Global mapping of transcription start sites and promoter motifs in the symbiotic a-proteobacterium Sinorhizobium meliloti 1021

Schlueter J-P, Reinkensmeier J, Barnett MJ, Lang C, Krol E, Giegerich R, Long SR, Becker A (2013)
Bmc Genomics 14(1): 156.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
Schlueter, Jan-Philip; Reinkensmeier, JanUniBi; Barnett, Melanie J.; Lang, Claus; Krol, Elizaveta; Giegerich, RobertUniBi; Long, Sharon R.; Becker, Anke
Abstract / Bemerkung
Background: Sinorhizobium meliloti is a soil-dwelling a-proteobacterium that possesses a large, tripartite genome and engages in a nitrogen fixing symbiosis with its plant hosts. Although much is known about this important model organism, global characterization of genetic regulatory circuits has been hampered by a lack of information about transcription and promoters. Results: Using an RNAseq approach and RNA populations representing 16 different growth and stress conditions, we comprehensively mapped S. meliloti transcription start sites (TSS). Our work identified 17,001 TSS that we grouped into six categories based on the genomic context of their transcripts: mRNA (4,430 TSS assigned to 2,657 protein-coding genes), leaderless mRNAs (171), putative mRNAs (425), internal sense transcripts (7,650), antisense RNA (3,720), and trans-encoded sRNAs (605). We used this TSS information to identify transcription factor binding sites and putative promoter sequences recognized by seven of the 15 known S. meliloti sigma factors sigma(70), sigma(54), sigma(H1), sigma(H2), sigma(E1), sigma(E2), and sigma(E9)). Altogether, we predicted 2,770 new promoter sequences, including 1,302 located upstream of protein coding genes and 722 located upstream of antisense RNA or trans-encoded sRNA genes. To validate promoter predictions for targets of the general stress response s factor, RpoE2 (sigma(E2)), we identified rpoE2-dependent genes using microarrays and confirmed TSS for a subset of these by 5' RACE mapping. Conclusions: By identifying TSS and promoters on a global scale, our work provides a firm foundation for the continued study of S. meliloti gene expression with relation to gene organization, s factors and other transcription factors, and regulatory RNAs.
sRNA; mRNA; Sinorhizobium meliloti; Sigma factor; Promoter; Transcription start site; Transcription; RNAseq; Antisense RNA
Bmc Genomics
Page URI


Schlueter J-P, Reinkensmeier J, Barnett MJ, et al. Global mapping of transcription start sites and promoter motifs in the symbiotic a-proteobacterium Sinorhizobium meliloti 1021. Bmc Genomics. 2013;14(1): 156.
Schlueter, J. - P., Reinkensmeier, J., Barnett, M. J., Lang, C., Krol, E., Giegerich, R., Long, S. R., et al. (2013). Global mapping of transcription start sites and promoter motifs in the symbiotic a-proteobacterium Sinorhizobium meliloti 1021. Bmc Genomics, 14(1), 156. doi:10.1186/1471-2164-14-156
Schlueter, Jan-Philip, Reinkensmeier, Jan, Barnett, Melanie J., Lang, Claus, Krol, Elizaveta, Giegerich, Robert, Long, Sharon R., and Becker, Anke. 2013. “Global mapping of transcription start sites and promoter motifs in the symbiotic a-proteobacterium Sinorhizobium meliloti 1021”. Bmc Genomics 14 (1): 156.
Schlueter, J. - P., Reinkensmeier, J., Barnett, M. J., Lang, C., Krol, E., Giegerich, R., Long, S. R., and Becker, A. (2013). Global mapping of transcription start sites and promoter motifs in the symbiotic a-proteobacterium Sinorhizobium meliloti 1021. Bmc Genomics 14:156.
Schlueter, J.-P., et al., 2013. Global mapping of transcription start sites and promoter motifs in the symbiotic a-proteobacterium Sinorhizobium meliloti 1021. Bmc Genomics, 14(1): 156.
J.-P. Schlueter, et al., “Global mapping of transcription start sites and promoter motifs in the symbiotic a-proteobacterium Sinorhizobium meliloti 1021”, Bmc Genomics, vol. 14, 2013, : 156.
Schlueter, J.-P., Reinkensmeier, J., Barnett, M.J., Lang, C., Krol, E., Giegerich, R., Long, S.R., Becker, A.: Global mapping of transcription start sites and promoter motifs in the symbiotic a-proteobacterium Sinorhizobium meliloti 1021. Bmc Genomics. 14, : 156 (2013).
Schlueter, Jan-Philip, Reinkensmeier, Jan, Barnett, Melanie J., Lang, Claus, Krol, Elizaveta, Giegerich, Robert, Long, Sharon R., and Becker, Anke. “Global mapping of transcription start sites and promoter motifs in the symbiotic a-proteobacterium Sinorhizobium meliloti 1021”. Bmc Genomics 14.1 (2013): 156.

74 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Characterization of HicAB toxin-antitoxin module of Sinorhizobium meliloti.
