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Volumn 11, Issue 2, 2015, Pages 1-31

A Nitric Oxide Regulated Small RNA Controls Expression of Genes Involved in Redox Homeostasis in Bacillus subtilis

Author keywords

[No Author keywords available]

Indexed keywords

NITRIC OXIDE; RIBONUCLEASE; RIBONUCLEASE III; RIBONUCLEASE Y; TRANSFER RNA; UNCLASSIFIED DRUG; 6S RNA; BACTERIAL RNA; MESSENGER RNA; UNTRANSLATED RNA;

EID: 84924354204     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1004957     Document Type: Article
Times cited : (61)

References (67)
  • 1
    • 80053019485 scopus 로고    scopus 로고
    • Regulation by small RNAs in bacteria: expanding frontiers
    • Storz G, Vogel J, Wassarman KM, (2011) Regulation by small RNAs in bacteria: expanding frontiers. Mol Cell 43: 880–891. doi: 10.1016/j.molcel.2011.08.022 21925377
    • (2011) Mol Cell , vol.43 , pp. 880-891
    • Storz, G.1    Vogel, J.2    Wassarman, K.M.3
  • 3
    • 78649989435 scopus 로고    scopus 로고
    • The group A Streptococcus small regulatory RNA FasX enhances streptokinase activity by increasing the stability of the ska mRNA transcript
    • Ramirez-Pena E, Trevino J, Liu Z, Perez N, Sumby P, (2010) The group A Streptococcus small regulatory RNA FasX enhances streptokinase activity by increasing the stability of the ska mRNA transcript. Mol Microbiol 78: 1332–1347. doi: 10.1111/j.1365-2958.2010.07427.x 21143309
    • (2010) Mol Microbiol , vol.78 , pp. 1332-1347
    • Ramirez-Pena, E.1    Trevino, J.2    Liu, Z.3    Perez, N.4    Sumby, P.5
  • 4
    • 77956631743 scopus 로고    scopus 로고
    • Stabilization of Clostridium perfringens collagenase mRNA by VR-RNA-dependent cleavage in 5′ leader sequence
    • Obana N, Shirahama Y, Abe K, Nakamura K, (2010) Stabilization of Clostridium perfringens collagenase mRNA by VR-RNA-dependent cleavage in 5′ leader sequence. Mol Microbiol 77: 1416–1428. doi: 10.1111/j.1365-2958.2010.07258.x 20572941
    • (2010) Mol Microbiol , vol.77 , pp. 1416-1428
    • Obana, N.1    Shirahama, Y.2    Abe, K.3    Nakamura, K.4
  • 5
    • 79151470965 scopus 로고    scopus 로고
    • RNase III participates in GadY-dependent cleavage of the gadX-gadW mRNA
    • Opdyke JA, Fozo EM, Hemm MR, Storz G, (2011) RNase III participates in GadY-dependent cleavage of the gadX-gadW mRNA. J Mol Biol 406: 29–43. doi: 10.1016/j.jmb.2010.12.009 21147125
    • (2011) J Mol Biol , vol.406 , pp. 29-43
    • Opdyke, J.A.1    Fozo, E.M.2    Hemm, M.R.3    Storz, G.4
  • 6
    • 68249156618 scopus 로고    scopus 로고
    • Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation
    • Pfeiffer V, Papenfort K, Lucchini S, Hinton JC, Vogel J, (2009) Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation. Nat Struct Mol Biol 16: 840–846. doi: 10.1038/nsmb.1631 19620966
    • (2009) Nat Struct Mol Biol , vol.16 , pp. 840-846
    • Pfeiffer, V.1    Papenfort, K.2    Lucchini, S.3    Hinton, J.C.4    Vogel, J.5
  • 7
    • 50149103524 scopus 로고    scopus 로고
    • The Bacillus subtilis iron-sparing response is mediated by a Fur-regulated small RNA and three small, basic proteins
    • Gaballa A, Antelmann H, Aguilar C, Khakh SK, Song KB, et al. (2008) The Bacillus subtilis iron-sparing response is mediated by a Fur-regulated small RNA and three small, basic proteins. Proc Natl Acad Sci U S A 105: 11927–11932. doi: 10.1073/pnas.0711752105 18697947
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 11927-11932
    • Gaballa, A.1    Antelmann, H.2    Aguilar, C.3    Khakh, S.K.4    Song, K.B.5
  • 8
    • 33749165741 scopus 로고    scopus 로고
    • The small untranslated RNA SR1 from the Bacillus subtilis genome is involved in the regulation of arginine catabolism
    • Heidrich N, Chinali A, Gerth U, Brantl S, (2006) The small untranslated RNA SR1 from the Bacillus subtilis genome is involved in the regulation of arginine catabolism. Mol Microbiol 62: 520–536. 17020585
