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 (2015)
PLOS GENETICS 11(3): e1005087.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
Autor*in
Nuss, Aaron M.; Heroven, Ann Kathrin; Waldmann, Barbara; Reinkensmeier, JanUniBi; Jarek, Michael; Beckstette, MichaelUniBi; Dersch, Petra
Abstract / Bemerkung
One hallmark of pathogenic yersiniae is their ability to rapidly adjust their life-style and pathogenesis upon host entry. In order to capture the range, magnitude and complexity of the underlying gene control mechanisms we used comparative RNA-seq-based transcriptomic profiling of the enteric pathogen Y. pseudotuberculosis under environmental and infection-relevant conditions. We identified 1151 individual transcription start sites, multiple ribos-witch-like RNA elements, and a global set of antisense RNAs and previously unrecognized trans-acting RNAs. Taking advantage of these data, we revealed a temperature-induced and growth phase-dependent reprogramming of a large set of catabolic/energy production genes and uncovered the existence of a thermo-regulated 'acetate switch', which appear to prime the bacteria for growth in the digestive tract. To elucidate the regulatory architecture linking nutritional status to virulence we also refined the CRP regulon. We identified a massive remodelling of the CRP-controlled network in response to temperature and discovered CRP as a transcriptional master regulator of numerous conserved and newly identified non-coding RNAs which participate in this process. This finding highlights a novel level of complexity of the regulatory network in which the concerted action of transcriptional regulators and multiple non-coding RNAs under control of CRP adjusts the control of Yersinia fitness and virulence to the requirements of their environmental and virulent life-styles.
Erscheinungsjahr
2015
Zeitschriftentitel
PLOS GENETICS
Band
11
Ausgabe
3
Art.-Nr.
e1005087
eISSN
1553-7404
Page URI
https://pub.uni-bielefeld.de/record/2917100

Zitieren

Nuss AM, Heroven AK, Waldmann B, et al. Transcriptomic Profiling of Yersinia pseudotuberculosis Reveals Reprogramming of the Crp Regulon by Temperature and Uncovers Crp as a Master Regulator of Small RNAs. PLOS GENETICS. 2015;11(3): e1005087.
Nuss, A. M., Heroven, A. K., Waldmann, B., Reinkensmeier, J., Jarek, M., Beckstette, M., & Dersch, P. (2015). Transcriptomic Profiling of Yersinia pseudotuberculosis Reveals Reprogramming of the Crp Regulon by Temperature and Uncovers Crp as a Master Regulator of Small RNAs. PLOS GENETICS, 11(3), e1005087. https://doi.org/10.1371/journal.pgen.1005087
Nuss, Aaron M., Heroven, Ann Kathrin, Waldmann, Barbara, Reinkensmeier, Jan, Jarek, Michael, Beckstette, Michael, and Dersch, Petra. 2015. “Transcriptomic Profiling of Yersinia pseudotuberculosis Reveals Reprogramming of the Crp Regulon by Temperature and Uncovers Crp as a Master Regulator of Small RNAs”. PLOS GENETICS 11 (3): e1005087.
Nuss, A. M., Heroven, A. K., Waldmann, B., Reinkensmeier, J., Jarek, M., Beckstette, M., and Dersch, P. (2015). Transcriptomic Profiling of Yersinia pseudotuberculosis Reveals Reprogramming of the Crp Regulon by Temperature and Uncovers Crp as a Master Regulator of Small RNAs. PLOS GENETICS 11:e1005087.
Nuss, A.M., et al., 2015. Transcriptomic Profiling of Yersinia pseudotuberculosis Reveals Reprogramming of the Crp Regulon by Temperature and Uncovers Crp as a Master Regulator of Small RNAs. PLOS GENETICS, 11(3): e1005087.
A.M. Nuss, et al., “Transcriptomic Profiling of Yersinia pseudotuberculosis Reveals Reprogramming of the Crp Regulon by Temperature and Uncovers Crp as a Master Regulator of Small RNAs”, PLOS GENETICS, vol. 11, 2015, : e1005087.