Thomet M, Trautwetter A, Ermel G, Blanco C., BMC Microbiol 19(1), 2019
PMID: 30630415
Stress-inducible NHEJ in bacteria: function in DNA repair and acquisition of heterologous DNA.
Dupuy P, Sauviac L, Bruand C., Nucleic Acids Res 47(3), 2019
PMID: 30517704
An Integrated Systems Approach Unveils New Aspects of Microoxia-Mediated Regulation in Bradyrhizobium diazoefficiens.
Fernández N, Cabrera JJ, Varadarajan AR, Lutz S, Ledermann R, Roschitzki B, Eberl L, Bedmar EJ, Fischer HM, Pessi G, Ahrens CH, Mesa S., Front Microbiol 10(), 2019
PMID: 31134003
Control of Bacterial Sulfite Detoxification by Conserved and Species-Specific Regulatory Circuits.
Tan YJC, Zhao C, Nasreen M, O'Rourke L, Dhouib R, Roberts L, Wan Y, Beatson SA, Kappler U., Front Microbiol 10(), 2019
PMID: 31139157
Transcription attenuation-derived small RNA rnTrpL regulates tryptophan biosynthesis gene expression in trans.
Melior H, Li S, Madhugiri R, Stötzel M, Azarderakhsh S, Barth-Weber S, Baumgardt K, Ziebuhr J, Evguenieva-Hackenberg E., Nucleic Acids Res 47(12), 2019
PMID: 30993322
RNAseq analysis of α-proteobacterium Gluconobacter oxydans 621H.
Kranz A, Busche T, Vogel A, Usadel B, Kalinowski J, Bott M, Polen T., BMC Genomics 19(1), 2018
PMID: 29304737
Polyamines are required for normal growth in Sinorhizobium meliloti.
Becerra-Rivera VA, Bergström E, Thomas-Oates J, Dunn MF., Microbiology 164(4), 2018
PMID: 29619919
An sRNA and Cold Shock Protein Homolog-Based Feedforward Loop Post-transcriptionally Controls Cell Cycle Master Regulator CtrA.
Robledo M, Schlüter JP, Loehr LO, Linne U, Albaum SP, Jiménez-Zurdo JI, Becker A., Front Microbiol 9(), 2018
PMID: 29740411
Most Sinorhizobium meliloti Extracytoplasmic Function Sigma Factors Control Accessory Functions.
Lang C, Barnett MJ, Fisher RF, Smith LS, Diodati ME, Long SR., mSphere 3(5), 2018
PMID: 30305320
Negative Regulation of Ectoine Uptake and Catabolism in Sinorhizobium meliloti: Characterization of the EhuR Gene.
Yu Q, Cai H, Zhang Y, He Y, Chen L, Merritt J, Zhang S, Dong Z., J Bacteriol 199(1), 2017
PMID: 27795315
Genome-Wide Transcriptional Start Site Mapping and sRNA Identification in the Pathogen Leptospira interrogans.
Zhukova A, Fernandes LG, Hugon P, Pappas CJ, Sismeiro O, Coppée JY, Becavin C, Malabat C, Eshghi A, Zhang JJ, Yang FX, Picardeau M., Front Cell Infect Microbiol 7(), 2017
PMID: 28154810
Sinorhizobium meliloti YbeY is an endoribonuclease with unprecedented catalytic features, acting as silencing enzyme in riboregulation.
Saramago M, Peregrina A, Robledo M, Matos RG, Hilker R, Serrania J, Becker A, Arraiano CM, Jiménez-Zurdo JI., Nucleic Acids Res 45(3), 2017
PMID: 28180335
Caulobacter crescentus CdnL is a non-essential RNA polymerase-binding protein whose depletion impairs normal growth and rRNA transcription.
Gallego-García A, Iniesta AA, González D, Collier J, Padmanabhan S, Elías-Arnanz M., Sci Rep 7(), 2017
PMID: 28233804
Regulation of Polyhydroxybutyrate Accumulation in Sinorhizobium meliloti by the Trans-Encoded Small RNA MmgR.
Lagares A, Borella GC, Linne U, Becker A, Valverde C., J Bacteriol 199(8), 2017
PMID: 28167519
Heterologous Complementation Reveals a Specialized Activity for BacA in the Medicago-Sinorhizobium meliloti Symbiosis.
diCenzo GC, Zamani M, Ludwig HN, Finan TM., Mol Plant Microbe Interact 30(4), 2017
PMID: 28398123
A conserved α-proteobacterial small RNA contributes to osmoadaptation and symbiotic efficiency of rhizobia on legume roots.
Robledo M, Peregrina A, Millán V, García-Tomsig NI, Torres-Quesada O, Mateos PF, Becker A, Jiménez-Zurdo JI., Environ Microbiol 19(7), 2017
PMID: 28401641
Structure, proteome and genome of Sinorhizobium meliloti phage ΦM5: A virus with LUZ24-like morphology and a highly mosaic genome.