    • (2006) Mol Microbiol , vol.62 , pp. 520-536
    • Heidrich, N.1    Chinali, A.2    Gerth, U.3    Brantl, S.4
  • 9
    • 84871240106 scopus 로고    scopus 로고
    • SR1- a small RNA with two remarkably conserved functions
    • Gimpel M, Preis H, Barth E, Gramzow L, Brantl S, (2012) SR1- a small RNA with two remarkably conserved functions. Nucleic Acids Res 40: 11659–11672. doi: 10.1093/nar/gks895 23034808
    • (2012) Nucleic Acids Res , vol.40 , pp. 11659-11672
    • Gimpel, M.1    Preis, H.2    Barth, E.3    Gramzow, L.4    Brantl, S.5
  • 10
    • 84861368192 scopus 로고    scopus 로고
    • The FsrA sRNA and FbpB protein mediate the iron-dependent induction of the Bacillus subtilis lutABC iron-sulfur-containing oxidases
    • Smaldone GT, Antelmann H, Gaballa A, Helmann JD, (2012) The FsrA sRNA and FbpB protein mediate the iron-dependent induction of the Bacillus subtilis lutABC iron-sulfur-containing oxidases. J Bacteriol 194: 2586–2593. doi: 10.1128/JB.05567-11 22427629
    • (2012) J Bacteriol , vol.194 , pp. 2586-2593
    • Smaldone, G.T.1    Antelmann, H.2    Gaballa, A.3    Helmann, J.D.4
  • 11
    • 84861412664 scopus 로고    scopus 로고
    • A global investigation of the Bacillus subtilis iron-sparing response identifies major changes in metabolism
    • Smaldone GT, Revelles O, Gaballa A, Sauer U, Antelmann H, et al. (2012) A global investigation of the Bacillus subtilis iron-sparing response identifies major changes in metabolism. J Bacteriol 194: 2594–2605. doi: 10.1128/JB.05990-11 22389480
    • (2012) J Bacteriol , vol.194 , pp. 2594-2605
    • Smaldone, G.T.1    Revelles, O.2    Gaballa, A.3    Sauer, U.4    Antelmann, H.5
  • 12
    • 20144380295 scopus 로고    scopus 로고
    • Staphylococcus aureus RNAIII and the endoribonuclease III coordinately regulate spa gene expression
    • Huntzinger E, Boisset S, Saveanu C, Benito Y, Geissmann T, et al. (2005) Staphylococcus aureus RNAIII and the endoribonuclease III coordinately regulate spa gene expression. EMBO J 24: 824–835. doi: 10.1038/sj.emboj.7600572 15678100
    • (2005) EMBO J , vol.24 , pp. 824-835
    • Huntzinger, E.1    Boisset, S.2    Saveanu, C.3    Benito, Y.4    Geissmann, T.5
  • 13
    • 84903291745 scopus 로고    scopus 로고
    • Impact of Hfq on the Bacillus subtilis transcriptome
    • Hammerle H, Amman F, Vecerek B, Stulke J, Hofacker I, et al. (2014) Impact of Hfq on the Bacillus subtilis transcriptome. PLoS One 9: e98661. doi: 10.1371/journal.pone.0098661 24932523
    • (2014) PLoS One , vol.9
    • Hammerle, H.1    Amman, F.2    Vecerek, B.3    Stulke, J.4    Hofacker, I.5
  • 14
    • 84874025965 scopus 로고    scopus 로고
    • Association of RNAs with Bacillus subtilis Hfq
    • Dambach M, Irnov I, Winkler WC, (2013) Association of RNAs with Bacillus subtilis Hfq. PLoS One 8: e55156. doi: 10.1371/journal.pone.0055156 23457461
    • (2013) PLoS One , vol.8
    • Dambach, M.1    Irnov, I.2    Winkler, W.C.3
  • 15
    • 17844361922 scopus 로고    scopus 로고
    • Ribonucleases J1 and J2: two novel endoribonucleases in B. subtilis with functional homology to E. coli RNase E
    • Even S, Pellegrini O, Zig L, Labas V, Vinh J, et al. (2005) Ribonucleases J1 and J2: two novel endoribonucleases in B. subtilis with functional homology to E. coli RNase E. Nucleic Acids Res 33: 2141–2152. doi: 10.1093/nar/gki505 15831787
    • (2005) Nucleic Acids Res , vol.33 , pp. 2141-2152
    • Even, S.1    Pellegrini, O.2    Zig, L.3    Labas, V.4    Vinh, J.5
  • 16
    • 34249101864 scopus 로고    scopus 로고
    • 5′-to-3′ exoribonuclease activity in bacteria: role of RNase J1 in rRNA maturation and 5′ stability of mRNA
    • Mathy N, Benard L, Pellegrini O, Daou R, Wen T, et al. (2007) 5′-to-3′ exoribonuclease activity in bacteria: role of RNase J1 in rRNA maturation and 5′ stability of mRNA. Cell 129: 681–692. 17512403
    • (2007) Cell , vol.129 , pp. 681-692
