PUB - Publikationen an der Universität Bielefeld

RhizoGATE - The gateway to rhizobial genomes
AUTHOR UNKNOWN, 0

Small RNAs in bacteria: diverse regulators of gene expression in response to environmental changes.
Wassarman KM., Cell 109(2), 2002
PMID: 12007399

The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae.
Lenz DH, Mok KC, Lilley BN, Kulkarni RV, Wingreen NS, Bassler BL., Cell 118(1), 2004
PMID: 15242645

Small toxic proteins and the antisense RNAs that repress them.
Fozo EM, Hemm MR, Storz G., Microbiol. Mol. Biol. Rev. 72(4), 2008
PMID: 19052321

An abundance of RNA regulators.
Storz G, Altuvia S, Wassarman KM., Annu. Rev. Biochem. 74(), 2005
PMID: 15952886

The Escherichia coli OxyS regulatory RNA represses fhlA translation by blocking ribosome binding.
Altuvia S, Zhang A, Argaman L, Tiwari A, Storz G., EMBO J. 17(20), 1998
PMID: 9774350

The function of micF RNA. micF RNA is a major factor in the thermal regulation of OmpF protein in Escherichia coli.
Andersen J, Forst SA, Zhao K, Inouye M, Delihas N., J. Biol. Chem. 264(30), 1989
PMID: 2478539

MicC, a second small-RNA regulator of Omp protein expression in Escherichia coli.
Chen S, Zhang A, Blyn LB, Storz G., J. Bacteriol. 186(20), 2004
PMID: 15466019

DsrA RNA regulates translation of RpoS message by an anti-antisense mechanism, independent of its action as an antisilencer of transcription.
Majdalani N, Cunning C, Sledjeski D, Elliott T, Gottesman S., Proc. Natl. Acad. Sci. U.S.A. 95(21), 1998
PMID: 9770508

Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli.
Masse E, Escorcia FE, Gottesman S., Genes Dev. 17(19), 2003
PMID: 12975324

Small RNAs controlling iron metabolism.
Masse E, Salvail H, Desnoyers G, Arguin M., Curr. Opin. Microbiol. 10(2), 2007
PMID: 17383226

GadY, a small-RNA regulator of acid response genes in Escherichia coli.
Opdyke JA, Kang JG, Storz G., J. Bacteriol. 186(20), 2004
PMID: 15466020

CsrB sRNA family: sequestration of RNA-binding regulatory proteins.
Babitzke P, Romeo T., Curr. Opin. Microbiol. 10(2), 2007
PMID: 17383221

Identification of novel small RNAs using comparative genomics and microarrays.
Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S., Genes Dev. 15(13), 2001
PMID: 11445539

Novel small RNA-encoding genes in the intergenic regions of Escherichia coli.
Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H, Altuvia S., Curr. Biol. 11(12), 2001
PMID: 11448770

Computational identification of noncoding RNAs in E. coli by comparative genomics.
Rivas E, Klein RJ, Jones TA, Eddy SR., Curr. Biol. 11(17), 2001
PMID: 11553332

A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome.
Chen S, Lesnik EA, Hall TA, Sampath R, Griffey RH, Ecker DJ, Blyn LB., BioSystems 65(2-3), 2002
PMID: 12069726

Identification of small noncoding RNAs in Helicobacter pylori by a bioinformatics-based approach.
Xiao B, Li W, Guo G, Li B, Liu Z, Jia K, Guo Y, Mao X, Zou Q., Curr. Microbiol. 58(3), 2009
PMID: 19123032

Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool sRNAPredict2.
Livny J, Brencic A, Lory S, Waldor MK., Nucleic Acids Res. 34(12), 2006
PMID: 16870723

Computational prediction and transcriptional analysis of sRNAs in Nitrosomonas europaea.
Gvakharia BO, Tjaden B, Vajrala N, Sayavedra-Soto LA, Arp DJ., FEMS Microbiol. Lett. 312(1), 2010
PMID: 20840601

