메뉴 건너뛰기




Volumn 8, Issue , 2007, Pages

Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in Sinorhizobium meliloti strain 1021

Author keywords

[No Author keywords available]

Indexed keywords

TRANSFER RNA; BACTERIAL RNA; NUCLEAR RNA; STEROID RECEPTOR RNA ACTIVATOR; UNCLASSIFIED DRUG; UNTRANSLATED RNA;

EID: 39149122829     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-8-467     Document Type: Article
Times cited : (49)

References (90)
  • 1
    • 0035656688 scopus 로고    scopus 로고
    • Non-coding RNA genes and the modern RNA world
    • 10.1038/35103511
    • Eddy SR Non-coding RNA genes and the modern RNA world Nature Rev Genet 2001, 2:919. 10.1038/35103511
    • (2001) Nature Rev Genet , vol.2 , pp. 919
    • Eddy, S.R.1
  • 2
    • 0035395606 scopus 로고    scopus 로고
    • Identification of novel small RNAs using comparative genomics and microarrays
    • 10.1101/gad.901001
    • Wassarman KM Repoila F Rosenow C Storz G Gottesman S Identification of novel small RNAs using comparative genomics and microarrays Genes Dev 2001, 13:1637-1651. 10.1101/gad.901001
    • (2001) Genes Dev , vol.13 , pp. 1637-1651
    • Wassarman, K.M.1    Repoila, F.2    Rosenow, C.3    Storz, G.4    Gottesman, S.5
  • 3
    • 0030856840 scopus 로고    scopus 로고
    • Analysis of the yeast genome: Identification of new non-coding and small ORF-containing RNAs
    • 147069 9358174 10.1093/nar/25.22.4619
    • Olivas WM Muhlrad D Parker R Analysis of the yeast genome: identification of new non-coding and small ORF-containing RNAs Nucleic Acids Res 1997, 25:4619. 147069 9358174 10.1093/nar/25.22.4619
    • (1997) Nucleic Acids Res , vol.25 , pp. 4619
    • Olivas, W.M.1    Muhlrad, D.2    Parker, R.3
  • 4
    • 0035954304 scopus 로고    scopus 로고
    • Novel small RNA-encoding genes in the intergenic regions of Escherichia coli
    • 10.1016/S0960-9822(01)00270-6
    • Argaman L Hershberg R Vogel J Bejerano G Wagner EG Margalit H Altuvia S Novel small RNA-encoding genes in the intergenic regions of Escherichia coli Curr Biol 2001, 2:941-950. 10.1016/S0960-9822(01)00270-6
    • (2001) Curr Biol , vol.2 , pp. 941-950
    • Argaman, L.1    Hershberg, R.2    Vogel, J.3    Bejerano, G.4    Wagner, E.G.5    Margalit, H.6    Altuvia, S.7
  • 5
    • 15944384666 scopus 로고    scopus 로고
    • The expanding world of small RNAs in the hyperthermophilic archaeon Sulfolobus solfataricus
    • 10.1111/j.1365-2958.2005.04505.x
    • Zago MA Dennis PP Omer AD The expanding world of small RNAs in the hyperthermophilic archaeon Sulfolobus solfataricus Mol Microbiol 2005, 6:1812-1828. 10.1111/j.1365-2958.2005.04505.x
    • (2005) Mol Microbiol , vol.6 , pp. 1812-1828
    • Zago, M.A.1    Dennis, P.P.2    Omer, A.D.3
  • 6
    • 29044436786 scopus 로고    scopus 로고
    • Identification of cyanobacterial non-coding RNAs by comparative genome analysis
    • 10.1186/gb-2005-6-9-r73
    • Axmann IM Kensche P Vogel J Kohl S Herzel H Hess WR Identification of cyanobacterial non-coding RNAs by comparative genome analysis Genome Biol 2005, 9:R73. 10.1186/gb-2005-6-9-r73
    • (2005) Genome Biol , vol.9
    • Axmann, I.M.1    Kensche, P.2    Vogel, J.3    Kohl, S.4    Herzel, H.5    Hess, W.R.6
  • 7
    • 0036271043 scopus 로고    scopus 로고
    • A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome
    • 10.1016/S0303-2647(02)00013-8
    • Chen S Lesnik EA Hall TA Sampath R Griffey RH Ecker DJ Blyn LB A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome Biosystems 2002, (2-3):157-177. 10.1016/ S0303-2647(02)00013-8
    • (2002) Biosystems , Issue.2-3 , pp. 157-177
    • Chen, S.1    Lesnik, E.A.2    Hall, T.A.3    Sampath, R.4    Griffey, R.H.5    Ecker, D.J.6    Blyn, L.B.7
  • 8
    • 0037188546 scopus 로고    scopus 로고
    • Noncoding RNA genes identified in AT-rich hyperthermophiles
    • 10.1073/pnas.112063799
    • Klein RJ Misulovin Z Eddy S Noncoding RNA genes identified in AT-rich hyperthermophiles Proc Natl Acad Sci USA 2002, 11:7542-7547. 10.1073/ pnas.112063799
    • (2002) Proc Natl Acad Sci USA , vol.11 , pp. 7542-7547
    • Klein, R.J.1    Misulovin, Z.2    Eddy, S.3
  • 9
    • 0036567632 scopus 로고    scopus 로고
    • Searching for RNA genes using base-composition statistics
    • 10.1093/nar/30.9.2076
    • Schattner P Searching for RNA genes using base-composition statistics Nucleic Acids Res 2002, 9:2076-2082. 10.1093/nar/30.9.2076
    • (2002) Nucleic Acids Res , vol.9 , pp. 2076-2082
    • Schattner, P.1
  • 10
    • 0035806973 scopus 로고    scopus 로고