    • Mathy, N.1    Benard, L.2    Pellegrini, O.3    Daou, R.4    Wen, T.5
  • 17
    • 73849116916 scopus 로고    scopus 로고
    • A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation
    • Geissmann T, Chevalier C, Cros MJ, Boisset S, Fechter P, et al. (2009) A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation. Nucleic Acids Res 37: 7239–7257. doi: 10.1093/nar/gkp668 19786493
    • (2009) Nucleic Acids Res , vol.37 , pp. 7239-7257
    • Geissmann, T.1    Chevalier, C.2    Cros, M.J.3    Boisset, S.4    Fechter, P.5
  • 18
    • 78049393967 scopus 로고    scopus 로고
    • Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism
    • Bohn C, Rigoulay C, Chabelskaya S, Sharma CM, Marchais A, et al. (2010) Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism. Nucleic Acids Res 38: 6620–6636. doi: 10.1093/nar/gkq462 20511587
    • (2010) Nucleic Acids Res , vol.38 , pp. 6620-6636
    • Bohn, C.1    Rigoulay, C.2    Chabelskaya, S.3    Sharma, C.M.4    Marchais, A.5
  • 19
    • 84861306939 scopus 로고    scopus 로고
    • The expression of small regulatory RNAs in clinical samples reflects the different life styles of Staphylococcus aureus in colonization vs. infection
    • Song J, Lays C, Vandenesch F, Benito Y, Bes M, et al. (2012) The expression of small regulatory RNAs in clinical samples reflects the different life styles of Staphylococcus aureus in colonization vs. infection. PLoS One 7: e37294. doi: 10.1371/journal.pone.0037294 22629378
    • (2012) PLoS One , vol.7
    • Song, J.1    Lays, C.2    Vandenesch, F.3    Benito, Y.4    Bes, M.5
  • 20
    • 0033220348 scopus 로고    scopus 로고
    • Genetic responses against nitric oxide toxicity
    • Demple B, (1999) Genetic responses against nitric oxide toxicity. Braz J Med Biol Res 32: 1417–1427. 10559844
    • (1999) Braz J Med Biol Res , vol.32 , pp. 1417-1427
    • Demple, B.1
  • 21
    • 77953641425 scopus 로고    scopus 로고
    • Bacterial nitric oxide synthases
    • Crane BR, Sudhamsu J, Patel BA, (2010) Bacterial nitric oxide synthases. Annu Rev Biochem 79: 445–470. doi: 10.1146/annurev-biochem-062608-103436 20370423
    • (2010) Annu Rev Biochem , vol.79 , pp. 445-470
    • Crane, B.R.1    Sudhamsu, J.2    Patel, B.A.3
  • 22
    • 25444434412 scopus 로고    scopus 로고
    • NO-mediated cytoprotection: instant adaptation to oxidative stress in bacteria
    • Gusarov I, Nudler E, (2005) NO-mediated cytoprotection: instant adaptation to oxidative stress in bacteria. Proc Natl Acad Sci U S A 102: 13855–13860. doi: 10.1073/pnas.0504307102 16172391
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 13855-13860
    • Gusarov, I.1    Nudler, E.2
  • 23
    • 38949187268 scopus 로고    scopus 로고
    • Bacillus anthracis-derived nitric oxide is essential for pathogen virulence and survival in macrophages
    • Shatalin K, Gusarov I, Avetissova E, Shatalina Y, McQuade LE, et al. (2008) Bacillus anthracis-derived nitric oxide is essential for pathogen virulence and survival in macrophages. Proc Natl Acad Sci U S A 105: 1009–1013. doi: 10.1073/pnas.0710950105 18215992
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 1009-1013
    • Shatalin, K.1    Gusarov, I.2    Avetissova, E.3    Shatalina, Y.4    McQuade, L.E.5
  • 24
    • 47249088762 scopus 로고    scopus 로고
    • Nitric oxide stress induces different responses but mediates comparable protein thiol protection in Bacillus subtilis and Staphylococcus aureus
    • Hochgrafe F, Wolf C, Fuchs S, Liebeke M, Lalk M, et al. (2008) Nitric oxide stress induces different responses but mediates comparable protein thiol protection in Bacillus subtilis and Staphylococcus aureus. J Bacteriol 190: 4997–5008. doi: 10.1128/JB.01846-07 18487332
    • (2008) J Bacteriol , vol.190 , pp. 4997-5008
    • Hochgrafe, F.1    Wolf, C.2    Fuchs, S.3    Liebeke, M.4    Lalk, M.5
  • 25
    • 70249096979 scopus 로고    scopus 로고
    • Endogenous nitric oxide protects bacteria against a wide spectrum of antibiotics
