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Volumn 44, Issue 14, 2016, Pages 6935-6948

Protection against deleterious nitrogen compounds: Role of σs-dependent small RNAs encoded adjacent to sdiA

Author keywords

[No Author keywords available]

Indexed keywords

AROMATIC NITRO COMPOUND; BETA GALACTOSIDASE; DIOXYGENASE; NITRIC OXIDE DIOXYGENASE; NITROGEN DERIVATIVE; NITROREDUCTASE; SMALL UNTRANSLATED RNA; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR CRL; TRANSCRIPTION FACTOR LUXR; TRANSCRIPTION FACTOR NARP; TRANSCRIPTION FACTOR SDIA; UNCLASSIFIED DRUG; BACTERIAL RNA; ESCHERICHIA COLI PROTEIN; HOST FACTOR 1; MESSENGER RNA; SDIA PROTEIN, E COLI; SIGMA FACTOR; SPACER DNA; TRANSACTIVATOR PROTEIN; URIDINE;

EID: 84984903707     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw404     Document Type: Article
Times cited : (33)

References (51)
  • 1
    • 80053019485 scopus 로고    scopus 로고
    • Regulation by small RNAs in bacteria: Expanding frontiers
    • Storz,G., Vogel,J. and Wassarman,K.M. (2011) Regulation by small RNAs in bacteria: expanding frontiers. Mol. Cell, 43, 880-891.
    • (2011) Mol. Cell , vol.43 , pp. 880-891
    • Storz, G.1    Vogel, J.2    Wassarman, K.M.3
  • 2
    • 84945484697 scopus 로고    scopus 로고
    • Small RNAs in bacteria and archaea: Who they are, what they do, and how they do it
    • Wagner,E.G.H. and Romby,P. (2015) Small RNAs in bacteria and archaea: who they are, what they do, and how they do it. Adv. Genet., 90, 133-208.
    • (2015) Adv. Genet. , vol.90 , pp. 133-208
    • Wagner, E.G.H.1    Romby, P.2
  • 3
    • 84866307118 scopus 로고    scopus 로고
    • The bacterial protein Hfq: Much more than a mere RNA-binding factor
    • Sobrero,P. and Valverde,C. (2012) The bacterial protein Hfq: much more than a mere RNA-binding factor. Crit. Rev. Microbiol., 38, 276-299.
    • (2012) Crit. Rev. Microbiol. , vol.38 , pp. 276-299
    • Sobrero, P.1    Valverde, C.2
  • 4
    • 79960433506 scopus 로고    scopus 로고
    • Hfq and its constellation of RNA
    • Vogel,J. and Luisi,B.F. (2011) Hfq and its constellation of RNA. Nat. Rev. Microbiol., 9, 578-589.
    • (2011) Nat. Rev. Microbiol. , vol.9 , pp. 578-589
    • Vogel, J.1    Luisi, B.F.2
  • 5
    • 84861442326 scopus 로고    scopus 로고
    • Regulating iron storage and metabolism with RNA: An overview of posttranscriptional controls of intracellular iron homeostasis
    • Salvail,H. and Massé,E. (2012) Regulating iron storage and metabolism with RNA: an overview of posttranscriptional controls of intracellular iron homeostasis. Wiley Interdiscip. Rev. RNA, 3, 26-36.
    • (2012) Wiley Interdiscip. Rev. RNA , vol.3 , pp. 26-36
    • Salvail, H.1    Massé, E.2
  • 6
    • 77349104885 scopus 로고    scopus 로고
    • Reprogramming of anaerobic metabolism by the FnrS small RNA
    • Durand,S. and Storz,G. (2010) Reprogramming of anaerobic metabolism by the FnrS small RNA. Mol. Microbiol., 75, 1215-1231.