Johnson MC, Sena-Velez M, Washburn BK, Platt GN, Lu S, Brewer TE, Lynn JS, Stroupe ME, Jones KM., J Struct Biol 200(3), 2017
PMID: 28842338
A Key Regulator of the Glycolytic and Gluconeogenic Central Metabolic Pathways in Sinorhizobium meliloti.
diCenzo GC, Muhammed Z, Østerås M, O'Brien SAP, Finan TM., Genetics 207(3), 2017
PMID: 28851745
RNA silencing in plant symbiotic bacteria: Insights from a protein-centric view.
Jiménez-Zurdo JI, Robledo M., RNA Biol 14(12), 2017
PMID: 28805544
Genome-Wide Analysis of the Transcription Start Sites and Promoter Motifs of Phytoplasmas.
Nijo T, Neriya Y, Koinuma H, Iwabuchi N, Kitazawa Y, Tanno K, Okano Y, Maejima K, Yamaji Y, Oshima K, Namba S., DNA Cell Biol 36(12), 2017
PMID: 29039971
Expression of the Sinorhizobium meliloti small RNA gene mmgR is controlled by the nitrogen source.
Ceizel Borella G, Lagares A, Valverde C., FEMS Microbiol Lett 363(9), 2016
PMID: 27010014
Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis - a rich resource to identify new transcripts, proteins and to study gene regulation.
Čuklina J, Hahn J, Imakaev M, Omasits U, Förstner KU, Ljubimov N, Goebel M, Pessi G, Fischer HM, Ahrens CH, Gelfand MS, Evguenieva-Hackenberg E., BMC Genomics 17(), 2016
PMID: 27107716
Genome-wide mapping of transcription start sites yields novel insights into the primary transcriptome of Pseudomonas putida.
D'Arrigo I, Bojanovič K, Yang X, Holm Rau M, Long KS., Environ Microbiol 18(10), 2016
PMID: 27111755
Global repositioning of transcription start sites in a plant-fermenting bacterium.
Boutard M, Ettwiller L, Cerisy T, Alberti A, Labadie K, Salanoubat M, Schildkraut I, Tolonen AC., Nat Commun 7(), 2016
PMID: 27982035
Genetic analysis of signal integration by the Sinorhizobium meliloti sensor kinase FeuQ.
VanYperen RD, Orton TS, Griffitts JS., Microbiology 161(pt 2), 2015
PMID: 25479839
Thermodynamic matchers for the construction of the cuckoo RNA family.
Reinkensmeier J, Giegerich R., RNA Biol 12(2), 2015
PMID: 25779873
The global regulatory architecture of transcription during the Caulobacter cell cycle.
Zhou B, Schrader JM, Kalogeraki VS, Abeliuk E, Dinh CB, Pham JQ, Cui ZZ, Dill DL, McAdams HH, Shapiro L., PLoS Genet 11(1), 2015
PMID: 25569173
Genetic redundancy is prevalent within the 6.7 Mb Sinorhizobium meliloti genome.
diCenzo GC, Finan TM., Mol Genet Genomics 290(4), 2015
PMID: 25638282
Genomic context drives transcription of insertion sequences in the bacterial endosymbiont Wolbachia wVulC.
Cerveau N, Gilbert C, Liu C, Garrett RA, Grève P, Bouchon D, Cordaux R., Gene 564(1), 2015
PMID: 25813874
Transcriptomic profiling of Yersinia pseudotuberculosis reveals reprogramming of the Crp regulon by temperature and uncovers Crp as a master regulator of small RNAs.
Nuss AM, Heroven AK, Waldmann B, Reinkensmeier J, Jarek M, Beckstette M, Dersch P., PLoS Genet 11(3), 2015
PMID: 25816203
A stress-induced small RNA modulates alpha-rhizobial cell cycle progression.
Robledo M, Frage B, Wright PR, Becker A., PLoS Genet 11(4), 2015
PMID: 25923724
Small RNA Deep-Sequencing Analyses Reveal a New Regulator of Virulence in Agrobacterium fabrum C58.
Dequivre M, Diel B, Villard C, Sismeiro O, Durot M, Coppée JY, Nesme X, Vial L, Hommais F., Mol Plant Microbe Interact 28(5), 2015
PMID: 26024442
Cell Cycle Control by the Master Regulator CtrA in Sinorhizobium meliloti.
Pini F, De Nisco NJ, Ferri L, Penterman J, Fioravanti A, Brilli M, Mengoni A, Bazzicalupo M, Viollier PH, Walker GC, Biondi EG., PLoS Genet 11(5), 2015
PMID: 25978424
Evolution of Intra-specific Regulatory Networks in a Multipartite Bacterial Genome.
Galardini M, Brilli M, Spini G, Rossi M, Roncaglia B, Bani A, Chiancianesi M, Moretto M, Engelen K, Bacci G, Pini F, Biondi EG, Bazzicalupo M, Mengoni A., PLoS Comput Biol 11(9), 2015
PMID: 26340565
Leaderless Transcripts and Small Proteins Are Common Features of the Mycobacterial Translational Landscape.