    • Computational identification of noncoding RNAs in E. coli by comparative genomics
    • 10.1016/S0960-9822(01)00401-8
    • Rivas E Klein RJ Jones TA Eddy SR Computational identification of noncoding RNAs in E. coli by comparative genomics Curr Biol 2001, 7:1369-1373. 10.1016/S0960-9822(01)00401-8
    • (2001) Curr Biol , vol.7 , pp. 1369-1373
    • Rivas, E.1    Klein, R.J.2    Jones, T.A.3    Eddy, S.R.4
  • 11
    • 0003157183 scopus 로고    scopus 로고
    • Noncoding RNA gene detection using comparative sequence analysis
    • 64605 11801179 10.1186/1471-2105-2-8
    • Rivas E Eddy SR Noncoding RNA gene detection using comparative sequence analysis BMC Bioinformatics 2001, 2:8. 64605 11801179 10.1186/ 1471-2105-2-8
    • (2001) BMC Bioinformatics , vol.2 , pp. 8
    • Rivas, E.1    Eddy, S.R.2
  • 12
    • 33744820625 scopus 로고    scopus 로고
    • Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change
    • 1570369 16566836 10.1186/1471-2105-7-173
    • Uzilov AV Keegan JM Mathews DH Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change BMC Bioinformatics 2006, 7:173. 1570369 16566836 10.1186/1471-2105-7-173
    • (2006) BMC Bioinformatics , vol.7 , pp. 173
    • Uzilov, A.V.1    Keegan, J.M.2    Mathews, D.H.3
  • 13
    • 33847628846 scopus 로고    scopus 로고
    • Considerations in the identification of functional RNA structural elements in genomic alignments
    • 1803800 17263882 10.1186/1471-2105-8-33
    • Babak T Blencowe BJ Hughes TR Considerations in the identification of functional RNA structural elements in genomic alignments BMC Bioinformatics 2007, 8:33. 1803800 17263882 10.1186/1471-2105-8-33
    • (2007) BMC Bioinformatics , vol.8 , pp. 33
    • Babak, T.1    Blencowe, B.J.2    Hughes, T.R.3
  • 14
    • 0033765362 scopus 로고    scopus 로고
    • Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs
    • 10.1093/bioinformatics/16.7.583
    • Rivas E Eddy SR Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs Bioinformatics 2000, 7:583-605. 10.1093/bioinformatics/16.7.583
    • (2000) Bioinformatics , vol.7 , pp. 583-605
    • Rivas, E.1    Eddy, S.R.2
  • 15
    • 33646029404 scopus 로고    scopus 로고
    • Prediction of non-coding and antisense RNA genes in Escherichia coli with Gapped Markov Model
    • 10.1016/j.gene.2005.12.034 16564143
    • Yachie N Numata K Saito R Kanai A Tomita M Prediction of non-coding and antisense RNA genes in Escherichia coli with Gapped Markov Model Gene 2006, 372:171-181. 10.1016/j.gene.2005.12.034 16564143
    • (2006) Gene , vol.372 , pp. 171-181
    • Yachie, N.1    Numata, K.2    Saito, R.3    Kanai, A.4    Tomita, M.5
  • 16
    • 20444495294 scopus 로고    scopus 로고
    • Predicting non-coding RNA genes in Escherichia coli with boosted genetic programming
    • 1143698 15942029 10.1093/nar/gki644
    • Saetrom P Sneve R Kristiansen KI Snøve O Jr Grünfeld T Rognes T Seeberg E Predicting non-coding RNA genes in Escherichia coli with boosted genetic programming Nucleic Acids Res 2005, 33(10):3263-3270. 1143698 15942029 10.1093/nar/gki644
    • (2005) Nucleic Acids Res , vol.33 , Issue.10 , pp. 3263-3270
    • Saetrom, P.1    Sneve, R.2    Kristiansen, K.I.3    Snøve Jr., O.4    Grünfeld, T.5    Rognes, T.6    Seeberg, E.7
  • 17
    • 22844436749 scopus 로고    scopus 로고
    • sRNAPredict: An integrative computational approach to identify sRNAs in bacterial genomes
    • 10.1093/nar/gki715
    • Livny J Fogel MA Davis BM Waldor MK sRNAPredict: An integrative computational approach to identify sRNAs in bacterial genomes Nucleic Acids Res 2005, 13:4096-4105. 10.1093/nar/gki715
    • (2005) Nucleic Acids Res , vol.13 , pp. 4096-4105
    • Livny, J.1    Fogel, M.A.2    Davis, B.M.3    Waldor, M.K.4
  • 18
    • 33746533172 scopus 로고    scopus 로고
    • Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool sRNAPredict2
    • 10.1093/nar/gkl453
    • Livny J Brencic A Lory S Waldor MK Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool sRNAPredict2 Nucleic Acids Res 2006, 12:3484-3493. 10.1093/nar/gkl453
    • (2006) Nucleic Acids Res , vol.12 , pp. 3484-3493
    • Livny, J.1    Brencic, A.2    Lory, S.3    Waldor, M.K.4
  • 19
    • 0344237410 scopus 로고    scopus 로고
    • RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria
    • 10.1093/nar/gkg867
    • Vogel J Bartels V Tang TH Churakov G Slagter-Jager JG Huttenhofer A Wagner EG RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria Nucleic Acids Res 2003, 22:6435-6443. 10.1093/nar/gkg867
    • (2003) Nucleic Acids Res , vol.22 , pp. 6435-6443