    • Gusarov I, Shatalin K, Starodubtseva M, Nudler E, (2009) Endogenous nitric oxide protects bacteria against a wide spectrum of antibiotics. Science 325: 1380–1384. doi: 10.1126/science.1175439 19745150
    • (2009) Science , vol.325 , pp. 1380-1384
    • Gusarov, I.1    Shatalin, K.2    Starodubtseva, M.3    Nudler, E.4
  • 26
    • 84874782570 scopus 로고    scopus 로고
    • Methicillin-resistant Staphylococcus aureus bacterial nitric-oxide synthase affects antibiotic sensitivity and skin abscess development
    • van Sorge NM, Beasley FC, Gusarov I, Gonzalez DJ, von Kockritz-Blickwede M, et al. (2013) Methicillin-resistant Staphylococcus aureus bacterial nitric-oxide synthase affects antibiotic sensitivity and skin abscess development. J Biol Chem 288: 6417–6426. doi: 10.1074/jbc.M112.448738 23322784
    • (2013) J Biol Chem , vol.288 , pp. 6417-6426
    • van Sorge, N.M.1    Beasley, F.C.2    Gusarov, I.3    Gonzalez, D.J.4    von Kockritz-Blickwede, M.5
  • 27
    • 84874041072 scopus 로고    scopus 로고
    • Bacterial nitric oxide extends the lifespan of C. elegans
    • Gusarov I, Gautier L, Smolentseva O, Shamovsky I, Eremina S, et al. (2013) Bacterial nitric oxide extends the lifespan of C. elegans. Cell 152: 818–830. doi: 10.1016/j.cell.2012.12.043 23415229
    • (2013) Cell , vol.152 , pp. 818-830
    • Gusarov, I.1    Gautier, L.2    Smolentseva, O.3    Shamovsky, I.4    Eremina, S.5
  • 28
    • 84857683425 scopus 로고    scopus 로고
    • Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis
    • Nicolas P, Mader U, Dervyn E, Rochat T, Leduc A, et al. (2012) Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis. Science 335: 1103–1106. doi: 10.1126/science.1206848 22383849
    • (2012) Science , vol.335 , pp. 1103-1106
    • Nicolas, P.1    Mader, U.2    Dervyn, E.3    Rochat, T.4    Leduc, A.5
  • 29
    • 1542376961 scopus 로고    scopus 로고
    • Mutational analysis of the signal-sensing domain of ResE histidine kinase from Bacillus subtilis
    • Baruah A, Lindsey B, Zhu Y, Nakano MM, (2004) Mutational analysis of the signal-sensing domain of ResE histidine kinase from Bacillus subtilis. J Bacteriol 186: 1694–1704. doi: 10.1128/JB.186.6.1694-1704.2004 14996800
    • (2004) J Bacteriol , vol.186 , pp. 1694-1704
    • Baruah, A.1    Lindsey, B.2    Zhu, Y.3    Nakano, M.M.4
  • 30
    • 84891605602 scopus 로고    scopus 로고
    • The Staphylococcus aureus SrrAB two-component system promotes resistance to nitrosative stress and hypoxia
    • Kinkel TL, Roux CM, Dunman PM, Fang FC, (2013) The Staphylococcus aureus SrrAB two-component system promotes resistance to nitrosative stress and hypoxia. MBio 4: e00696–00613. doi: 10.1128/mBio.00696-13 24222487
    • (2013) MBio , vol.4
    • Kinkel, T.L.1    Roux, C.M.2    Dunman, P.M.3    Fang, F.C.4
  • 31
    • 4544279117 scopus 로고    scopus 로고
    • Bacillus subtilis ResD induces expression of the potential regulatory genes yclJK upon oxygen limitation
    • Hartig E, Geng H, Hartmann A, Hubacek A, Munch R, et al. (2004) Bacillus subtilis ResD induces expression of the potential regulatory genes yclJK upon oxygen limitation. J Bacteriol 186: 6477–6484. doi: 10.1128/JB.186.19.6477-6484.2004 15375128
    • (2004) J Bacteriol , vol.186 , pp. 6477-6484
    • Hartig, E.1    Geng, H.2    Hartmann, A.3    Hubacek, A.4    Munch, R.5
  • 32
    • 84890912786 scopus 로고    scopus 로고
    • The ResD Response Regulator, through Functional Interaction with NsrR and Fur, Plays Three Distinct Roles in Bacillus subtilis Transcriptional Control
    • Henares B, Kommineni S, Chumsakul O, Ogasawara N, Ishikawa S, et al. (2014) The ResD Response Regulator, through Functional Interaction with NsrR and Fur, Plays Three Distinct Roles in Bacillus subtilis Transcriptional Control. J Bacteriol 196: 493–503. doi: 10.1128/JB.01166-13 24214949
    • (2014) J Bacteriol , vol.196 , pp. 493-503