    • (2010) Mol. Microbiol. , vol.75 , pp. 1215-1231
    • Durand, S.1    Storz, G.2
  • 7
    • 77349101808 scopus 로고    scopus 로고
    • Translational regulation of gene expression by an anaerobically induced small non-coding RNA in Escherichia coli
    • Boysen,A., Møller-Jensen,J., Kallipolitis,B., Valentin-Hansen,P. and 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.
    • (2010) J. Biol. Chem. , vol.285 , pp. 10690-10702
    • Boysen, A.1    Møller-Jensen, J.2    Kallipolitis, B.3    Valentin-Hansen, P.4    Overgaard, M.5
  • 8
    • 84904362234 scopus 로고    scopus 로고
    • MicL, a new -E-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein
    • Guo,M.S., Updegrove,T.B., Gogol,E.B., Shabalina,S.A., Gross,C.A. and Storz,G. (2014) MicL, a new -E-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein. Genes Dev., 28, 1620-1634.
    • (2014) Genes Dev. , vol.28 , pp. 1620-1634
    • Guo, M.S.1    Updegrove, T.B.2    Gogol, E.B.3    Shabalina, S.A.4    Gross, C.A.5    Storz, G.6
  • 9
    • 84867577054 scopus 로고    scopus 로고
    • An atlas of Hfq-bound transcripts reveals 3' UTRs as a genomic reservoir of regulatory small RNAs
    • Chao,Y., Papenfort,K., Reinhardt,R., Sharma,C.M. and Vogel,J. (2012) An atlas of Hfq-bound transcripts reveals 3' UTRs as a genomic reservoir of regulatory small RNAs. EMBO J., 31, 4005-1019.
    • (2012) EMBO J. , vol.31 , pp. 1019-4005
    • Chao, Y.1    Papenfort, K.2    Reinhardt, R.3    Sharma, C.M.4    Vogel, J.5
  • 10
    • 80053226878 scopus 로고    scopus 로고
    • The RpoS-mediated general stress response in Escherichia coli
    • Battesti,A., Majdalani,N. and Gottesman,S. (2011) The RpoS-mediated general stress response in Escherichia coli. Annu. Rev. Microbiol., 65, 189-213.
    • (2011) Annu. Rev. Microbiol. , vol.65 , pp. 189-213
    • Battesti, A.1    Majdalani, N.2    Gottesman, S.3
  • 11
    • 84900310041 scopus 로고    scopus 로고
    • Elucidating the function of the RpoS regulon
    • Schellhorn,H.E. (2014) Elucidating the function of the RpoS regulon. Future Microbiol., 9, 497-507.
    • (2014) Future Microbiol. , vol.9 , pp. 497-507
    • Schellhorn, H.E.1
  • 12
    • 84858860817 scopus 로고    scopus 로고
    • A conserved RpoS-dependent small RNA controls the synthesis of major porin OmpD
    • Fr öhlich,K.S., Papenfort,K., Berger,A.A. and Vogel,J. (2012) A conserved RpoS-dependent small RNA controls the synthesis of major porin OmpD. Nucleic Acids Res., 40, 3623-3640.
    • (2012) Nucleic Acids Res. , vol.40 , pp. 3623-3640
    • Frohlich, K.S.1    Papenfort, K.2    Berger, A.A.3    Vogel, J.4
  • 13
    • 4944264194 scopus 로고    scopus 로고
    • GadY, a small-RNA regulator of acid response genes in Escherichia coli
    • Opdyke,J.A., Kang,J.G. and Storz,G. (2004) GadY, a small-RNA regulator of acid response genes in Escherichia coli. J. Bacteriol., 186, 6698-6705.
    • (2004) J. Bacteriol. , vol.186 , pp. 6698-6705
    • Opdyke, J.A.1    Kang, J.G.2    Storz, G.3
  • 14
    • 84883161741 scopus 로고    scopus 로고
    • An RpoS-dependent sRNA regulates the expression of a chaperone involved in protein folding
    • Silva,I.J., Ortega,A.D., Viegas,S.C., Garcá-Del Portillo,F. and Arraiano,C.M. (2013) An RpoS-dependent sRNA regulates the expression of a chaperone involved in protein folding. RNA, 19, 1253-1265.