    • Vogel, J.1    Bartels, V.2    Tang, T.H.3    Churakov, G.4    Slagter-Jager, J.G.5    Huttenhofer, A.6    Wagner, E.G.7
  • 20
    • 32644439243 scopus 로고    scopus 로고
    • Experimental approaches to identify non-coding RNAs
    • 10.1093/nar/gkj469
    • Huttenhofer A Vogel J Experimental approaches to identify non-coding RNAs Nucleic Acids Res 2006, 2:635-646. 10.1093/nar/gkj469
    • (2006) Nucleic Acids Res , vol.2 , pp. 635-646
    • Huttenhofer, A.1    Vogel, J.2
  • 21
    • 17144365857 scopus 로고    scopus 로고
    • Experimental RNomics in Aquifex aeolicus: Identification of small non-coding RNAs and the putative 6S RNA homolog
    • 10.1093/nar/gki334
    • Willkomm DK Minnerup J Huttenhofer A Hartmann RK Experimental RNomics in Aquifex aeolicus: Identification of small non-coding RNAs and the putative 6S RNA homolog Nucleic Acids Res 2005, 6:1949-1960. 10.1093/nar/ gki334
    • (2005) Nucleic Acids Res , vol.6 , pp. 1949-1960
    • Willkomm, D.K.1    Minnerup, J.2    Huttenhofer, A.3    Hartmann, R.K.4
  • 22
    • 0024365785 scopus 로고
    • Genetic evidence that DicF, a second division inhibitor encoded by the Escherichia coli dicB operon, is probably RNA
    • 10.1111/j.1365-2958.1989.tb00249.x 2477663
    • Bouche F Bouche JP Genetic evidence that DicF, a second division inhibitor encoded by the Escherichia coli dicB operon, is probably RNA Mol Microbiol 1989, 3:991-994. 10.1111/j.1365-2958.1989.tb00249.x 2477663
    • (1989) Mol Microbiol , vol.3 , pp. 991-994
    • Bouche, F.1    Bouche, J.P.2
  • 23
    • 0034625237 scopus 로고    scopus 로고
    • 6S RNA regulates E. coli RNA polymerase activity
    • 10.1016/S0092-8674(00)80873-9 10892648
    • Wassarman KM Storz G 6S RNA regulates E. coli RNA polymerase activity Cell 2000, 101:613-623. 10.1016/S0092-8674(00)80873-9 10892648
    • (2000) Cell , vol.101 , pp. 613-623
    • Wassarman, K.M.1    Storz, G.2
  • 24
    • 0031711821 scopus 로고    scopus 로고
    • Ribonuclease P: Unity and diversity in a tRNA processing ribozyme
    • 10.1146/annurev.biochem.67.1.153 9759486
    • Frank DN Pace NR Ribonuclease P: Unity and diversity in a tRNA processing ribozyme Annu Rev Biochem 1998, 67:153-180. 10.1146/ annurev.biochem.67.1.153 9759486
    • (1998) Annu Rev Biochem , vol.67 , pp. 153-180
    • Frank, D.N.1    Pace, N.R.2
  • 25
    • 0036645490 scopus 로고    scopus 로고
    • Spot 42 RNA mediates discoordinate expression of the E. coli galactose operon
    • 186370 12101127 10.1101/gad.231702
    • Moller T Franch T Udesen C Gerdes K Valentin-Hansen P Spot 42 RNA mediates discoordinate expression of the E. coli galactose operon Genes Dev 2002, 16:1696-1706. 186370 12101127 10.1101/gad.231702
    • (2002) Genes Dev , vol.16 , pp. 1696-1706
    • Moller, T.1    Franch, T.2    Udesen, C.3    Gerdes, K.4    Valentin-Hansen, P.5
  • 28
    • 0032531720 scopus 로고    scopus 로고
    • The Escherichia coli OxyS regulatory RNA represses fhlA translationby blocking ribosome binding
    • 1170933 9774350 10.1093/emboj/17.20.6069
    • Altuvia S Zhang A Argaman L Tiwari A Storz G The Escherichia coli OxyS regulatory RNA represses fhlA translationby blocking ribosome binding EMBO J 1998, 17:6069-6075. 1170933 9774350 10.1093/emboj/17.20.6069
    • (1998) EMBO J , vol.17 , pp. 6069-6075
    • Altuvia, S.1    Zhang, A.2    Argaman, L.3    Tiwari, A.4    Storz, G.5
  • 29
    • 0032514739 scopus 로고    scopus 로고
    • DsrA RNA regulates translation of RpoS message by an anti-antisense mechanism, independent of its action as an antisilencer of transcription
    • 22853 9770508 10.1073/pnas.95.21.12462
    • Majdalani N Cunning C Sledjeski D Elliott T Gottesman S 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 USA 1998, 95:12462-12467. 22853 9770508 10.1073/pnas.95.21.12462
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 12462-12467
    • Majdalani, N.1    Cunning, C.2    Sledjeski, D.3    Elliott, T.4    Gottesman, S.5
  • 30
    • 0036437019 scopus 로고    scopus 로고
    • Regulation and mode of action of the second small RNA activator of RpoS translation, RprA
    • 10.1046/j.1365-2958.2002.03203.x 12410838
    • Majdalani N Hernandez D Gottesman S Regulation and mode of action of the second small RNA activator of RpoS translation, RprA Mol Microbiol 2002, 46:813-826. 10.1046/j.1365-2958.2002.03203.x 12410838
    • (2002) Mol Microbiol , vol.46 , pp. 813-826
    • Majdalani, N.1    Hernandez, D.2    Gottesman, S.3
  • 31
    • 3142564584 scopus 로고    scopus 로고
    • The Small RNA Chaperone Hfq and Multiple Small RNAs Control QuorumSensing in Vibrio harveyi and Vibrio cholerae
