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Volumn 7, Issue 4, 2012, Pages 535-547

Identification by cDNA cloning of abundant sRNAs in a human-avirulent Yersinia pestis strain grown under five different growth conditions

Author keywords

cDNA library construction; small RNA; Yersinia pestis

Indexed keywords

COMPLEMENTARY DNA; COMPLEMENTARY RNA; TRANSFER RNA; UNTRANSLATED RNA;

EID: 84858962249     PISSN: 17460913     EISSN: 17460921     Source Type: Journal    
DOI: 10.2217/fmb.12.13     Document Type: Article
Times cited : (17)

References (46)
  • 1
    • 60149089144 scopus 로고    scopus 로고
    • Regulatory RNAs in bacteria
    • Waters LS, Storz G. Regulatory RNAs in bacteria. Cell 136(4), 615-628 (2009).
    • (2009) Cell , vol.136 , Issue.4 , pp. 615-628
    • Waters, L.S.1    Storz, G.2
  • 2
    • 4344682527 scopus 로고    scopus 로고
    • The small RNA regulators of Escherichia coli: Roles and mechanisms
    • Gottesman S. The small RNA regulators of Escherichia coli: roles and mechanisms. Annu. Rev. Microbiol. 58, 303-328 (2004).
    • (2004) Annu. Rev. Microbiol. , vol.58 , pp. 303-328
    • Gottesman, S.1
  • 3
    • 50849105413 scopus 로고    scopus 로고
    • Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq
    • Sittka A, Lucchini S, Papenfort K et al. Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq. PLoS Genet. 4(8), E1000163 (2008).
    • (2008) PLoS Genet. , vol.4 , Issue.8
    • Sittka, A.1    Lucchini, S.2    Papenfort, K.3
  • 4
    • 67349278437 scopus 로고    scopus 로고
    • Deep sequencing of Salmonella RNA associated with heterologous Hfq proteins in vivo reveals small RNAs as a major target class and identifies RNA processing phenotypes
    • Sittka A, Sharma CM, Rolle K, Vogel J. Deep sequencing of Salmonella RNA associated with heterologous Hfq proteins in vivo reveals small RNAs as a major target class and identifies RNA processing phenotypes. RNA Biol. 6(3), 266-275 (2009).
    • (2009) RNA Biol. , vol.6 , Issue.3 , pp. 266-275
    • Sittka, A.1    Sharma, C.M.2    Rolle, K.3    Vogel, J.4
  • 5
    • 0344237410 scopus 로고    scopus 로고
    • RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria
    • New sRNA species were identified by generating cDNA libraries of sRNAs
    • Vogel J, Bartels V, Tang TH et al. RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria. Nucleic Acids Res. 31(22), 6435-6443 (2003). New sRNA species were identified by generating cDNA libraries of sRNAs.
    • (2003) Nucleic Acids Res. , vol.31 , Issue.22 , pp. 6435-6443
    • Vogel, J.1    Bartels, V.2    Tang, T.H.3
  • 6
    • 70349906229 scopus 로고    scopus 로고
    • Regulatory RNAs in prokaryotes: Here, there and everywhere
    • Narberhaus F, Vogel J. Regulatory RNAs in prokaryotes: here, there and everywhere. Mol. Microbiol. 74(2), 261-269 (2009).
    • (2009) Mol. Microbiol. , vol.74 , Issue.2 , pp. 261-269
    • Narberhaus, F.1    Vogel, J.2
  • 7
    • 70449435697 scopus 로고    scopus 로고
    • A genome-wide analysis of small regulatory RNAs in the human pathogen group A Streptococcus
    • Perez N, Trevino J, Liu Z, Ho SC, Babitzke P, Sumby P. A genome-wide analysis of small regulatory RNAs in the human pathogen group A Streptococcus. PLoS ONE 4(11), E7668 (2009).
    • (2009) PLoS ONE , vol.4 , Issue.11
    • Perez, N.1    Trevino, J.2    Liu, Z.3    Ho, S.C.4    Babitzke, P.5    Sumby, P.6
  • 8
    • 73849125970 scopus 로고    scopus 로고
    • Identification and characterization of noncoding small RNAs in Streptococcus pneumoniae serotype 2 strain D39
    • Tsui HC, Mukherjee D, Ray VA, Sham LT, Feig AL, Winkler ME. Identification and characterization of noncoding small RNAs in Streptococcus pneumoniae serotype 2 strain D39. J. Bacteriol. 192(1), 264-279 (2010).