    • (2013) RNA , vol.19 , pp. 1253-1265
    • Silva, I.J.1    Ortega, A.D.2    Viegas, S.C.3    Garcá-Del Portillo, F.4    Arraiano, C.M.5
  • 15
    • 79151470965 scopus 로고    scopus 로고
    • RNase III participates in GadY-dependent cleavage of the gadX-gadW mRNA
    • Opdyke,J.A., Fozo,E.M., Hemm,M.R. and Storz,G. (2011) RNase III participates in GadY-dependent cleavage of the gadX-gadW mRNA. J. Mol. Biol., 406, 29-43.
    • (2011) J. Mol. Biol. , vol.406 , pp. 29-43
    • Opdyke, J.A.1    Fozo, E.M.2    Hemm, M.R.3    Storz, G.4
  • 17
    • 84961164800 scopus 로고    scopus 로고
    • Small RNA regulation of TolC, the outer membrane component of bacterial multidrug transporters
    • Parker,A. and Gottesman,S. (2016) Small RNA regulation of TolC, the outer membrane component of bacterial multidrug transporters. J. Bacteriol., 198, 1101-1113.
    • (2016) J. Bacteriol. , vol.198 , pp. 1101-1113
    • Parker, A.1    Gottesman, S.2
  • 18
    • 0034612342 scopus 로고    scopus 로고
    • One-step inactivation of chromosomal genes in Escherichiacoli K-12 using PCR products
    • Datsenko,K.A. and Wanner,B.L. (2000) One-step inactivation of chromosomal genes in Escherichiacoli K-12 using PCR products. Proc. Natl. Acad. Sci. U.S.A., 97, 6640-6645.
    • (2000) Proc. Natl. Acad. Sci. U.S.A , vol.97 , pp. 6640-6645
    • Datsenko, K.A.1    Wanner, B.L.2
  • 19
    • 84858866772 scopus 로고    scopus 로고
    • A small RNA that regulates motility and biofilm formation in response to changes in nutrient availability in Escherichia coli
    • Thomason,M.K., Fontaine,F., De Lay,N. and Storz,G. (2012) A small RNA that regulates motility and biofilm formation in response to changes in nutrient availability in Escherichia coli. Mol. Microbiol., 84, 17-35.
    • (2012) Mol. Microbiol. , vol.84 , pp. 17-35
    • Thomason, M.K.1    Fontaine, F.2    De Lay, N.3    Storz, G.4
  • 20
    • 84883809477 scopus 로고    scopus 로고
    • Mutations in interaction surfaces differentially impact E.coli Hfq association with small RNAs and their mRNA targets
    • Zhang,A., Schu,D.J., Tjaden,B.C., Storz,G. and Gottesman,S. (2013) Mutations in interaction surfaces differentially impact E. coli Hfq association with small RNAs and their mRNA targets. J. Mol. Biol., 425, 3678-3697.
    • (2013) J. Mol. Biol. , vol.425 , pp. 3678-3697
    • Zhang, A.1    Schu, D.J.2    Tjaden, B.C.3    Storz, G.4    Gottesman, S.5
  • 21
    • 65349177758 scopus 로고    scopus 로고
    • A genetic approach for finding small RNAs regulators of genes of interest identifies RybC as regulating the DpiA/DpiB two-component system
    • Mandin,P. and Gottesman,S. (2009) A genetic approach for finding small RNAs regulators of genes of interest identifies RybC as regulating the DpiA/DpiB two-component system. Mol. Microbiol., 72, 551-565.
    • (2009) Mol. Microbiol. , vol.72 , pp. 551-565
    • Mandin, P.1    Gottesman, S.2
  • 22
    • 33645066654 scopus 로고    scopus 로고
    • Remodelling of the Escherichiacoli outer membrane by two small regulatory RNAs
    • Guillier,M. and Gottesman,S. (2006) Remodelling of the Escherichiacoli outer membrane by two small regulatory RNAs. Mol. Microbiol., 59, 231-247.