Nuss, A.M., Heroven, A.K., Waldmann, B., Reinkensmeier, J., Jarek, M., Beckstette, M., Dersch, P.: Transcriptomic Profiling of Yersinia pseudotuberculosis Reveals Reprogramming of the Crp Regulon by Temperature and Uncovers Crp as a Master Regulator of Small RNAs. PLOS GENETICS. 11, : e1005087 (2015).
Nuss, Aaron M., Heroven, Ann Kathrin, Waldmann, Barbara, Reinkensmeier, Jan, Jarek, Michael, Beckstette, Michael, and Dersch, Petra. “Transcriptomic Profiling of Yersinia pseudotuberculosis Reveals Reprogramming of the Crp Regulon by Temperature and Uncovers Crp as a Master Regulator of Small RNAs”. PLOS GENETICS 11.3 (2015): e1005087.

30 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Metabolome and transcriptome-wide effects of the carbon storage regulator A in enteropathogenic Escherichia coli.
Berndt V, Beckstette M, Volk M, Dersch P, Brönstrup M., Sci Rep 9(1), 2019
PMID: 30644424
A bacterial secreted translocator hijacks riboregulators to control type III secretion in response to host cell contact.
Kusmierek M, Hoßmann J, Witte R, Opitz W, Vollmer I, Volk M, Heroven AK, Wolf-Watz H, Dersch P., PLoS Pathog 15(6), 2019
PMID: 31173606
Loss of CNFY toxin-induced inflammation drives Yersinia pseudotuberculosis into persistency.
Heine W, Beckstette M, Heroven AK, Thiemann S, Heise U, Nuss AM, Pisano F, Strowig T, Dersch P., PLoS Pathog 14(2), 2018
PMID: 29390040
Depletion of Glucose Activates Catabolite Repression during Pneumonic Plague.
Ritzert JT, Lathem WW., J Bacteriol 200(11), 2018
PMID: 29555700
CRP-cAMP mediates silencing of Salmonella virulence at the post-transcriptional level.
El Mouali Y, Gaviria-Cantin T, Sánchez-Romero MA, Gibert M, Westermann AJ, Vogel J, Balsalobre C., PLoS Genet 14(6), 2018
PMID: 29879120
Discovering RNA-Based Regulatory Systems for Yersinia Virulence.
Knittel V, Vollmer I, Volk M, Dersch P., Front Cell Infect Microbiol 8(), 2018
PMID: 30460205
Iron Regulation in Clostridioides difficile.
Berges M, Michel AM, Lassek C, Nuss AM, Beckstette M, Dersch P, Riedel K, Sievers S, Becher D, Otto A, Maaß S, Rohde M, Eckweiler D, Borrero-de Acuña JM, Jahn M, Neumann-Schaal M, Jahn D., Front Microbiol 9(), 2018
PMID: 30619231
RNA-based mechanisms of virulence control in Enterobacteriaceae.
Heroven AK, Nuss AM, Dersch P., RNA Biol 14(5), 2017
PMID: 27442607
RNA Regulators: Formidable Modulators of Yersinia Virulence.
Nuss AM, Heroven AK, Dersch P., Trends Microbiol 25(1), 2017
PMID: 27651123
In vivo expression technology and 5' end mapping of the Borrelia burgdorferi transcriptome identify novel RNAs expressed during mammalian infection.
Adams PP, Flores Avile C, Popitsch N, Bilusic I, Schroeder R, Lybecker M, Jewett MW., Nucleic Acids Res 45(2), 2017
PMID: 27913725
Tissue dual RNA-seq allows fast discovery of infection-specific functions and riboregulators shaping host-pathogen transcriptomes.
Nuss AM, Beckstette M, Pimenova M, Schmühl C, Opitz W, Pisano F, Heroven AK, Dersch P., Proc Natl Acad Sci U S A 114(5), 2017
PMID: 28096329
Several Hfq-dependent alterations in physiology of Yersinia enterocolitica O:3 are mediated by derepression of the transcriptional regulator RovM.
Leskinen K, Pajunen MI, Varjosalo M, Fernández-Carrasco H, Bengoechea JA, Skurnik M., Mol Microbiol 103(6), 2017
PMID: 28010054
Riboregulation of bacterial and archaeal transposition.