    • 10.1016/j.cell.2004.06.009 15242645
    • Lenz DH Mok KC Lilley BN Kulkarni RV Wingreen NS Bassler BL The Small RNA Chaperone Hfq and Multiple Small RNAs Control QuorumSensing in Vibrio harveyi and Vibrio cholerae Cell 2004, 118:69-82. 10.1016/ j.cell.2004.06.009 15242645
    • (2004) Cell , vol.118 , pp. 69-82
    • Lenz, D.H.1    Mok, K.C.2    Lilley, B.N.3    Kulkarni, R.V.4    Wingreen, N.S.5    Bassler, B.L.6
  • 32
    • 0027423483 scopus 로고
    • PcnB is required for the rapid degradation of RNAI, the antisense RNA that controls the copy number of ColE1-related plasmids
    • 10.1111/j.1365-2958.1993.tb01243.x 7523833
    • He L Soderbom F Wagner EG Binnie U Binns N Masters M PcnB is required for the rapid degradation of RNAI, the antisense RNA that controls the copy number of ColE1-related plasmids Mol Microbiol 1993, 9:1131-1142. 10.1111/j.1365-2958.1993.tb01243.x 7523833
    • (1993) Mol Microbiol , vol.9 , pp. 1131-1142
    • He, L.1    Soderbom, F.2    Wagner, E.G.3    Binnie, U.4    Binns, N.5    Masters, M.6
  • 33
    • 0034072868 scopus 로고    scopus 로고
    • Probing the structure of RNAIII, the Staphylococcus aureus agr regulatory RNA, and identification of the RNA domain involved in repression of protein A expression
    • 1369947 10836788 10.1017/S1355838200992550
    • Benito Y Kolb FA Romby P Lina G Etienne J Vandenesch F Probing the structure of RNAIII, the Staphylococcus aureus agr regulatory RNA, and identification of the RNA domain involved in repression of protein A expression RNA 2000, 6:668-679. 1369947 10836788 10.1017/ S1355838200992550
    • (2000) RNA , vol.6 , pp. 668-679
    • Benito, Y.1    Kolb, F.A.2    Romby, P.3    Lina, G.4    Etienne, J.5    Vandenesch, F.6
  • 35
    • 0033854238 scopus 로고    scopus 로고
    • The gcvB gene encodes a small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli
    • 10.1046/j.1365-2958.2000.02051.x
    • Urbanowski ML Stauffer LT Stauffer GV The gcvB gene encodes a small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli Mol Microbiol 2003, 37:856-868. 10.1046/j.1365-2958.2000.02051.x
    • (2003) Mol Microbiol , vol.37 , pp. 856-868
    • Urbanowski, M.L.1    Stauffer, L.T.2    Stauffer, G.V.3
  • 36
    • 33751202938 scopus 로고    scopus 로고
    • Small non-coding RNAs and the bacterial outer membrane
    • 10.1016/j.mib.2006.10.006 17055775
    • Vogel J Papenfort K Small non-coding RNAs and the bacterial outer membrane Curr Opin Microbiol 2006, 9:605-611. 10.1016/j.mib.2006.10.006 17055775
    • (2006) Curr Opin Microbiol , vol.9 , pp. 605-611
    • Vogel, J.1    Papenfort, K.2
  • 37
    • 33748257975 scopus 로고    scopus 로고
    • Modulating the outer membrane with small RNAs
    • 10.1101/gad.1457506 16951250
    • Guillier M Gottesman S Storz G Modulating the outer membrane with small RNAs Genes Dev 2006, 20:2338-2348. 10.1101/gad.1457506 16951250
    • (2006) Genes Dev , vol.20 , pp. 2338-2348
    • Guillier, M.1    Gottesman, S.2    Storz, G.3
  • 38
    • 0036163624 scopus 로고    scopus 로고
    • The Sm-like Hfq protein increases OxyS RNA interaction with target mRNAs
    • 10.1016/S1097-2765(01)00437-3 11804582
    • Zhang A Wassarman KM Ortega J Steven AC Storz G The Sm-like Hfq protein increases OxyS RNA interaction with target mRNAs Mol Cell 2002, 9:11-22. 10.1016/S1097-2765(01)00437-3 11804582
    • (2002) Mol Cell , vol.9 , pp. 11-22
    • Zhang, A.1    Wassarman, K.M.2    Ortega, J.3    Steven, A.C.4    Storz, G.5
  • 39
    • 34248368843 scopus 로고    scopus 로고
    • SsrA-SmpB Ribosome Rescue System is Important for Growth of Bacillus subtilis at Low and High Temperatures
    • 1913333 17369301 10.1128/JB.00062-07
    • Shin JH Price CW SsrA-SmpB Ribosome Rescue System is Important for Growth of Bacillus subtilis at Low and High Temperatures J Bacteriol 2007, 189(10):3729-37. 1913333 17369301 10.1128/JB.00062-07
    • (2007) J Bacteriol , vol.189 , Issue.10 , pp. 3729-3737
    • Shin, J.H.1    Price, C.W.2
  • 40
    • 0035958746 scopus 로고    scopus 로고
    • The composite genome of the legume symbiont Sinorhizobium meliloti
    • 10.1126/science.1060966
    • Galibert F The composite genome of the legume symbiont Sinorhizobium meliloti Science 2001, 5530:668-72. 10.1126/science.1060966
    • (2001) Science , vol.5530 , pp. 668-672
    • Galibert, F.1
  • 41
    • 33847611227 scopus 로고    scopus 로고
    • Characterization and expression patterns of Sinorhizobium meliloti tmRNA (ssrA)
    • 10.1111/j.1574-6968.2006.00616.x