    • (2006) Mol. Microbiol. , vol.59 , pp. 231-247
    • Guillier, M.1    Gottesman, S.2
  • 23
    • 0141860088 scopus 로고    scopus 로고
    • Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli
    • Massé,E., Escorcia,F.E. and Gottesman,S. (2003) Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli. Genes Dev., 17, 2374-2383.
    • (2003) Genes Dev. , vol.17 , pp. 2374-2383
    • Massé, E.1    Escorcia, F.E.2    Gottesman, S.3
  • 24
    • 84944442094 scopus 로고    scopus 로고
    • Alternative Hfq-sRNA interaction modes dictate alternative mRNA recognition
    • Schu,D.J., Zhang,A., Gottesman,S. and Storz,G. (2015) Alternative Hfq-sRNA interaction modes dictate alternative mRNA recognition. EMBO J., 34, 2557-2573.
    • (2015) EMBO J. , vol.34 , pp. 2557-2573
    • Schu, D.J.1    Zhang, A.2    Gottesman, S.3    Storz, G.4
  • 26
    • 80052526246 scopus 로고    scopus 로고
    • Genome-wide detection of novel regulatory RNAs in e
    • Raghavan,R., Groisman,E.A. and Ochman,H. (2011) Genome-wide detection of novel regulatory RNAs in E. coli. Genome Res., 21, 1487-1497.
    • (2011) Coli. Genome Res. , vol.21 , pp. 1487-1497
    • Raghavan, R.1    Groisman, E.A.2    Ochman, H.3
  • 28
    • 2442456738 scopus 로고    scopus 로고
    • Crl, a low temperature-induced protein in Escherichia coli that binds directly to the stationary phase sigma subunit of RNA polymerase
    • Bougdour,A., Lelong,C. and Geiselmann,J. (2004) Crl, a low temperature-induced protein in Escherichia coli that binds directly to the stationary phase sigma subunit of RNA polymerase. J. Biol. Chem., 279, 19540-19550.
    • (2004) J. Biol. Chem. , vol.279 , pp. 19540-19550
    • Bougdour, A.1    Lelong, C.2    Geiselmann, J.3
  • 29
    • 33751096730 scopus 로고    scopus 로고
    • Crl facilitates RNA polymerase holoenzyme formation
    • Gaal,T., Mandel,M.J., Silhavy,T.J. and Gourse,R. (2006) Crl facilitates RNA polymerase holoenzyme formation. J. Bacteriol., 188, 7966-7970.
    • (2006) J. Bacteriol. , vol.188 , pp. 7966-7970
    • Gaal, T.1    Mandel, M.J.2    Silhavy, T.J.3    Gourse, R.4
  • 31
    • 0028142101 scopus 로고
    • Dual interacting two-component regulatory systems mediate nitrate-and nitrite-regulated gene expression in Escherichia coli
    • Stewart,V. (1994) Dual interacting two-component regulatory systems mediate nitrate-and nitrite-regulated gene expression in Escherichia coli. Res. Microbiol., 145, 450-454.
    • (1994) Res. Microbiol. , vol.145 , pp. 450-454
    • Stewart, V.1
  • 32
    • 0030064119 scopus 로고    scopus 로고
    • Control of cell division in Escherichia coli: Regulation of transcription of ftsQA involves both rpoS and SdiA-mediated autoinduction
    • Sitnikov,D.M., Schineller,J.B. and Baldwin,T.O. (1996) Control of cell division in Escherichia coli: regulation of transcription of ftsQA involves both rpoS and SdiA-mediated autoinduction. Proc. Natl. Acad. Sci. U.S.A., 93, 336-341.