    • (2010) J. Bacteriol. , vol.192 , Issue.1 , pp. 264-279
    • Tsui, H.C.1    Mukherjee, D.2    Ray, V.A.3    Sham, L.T.4    Feig, A.L.5    Winkler, M.E.6
  • 9
    • 76949103628 scopus 로고    scopus 로고
    • Genome-wide detection of predicted non-coding RNAs in Rhizobium etli expressed during free-living and host-associated growth using a high-resolution tiling array
    • Vercruysse M, Fauvart M, Cloots L et al. Genome-wide detection of predicted non-coding RNAs in Rhizobium etli expressed during free-living and host-associated growth using a high-resolution tiling array. BMC Genomics 11, 53 (2010).
    • (2010) BMC Genomics , vol.11 , pp. 53
    • Vercruysse, M.1    Fauvart, M.2    Cloots, L.3
  • 10
    • 78149264799 scopus 로고    scopus 로고
    • Identification of small RNAs in Francisella tularensis
    • Postic G, Frapy E, Dupuis M et al. Identification of small RNAs in Francisella tularensis. BMC Genomics 11, 625 (2010).
    • (2010) BMC Genomics , vol.11 , pp. 625
    • Postic, G.1    Frapy, E.2    Dupuis, M.3
  • 11
    • 64549149245 scopus 로고    scopus 로고
    • Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing
    • Liu JM, Livny J, Lawrence MS, Kimball MD, Waldor MK, Camilli A. Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing. Nucleic Acids Res. 37(6), E46 (2009).
    • (2009) Nucleic Acids Res. , vol.37 , Issue.6
    • Liu, J.M.1    Livny, J.2    Lawrence, M.S.3    Kimball, M.D.4    Waldor, M.K.5    Camilli, A.6
  • 12
    • 77949425194 scopus 로고    scopus 로고
    • The primary transcriptome of the major human pathogen Helicobacter pylori
    • Sharma CM, Hoffmann S, Darfeuille F et al. The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 464(7286), 250-255 (2010).
    • (2010) Nature , vol.464 , Issue.7286 , pp. 250-255
    • Sharma, C.M.1    Hoffmann, S.2    Darfeuille, F.3
  • 13
    • 78049392640 scopus 로고    scopus 로고
    • Identification of regulatory RNAs in Bacillus subtilis
    • Irnov I, Sharma CM, Vogel J, Winkler WC. Identification of regulatory RNAs in Bacillus subtilis. Nucleic Acids Res. 38(19), 6637-6651 (2010).
    • (2010) Nucleic Acids Res. , vol.38 , Issue.19 , pp. 6637-6651
    • Irnov, I.1    Sharma, C.M.2    Vogel, J.3    Winkler, W.C.4
  • 14
    • 0035395606 scopus 로고    scopus 로고
    • Identification of novel small RNAs using comparative genomics and microarrays
    • Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S. Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev. 15(13), 1637-1651 (2001).
    • (2001) Genes Dev. , vol.15 , Issue.13 , pp. 1637-1651
    • Wassarman, K.M.1    Repoila, F.2    Rosenow, C.3    Storz, G.4    Gottesman, S.5
  • 15
    • 78149421813 scopus 로고    scopus 로고
    • Bacterial antisense RNAs: How many are there, and what are they doing?
    • Thomason MK, Storz G. Bacterial antisense RNAs: how many are there, and what are they doing? Annu. Rev. Genet. 44, 167-188 (2010).
    • (2010) Annu. Rev. Genet. , vol.44 , pp. 167-188
    • Thomason, M.K.1    Storz, G.2
  • 16
    • 0031029062 scopus 로고    scopus 로고
    • Yersinia pestis - Etiologic agent of plague
    • Perry RD, Fetherston JD. Yersinia pestis - etiologic agent of plague. Clin. Microbiol. Rev. 10(1), 35-66 (1997).
    • (1997) Clin. Microbiol. Rev. , vol.10 , Issue.1 , pp. 35-66
    • Perry, R.D.1    Fetherston, J.D.2
  • 17
    • 22944434548 scopus 로고    scopus 로고
    • The evolution of flea-borne transmission in Yersinia pestis
    • Hinnebusch BJ. The evolution of flea-borne transmission in Yersinia pestis. Curr. Issues Mol. Biol. 7(2), 197-212 (2005).