Ellis MJ, Haniford DB., Wiley Interdiscip Rev RNA 7(3), 2016
PMID: 26846462
Environmental Regulation of Yersinia Pathophysiology.
Chen S, Thompson KM, Francis MS., Front Cell Infect Microbiol 6(), 2016
PMID: 26973818
Temperature-responsive in vitro RNA structurome of Yersinia pseudotuberculosis.
Righetti F, Nuss AM, Twittenhoff C, Beele S, Urban K, Will S, Bernhart SH, Stadler PF, Dersch P, Narberhaus F., Proc Natl Acad Sci U S A 113(26), 2016
PMID: 27298343
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
Increased plasmid copy number is essential for Yersinia T3SS function and virulence.
Wang H, Avican K, Fahlgren A, Erttmann SF, Nuss AM, Dersch P, Fallman M, Edgren T, Wolf-Watz H., Science 353(6298), 2016
PMID: 27365311
Distribution and Evolution of Yersinia Leucine-Rich Repeat Proteins.
Hu Y, Huang H, Hui X, Cheng X, White AP, Zhao Z, Wang Y., Infect Immun 84(8), 2016
PMID: 27217422
The Conserved Dcw Gene Cluster of R. sphaeroides Is Preceded by an Uncommonly Extended 5' Leader Featuring the sRNA UpsM.
Weber L, Thoelken C, Volk M, Remes B, Lechner M, Klug G., PLoS One 11(11), 2016
PMID: 27802301
Regulatory principles governing Salmonella and Yersinia virulence.
Erhardt M, Dersch P., Front Microbiol 6(), 2015
PMID: 26441883
Yersinia pestis and Yersinia pseudotuberculosis infection: a regulatory RNA perspective.
Martínez-Chavarría LC, Vadyvaloo V., Front Microbiol 6(), 2015
PMID: 26441890
Yersinia Type III Secretion System Master Regulator LcrF.
Schwiesow L, Lam H, Dersch P, Auerbuch V., J Bacteriol 198(4), 2015
PMID: 26644429
From Insect to Man: Photorhabdus Sheds Light on the Emergence of Human Pathogenicity.
Mulley G, Beeton ML, Wilkinson P, Vlisidou I, Ockendon-Powell N, Hapeshi A, Tobias NJ, Nollmann FI, Bode HB, van den Elsen J, ffrench-Constant RH, Waterfield NR., PLoS One 10(12), 2015
PMID: 26681201

98 References

Daten bereitgestellt von Europe PubMed Central.

Bacterial virulence and Fis: adapting regulatory networks to the host environment.
Duprey A, Reverchon S, Nasser W., Trends Microbiol. 22(2), 2013
PMID: 24370464
Coordinate regulation and sensory transduction in the control of bacterial virulence.
Miller JF, Mekalanos JJ, Falkow S., Science 243(4893), 1989
PMID: 2537530
Temperature-regulated expression of bacterial virulence genes.
Konkel ME, Tilly K., Microbes Infect. 2(2), 2000
PMID: 10742688
The role of mRNA structure in translational control in bacteria.
Geissmann T, Marzi S, Romby P., RNA Biol 6(2), 2009
PMID: 19885993
Post-transcriptional regulation of gene expression in Yersinia species.
Schiano CA, Lathem WW., Front Cell Infect Microbiol 2(), 2012
PMID: 23162797
Small RNA functions in carbon metabolism and virulence of enteric pathogens.
Papenfort K, Vogel J., Front Cell Infect Microbiol 4(), 2014
PMID: 25077072
The Csr/Rsm system of Yersinia and related pathogens: A post-transcriptional strategy for managing virulence
AUTHOR UNKNOWN, 2012
Small RNA-mediated regulation of host-pathogen interactions.
Harris JF, Micheva-Viteva S, Li N, Hong-Geller E., Virulence 4(8), 2013
PMID: 23958954
Riboswitch RNAs: using RNA to sense cellular metabolism.