    • Ulve VM Cheron A Trautwetter A Fontenelle C Barloy-Hubler F Characterization and expression patterns of Sinorhizobium meliloti tmRNA (ssrA) FEMS Microbio Lett 2007, 269(1):117-123. 10.1111/ j.1574-6968.2006.00616.x
    • (2007) FEMS Microbio Lett , vol.269 , Issue.1 , pp. 117-123
    • Ulve, V.M.1    Cheron, A.2    Trautwetter, A.3    Fontenelle, C.4    Barloy-Hubler, F.5
  • 42
    • 0344298926 scopus 로고    scopus 로고
    • The ribonuclease P Database
    • 148169 9847214 10.1093/nar/27.1.314
    • Brown JW The ribonuclease P Database Nucleic Acids Res 1999, 27:314. 148169 9847214 10.1093/nar/27.1.314
    • (1999) Nucleic Acids Res , vol.27 , pp. 314
    • Brown, J.W.1
  • 43
    • 13144275222 scopus 로고    scopus 로고
    • The expression of a novel antisense gene mediates incompatibility within the large repABC family of alpha-proteobacterial plasmids
    • 10.1111/j.1365-2958.2004.04412.x 15659174
    • MacLellan SR Smallbone LA Sibley CD Finan TM The expression of a novel antisense gene mediates incompatibility within the large repABC family of alpha-proteobacterial plasmids Mol Microbiol 2005, 55(2):611-623. 10.1111/j.1365-2958.2004.04412.x 15659174
    • (2005) Mol Microbiol , vol.55 , Issue.2 , pp. 611-623
    • MacLellan, S.R.1    Smallbone, L.A.2    Sibley, C.D.3    Finan, T.M.4
  • 46
  • 48
    • 0036667443 scopus 로고    scopus 로고
    • Identification and characterization of novel small RNAs in the aspS-yrvM intergenic region of the Bacillus subtilis genome
    • 12177353
    • Suzuma S Asari S Bunai K Yoshino K Ando Y Kakeshita H Fujita M Nakamura K Yamane K Identification and characterization of novel small RNAs in the aspS-yrvM intergenic region of the Bacillus subtilis genome Microbiology 2002, 148:2591-2598. 12177353
    • (2002) Microbiology , vol.148 , pp. 2591-2598
    • Suzuma, S.1    Asari, S.2    Bunai, K.3    Yoshino, K.4    Ando, Y.5    Kakeshita, H.6    Fujita, M.7    Nakamura, K.8    Yamane, K.9
  • 49
    • 0037154430 scopus 로고    scopus 로고
    • Expression of a small RNA, BS203 RNA, from the yocI-yocJ intergenic region of Bacillus subtilis genome
    • 11886746
    • Ando Y Asari S Suzuma S Yamane K Nakamura K Expression of a small RNA, BS203 RNA, from the yocI-yocJ intergenic region of Bacillus subtilis genome FEMS Microbiol Lett 2002, 207:29-33. 11886746
    • (2002) FEMS Microbiol Lett , vol.207 , pp. 29-33
    • Ando, Y.1    Asari, S.2    Suzuma, S.3    Yamane, K.4    Nakamura, K.5
  • 50
    • 0034072990 scopus 로고    scopus 로고
    • Identification of a small RNA within the pdh gene cluster of Mycoplasma pneumoniae and Mycoplasma genitalium
    • 94519 10809712 10.1128/JB.182.11.3281-3284.2000
    • Gohlmann HW Weiner J Schon A Herrmann R Identification of a small RNA within the pdh gene cluster of Mycoplasma pneumoniae and Mycoplasma genitalium J Bacteriol 2000, 182:3281-3284. 94519 10809712 10.1128/ JB.182.11.3281-3284.2000
    • (2000) J Bacteriol , vol.182 , pp. 3281-3284
    • Gohlmann, H.W.1    Weiner, J.2    Schon, A.3    Herrmann, R.4
  • 51
    • 26444600764 scopus 로고    scopus 로고
    • Small RNA genes expressed from Staphylococcus aureus genomic and pathogenicity islands with specific expression among pathogenic strains
    • 1242290 16183745 10.1073/pnas.0503838102
    • Pichon C Felden B Small RNA genes expressed from Staphylococcus aureus genomic and pathogenicity islands with specific expression among pathogenic strains Proc Natl Acad Sci USA 2005, 102:14249-14254. 1242290 16183745 10.1073/pnas.0503838102
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 14249-14254
    • Pichon, C.1    Felden, B.2
  • 52
    • 29044436786 scopus 로고    scopus 로고
    • Identification of cyanobacterial non-coding RNAs by comparative genome analysis
    • 1242208 16168080 10.1186/gb-2005-6-9-r73
    • Axmann IM Kensche P Vogel J Kohl S Herze H Hess WR Identification of cyanobacterial non-coding RNAs by comparative genome analysis Genome Biol 2005, 6:R73. 1242208 16168080 10.1186/gb-2005-6-9-r73
    • (2005) Genome Biol , vol.6
    • Axmann, I.M.1    Kensche, P.2    Vogel, J.3    Kohl, S.4    Herze, H.5    Hess, W.R.6
  • 53
    • 18344371528 scopus 로고    scopus 로고
    • A highly conserved 6S RNA structure is required for regulation of transcription
    • 10.1038/nsmb917 15793584
    • Trotochaud AE Wassarman KM A highly conserved 6S RNA structure is required for regulation of transcription Nat Struct Mol Biol 2005, 12:313-319. 10.1038/nsmb917 15793584
    • (2005) Nat Struct Mol Biol , vol.12 , pp. 313-319