    • (2005) Curr. Issues Mol. Biol. , vol.7 , Issue.2 , pp. 197-212
    • Hinnebusch, B.J.1
  • 18
    • 77955958425 scopus 로고    scopus 로고
    • The importance of the small RNA chaperone Hfq for growth of epidemic Yersinia pestis, but not Yersinia pseudotuberculosis, with implications for plague biology
    • Bai G, Golubov A, Smith EA, Mcdonough KA. The importance of the small RNA chaperone Hfq for growth of epidemic Yersinia pestis, but not Yersinia pseudotuberculosis, with implications for plague biology. J. Bacteriol. 192(16), 4239-4245 (2010).
    • (2010) J. Bacteriol. , vol.192 , Issue.16 , pp. 4239-4245
    • Bai, G.1    Golubov, A.2    Smith, E.A.3    Mcdonough, K.A.4
  • 19
    • 67650550777 scopus 로고    scopus 로고
    • Involvement of the post-transcriptional regulator Hfq in Yersinia pestis virulence
    • Indirect evidence indicating that Hfq-associated sRNAs might be involved in the virulence of Yersinia pestis
    • Geng J, Song Y, Yang L et al. Involvement of the post-transcriptional regulator Hfq in Yersinia pestis virulence. PLoS ONE 4(7), E6213 (2009). Indirect evidence indicating that Hfq-associated sRNAs might be involved in the virulence of Yersinia pestis.
    • (2009) PLoS ONE , vol.4 , Issue.7
    • Geng, J.1    Song, Y.2    Yang, L.3
  • 20
    • 80053062656 scopus 로고    scopus 로고
    • Global discovery of small RNAs in Yersinia pseudotuberculosis identifies Yersinia-specific small, noncoding RNAs required for virulence
    • One hundred and fifty sRNAs identified in Yersinia pseudotuberculosis are Yersinia-specific or Y. pseudotuberculosis-specific, indicating many sRNAs remain to be characterized in Y. pestis
    • Koo JT, Alleyne TM, Schiano CA, Jafari N, Lathem WW. Global discovery of small RNAs in Yersinia pseudotuberculosis identifies Yersinia-specific small, noncoding RNAs required for virulence. Proc. Natl Acad. Sci. USA 108(37), E709-E717 (2011). One hundred and fifty sRNAs identified in Yersinia pseudotuberculosis are Yersinia-specific or Y. pseudotuberculosis-specific, indicating many sRNAs remain to be characterized in Y. pestis.
    • (2011) Proc. Natl Acad. Sci. USA , vol.108 , Issue.37
    • Koo, J.T.1    Alleyne, T.M.2    Schiano, C.A.3    Jafari, N.4    Lathem, W.W.5
  • 21
    • 3242796606 scopus 로고    scopus 로고
    • Genetics of metabolic variations between Yersinia pestis biovars and the proposal of a new biovar, microtus
    • Zhou D, Tong Z, Song Y et al. Genetics of metabolic variations between Yersinia pestis biovars and the proposal of a new biovar, microtus. J. Bacteriol. 186(15), 5147-5152 (2004).
    • (2004) J. Bacteriol. , vol.186 , Issue.15 , pp. 5147-5152
    • Zhou, D.1    Tong, Z.2    Song, Y.3
  • 22
    • 42249096457 scopus 로고    scopus 로고
    • Identification and characterization of PhoP regulon members in Yersinia pestis biovar Microtus
    • Li Y, Gao H, Qin L et al. Identification and characterization of PhoP regulon members in Yersinia pestis biovar Microtus. BMC Genomics 9, 143 (2008).
    • (2008) BMC Genomics , vol.9 , pp. 143
    • Li, Y.1    Gao, H.2    Qin, L.3
  • 23
    • 0022629859 scopus 로고
    • Virulence genes regulated at the transcriptional level by Ca2+ in Yersinia pestis include structural genes for outer membrane proteins
    • Straley SC, Bowmer WS. Virulence genes regulated at the transcriptional level by Ca2+ in Yersinia pestis include structural genes for outer membrane proteins. Infect. Immun. 51(2), 445-454 (1986).
    • (1986) Infect. Immun. , vol.51 , Issue.2 , pp. 445-454
    • Straley, S.C.1    Bowmer, W.S.2
  • 24
    • 55549099601 scopus 로고    scopus 로고
    • Detection of small RNAs in Pseudomonas aeruginosa by RNomics and structure-based bioinformatic tools
    • Sonnleitner E, Sorger-Domenigg T, Madej MJ et al. Detection of small RNAs in Pseudomonas aeruginosa by RNomics and structure-based bioinformatic tools. Microbiology 154(Pt 10), 3175-3187 (2008).