    • Henares, B.1    Kommineni, S.2    Chumsakul, O.3    Ogasawara, N.4    Ishikawa, S.5
  • 33
    • 84868101287 scopus 로고    scopus 로고
    • Genome-wide identification of genes directly regulated by the pleiotropic transcription factor Spx in Bacillus subtilis
    • Rochat T, Nicolas P, Delumeau O, Rabatinova A, Korelusova J, et al. (2012) Genome-wide identification of genes directly regulated by the pleiotropic transcription factor Spx in Bacillus subtilis. Nucleic Acids Res 40: 9571–9583. doi: 10.1093/nar/gks755 22904090
    • (2012) Nucleic Acids Res , vol.40 , pp. 9571-9583
    • Rochat, T.1    Nicolas, P.2    Delumeau, O.3    Rabatinova, A.4    Korelusova, J.5
  • 34
    • 0036189830 scopus 로고    scopus 로고
    • Induction of ResDE-dependent gene expression in Bacillus subtilis in response to nitric oxide and nitrosative stress
    • Nakano MM, (2002) Induction of ResDE-dependent gene expression in Bacillus subtilis in response to nitric oxide and nitrosative stress. J Bacteriol 184: 1783–1787. doi: 10.1128/JB.184.6.1783-1787.2002 11872732
    • (2002) J Bacteriol , vol.184 , pp. 1783-1787
    • Nakano, M.M.1
  • 35
    • 0030665283 scopus 로고    scopus 로고
    • Expression of a stress- and starvation-induced dps/pexB-homologous gene is controlled by the alternative sigma factor sigmaB in Bacillus subtilis
    • Antelmann H, Engelmann S, Schmid R, Sorokin A, Lapidus A, et al. (1997) Expression of a stress- and starvation-induced dps/pexB-homologous gene is controlled by the alternative sigma factor sigmaB in Bacillus subtilis. J Bacteriol 179: 7251–7256. 9393687
    • (1997) J Bacteriol , vol.179 , pp. 7251-7256
    • Antelmann, H.1    Engelmann, S.2    Schmid, R.3    Sorokin, A.4    Lapidus, A.5
  • 36
    • 50049105557 scopus 로고    scopus 로고
    • Spx mediates oxidative stress regulation of the methionine sulfoxide reductases operon in Bacillus subtilis
    • You C, Sekowska A, Francetic O, Martin-Verstraete I, Wang Y, et al. (2008) Spx mediates oxidative stress regulation of the methionine sulfoxide reductases operon in Bacillus subtilis. BMC Microbiol 8: 128. doi: 10.1186/1471-2180-8-128 18662407
    • (2008) BMC Microbiol , vol.8 , pp. 128
    • You, C.1    Sekowska, A.2    Francetic, O.3    Martin-Verstraete, I.4    Wang, Y.5
  • 37
    • 85120658674 scopus 로고    scopus 로고
    • Kiran MD, Bala S, Hirshberg M, Balaban N (2010) YhgC protects Bacillus anthracis from oxidative stress. Int J Artif Organs.
  • 38
    • 34047252713 scopus 로고    scopus 로고
    • Bacterial flavodoxins support nitric oxide production by Bacillus subtilis nitric-oxide synthase
    • Wang ZQ, Lawson RJ, Buddha MR, Wei CC, Crane BR, et al. (2007) Bacterial flavodoxins support nitric oxide production by Bacillus subtilis nitric-oxide synthase. J Biol Chem 282: 2196–2202. 17127770
    • (2007) J Biol Chem , vol.282 , pp. 2196-2202
    • Wang, Z.Q.1    Lawson, R.J.2    Buddha, M.R.3    Wei, C.C.4    Crane, B.R.5
  • 39
    • 84859229689 scopus 로고    scopus 로고
    • Three essential ribonucleases-RNase Y, J1, and III-control the abundance of a majority of Bacillus subtilis mRNAs
    • Durand S, Gilet L, Bessieres P, Nicolas P, Condon C, (2012) Three essential ribonucleases-RNase Y, J1, and III-control the abundance of a majority of Bacillus subtilis mRNAs. PLoS Genet 8: e1002520. doi: 10.1371/journal.pgen.1002520 22412379
    • (2012) PLoS Genet , vol.8
    • Durand, S.1    Gilet, L.2    Bessieres, P.3    Nicolas, P.4    Condon, C.5
  • 40
    • 84864146468 scopus 로고    scopus 로고
    • Computational identification of sRNA targets
    • Tjaden B, (2012) Computational identification of sRNA targets. Methods Mol Biol 905: 227–234. doi: 10.1007/978-1-61779-949-5_14 22736007
    • (2012) Methods Mol Biol , vol.905 , pp. 227-234
    • Tjaden, B.1
  • 41
    • 84883772639 scopus 로고    scopus 로고
    • Comparative genomics boosts target prediction for bacterial small RNAs