    • (1996) Proc. Natl. Acad. Sci. U.S.A , vol.93 , pp. 336-341
    • Sitnikov, D.M.1    Schineller, J.B.2    Baldwin, T.O.3
  • 33
    • 80655125468 scopus 로고    scopus 로고
    • CsrA represses translation of sdiA, which encodes the N-acylhomoserine-L-lactone receptor of Escherichia coli, by binding exclusively within the coding region of sdiA mRNA
    • Yakhnin,H., Baker,C.S., Berezin,I., Evangelista,M.A., Rassin,A., Romeo,T. and Babitzke,P. (2011) CsrA represses translation of sdiA, which encodes the N-acylhomoserine-L-lactone receptor of Escherichia coli, by binding exclusively within the coding region of sdiA mRNA. J. Bacteriol., 193, 6162-6170.
    • (2011) J. Bacteriol. , vol.193 , pp. 6162-6170
    • Yakhnin, H.1    Baker, C.S.2    Berezin, I.3    Evangelista, M.A.4    Rassin, A.5    Romeo, T.6    Babitzke, P.7
  • 34
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • Zuker,M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3406-3415
    • Zuker, M.1
  • 35
    • 80053440900 scopus 로고    scopus 로고
    • The influence of Escherichia coli Hfq mutations on RNA binding and sRNAmRNA duplex formation in rpoS riboregulation
    • Updegrove,T.B. andWartell,R.M. (2011) The influence of Escherichia coli Hfq mutations on RNA binding and sRNAmRNA duplex formation in rpoS riboregulation. Biochim. Biophys. Acta, 1809, 532-540.
    • (2011) Biochim. Biophys. Acta , vol.1809 , pp. 532-540
    • Updegrove, T.B.1    AndWartell, R.M.2
  • 36
    • 0029745672 scopus 로고    scopus 로고
    • Biochemical characterization of NfsA, the Escherichia coli major nitroreductase exhibiting a high amino acid sequence homology to Frp, a Vibrio harveyi flavin oxidoreductase
    • Zenno,S., Koike,H., Kumar,A.N., Jayaraman,R., Tanokura,M. and Saigo,K. (1996) Biochemical characterization of NfsA, the Escherichia coli major nitroreductase exhibiting a high amino acid sequence homology to Frp, a Vibrio harveyi flavin oxidoreductase. J. Bacteriol., 178, 4508-4514.
    • (1996) J. Bacteriol. , vol.178 , pp. 4508-4514
    • Zenno, S.1    Koike, H.2    Kumar, A.N.3    Jayaraman, R.4    Tanokura, M.5    Saigo, K.6
  • 39
    • 57249083988 scopus 로고    scopus 로고
    • IntaRNA: Efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions
    • Busch,A., Richter,A.S. and Backofen,R. (2008) IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinformatics, 24, 2849-2856.
    • (2008) Bioinformatics , vol.24 , pp. 2849-2856
    • Busch, A.1    Richter, A.S.2    Backofen, R.3
  • 40
    • 0017877955 scopus 로고
    • Genetics of nitrofurazone resistance in Escherichia coli
    • McCalla,D.R., Kaiser,C. and Green,M.H. (1978) Genetics of nitrofurazone resistance in Escherichia coli. J. Bacteriol., 133, 10-16.
    • (1978) J. Bacteriol. , vol.133 , pp. 10-16
    • McCalla, D.R.1    Kaiser, C.2    Green, M.H.3
  • 41
    • 0031771290 scopus 로고    scopus 로고
    • Oxygen-insensitive nitroreductases: Analysis of the roles of nfsA and nfsB in development of resistance to 5-nitrofuran derivatives in Escherichia coli
    • Whiteway,J., Koziarz,P., Veall,J., Sandhu,N., Kumar,P., Hoecher,B. and Lambert,I.B. (1998) Oxygen-insensitive nitroreductases: analysis of the roles of nfsA and nfsB in development of resistance to 5-nitrofuran derivatives in Escherichia coli. J. Bacteriol., 180, 5529-5539.