    • (2008) Microbiology , vol.154 , Issue.PART 10 , pp. 3175-3187
    • Sonnleitner, E.1    Sorger-Domenigg, T.2    Madej, M.J.3
  • 25
    • 34447499141 scopus 로고    scopus 로고
    • Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake
    • Kingsford CL, Ayanbule K, Salzberg SL. Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biol. 8(2), R22 (2007).
    • (2007) Genome Biol. , vol.8 , Issue.2
    • Kingsford, C.L.1    Ayanbule, K.2    Salzberg, S.L.3
  • 26
    • 38549140094 scopus 로고    scopus 로고
    • RegulonDB (version 6.0): Gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation
    • Gama-Castro S, Jimenez-Jacinto V, Peralta-Gil M et al. RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res. 36(Database issue), D120-D124 (2008).
    • (2008) Nucleic Acids Res. , vol.36 , Issue.DATABASE ISSUE
    • Gama-Castro, S.1    Jimenez-Jacinto, V.2    Peralta-Gil, M.3
  • 27
    • 77955821310 scopus 로고    scopus 로고
    • Northern blot detection of endogenous small RNAs (approximately 14 nt) in bacterial total RNA extracts
    • Beckmann BM, Grunweller A, Weber MH, Hartmann RK. Northern blot detection of endogenous small RNAs (approximately 14 nt) in bacterial total RNA extracts. Nucleic Acids Res. 38(14), E147 (2010).
    • (2010) Nucleic Acids Res. , vol.38 , Issue.14
    • Beckmann, B.M.1    Grunweller, A.2    Weber, M.H.3    Hartmann, R.K.4
  • 28
    • 34247099372 scopus 로고    scopus 로고
    • Regulatory mechanisms employed by cis-encoded antisense RNAs
    • Brantl S. Regulatory mechanisms employed by cis-encoded antisense RNAs. Curr. Opin. Microbiol. 10(2), 102-109 (2007).
    • (2007) Curr. Opin. Microbiol. , vol.10 , Issue.2 , pp. 102-109
    • Brantl, S.1
  • 29
    • 85041131924 scopus 로고
    • Antisense RNA control in bacteria, phages and plasmids
    • Wagner EG. Antisense RNA control in bacteria, phages and plasmids. Annu. Rev. Microbiol. 48, 713-742 (1994).
    • (1994) Annu. Rev. Microbiol. , vol.48 , pp. 713-742
    • Wagner, E.G.1
  • 30
    • 0031823250 scopus 로고    scopus 로고
    • Degradation pathway of CopA, the antisense RNA that controls replication of plasmid R1
    • Soderbom F, Wagner EG. Degradation pathway of CopA, the antisense RNA that controls replication of plasmid R1. Microbiology 144(Pt 7), 1907-1917 (1998).
    • (1998) Microbiology , vol.144 , Issue.PART 7 , pp. 1907-1917
    • Soderbom, F.1    Wagner, E.G.2
  • 32
    • 33845450357 scopus 로고    scopus 로고
    • Synthesis-mediated release of a small RNA inhibitor of RNA polymerase
    • Wassarman KM, Saecker RM. Synthesis-mediated release of a small RNA inhibitor of RNA polymerase. Science 314(5805), 1601-1603 (2006).
    • (2006) Science , vol.314 , Issue.5805 , pp. 1601-1603
    • Wassarman, K.M.1    Saecker, R.M.2
  • 33
    • 77953615968 scopus 로고    scopus 로고
    • Avoidance of antisense, antiterminator tRNA anticodons in vertebrate mitochondria
    • Seligmann H. Avoidance of antisense, antiterminator tRNA anticodons in vertebrate mitochondria. Biosystems 101(1), 42-50 (2010).
    • (2010) Biosystems , vol.101 , Issue.1 , pp. 42-50
    • Seligmann, H.1
  • 34
    • 13444249920 scopus 로고    scopus 로고
    • Mutation and selection on the anticodon of tRNA genes in vertebrate mitochondrial genomes
    • Xia X. Mutation and selection on the anticodon of tRNA genes in vertebrate mitochondrial genomes. Gene 345(1), 13-20 (2005).
    • (2005) Gene , vol.345 , Issue.1 , pp. 13-20
    • Xia, X.1
  • 35
    • 0020826922 scopus 로고
    • Translational control of IS10 transposition
    • Simons RW, Kleckner N. Translational control of IS10 transposition. Cell 34, 683-691 (1983).