    • Wright PR, Richter AS, Papenfort K, Mann M, Vogel J, et al. (2013) Comparative genomics boosts target prediction for bacterial small RNAs. Proc Natl Acad Sci U S A 110: E3487–3496. doi: 10.1073/pnas.1303248110 23980183
    • (2013) Proc Natl Acad Sci U S A , vol.110 , pp. 3487-3496
    • Wright, P.R.1    Richter, A.S.2    Papenfort, K.3    Mann, M.4    Vogel, J.5
  • 42
    • 79959937873 scopus 로고    scopus 로고
    • RNApredator: fast accessibility-based prediction of sRNA targets
    • Eggenhofer F, Tafer H, Stadler PF, Hofacker IL, (2011) RNApredator: fast accessibility-based prediction of sRNA targets. Nucleic Acids Res 39: W149–154. doi: 10.1093/nar/gkr467 21672960
    • (2011) Nucleic Acids Res , vol.39 , pp. 149-154
    • Eggenhofer, F.1    Tafer, H.2    Stadler, P.F.3    Hofacker, I.L.4
  • 43
    • 1642329678 scopus 로고    scopus 로고
    • Transcriptional activation by Bacillus subtilis ResD: tandem binding to target elements and phosphorylation-dependent and -independent transcriptional activation
    • Geng H, Nakano S, Nakano MM, (2004) Transcriptional activation by Bacillus subtilis ResD: tandem binding to target elements and phosphorylation-dependent and -independent transcriptional activation. J Bacteriol 186: 2028–2037. doi: 10.1128/JB.186.7.2028-2037.2004 15028686
    • (2004) J Bacteriol , vol.186 , pp. 2028-2037
    • Geng, H.1    Nakano, S.2    Nakano, M.M.3
  • 44
    • 0035933597 scopus 로고    scopus 로고
    • Quinones as the redox signal for the arc two-component system of bacteria
    • Georgellis D, Kwon O, Lin EC, (2001) Quinones as the redox signal for the arc two-component system of bacteria. Science 292: 2314–2316. 11423658
    • (2001) Science , vol.292 , pp. 2314-2316
    • Georgellis, D.1    Kwon, O.2    Lin, E.C.3
  • 45
    • 0033891425 scopus 로고    scopus 로고
    • Global gene expression profiles of Bacillus subtilis grown under anaerobic conditions
    • Ye RW, Tao W, Bedzyk L, Young T, Chen M, et al. (2000) Global gene expression profiles of Bacillus subtilis grown under anaerobic conditions. J Bacteriol 182: 4458–4465. 10913079
    • (2000) J Bacteriol , vol.182 , pp. 4458-4465
    • Ye, R.W.1    Tao, W.2    Bedzyk, L.3    Young, T.4    Chen, M.5
  • 46
    • 84902332213 scopus 로고    scopus 로고
    • Quantitative flux analysis reveals folate-dependent NADPH production
    • Fan J, Ye J, Kamphorst JJ, Shlomi T, Thompson CB, et al. (2014) Quantitative flux analysis reveals folate-dependent NADPH production. Nature 510: 298–302. doi: 10.1038/nature13236 24805240
    • (2014) Nature , vol.510 , pp. 298-302
    • Fan, J.1    Ye, J.2    Kamphorst, J.J.3    Shlomi, T.4    Thompson, C.B.5
  • 47
    • 70450222923 scopus 로고    scopus 로고
    • RNase Y, a novel endoribonuclease, initiates riboswitch turnover in Bacillus subtilis
    • Shahbabian K, Jamalli A, Zig L, Putzer H, (2009) RNase Y, a novel endoribonuclease, initiates riboswitch turnover in Bacillus subtilis. EMBO J 28: 3523–3533. doi: 10.1038/emboj.2009.283 19779461
    • (2009) EMBO J , vol.28 , pp. 3523-3533
    • Shahbabian, K.1    Jamalli, A.2    Zig, L.3    Putzer, H.4
  • 48
    • 84873022664 scopus 로고    scopus 로고
    • DEAD-Box RNA helicases in Bacillus subtilis have multiple functions and act independently from each other
    • Lehnik-Habrink M, Rempeters L, Kovacs AT, Wrede C, Baierlein C, et al. (2013) DEAD-Box RNA helicases in Bacillus subtilis have multiple functions and act independently from each other. J Bacteriol 195: 534–544. doi: 10.1128/JB.01475-12 23175651
    • (2013) J Bacteriol , vol.195 , pp. 534-544
    • Lehnik-Habrink, M.1    Rempeters, L.2    Kovacs, A.T.3    Wrede, C.4    Baierlein, C.5
  • 49
    • 0025355785 scopus 로고
    • Escherichia coli cell division inhibitor DicF-RNA of the dicB operon. Evidence for its generation in vivo by transcription termination and by RNase III and RNase E-dependent processing