    • Trotochaud, A.E.1    Wassarman, K.M.2
  • 54
    • 0141850376 scopus 로고    scopus 로고
    • Intergenic sequence inspector: Searching and identifying bacterial RNAs
    • Sep 1 10.1093/bioinformatics/btg235 15593399
    • Pichon C Felden B Intergenic sequence inspector: Searching and identifying bacterial RNAs Bioinformatics 19(13):1707-9. 2003, Sep 1 10.1093/bioinformatics/btg235 15593399
    • (2003) Bioinformatics , vol.19 , Issue.13 , pp. 1707-1709
    • Pichon, C.1    Felden, B.2
  • 55
    • 0029412082 scopus 로고
    • Identification of Rhizobium-specific intergenic mosaic elements within an essential two-component regulatory system of Rhizobium species
    • 177356 7559334
    • Osteras M Stanley J Finan TM Identification of Rhizobium-specific intergenic mosaic elements within an essential two-component regulatory system of Rhizobium species J Bacteriol 1995, 177:5485-5494. 177356 7559334
    • (1995) J Bacteriol , vol.177 , pp. 5485-5494
    • Osteras, M.1    Stanley, J.2    Finan, T.M.3
  • 56
    • 0032530166 scopus 로고    scopus 로고
    • Presence of a gene encoding choline sulfatase in Sinorhizobium meliloti bet operon: Choline-o-sulfate is metabolized into glycine betaine
    • 21653 9736747 10.1073/pnas.95.19.11394
    • Osteras M Boncompagni E Vincent N Poggi MC Le Rudulier D Presence of a gene encoding choline sulfatase in Sinorhizobium meliloti bet operon: choline-O-sulfate is metabolized into glycine betaine Proc Natl Acad Sci USA 1998, 95:11394-11399. 21653 9736747 10.1073/pnas.95.19.11394
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 11394-11399
    • Osteras, M.1    Boncompagni, E.2    Vincent, N.3    Poggi, M.C.4    Le Rudulier, D.5
  • 57
    • 0032574728 scopus 로고    scopus 로고
    • Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene
    • Erratum in: 15:9059 10.1073/pnas.95.9.5145
    • Sullivan JT Ronson CW Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene Proc Natl Acad Sci USA 1998, 9:5145-5149. Erratum in: Proc. Natl. Acad. Sci. USA 15:9059 10.1073/pnas.95.9.5145
    • (1998) Proc Natl Acad Sci USA , vol.9 , pp. 5145-5149
    • Sullivan, J.T.1    Ronson, C.W.2
  • 58
    • 0028251157 scopus 로고
    • Diverse mechanisms for regulating ribosomal protein synthesis in Escherichia coli
    • 7517053
    • Zengel JM Lindahl L Diverse mechanisms for regulating ribosomal protein synthesis in Escherichia coli Prog Nucleic Acid Res Mol Biol 1994, 47:331-370. 7517053
    • (1994) Prog Nucleic Acid Res Mol Biol , vol.47 , pp. 331-370
    • Zengel, J.M.1    Lindahl, L.2
  • 59
    • 0029965652 scopus 로고    scopus 로고
    • Pseudoknot and translational control in the expression of the S15 ribosomal protein
    • 10.1016/S0300-9084(96)80003-4 8955900
    • Benard L Philippe C Ehresmann B Ehresmann C Portier C Pseudoknot and translational control in the expression of the S15 ribosomal protein Biochimie 1996, 78:568-576. 10.1016/S0300-9084(96)80003-4 8955900
    • (1996) Biochimie , vol.78 , pp. 568-576
    • Benard, L.1    Philippe, C.2    Ehresmann, B.3    Ehresmann, C.4    Portier, C.5
  • 60
    • 0347756648 scopus 로고    scopus 로고
    • Islander: A database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities
    • 32 Database 308793 14681358 10.1093/nar/gkh059
    • Mantri Y Williams KP Islander: A database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities Nucleic Acids Res 2004 32 Database D55-8. 308793 14681358 10.1093/nar/gkh059
    • (2004) Nucleic Acids Res
    • Mantri, Y.1    Williams, K.P.2
  • 62
    • 0030817277 scopus 로고    scopus 로고
    • Unusual structure of the tonB-exb DNA region of Xanthomonas campestris pv. campestris: tonB, exbB, and exbD1 are essential for ferric iron uptake, but exbD2 is not
    • 179653 9371459
    • Wiggerich HG Klauke B Koplin R Priefer UB Puhler A Unusual structure of the tonB-exb DNA region of Xanthomonas campestris pv. campestris: tonB, exbB, and exbD1 are essential for ferric iron uptake, but exbD2 is not J Bacteriol 1997, 179:7103-7110. 179653 9371459
    • (1997) J Bacteriol , vol.179 , pp. 7103-7110
    • Wiggerich, H.G.1    Klauke, B.2    Koplin, R.3    Priefer, U.B.4    Puhler, A.5
  • 63
    • 33750443276 scopus 로고    scopus 로고
    • RyhB small RNA modulates the free intracellular iron pool and is essential for normal growth during iron limitation in Escherichia coli
    • 10.1111/j.1365-2958.2006.05439.x 17078818
    • Jacques JF Jang S Prevost K Desnoyers G Desmarais M Imlay J Masse E RyhB small RNA modulates the free intracellular iron pool and is essential for normal growth during iron limitation in Escherichia coli Mol Microbiol 2006, 62:1181-1190. 10.1111/j.1365-2958.2006.05439.x 17078818