    • (1998) J. Bacteriol. , vol.180 , pp. 5529-5539
    • Whiteway, J.1    Koziarz, P.2    Veall, J.3    Sandhu, N.4    Kumar, P.5    Hoecher, B.6    Lambert, I.B.7
  • 43
    • 0037929111 scopus 로고    scopus 로고
    • Escherichia coli flavohemoglobin is an efficient alkylhydroperoxide reductase
    • Bonamore,A., Gentili,P., Ilari,A., Schininà,M.E. and Boffi,A. (2003) Escherichia coli flavohemoglobin is an efficient alkylhydroperoxide reductase. J. Biol. Chem., 278, 22272-22277.
    • (2003) J. Biol. Chem. , vol.278 , pp. 22272-22277
    • Bonamore, A.1    Gentili, P.2    Ilari, A.3    Schininà, M.E.4    Boffi, A.5
  • 45
    • 84898058733 scopus 로고    scopus 로고
    • NrsZ: A novel, processed, nitrogen-dependent, small non-coding RNA that regulates Pseudomonas aeruginosa PAO1 virulence
    • Wenner,N., Maes,A., Cotado-Sampayo,M. and Lapouge,K. (2014) NrsZ: a novel, processed, nitrogen-dependent, small non-coding RNA that regulates Pseudomonas aeruginosa PAO1 virulence. Environ. Microbiol., 16, 1053-1068.
    • (2014) Environ. Microbiol. , vol.16 , pp. 1053-1068
    • Wenner, N.1    Maes, A.2    Cotado-Sampayo, M.3    Lapouge, K.4
  • 46
    • 77951765424 scopus 로고    scopus 로고
    • Heterocyst-specific transcription of NsiR1, a non-coding RNA encoded in a tandem array of direct repeats in cyanobacteria
    • Ionescu,D., Voss,B., Oren,A., Hess,W.R. and Muro-Pastor,A.M. (2010) Heterocyst-specific transcription of NsiR1, a non-coding RNA encoded in a tandem array of direct repeats in cyanobacteria. J. Mol. Biol., 398, 177-188.
    • (2010) J. Mol. Biol. , vol.398 , pp. 177-188
    • Ionescu, D.1    Voss, B.2    Oren, A.3    Hess, W.R.4    Muro-Pastor, A.M.5
  • 48
    • 84866788439 scopus 로고    scopus 로고
    • The seed region of a small RNA drives the controlled destruction of the target mRNA by the endoribonuclease RNase e
    • Bandyra,K.J., Said,N., Pfeiffer,V., Górna,M.W., Vogel,J. and Luisi,B.F. (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.
    • (2012) Mol. Cell , vol.47 , pp. 943-953
    • Bandyra, K.J.1    Said, N.2    Pfeiffer, V.3    Górna, M.W.4    Vogel, J.5    Luisi, B.F.6
  • 49
    • 84940404135 scopus 로고    scopus 로고
    • Small RNA-based feedforward loop with AND-gate logic regulates extrachromosomal DNA transfer in Salmonella
    • Papenfort,K., Espinosa,E., Casades us,J. and Vogel,J. (2015) Small RNA-based feedforward loop with AND-gate logic regulates extrachromosomal DNA transfer in Salmonella. Proc. Natl. Acad. Sci. U.S.A., 112, E4772-E4781.
    • (2015) Proc. Natl. Acad. Sci. U.S.A , vol.112 , pp. E4772-E4781
    • Papenfort, K.1    Espinosa, E.2    Casadesus, J.3    Vogel, J.4
  • 51
    • 84948163933 scopus 로고    scopus 로고
    • Every little piece counts: The many faces of tRNA transcripts
    • Lalaouna,D., Carrier,M.C. and Massé,E. (2015) Every little piece counts: the many faces of tRNA transcripts. Transcription, 6, 74-77.
    • (2015) Transcription , vol.6 , pp. 74-77
    • Lalaouna, D.1    Carrier, M.C.2    Massé, E.3


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