    • Faubladier M, Cam K, Bouche JP, (1990) Escherichia coli cell division inhibitor DicF-RNA of the dicB operon. Evidence for its generation in vivo by transcription termination and by RNase III and RNase E-dependent processing. J Mol Biol 212: 461–471. 1691299
    • (1990) J Mol Biol , vol.212 , pp. 461-471
    • Faubladier, M.1    Cam, K.2    Bouche, J.P.3
  • 50
    • 84904362234 scopus 로고    scopus 로고
    • MicL, a new sigmaE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein
    • Guo MS, Updegrove TB, Gogol EB, Shabalina SA, Gross CA, et al. (2014) MicL, a new sigmaE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein. Genes Dev 28: 1620–1634. doi: 10.1101/gad.243485.114 25030700
    • (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
  • 51
    • 70350176597 scopus 로고    scopus 로고
    • Specific and pleiotropic patterns of mRNA regulation by ArcZ, a conserved, Hfq-dependent small RNA
    • Papenfort K, Said N, Welsink T, Lucchini S, Hinton JC, et al. (2009) Specific and pleiotropic patterns of mRNA regulation by ArcZ, a conserved, Hfq-dependent small RNA. Mol Microbiol 74: 139–158. doi: 10.1111/j.1365-2958.2009.06857.x 19732340
    • (2009) Mol Microbiol , vol.74 , pp. 139-158
    • Papenfort, K.1    Said, N.2    Welsink, T.3    Lucchini, S.4    Hinton, J.C.5
  • 52
    • 77956879952 scopus 로고    scopus 로고
    • Integrating anaerobic/aerobic sensing and the general stress response through the ArcZ small RNA
    • Mandin P, Gottesman S, (2010) Integrating anaerobic/aerobic sensing and the general stress response through the ArcZ small RNA. EMBO J 29: 3094–3107. doi: 10.1038/emboj.2010.179 20683441
    • (2010) EMBO J , vol.29 , pp. 3094-3107
    • Mandin, P.1    Gottesman, S.2
  • 53
    • 34447328708 scopus 로고    scopus 로고
    • RNase E-dependent processing stabilizes MicX, a Vibrio cholerae sRNA
    • Davis BM, Waldor MK, (2007) RNase E-dependent processing stabilizes MicX, a Vibrio cholerae sRNA. Mol Microbiol 65: 373–385. doi: 10.1111/j.1365-2958.2007.05796.x 17590231
    • (2007) Mol Microbiol , vol.65 , pp. 373-385
    • Davis, B.M.1    Waldor, M.K.2
  • 55
    • 79954601376 scopus 로고    scopus 로고
    • Regulation of the small regulatory RNA MicA by ribonuclease III: a target-dependent pathway
    • 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. doi: 10.1093/nar/gkq1239 21138960
    • (2011) Nucleic Acids Res , vol.39 , pp. 2918-2930
    • Viegas, S.C.1    Silva, I.J.2    Saramago, M.3    Domingues, S.4    Arraiano, C.M.5
  • 56
    • 15044340366 scopus 로고    scopus 로고
    • Both RNase E and RNase III control the stability of sodB mRNA upon translational inhibition by the small regulatory RNA RyhB
    • Afonyushkin T, Vecerek B, Moll I, Blasi U, Kaberdin VR, (2005) Both RNase E and RNase III control the stability of sodB mRNA upon translational inhibition by the small regulatory RNA RyhB. Nucleic Acids Res 33: 1678–1689. doi: 10.1093/nar/gki313 15781494
    • (2005) Nucleic Acids Res , vol.33 , pp. 1678-1689
    • Afonyushkin, T.1    Vecerek, B.2    Moll, I.3    Blasi, U.4    Kaberdin, V.R.5
  • 57
    • 79956068747 scopus 로고    scopus 로고
    • CsfG, a sporulation-specific, small non-coding RNA highly conserved in endospore formers
    • Marchais A, Duperrier S, Durand S, Gautheret D, Stragier P, (2011) CsfG, a sporulation-specific, small non-coding RNA highly conserved in endospore formers. RNA Biol 8: 358–364. doi: 10.4161/rna.8.3.14998 21532344
    • (2011) RNA Biol , vol.8 , pp. 358-364
    • Marchais, A.1    Duperrier, S.2    Durand, S.3    Gautheret, D.4    Stragier, P.5
  • 58
    • 0029590029 scopus 로고
    • Antibiotic-resistance cassettes for Bacillus subtilis
    • Guerout-Fleury AM, Shazand K, Frandsen N, Stragier P, (1995) Antibiotic-resistance cassettes for Bacillus subtilis. Gene 167: 335–336. 8566804
    • (1995) Gene , vol.167 , pp. 335-336
    • Guerout-Fleury, A.M.1    Shazand, K.2    Frandsen, N.3    Stragier, P.4