    • (2006) Mol Microbiol , vol.62 , pp. 1181-1190
    • Jacques, J.F.1    Jang, S.2    Prevost, K.3    Desnoyers, G.4    Desmarais, M.5    Imlay, J.6    Masse, E.7
  • 64
    • 0037387973 scopus 로고    scopus 로고
    • A survey of small RNA-encoding genes in Escherichia coli
    • 152812 12654996 10.1093/nar/gkg297
    • Hershberg R Altuvia S Margalit H A survey of small RNA-encoding genes in Escherichia coli Nucleic Acids Res 2003, 31:1813-20. 152812 12654996 10.1093/nar/gkg297
    • (2003) Nucleic Acids Res , vol.31 , pp. 1813-1820
    • Hershberg, R.1    Altuvia, S.2    Margalit, H.3
  • 65
    • 0345465673 scopus 로고    scopus 로고
    • SmpB, a unique RNA-binding protein essential for the peptide-tagging activity of SsrA (tmRNA)
    • 1171456 10393194 10.1093/emboj/18.13.3793
    • Karzai AW Susskind MM Sauer RT SmpB, a unique RNA-binding protein essential for the peptide-tagging activity of SsrA (tmRNA) EMBO J 1999, 18:3793-3799. 1171456 10393194 10.1093/emboj/18.13.3793
    • (1999) EMBO J , vol.18 , pp. 3793-3799
    • Karzai, A.W.1    Susskind, M.M.2    Sauer, R.T.3
  • 66
    • 13144275222 scopus 로고    scopus 로고
    • The expression of a novel antisense gene mediates incompatibility within the large repABC family of alpha-proteobacterial plasmids
    • 10.1111/j.1365-2958.2004.04412.x 15659174
    • MacLellan SR Smallbone LA Sibley CD Finan TM The expression of a novel antisense gene mediates incompatibility within the large repABC family of alpha-proteobacterial plasmids Mol Microbiol 2005, 55:611-623. 10.1111/j.1365-2958.2004.04412.x 15659174
    • (2005) Mol Microbiol , vol.55 , pp. 611-623
    • MacLellan, S.R.1    Smallbone, L.A.2    Sibley, C.D.3    Finan, T.M.4
  • 67
    • 0038313116 scopus 로고    scopus 로고
    • Prediction and overview of the RpoN-regulon in closely related species of the Rhizobiales
    • 151178 12537565
    • Dombrecht B Marchal K Vanderleyden J Michiels J Prediction and overview of the RpoN-regulon in closely related species of the Rhizobiales Genome Biol 2002, 3(12) 151178 12537565
    • (2002) Genome Biol , vol.3 , Issue.12
    • Dombrecht, B.1    Marchal, K.2    Vanderleyden, J.3    Michiels, J.4
  • 68
    • 34547555385 scopus 로고    scopus 로고
    • Melina II: A web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions
    • 1933176 17537821 10.1093/nar/gkm362
    • Okumura T Makiguchi H Makita Y Yamashita R Nakai K Melina II: A web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions Nucleic Acids Res 2007, 35:W227-231. 1933176 17537821 10.1093/nar/gkm362
    • (2007) Nucleic Acids Res , vol.35
    • Okumura, T.1    Makiguchi, H.2    Makita, Y.3    Yamashita, R.4    Nakai, K.5
  • 69
    • 0036464509 scopus 로고    scopus 로고
    • Conserved economics of transcription termination in eubacteria
    • 100295 11809879 10.1093/nar/30.3.675
    • Unniraman S Prakash R Nagaraja V Conserved economics of transcription termination in eubacteria Nucleic Acids Res 2002, 30:675-684. 100295 11809879 10.1093/nar/30.3.675
    • (2002) Nucleic Acids Res , vol.30 , pp. 675-684
    • Unniraman, S.1    Prakash, R.2    Nagaraja, V.3
  • 70
    • 0043123153 scopus 로고    scopus 로고
    • Vienna RNA secondary structure server
    • 169005 12824340 10.1093/nar/gkg599
    • Hofacker IL Vienna RNA secondary structure server Nucleic Acids Res 2003, 31:3429-3431. 169005 12824340 10.1093/nar/gkg599
    • (2003) Nucleic Acids Res , vol.31 , pp. 3429-3431
    • Hofacker, I.L.1
  • 72
    • 34547556305 scopus 로고    scopus 로고
    • The RNAz web server: Prediction of thermodynamically stable and evolutionarily conserved RNA structures
    • 1933143 17452347 10.1093/nar/gkm222
    • Gruber AR Neubock R Hofacker IL Washietl S The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures Nucleic Acids Res 2007, 35:W335-338. 1933143 17452347 10.1093/ nar/gkm222
    • (2007) Nucleic Acids Res , vol.35
    • Gruber, A.R.1    Neubock, R.2    Hofacker, I.L.3    Washietl, S.4
  • 73
    • 0035933778 scopus 로고    scopus 로고
    • Minimal functional structure of Escherichia coli 4.5 S RNA required for binding to elongation factor G
    • 10.1074/jbc.M101376200 11294875
    • Nakamura K Miyamoto H Suzuma S Sakamoto T Kawai G Yamane K Minimal functional structure of Escherichia coli 4.5 S RNA required for binding to elongation factor G J Biol Chem 2001, 276:22844-22849. 10.1074/ jbc.M101376200 11294875