Shell SS, Wang J, Lapierre P, Mir M, Chase MR, Pyle MM, Gawande R, Ahmad R, Sarracino DA, Ioerger TR, Fortune SM, Derbyshire KM, Wade JT, Gray TA., PLoS Genet 11(11), 2015
PMID: 26536359
Host plant peptides elicit a transcriptional response to control the Sinorhizobium meliloti cell cycle during symbiosis.
Penterman J, Abo RP, De Nisco NJ, Arnold MF, Longhi R, Zanda M, Walker GC., Proc Natl Acad Sci U S A 111(9), 2014
PMID: 24501120
Global analysis of cell cycle gene expression of the legume symbiont Sinorhizobium meliloti.
De Nisco NJ, Abo RP, Wu CM, Penterman J, Walker GC., Proc Natl Acad Sci U S A 111(9), 2014
PMID: 24501121
Genome-wide profiling of Hfq-binding RNAs uncovers extensive post-transcriptional rewiring of major stress response and symbiotic regulons in Sinorhizobium meliloti.
Torres-Quesada O, Reinkensmeier J, Schlüter JP, Robledo M, Peregrina A, Giegerich R, Toro N, Becker A, Jiménez-Zurdo JI., RNA Biol 11(5), 2014
PMID: 24786641
TSSAR: TSS annotation regime for dRNA-seq data.
Amman F, Wolfinger MT, Lorenz R, Hofacker IL, Stadler PF, Findeiß S., BMC Bioinformatics 15(), 2014
PMID: 24674136
The Sinorhizobium meliloti EmrAB efflux system is regulated by flavonoids through a TetR-like regulator (EmrR).
Rossbach S, Kunze K, Albert S, Zehner S, Göttfert M., Mol Plant Microbe Interact 27(4), 2014
PMID: 24224534
RNA sequencing and proteogenomics reveal the importance of leaderless mRNAs in the radiation-tolerant bacterium Deinococcus deserti.
de Groot A, Roche D, Fernandez B, Ludanyi M, Cruveiller S, Pignol D, Vallenet D, Armengaud J, Blanchard L., Genome Biol Evol 6(4), 2014
PMID: 24723731
Differential RNA-seq: the approach behind and the biological insight gained.
Sharma CM, Vogel J., Curr Opin Microbiol 19(), 2014
PMID: 25024085
Riboregulation in plant-associated α-proteobacteria.
Becker A, Overlöper A, Schlüter JP, Reinkensmeier J, Robledo M, Giegerich R, Narberhaus F, Evguenieva-Hackenberg E., RNA Biol 11(5), 2014
PMID: 25003187
The coding and noncoding architecture of the Caulobacter crescentus genome.
Schrader JM, Zhou B, Li GW, Lasker K, Childers WS, Williams B, Long T, Crosson S, McAdams HH, Weissman JS, Shapiro L., PLoS Genet 10(7), 2014
PMID: 25078267
RNA-Seq analysis of the multipartite genome of Rhizobium etli CE3 shows different replicon contributions under heat and saline shock.
López-Leal G, Tabche ML, Castillo-Ramírez S, Mendoza-Vargas A, Ramírez-Romero MA, Dávila G., BMC Genomics 15(), 2014
PMID: 25201548
Profound impact of Hfq on nutrient acquisition, metabolism and motility in the plant pathogen Agrobacterium tumefaciens.
Möller P, Overlöper A, Förstner KU, Wen TN, Sharma CM, Lai EM, Narberhaus F., PLoS One 9(10), 2014
PMID: 25330313
Analysis of a taurine-dependent promoter in Sinorhizobium meliloti that offers tight modulation of gene expression.
Mostafavi M, Lewis JC, Saini T, Bustamante JA, Gao IT, Tran TT, King SN, Huang Z, Chen JC., BMC Microbiol 14(), 2014
PMID: 25420869
Temporal expression program of quorum sensing-based transcription regulation in Sinorhizobium meliloti.
Charoenpanich P, Meyer S, Becker A, McIntosh M., J Bacteriol 195(14), 2013
PMID: 23687265
Independent activity of the homologous small regulatory RNAs AbcR1 and AbcR2 in the legume symbiont Sinorhizobium meliloti.
Torres-Quesada O, Millán V, Nisa-Martínez R, Bardou F, Crespi M, Toro N, Jiménez-Zurdo JI., PLoS One 8(7), 2013
PMID: 23869210
Parallel evolution of genome structure and transcriptional landscape in the Epsilonproteobacteria.
Porcelli I, Reuter M, Pearson BM, Wilhelm T, van Vliet AH., BMC Genomics 14(), 2013
PMID: 24028687

104 References

Daten bereitgestellt von Europe PubMed Central.

Regulatory RNAs in bacteria.
Waters LS, Storz G., Cell 136(4), 2009
PMID: 19239884
Regulation by small RNAs in bacteria: expanding frontiers.
Storz G, Vogel J, Wassarman KM., Mol. Cell 43(6), 2011
PMID: 21925377
Activating transcription in bacteria.
Lee DJ, Minchin SD, Busby SJ., Annu. Rev. Microbiol. 66(), 2012
PMID: 22726217
The primary transcriptome of the major human pathogen Helicobacter pylori.
Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A, Chabas S, Reiche K, Hackermuller J, Reinhardt R, Stadler PF, Vogel J., Nature 464(7286), 2010
PMID: 20164839
An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803.
Mitschke J, Georg J, Scholz I, Sharma CM, Dienst D, Bantscheff J, Voss B, Steglich C, Wilde A, Vogel J, Hess WR., Proc. Natl. Acad. Sci. U.S.A. 108(5), 2011
PMID: 21245330
Dynamics of transcriptional start site selection during nitrogen stress-induced cell differentiation in Anabaena sp. PCC7120.
Mitschke J, Vioque A, Haas F, Hess WR, Muro-Pastor AM., Proc. Natl. Acad. Sci. U.S.A. 108(50), 2011
PMID: 22135468
A high resolution map of a cyanobacterial transcriptome.
Vijayan V, Jain IH, O'Shea EK., Genome Biol. 12(5), 2011
PMID: 21612627
Structure and complexity of a bacterial transcriptome.
Passalacqua KD, Varadarajan A, Ondov BD, Okou DT, Zwick ME, Bergman NH., J. Bacteriol. 191(10), 2009
PMID: 19304856
Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs.
Oliver HF, Orsi RH, Ponnala L, Keich U, Wang W, Sun Q, Cartinhour SW, Filiatrault MJ, Wiedmann M, Boor KJ., BMC Genomics 10(), 2009
PMID: 20042087
Transcriptome complexity in a genome-reduced bacterium.
Guell M, van Noort V, Yus E, Chen WH, Leigh-Bell J, Michalodimitrakis K, Yamada T, Arumugam M, Doerks T, Kuhner S, Rode M, Suyama M, Schmidt S, Gavin AC, Bork P, Serrano L., Science 326(5957), 2009
PMID: 19965477
Sequence-based analysis uncovers an abundance of non-coding RNA in the total transcriptome of Mycobacterium tuberculosis.
Arnvig KB, Comas I, Thomson NR, Houghton J, Boshoff HI, Croucher NJ, Rose G, Perkins TT, Parkhill J, Dougan G, Young DB., PLoS Pathog. 7(11), 2011
PMID: 22072964
Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome.
Albrecht M, Sharma CM, Reinhardt R, Vogel J, Rudel T., Nucleic Acids Res. 38(3), 2009
PMID: 19923228
Genome-wide identification of transcriptional start sites in the plant pathogen Pseudomonas syringae pv. tomato str. DC3000.
Filiatrault MJ, Stodghill PV, Myers CR, Bronstein PA, Butcher BG, Lam H, Grills G, Schweitzer P, Wang W, Schneider DJ, Cartinhour SW., PLoS ONE 6(12), 2011
PMID: 22216251
A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi.
Perkins TT, Kingsley RA, Fookes MC, Gardner PP, James KD, Yu L, Assefa SA, He M, Croucher NJ, Pickard DJ, Maskell DJ, Parkhill J, Choudhary J, Thomson NR, Dougan G., PLoS Genet. 5(7), 2009
PMID: 19609351
The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium.
Kroger C, Dillon SC, Cameron AD, Papenfort K, Sivasankaran SK, Hokamp K, Chao Y, Sittka A, Hebrard M, Handler K, Colgan A, Leekitcharoenphon P, Langridge GC, Lohan AJ, Loftus B, Lucchini S, Ussery DW, Dorman CJ, Thomson NR, Vogel J, Hinton JC., Proc. Natl. Acad. Sci. U.S.A. 109(20), 2012
PMID: 22538806
Deep sequencing uncovers numerous small RNAs on all four replicons of the plant pathogen Agrobacterium tumefaciens.
Wilms I, Overloper A, Nowrousian M, Sharma CM, Narberhaus F., RNA Biol 9(4), 2012
PMID: 22336765
A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti.
Schluter JP, Reinkensmeier J, Daschkey S, Evguenieva-Hackenberg E, Janssen S, Janicke S, Becker JD, Giegerich R, Becker A., BMC Genomics 11(), 2010
PMID: 20398411
The evolution of chronic infection strategies in the alpha-proteobacteria.
Batut J, Andersson SG, O'Callaghan D., Nat. Rev. Microbiol. 2(12), 2004
PMID: 15550939
How rhizobial symbionts invade plants: the Sinorhizobium-Medicago model.
Jones KM, Kobayashi H, Davies BW, Taga ME, Walker GC., Nat. Rev. Microbiol. 5(8), 2007
PMID: 17632573
The composite genome of the legume symbiont Sinorhizobium meliloti.