Fast and reliable prediction of noncoding RNAs.
Washietl S, Hofacker IL, Stadler PF., Proc. Natl. Acad. Sci. U.S.A. 102(7), 2005
PMID: 15665081

Identification and classification of conserved RNA secondary structures in the human genome.
Pedersen JS, Bejerano G, Siepel A, Rosenbloom K, Lindblad-Toh K, Lander ES, Kent J, Miller W, Haussler D., PLoS Comput. Biol. 2(4), 2006
PMID: 16628248

Infernal 1.0: inference of RNA alignments.
Nawrocki EP, Kolbe DL, Eddy SR., Bioinformatics 25(10), 2009
PMID: 19307242

Structured RNAs in the ENCODE selected regions of the human genome.
Washietl S, Pedersen JS, Korbel JO, Stocsits C, Gruber AR, Hackermuller J, Hertel J, Lindemeyer M, Reiche K, Tanzer A, Ucla C, Wyss C, Antonarakis SE, Denoeud F, Lagarde J, Drenkow J, Kapranov P, Gingeras TR, Guigo R, Snyder M, Gerstein MB, Reymond A, Hofacker IL, Stadler PF., Genome Res. 17(6), 2007
PMID: 17568003

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

Small non-coding RNAs in Caulobacter crescentus.
Landt SG, Abeliuk E, McGrath PT, Lesley JA, McAdams HH, Shapiro L., Mol. Microbiol. 68(3), 2008
PMID: 18373523

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

High-throughput, kingdom-wide prediction and annotation of bacterial non-coding RNAs.
Livny J, Teonadi H, Livny M, Waldor MK., PLoS ONE 3(9), 2008
PMID: 18787707

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, Engelen K, Thijs IM, Marchal K, Michiels J., BMC Genomics 11(), 2010
PMID: 20089193

Deep sequencing uncovers numerous small RNAs on all four replicons of the plant pathogen Agrobacterium tumefaciens
Wilms I., Overlöper A., Nowrousian M., Sharma C.M., Narberhaus F.., 2012

Two discrete elements are required for the replication of a repABC plasmid: an antisense RNA and a stem-loop structure.
Venkova-Canova T, Soberon NE, Ramirez-Romero MA, Cevallos MA., Mol. Microbiol. 54(5), 2004
PMID: 15554980

The expression of a novel antisense gene mediates incompatibility within the large repABC family of alpha-proteobacterial plasmids.
MacLellan SR, Smallbone LA, Sibley CD, Finan TM., Mol. Microbiol. 55(2), 2005
PMID: 15659174

Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in Sinorhizobium meliloti strain 1021.
Ulve VM, Sevin EW, Cheron A, Barloy-Hubler F., BMC Genomics 8(), 2007
PMID: 18093320

Characterization and expression patterns of Sinorhizobium meliloti tmRNA (ssrA).
Ulve VM, Cheron A, Trautwetter A, Fontenelle C, Barloy-Hubler F., FEMS Microbiol. Lett. 269(1), 2007
PMID: 17241239

Identification of differentially expressed small non-coding RNAs in the legume endosymbiont Sinorhizobium meliloti by comparative genomics.
del Val C, Rivas E, Torres-Quesada O, Toro N, Jimenez-Zurdo JI., Mol. Microbiol. 66(5), 2007
PMID: 17971083

Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011.
Valverde C, Livny J, Schluter JP, Reinkensmeier J, Becker A, Parisi G., BMC Genomics 9(), 2008
PMID: 18793445

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

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

Brucellosis.
Pappas G, Akritidis N, Bosilkovski M, Tsianos E., N. Engl. J. Med. 352(22), 2005
PMID: 15930423

Beyond cat scratch disease: widening spectrum of Bartonella henselae infection.
Florin TA, Zaoutis TE, Zaoutis LB., Pediatrics 121(5), 2008
PMID: 18443019

Agrobacterium tumefaciens and plant cell interactions and activities required for interkingdom macromolecular transfer.
McCullen CA, Binns AN., Annu. Rev. Cell Dev. Biol. 22(), 2006
PMID: 16709150