    • (1983) Cell , vol.34 , pp. 683-691
    • Simons, R.W.1    Kleckner, N.2
  • 36
    • 28844473478 scopus 로고    scopus 로고
    • Short retroposons in eukaryotic genomes
    • Kramerov DA, Vassetzky NS. Short retroposons in eukaryotic genomes. Int. Rev. Cytol. 247, 165-221 (2005).
    • (2005) Int. Rev. Cytol. , vol.247 , pp. 165-221
    • Kramerov, D.A.1    Vassetzky, N.S.2
  • 37
    • 0014220139 scopus 로고
    • 32P-labeled ribonucleic acids on polyacrylamide gels and their characterization by fingerprinting
    • 32P-labeled ribonucleic acids on polyacrylamide gels and their characterization by fingerprinting. J. Mol. Biol. 30, 125-136 (1967).
    • (1967) J. Mol. Biol. , vol.30 , pp. 125-136
    • Hindley, J.1
  • 38
    • 0345465673 scopus 로고    scopus 로고
    • SmpB, a unique RNA-binding protein essential for the peptide-tagging activity of SsrA (tmRNA)
    • Karzai Aw, Susskind MM, Sauer RT. SmpB, a unique RNA-binding protein essential for the peptide-tagging activity of SsrA (tmRNA). EMBO J. 18(13), 3793-3799 (1999).
    • (1999) EMBO J. , vol.18 , Issue.13 , pp. 3793-3799
    • Karzai, Aw.1    Susskind, M.M.2    Sauer, R.T.3
  • 39
    • 33645765576 scopus 로고    scopus 로고
    • A role for the SmpB-SsrA system in Yersinia pseudotuberculosis pathogenesis
    • Okan NA, Bliska JB, Karzai AW. A role for the SmpB-SsrA system in Yersinia pseudotuberculosis pathogenesis. PLoS Pathog. 2, E6 (2006).
    • (2006) PLoS Pathog. , vol.2
    • Okan, N.A.1    Bliska, J.B.2    Karzai, A.W.3
  • 40
    • 62849101179 scopus 로고    scopus 로고
    • Global systems-level analysis of Hfq and SmpB deletion mutants in Salmonella: Implications for virulence and global protein translation
    • Ansong C, Yoon H, Porwollik S et al. Global systems-level analysis of Hfq and SmpB deletion mutants in Salmonella: implications for virulence and global protein translation. PLoS ONE 4(3), E4809 (2009).
    • (2009) PLoS ONE , vol.4 , Issue.3
    • Ansong, C.1    Yoon, H.2    Porwollik, S.3
  • 41
    • 77349125807 scopus 로고    scopus 로고
    • The smpB-ssrA mutant of Yersinia pestis functions as a live attenuated vaccine to protect mice against pulmonary plague infection
    • Okan NA, Mena P, Benach JL, Bliska JB, Karzai AW. The smpB-ssrA mutant of Yersinia pestis functions as a live attenuated vaccine to protect mice against pulmonary plague infection. Infect. Immun. 78(3), 1284-1293 (2010).
    • (2010) Infect. Immun. , vol.78 , Issue.3 , pp. 1284-1293
    • Okan, N.A.1    Mena, P.2    Benach, J.L.3    Bliska, J.B.4    Karzai, A.W.5
  • 42
    • 58649085492 scopus 로고    scopus 로고
    • The CRP-activated small noncoding regulatory RNA CyaR (RyeE) links nutritional status to group behavior
    • De Lay N, Gottesman S. The CRP-activated small noncoding regulatory RNA CyaR (RyeE) links nutritional status to group behavior. J. Bacteriol. 191(2), 461-476 (2009).
    • (2009) J. Bacteriol. , vol.191 , Issue.2 , pp. 461-476
    • De Lay, N.1    Gottesman, S.2
  • 43
    • 48449101958 scopus 로고    scopus 로고
    • TargetRNA: A tool for predicting targets of small RNA action in bacteria
    • Tjaden B. TargetRNA: a tool for predicting targets of small RNA action in bacteria. Nucleic Acids Res. 36, W109-W113 (2008).
    • (2008) Nucleic Acids Res. , vol.36
    • Tjaden, B.1
  • 44
    • 84858982204 scopus 로고    scopus 로고
    • Softberry. http://linux1.softberry.com


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