Galibert F, Finan TM, Long SR, Puhler A, Abola P, Ampe F, Barloy-Hubler F, Barnett MJ, Becker A, Boistard P, Bothe G, Boutry M, Bowser L, Buhrmester J, Cadieu E, Capela D, Chain P, Cowie A, Davis RW, Dreano S, Federspiel NA, Fisher RF, Gloux S, Godrie T, Goffeau A, Golding B, Gouzy J, Gurjal M, Hernandez-Lucas I, Hong A, Huizar L, Hyman RW, Jones T, Kahn D, Kahn ML, Kalman S, Keating DH, Kiss E, Komp C, Lelaure V, Masuy D, Palm C, Peck MC, Pohl TM, Portetelle D, Purnelle B, Ramsperger U, Surzycki R, Thebault P, Vandenbol M, Vorholter FJ, Weidner S, Wells DH, Wong K, Yeh KC, Batut J., Science 293(5530), 2001
PMID: 11474104
Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid.
Barnett MJ, Fisher RF, Jones T, Komp C, Abola AP, Barloy-Hubler F, Bowser L, Capela D, Galibert F, Gouzy J, Gurjal M, Hong A, Huizar L, Hyman RW, Kahn D, Kahn ML, Kalman S, Keating DH, Palm C, Peck MC, Surzycki R, Wells DH, Yeh KC, Davis RW, Federspiel NA, Long SR., Proc. Natl. Acad. Sci. U.S.A. 98(17), 2001
PMID: 11481432
The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti.
Finan TM, Weidner S, Wong K, Buhrmester J, Chain P, Vorholter FJ, Hernandez-Lucas I, Becker A, Cowie A, Gouzy J, Golding B, Puhler A., Proc. Natl. Acad. Sci. U.S.A. 98(17), 2001
PMID: 11481431
The role of sigma factor RpoH1 in the pH stress response of Sinorhizobium meliloti.
de Lucena DK, Puhler A, Weidner S., BMC Microbiol. 10(), 2010
PMID: 20955556
Mechanisms for activating bacterial RNA polymerase.
Ghosh T, Bose D, Zhang X., FEMS Microbiol. Rev. 34(5), 2010
PMID: 20629756
Prediction and overview of the RpoN-regulon in closely related species of the Rhizobiales
Identification of the heat-shock sigma factor RpoH and a second RpoH-like protein in Sinorhizobium meliloti.
Oke V, Rushing BG, Fisher EJ, Moghadam-Tabrizi M, Long SR., Microbiology (Reading, Engl.) 147(Pt 9), 2001
PMID: 11535780
RpoE2 of Sinorhizobium meliloti is necessary for trehalose synthesis and growth in hyperosmotic media.
Flechard M, Fontenelle C, Blanco C, Goude R, Ermel G, Trautwetter A., Microbiology (Reading, Engl.) 156(Pt 6), 2010
PMID: 20223801
Rhizobium--plant signal exchange.
Fisher RF, Long SR., Nature 357(6380), 1992
PMID: 1614514
Quorum sensing controls exopolysaccharide production in Sinorhizobium meliloti.
Marketon MM, Glenn SA, Eberhard A, Gonzalez JE., J. Bacteriol. 185(1), 2003
PMID: 12486070
Role of quorum sensing in Sinorhizobium meliloti-Alfalfa symbiosis.
Gurich N, Gonzalez JE., J. Bacteriol. 191(13), 2009
PMID: 19395488
A portal for rhizobial genomes: RhizoGATE integrates a Sinorhizobium meliloti genome annotation update with postgenome data.
Becker A, Barnett MJ, Capela D, Dondrup M, Kamp PB, Krol E, Linke B, Ruberg S, Runte K, Schroeder BK, Weidner S, Yurgel SN, Batut J, Long SR, Puhler A, Goesmann A., J. Biotechnol. 140(1-2), 2008
PMID: 19103235
RhizoRegNet--a database of rhizobial transcription factors and regulatory networks.
Krol E, Blom J, Winnebald J, Berhorster A, Barnett MJ, Goesmann A, Baumbach J, Becker A., J. Biotechnol. 155(1), 2010
PMID: 21087643
Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli.
Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E., PLoS ONE 4(10), 2009
PMID: 19838305
A homolog of the CtrA cell cycle regulator is present and essential in Sinorhizobium meliloti.
Barnett MJ, Hung DY, Reisenauer A, Shapiro L, Long SR., J. Bacteriol. 183(10), 2001
PMID: 11325950
GenDB--an open source genome annotation system for prokaryote genomes.
Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Puhler A., Nucleic Acids Res. 31(8), 2003
PMID: 12682369
Selective translation of leaderless mRNAs by specialized ribosomes generated by MazF in Escherichia coli.
Vesper O, Amitai S, Belitsky M, Byrgazov K, Kaberdina AC, Engelberg-Kulka H, Moll I., Cell 147(1), 2011
PMID: 21944167
Unusual regulation of a leaderless operon involved in the catabolism of dimethylsulfoniopropionate in Rhodobacter sphaeroides.
Sullivan MJ, Curson AR, Shearer N, Todd JD, Green RT, Johnston AW., PLoS ONE 6(1), 2011
PMID: 21249136
Pseudomonas putida KT2440 genome update by cDNA sequencing and microarray transcriptomics.
Frank S, Klockgether J, Hagendorf P, Geffers R, Schock U, Pohl T, Davenport CF, Tummler B., Environ. Microbiol. 13(5), 2011
PMID: 21355971
Ribosomes bind leaderless mRNA in Escherichia coli through recognition of their 5'-terminal AUG.