    • (2001) J Biol Chem , vol.276 , pp. 22844-22849
    • Nakamura, K.1    Miyamoto, H.2    Suzuma, S.3    Sakamoto, T.4    Kawai, G.5    Yamane, K.6
  • 74
    • 17844379221 scopus 로고    scopus 로고
    • 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter
    • 10.1261/rna.7286705
    • Barrick JE Sudarsan N Weinberg Z Ruzzo WL Breaker RR 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter RNA 2005, 5:774-784. 10.1261/rna.7286705
    • (2005) RNA , vol.5 , pp. 774-784
    • Barrick, J.E.1    Sudarsan, N.2    Weinberg, Z.3    Ruzzo, W.L.4    Breaker, R.R.5
  • 75
    • 34247495145 scopus 로고    scopus 로고
    • FtsZ polymer-bundling by the Escherichia coli ZapA orthologue, YgfE, involves a conformational change in bound GTP
    • 10.1016/j.jmb.2007.03.025 17428494
    • Small E Marrington R Rodger A Scott DJ Sloan K Roper D Dafforn TR Addinall SG FtsZ polymer-bundling by the Escherichia coli ZapA orthologue, YgfE, involves a conformational change in bound GTP J Mol Biol 2007, 369:210-221. 10.1016/j.jmb.2007.03.025 17428494
    • (2007) J Mol Biol , vol.369 , pp. 210-221
    • Small, E.1    Marrington, R.2    Rodger, A.3    Scott, D.J.4    Sloan, K.5    Roper, D.6    Dafforn, T.R.7    Addinall, S.G.8
  • 76
    • 0030914642 scopus 로고    scopus 로고
    • Host regulation of lysogenic decision in bacteriophage lambda: Transmembrane modulation of FtsH (HflB), the cII degrading protease, by HflKC (HflA)
    • 20815 9159109 10.1073/pnas.94.11.5544
    • Kihara A Akiyama Y Ito K Host regulation of lysogenic decision in bacteriophage lambda: Transmembrane modulation of FtsH (HflB), the cII degrading protease, by HflKC (HflA) Proc Natl Acad Sci USA 1997, 94:5544-5549. 20815 9159109 10.1073/pnas.94.11.5544
    • (1997) Proc Natl Acad Sci USA , vol.94 , pp. 5544-5549
    • Kihara, A.1    Akiyama, Y.2    Ito, K.3
  • 77
    • 34247148876 scopus 로고    scopus 로고
    • RNA antitoxins
    • 10.1016/j.mib.2007.03.003 17376733
    • Gerdes K Wagner EG RNA antitoxins Curr Opin Microbiol 2007, 10:117-124. 10.1016/j.mib.2007.03.003 17376733
    • (2007) Curr Opin Microbiol , vol.10 , pp. 117-124
    • Gerdes, K.1    Wagner, E.G.2
  • 78
    • 39149110856 scopus 로고    scopus 로고
    • RASTA-Bacteria: A web-based tool for identifying toxin-antitoxin loci in prokaryotes
    • 10.1186/gb-2007-8-8-r155 17678530
    • Sevin EW Barloy-Hubler F RASTA-Bacteria: A web-based tool for identifying toxin-antitoxin loci in prokaryotes Genome Biol 2007, 8:R155. 10.1186/gb-2007-8-8-r155 17678530
    • (2007) Genome Biol , vol.8
    • Sevin, E.W.1    Barloy-Hubler, F.2
  • 79
    • 34247158257 scopus 로고    scopus 로고
    • Mechanism of RNA silencing by Hfq-binding small RNAs
    • 10.1016/j.mib.2007.03.010 17383928
    • Aiba H Mechanism of RNA silencing by Hfq-binding small RNAs Curr Opin Microbiol 2007, 10:134-139. 10.1016/j.mib.2007.03.010 17383928
    • (2007) Curr Opin Microbiol , vol.10 , pp. 134-139
    • Aiba, H.1
  • 82
    • 33845413333 scopus 로고    scopus 로고
    • A new approach to intensity-dependent normalization of two-channel microarrays
    • 10.1093/biostatistics/kxj038 16636140
    • Dabney AR Storey JD A new approach to intensity-dependent normalization of two-channel microarrays Biostatistics 2007, 8(1):128-139. 10.1093/ biostatistics/kxj038 16636140
    • (2007) Biostatistics , vol.8 , Issue.1 , pp. 128-139
    • Dabney, A.R.1    Storey, J.D.2
  • 86
    • 3142543406 scopus 로고    scopus 로고
    • ftp://ftp.ncbi.nih.gov/genomes/Bacteria/
    • The Refseq Database ftp://ftp.ncbi.nih.gov/genomes/Bacteria/
    • The Refseq Database
  • 88
    • 33644873202 scopus 로고    scopus 로고
    • Transterm - Extended search facilities and improved integration with other databases
    • 1347521 16381889 10.1093/nar/gkj159
    • Jacobs GH Stockwell PA Tate WP Brown CM Transterm - extended search facilities and improved integration with other databases Nucleic Acids Res 2006, 34:D37-40. 1347521 16381889 10.1093/nar/gkj159
    • (2006) Nucleic Acids Res , vol.34
    • Jacobs, G.H.1    Stockwell, P.A.2    Tate, W.P.3    Brown, C.M.4
  • 90
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • 308517 7984417 10.1093/nar/22.22.4673
    • Higgins D Thompson J Gibson T Thompson JD Higgins DG Gibson TJ CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res 1994, 22:4673-4680. 308517 7984417 10.1093/nar/22.22.4673
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Higgins, D.1    Thompson, J.2    Gibson, T.3    Thompson, J.D.4    Higgins, D.G.5    Gibson, T.J.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.