Thermodynamic Matchers: Strengthening the Significance of RNA Folding Energies
Höchsmann T., Höchsmann M., Giegerich R.., 0

Locomotif: from graphical motif description to RNA motif search.
Reeder J, Reeder J, Giegerich R., Bioinformatics 23(13), 2007
PMID: 17646322

PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species.
Gillespie JJ, Wattam AR, Cammer SA, Gabbard JL, Shukla MP, Dalay O, Driscoll T, Hix D, Mane SP, Mao C, Nordberg EK, Scott M, Schulman JR, Snyder EE, Sullivan DE, Wang C, Warren A, Williams KP, Xue T, Yoo HS, Zhang C, Zhang Y, Will R, Kenyon RW, Sobral BW., Infect. Immun. 79(11), 2011
PMID: 21896772

Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti.
Galardini M, Mengoni A, Brilli M, Pini F, Fioravanti A, Lucas S, Lapidus A, Cheng JF, Goodwin L, Pitluck S, Land M, Hauser L, Woyke T, Mikhailova N, Ivanova N, Daligault H, Bruce D, Detter C, Tapia R, Han C, Teshima H, Mocali S, Bazzicalupo M, Biondi EG., BMC Genomics 12(), 2011
PMID: 21569405

Conserved symbiotic plasmid DNA sequences in the multireplicon pangenomic structure of Rhizobium etli.
Gonzalez V, Acosta JL, Santamaria RI, Bustos P, Fernandez JL, Hernandez Gonzalez IL, Diaz R, Flores M, Palacios R, Mora J, Davila G., Appl. Environ. Microbiol. 76(5), 2010
PMID: 20048063

Rhizobium sp. strain NGR234 possesses a remarkable number of secretion systems.
Schmeisser C, Liesegang H, Krysciak D, Bakkou N, Le Quere A, Wollherr A, Heinemeyer I, Morgenstern B, Pommerening-Roser A, Flores M, Palacios R, Brenner S, Gottschalk G, Schmitz RA, Broughton WJ, Perret X, Strittmatter AW, Streit WR., Appl. Environ. Microbiol. 75(12), 2009
PMID: 19376903

Complete genome sequence of the Medicago microsymbiont Ensifer (Sinorhizobium) medicae strain WSM419.
Reeve W, Chain P, O'Hara G, Ardley J, Nandesena K, Brau L, Tiwari R, Malfatti S, Kiss H, Lapidus A, Copeland A, Nolan M, Land M, Hauser L, Chang YJ, Ivanova N, Mavromatis K, Markowitz V, Kyrpides N, Gollagher M, Yates R, Dilworth M, Howieson J., Stand Genomic Sci 2(1), 2010
PMID: 21304680

Genome sequences of three agrobacterium biovars help elucidate the evolution of multichromosome genomes in bacteria.
Slater SC, Goldman BS, Goodner B, Setubal JC, Farrand SK, Nester EW, Burr TJ, Banta L, Dickerman AW, Paulsen I, Otten L, Suen G, Welch R, Almeida NF, Arnold F, Burton OT, Du Z, Ewing A, Godsy E, Heisel S, Houmiel KL, Jhaveri J, Lu J, Miller NM, Norton S, Chen Q, Phoolcharoen W, Ohlin V, Ondrusek D, Pride N, Stricklin SL, Sun J, Wheeler C, Wilson L, Zhu H, Wood DW., J. Bacteriol. 191(8), 2009
PMID: 19251847

Biocomputational prediction of non-coding RNAs in model cyanobacteria.
Voss B, Georg J, Schon V, Ude S, Hess WR., BMC Genomics 10(), 2009
PMID: 19309518

Complete genome sequence of citrus huanglongbing bacterium, 'Candidatus Liberibacter asiaticus' obtained through metagenomics.
Duan Y, Zhou L, Hall DG, Li W, Doddapaneni H, Lin H, Liu L, Vahling CM, Gabriel DW, Williams KP, Dickerman A, Sun Y, Gottwald T., Mol. Plant Microbe Interact. 22(8), 2009
PMID: 19589076