  • 59
    • 33845719997 scopus 로고    scopus 로고
    • Maturation of the 5′ end of Bacillus subtilis 16S rRNA by the essential ribonuclease YkqC/RNase J1
    • Britton RA, Wen T, Schaefer L, Pellegrini O, Uicker WC, et al. (2007) Maturation of the 5′ end of Bacillus subtilis 16S rRNA by the essential ribonuclease YkqC/RNase J1. Mol Microbiol 63: 127–138. 17229210
    • (2007) Mol Microbiol , vol.63 , pp. 127-138
    • Britton, R.A.1    Wen, T.2    Schaefer, L.3    Pellegrini, O.4    Uicker, W.C.5
  • 60
  • 61
    • 84869010693 scopus 로고    scopus 로고
    • RNAsnap: a rapid, quantitative and inexpensive, method for isolating total RNA from bacteria
    • Stead MB, Agrawal A, Bowden KE, Nasir R, Mohanty BK, et al. (2012) RNAsnap: a rapid, quantitative and inexpensive, method for isolating total RNA from bacteria. Nucleic Acids Res 40: e156. doi: 10.1093/nar/gks680 22821568
    • (2012) Nucleic Acids Res , vol.40 , pp. 156
    • Stead, M.B.1    Agrawal, A.2    Bowden, K.E.3    Nasir, R.4    Mohanty, B.K.5
  • 62
    • 4544341015 scopus 로고    scopus 로고
    • Linear models and empirical bayes methods for assessing differential expression in microarray experiments
    • Smyth GK, (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3: Article3. 16646809
    • (2004) Stat Appl Genet Mol Biol , vol.3
    • Smyth, G.K.1
  • 63
    • 47749156020 scopus 로고    scopus 로고
    • A unified approach to false discovery rate estimation
    • Strimmer K, (2008) A unified approach to false discovery rate estimation. BMC Bioinformatics 9: 303. doi: 10.1186/1471-2105-9-303 18613966
    • (2008) BMC Bioinformatics , vol.9 , pp. 303
    • Strimmer, K.1
  • 64
    • 26444506068 scopus 로고    scopus 로고
    • Correlation of relative abundance ratios derived from peptide ion chromatograms and spectrum counting for quantitative proteomic analysis using stable isotope labeling
    • Zybailov B, Coleman MK, Florens L, Washburn MP, (2005) Correlation of relative abundance ratios derived from peptide ion chromatograms and spectrum counting for quantitative proteomic analysis using stable isotope labeling. Anal Chem 77: 6218–6224. 16194081
    • (2005) Anal Chem , vol.77 , pp. 6218-6224
    • Zybailov, B.1    Coleman, M.K.2    Florens, L.3    Washburn, M.P.4
  • 65
    • 84862994718 scopus 로고    scopus 로고
    • Comparative label-free LC-MS/MS analysis of colorectal adenocarcinoma and metastatic cells treated with 5-fluorouracil
    • Bauer KM, Lambert PA, Hummon AB, (2012) Comparative label-free LC-MS/MS analysis of colorectal adenocarcinoma and metastatic cells treated with 5-fluorouracil. Proteomics 12: 1928–1937. doi: 10.1002/pmic.201200041 22623418
    • (2012) Proteomics , vol.12 , pp. 1928-1937
    • Bauer, K.M.1    Lambert, P.A.2    Hummon, A.B.3
  • 66
    • 65649150695 scopus 로고    scopus 로고
    • Ribosomal initiation complexes probed by toeprinting and effect of trans-acting translational regulators in bacteria
    • Fechter P, Chevalier C, Yusupova G, Yusupov M, Romby P, et al. (2009) Ribosomal initiation complexes probed by toeprinting and effect of trans-acting translational regulators in bacteria. Methods Mol Biol 540: 247–263. doi: 10.1007/978-1-59745-558-9_18 19381565
    • (2009) Methods Mol Biol , vol.540 , pp. 247-263
    • Fechter, P.1    Chevalier, C.2    Yusupova, G.3    Yusupov, M.4    Romby, P.5
  • 67
    • 65649135085 scopus 로고    scopus 로고
    • Probing mRNA structure and sRNA-mRNA interactions in bacteria using enzymes and lead(II)
    • Chevalier C, Geissmann T, Helfer AC, Romby P, (2009) Probing mRNA structure and sRNA-mRNA interactions in bacteria using enzymes and lead(II). Methods Mol Biol 540: 215–232. doi: 10.1007/978-1-59745-558-9_16 19381563
    • (2009) Methods Mol Biol , vol.540 , pp. 215-232
    • Chevalier, C.1    Geissmann, T.2    Helfer, A.C.3    Romby, P.4


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