM,, Caza M,, Benjamin JA,, Mendieta ME,, Lepine F,, Dozois CM,, Imlay J,, Masse E . 2010. A small RNA promotes siderophore production through transcriptional and metabolic remodeling. Proc Natl Acad Sci U S A 107 : 15223 15228.[PubMed] [CrossRef]
213. Ochsner UA,, Wilderman PJ,, Vasil AI,, Vasil ML . 2002. GeneChip expression analysis of the iron starvation response in Pseudomonas aeruginosa: identification of novel pyoverdine biosynthesis genes. Mol Microbiol 45 : 1277 1287.[PubMed] [CrossRef]