Brock JE, Pourshahian S, Giliberti J, Limbach PA, Janssen GR., RNA 14(10), 2008
PMID: 18755843
Cartography of methicillin-resistant S. aureus transcripts: detection, orientation and temporal expression during growth phase and stress conditions.
Beaume M, Hernandez D, Farinelli L, Deluen C, Linder P, Gaspin C, Romby P, Schrenzel J, Francois P., PLoS ONE 5(5), 2010
PMID: 20505759
Transcriptome analysis of Pseudomonas syringae identifies new genes, noncoding RNAs, and antisense activity.
Filiatrault MJ, Stodghill PV, Bronstein PA, Moll S, Lindeberg M, Grills G, Schweitzer P, Wang W, Schroth GP, Luo S, Khrebtukova I, Yang Y, Thannhauser T, Butcher BG, Cartinhour S, Schneider DJ., J. Bacteriol. 192(9), 2010
PMID: 20190049
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., Nucleic Acids Res. 37(6), 2009
PMID: 19223322
S-box and T-box riboswitches and antisense RNA control a sulfur metabolic operon of Clostridium acetobutylicum.
Andre G, Even S, Putzer H, Burguiere P, Croux C, Danchin A, Martin-Verstraete I, Soutourina O., Nucleic Acids Res. 36(18), 2008
PMID: 18812398
Evidence for a major role of antisense RNAs in cyanobacterial gene regulation.
Georg J, Voss B, Scholz I, Mitschke J, Wilde A, Hess WR., Mol. Syst. Biol. 5(), 2009
PMID: 19756044
Antisense RNA protects mRNA from RNase E degradation by RNA-RNA duplex formation during phage infection.
Stazic D, Lindell D, Steglich C., Nucleic Acids Res. 39(11), 2011
PMID: 21325266
An antisense RNA controls synthesis of an SOS-induced toxin evolved from an antitoxin.
Kawano M, Aravind L, Storz G., Mol. Microbiol. 64(3), 2007
PMID: 17462020
A novel antisense RNA regulates at transcriptional level the virulence gene icsA of Shigella flexneri.
Giangrossi M, Prosseda G, Tran CN, Brandi A, Colonna B, Falconi M., Nucleic Acids Res. 38(10), 2010
PMID: 20129941
Small untranslated RNA antitoxin in Bacillus subtilis.
Silvaggi JM, Perkins JB, Losick R., J. Bacteriol. 187(19), 2005
PMID: 16166525
Regulatory mechanisms employed by cis-encoded antisense RNAs.
Brantl S., Curr. Opin. Microbiol. 10(2), 2007
PMID: 17387036
An internal antisense RNA regulates expression of the photosynthesis gene isiA.
Duhring U, Axmann IM, Hess WR, Wilde A., Proc. Natl. Acad. Sci. U.S.A. 103(18), 2006
PMID: 16636284
Small RNAs establish delays and temporal thresholds in gene expression.
Legewie S, Dienst D, Wilde A, Herzel H, Axmann IM., Biophys. J. 95(7), 2008
PMID: 18599624
cis-antisense RNA, another level of gene regulation in bacteria.
Georg J, Hess WR., Microbiol. Mol. Biol. Rev. 75(2), 2011
PMID: 21646430
Conservation and Occurrence of Trans-Encoded sRNAs in the Rhizobiales.
Reinkensmeier J, Schluter JP, Giegerich R, Becker A., Genes (Basel) 2(4), 2011
PMID: 24710299
Dual RpoH sigma factors and transcriptional plasticity in a symbiotic bacterium.
Barnett MJ, Bittner AN, Toman CJ, Oke V, Long SR., J. Bacteriol. 194(18), 2012
PMID: 22773790
Transcription start sites for syrM and nodD3 flank an insertion sequence relic in Rhizobium meliloti.
Barnett MJ, Rushing BG, Fisher RF, Long SR., J. Bacteriol. 178(7), 1996
PMID: 8606148
Promoter prediction in the rhizobia.
MacLellan SR, MacLean AM, Finan TM., Microbiology (Reading, Engl.) 152(Pt 6), 2006
PMID: 16735738
The third pillar of bacterial signal transduction: classification of the extracytoplasmic function (ECF) sigma factor protein family.
Staron A, Sofia HJ, Dietrich S, Ulrich LE, Liesegang H, Mascher T., Mol. Microbiol. 74(3), 2009
PMID: 19737356
Identification and characterization of large plasmids in Rhizobium meliloti using agarose-gel electrophoresis

Extracytoplasmic function σ factors of the widely distributed group ECF41 contain a fused regulatory domain.
Wecke T, Halang P, Staron A, Dufour YS, Donohue TJ, Mascher T., Microbiologyopen 1(2), 2012
PMID: 22950025
Genome prediction of PhoB regulated promoters in Sinorhizobium meliloti and twelve proteobacteria.