Comparative genomic structure of prokaryotes.
Bentley SD, Parkhill J., Annu. Rev. Genet. 38(), 2004
PMID: 15568993

Gene order is not conserved in bacterial evolution.
Mushegian AR, Koonin EV., Trends Genet. 12(8), 1996
PMID: 8783936

Evolution of prokaryotic gene order: genome rearrangements in closely related species.
Suyama M, Bork P., Trends Genet. 17(1), 2001
PMID: 11163906

IS Rm31, a new insertion sequence of the IS 66 family in Sinorhizobium meliloti.
Biondi EG, Femia AP, Favilli F, Bazzicalupo M., Arch. Microbiol. 180(2), 2003
PMID: 12819859

Modeling conserved structure patterns for functional noncoding RNA.
Chen Q, Chen YP., IEEE Trans Biomed Eng 58(6), 2010
PMID: 21041153

A motif-based search in bacterial genomes identifies the ortholog of the small RNA Yfr1 in all lineages of cyanobacteria.
Voss B, Gierga G, Axmann IM, Hess WR., BMC Genomics 8(), 2007
PMID: 17941988

Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake.
Kingsford CL, Ayanbule K, Salzberg SL., Genome Biol. 8(2), 2007
PMID: 17313685

Activation of gene expression by small RNA.
Frohlich KS, Vogel J., Curr. Opin. Microbiol. 12(6), 2009
PMID: 19880344

PolyU tail of rho-independent terminator of bacterial small RNAs is essential for Hfq action.
Otaka H, Ishikawa H, Morita T, Aiba H., Proc. Natl. Acad. Sci. U.S.A. 108(32), 2011
PMID: 21788484

The Vienna RNA websuite.
Gruber AR, Lorenz R, Bernhart SH, Neubock R, Hofacker IL., Nucleic Acids Res. 36(Web Server issue), 2008
PMID: 18424795

Interactions of the RNA-binding protein Hfq with cspA mRNA, encoding the major cold shock protein.
Hankins JS, Denroche H, Mackie GA., J. Bacteriol. 192(10), 2010
PMID: 20233932

Hfq structure, function and ligand binding.
Brennan RG, Link TM., Curr. Opin. Microbiol. 10(2), 2007
PMID: 17395525

Common and divergent features in transcriptional control of the homologous small RNAs GlmY and GlmZ in Enterobacteriaceae.
Gopel Y, Luttmann D, Heroven AK, Reichenbach B, Dersch P, Gorke B., Nucleic Acids Res. 39(4), 2010
PMID: 20965974

An upstream Hfq binding site in the fhlA mRNA leader region facilitates the OxyS-fhlA interaction.
Salim NN, Feig AL., PLoS ONE 5(9), 2010
PMID: 20927406

Antisense-RNA regulation and RNA interference.
Brantl S., Biochim. Biophys. Acta 1575(1-3), 2002
PMID: 12020814

A small bacterial RNA regulates a putative ABC transporter.
Antal M, Bordeau V, Douchin V, Felden B., J. Biol. Chem. 280(9), 2004
PMID: 15618228

Regulatory RNAs in cyanobacteria: developmental decisions, stress responses and a plethora of chromosomally encoded cis-antisense RNAs.
Georg J, Hess WR., Biol. Chem. 392(4), 2011
PMID: 21294678

Small RNA-mediated control of the Agrobacterium tumefaciens GABA binding protein.
Wilms I, Voss B, Hess WR, Leichert LI, Narberhaus F., Mol. Microbiol. 80(2), 2011
PMID: 21320185

Probing the structure of RNAIII, the Staphylococcus aureus agr regulatory RNA, and identification of the RNA domain involved in repression of protein A expression.
Benito Y, Kolb FA, Romby P, Lina G, Etienne J, Vandenesch F., RNA 6(5), 2000
PMID: 10836788

Staphylococcus aureus RNAIII and the endoribonuclease III coordinately regulate spa gene expression.
Huntzinger E, Boisset S, Saveanu C, Benito Y, Geissmann T, Namane A, Lina G, Etienne J, Ehresmann B, Ehresmann C, Jacquier A, Vandenesch F, Romby P., EMBO J. 24(4), 2005
PMID: 15678100

Staphylococcus aureus RNAIII coordinately represses the synthesis of virulence factors and the transcription regulator Rot by an antisense mechanism.
Boisset S, Geissmann T, Huntzinger E, Fechter P, Bendridi N, Possedko M, Chevalier C, Helfer AC, Benito Y, Jacquier A, Gaspin C, Vandenesch F, Romby P., Genes Dev. 21(11), 2007
PMID: 17545468

Down-regulation of outer membrane proteins by noncoding RNAs: unraveling the cAMP-CRP- and sigmaE-dependent CyaR-ompX regulatory case.
Johansen J, Eriksen M, Kallipolitis B, Valentin-Hansen P., J. Mol. Biol. 383(1), 2008
PMID: 18619465

Systematic deletion of Salmonella small RNA genes identifies CyaR, a conserved CRP-dependent riboregulator of OmpX synthesis.
Papenfort K, Pfeiffer V, Lucchini S, Sonawane A, Hinton JC, Vogel J., Mol. Microbiol. 68(4), 2008
PMID: 18399940

The Crp-activated small noncoding regulatory RNA CyaR (RyeE) links nutritional status to group behavior.
De Lay N, Gottesman S., J. Bacteriol. 191(2), 2008
PMID: 18978044

Photooxidative stress-induced and abundant small RNAs in Rhodobacter sphaeroides.
Berghoff BA, Glaeser J, Sharma CM, Vogel J, Klug G., Mol. Microbiol. 74(6), 2009
PMID: 19906181

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

NCBI genomes FTP site
AUTHOR UNKNOWN, 0

The tedious task of finding homologous noncoding RNA genes.
Menzel P, Gorodkin J, Stadler PF., RNA 15(12), 2009
PMID: 19861422

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ., Nucleic Acids Res. 25(17), 1997
PMID: 9254694

Non-coding RNA annotation of the genome of Trichoplax adhaerens.
Hertel J, de Jong D, Marz M, Rose D, Tafer H, Tanzer A, Schierwater B, Stadler PF., Nucleic Acids Res. 37(5), 2009
PMID: 19151082

Large scale hierarchical clustering of protein sequences
Krause A., Stoye J., Vingron M.., 2005

Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering.
Will S, Reiche K, Hofacker IL, Stadler PF, Backofen R., PLoS Comput. Biol. 3(4), 2007
PMID: 17432929

Secondary structure prediction for aligned RNA sequences.
Hofacker IL, Fekete M, Stadler PF., J. Mol. Biol. 319(5), 2002
PMID: 12079347

RNAalifold: Improved consensus structure prediction for RNA alignments
Bernhart S.H., Hofacker I.L., Will S., Gruber A.R., Stadler P.F.., 2008

AUTHOR UNKNOWN, 0

Fast folding and comparison of RNA secondary structures
Hofacker I.L., Fontana W., Stadler P.F., Bonhoeffer L.S., Tacker M., Schuster P.., 1994

Abstract shapes of RNA.
Giegerich R, Voss B, Rehmsmeier M., Nucleic Acids Res. 32(16), 2004
PMID: 15371549

RNAshapes: an integrated RNA analysis package based on abstract shapes.
Steffen P, Voss B, Rehmsmeier M, Reeder J, Giegerich R., Bioinformatics 22(4), 2005
PMID: 16357029

RNAHeliCes—Folding Space Analysis Based on Position Aware Structure Abstraction
Huang J., Voss B.., 0

Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction.
Reeder J, Giegerich R., Bioinformatics 21(17), 2005
PMID: 16020472