Yuan ZC, Zaheer R, Morton R, Finan TM., Nucleic Acids Res. 34(9), 2006
PMID: 16717279
The structure of a transcription activation subcomplex reveals how σ(70) is recruited to PhoB promoters.
Blanco AG, Canals A, Bernues J, Sola M, Coll M., EMBO J. 30(18), 2011
PMID: 21829166
Phosphate assimilation in Rhizobium (Sinorhizobium) meliloti: identification of a pit-like gene.
Bardin SD, Voegele RT, Finan TM., J. Bacteriol. 180(16), 1998
PMID: 9696772
Genes directly controlled by CtrA, a master regulator of the Caulobacter cell cycle.
Laub MT, Chen SL, Shapiro L, McAdams HH., Proc. Natl. Acad. Sci. U.S.A. 99(7), 2002
PMID: 11930012
A Sinorhizobium meliloti minE mutant has an altered morphology and exhibits defects in legume symbiosis.
Cheng J, Sibley CD, Zaheer R, Finan TM., Microbiology (Reading, Engl.) 153(Pt 2), 2007
PMID: 17259609
The diversity and evolution of cell cycle regulation in alpha-proteobacteria: a comparative genomic analysis.
Brilli M, Fondi M, Fani R, Mengoni A, Ferri L, Bazzicalupo M, Biondi EG., BMC Syst Biol 4(), 2010
PMID: 20426835
Plasticity of a transcriptional regulation network among alpha-proteobacteria is supported by the identification of CtrA targets in Brucella abortus.
Bellefontaine AF, Pierreux CE, Mertens P, Vandenhaute J, Letesson JJ, De Bolle X., Mol. Microbiol. 43(4), 2002
PMID: 11929544
MEME: discovering and analyzing DNA and protein sequence motifs.
Bailey TL, Williams N, Misleh C, Li WW., Nucleic Acids Res. 34(Web Server issue), 2006
PMID: 16845028
A dual-genome Symbiosis Chip for coordinate study of signal exchange and development in a prokaryote-host interaction.
Barnett MJ, Toman CJ, Fisher RF, Long SR., Proc. Natl. Acad. Sci. U.S.A. 101(47), 2004
PMID: 15542588
RegTransBase--a database of regulatory sequences and interactions in a wide range of prokaryotic genomes.
Kazakov AE, Cipriano MJ, Novichkov PS, Minovitsky S, Vinogradov DV, Arkin A, Mironov AA, Gelfand MS, Dubchak I., Nucleic Acids Res. 35(Database issue), 2006
PMID: 17142223
A Sinorhizobium meliloti osmosensory two-component system required for cyclic glucan export and symbiosis.
Griffitts JS, Carlyon RE, Erickson JH, Moulton JL, Barnett MJ, Toman CJ, Long SR., Mol. Microbiol. 69(2), 2008
PMID: 18630344
FeuN, a novel modulator of two-component signalling identified in Sinorhizobium meliloti.
Carlyon RE, Ryther JL, VanYperen RD, Griffitts JS., Mol. Microbiol. 77(1), 2010
PMID: 20487268
Sinorhizobium meliloti rpoE2 is necessary for H(2)O(2) stress resistance during the stationary growth phase.
Flechard M, Fontenelle C, Trautwetter A, Ermel G, Blanco C., FEMS Microbiol. Lett. 290(1), 2008
PMID: 19025578
General stress response in α-proteobacteria: PhyR and beyond.
Staron A, Mascher T., Mol. Microbiol. 78(2), 2010
PMID: 20979331
A LuxR homolog controls production of symbiotically active extracellular polysaccharide II by Sinorhizobium meliloti.
Pellock BJ, Teplitski M, Boinay RP, Bauer WD, Walker GC., J. Bacteriol. 184(18), 2002
PMID: 12193623

R factor transfer in Rhizobium leguminosarum.
Beringer JE., J. Gen. Microbiol. 84(1), 1974
PMID: 4612098

Fast mapping of short sequences with mismatches, insertions and deletions using index structures.
Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermuller J., PLoS Comput. Biol. 5(9), 2009
PMID: 19750212
Predicting Shine-Dalgarno sequence locations exposes genome annotation errors.
Starmer J, Stomp A, Vouk M, Bitzer D., PLoS Comput. Biol. 2(5), 2006
PMID: 16710451
Compilation and analysis of sigma(54)-dependent promoter sequences.
Barrios H, Valderrama B, Morett E., Nucleic Acids Res. 27(22), 1999
PMID: 10536136
Fast index based algorithms and software for matching position specific scoring matrices.
Beckstette M, Homann R, Giegerich R, Kurtz S., BMC Bioinformatics 7(), 2006
PMID: 16930469
Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules.
Turatsinze JV, Thomas-Chollier M, Defrance M, van Helden J., Nat Protoc 3(10), 2008
PMID: 18802439
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository.
Edgar R, Domrachev M, Lash AE., Nucleic Acids Res. 30(1), 2002
PMID: 11752295

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

PMID: 23497287
PubMed | Europe PMC

Suchen in

Google Scholar