Henkin TM., Genes Dev. 22(24), 2008
PMID: 19141470
Prospects for riboswitch discovery and analysis.
Breaker RR., Mol. Cell 43(6), 2011
PMID: 21925376
Bacterial RNA thermometers: molecular zippers and switches.
Kortmann J, Narberhaus F., Nat. Rev. Microbiol. 10(4), 2012
PMID: 22421878
A decade of riboswitches.
Serganov A, Nudler E., Cell 152(1-2), 2013
PMID: 23332744
The intricate world of riboswitches.
Coppins RL, Hall KB, Groisman EA., Curr. Opin. Microbiol. 10(2), 2007
PMID: 17383225
The role of Hfq in bacterial pathogens.
Chao Y, Vogel J., Curr. Opin. Microbiol. 13(1), 2010
PMID: 20080057
Global discovery of small RNAs in Yersinia pseudotuberculosis identifies Yersinia-specific small, noncoding RNAs required for virulence.
Koo JT, Alleyne TM, Schiano CA, Jafari N, Lathem WW., Proc. Natl. Acad. Sci. U.S.A. 108(37), 2011
PMID: 21876162
Genome-wide analysis of small RNAs expressed by Yersinia pestis identifies a regulator of the Yop-Ysc type III secretion system.
Schiano CA, Koo JT, Schipma MJ, Caulfield AJ, Jafari N, Lathem WW., J. Bacteriol. 196(9), 2014
PMID: 24532772
Identification and characterization of small RNAs in Yersinia pestis.
Beauregard A, Smith EA, Petrone BL, Singh N, Karch C, McDonough KA, Wade JT., RNA Biol 10(3), 2013
PMID: 23324607
Identification by cDNA cloning of abundant sRNAs in a human-avirulent Yersinia pestis strain grown under five different growth conditions.
Qu Y, Bi L, Ji X, Deng Z, Zhang H, Yan Y, Wang M, Li A, Huang X, Yang R, Han Y., Future Microbiol 7(4), 2012
PMID: 22439729
Determination of sRNA expressions by RNA-seq in Yersinia pestis grown in vitro and during infection.
Yan Y, Su S, Meng X, Ji X, Qu Y, Liu Z, Wang X, Cui Y, Deng Z, Zhou D, Jiang W, Yang R, Han Y., PLoS ONE 8(9), 2013
PMID: 24040259
Regulatory RNA in bacterial pathogens.
Papenfort K, Vogel J., Cell Host Microbe 8(1), 2010
PMID: 20638647
[Intestinal yersiniosis. Clinical importance, epidemiology, diagnosis, and prevention].
Bockemuhl J, Roggentin P., Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 47(7), 2004
PMID: 15254824
Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis.
Achtman M, Zurth K, Morelli G, Torrea G, Guiyoule A, Carniel E., Proc. Natl. Acad. Sci. U.S.A. 96(24), 1999
PMID: 10570195
Parallel independent evolution of pathogenicity within the genus Yersinia.
Reuter S, Connor TR, Barquist L, Walker D, Feltwell T, Harris SR, Fookes M, Hall ME, Petty NK, Fuchs TM, Corander J, Dufour M, Ringwood T, Savin C, Bouchier C, Martin L, Miettinen M, Shubin M, Riehm JM, Laukkanen-Ninios R, Sihvonen LM, Siitonen A, Skurnik M, Falcao JP, Fukushima H, Scholz HC, Prentice MB, Wren BW, Parkhill J, Carniel E, Achtman M, McNally A, Thomson NR., Proc. Natl. Acad. Sci. U.S.A. 111(18), 2014
PMID: 24753568
Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis.
Chain PS, Carniel E, Larimer FW, Lamerdin J, Stoutland PO, Regala WM, Georgescu AM, Vergez LM, Land ML, Motin VL, Brubaker RR, Fowler J, Hinnebusch J, Marceau M, Medigue C, Simonet M, Chenal-Francisque V, Souza B, Dacheux D, Elliott JM, Derbise A, Hauser LJ, Garcia E., Proc. Natl. Acad. Sci. U.S.A. 101(38), 2004
PMID: 15358858
Yersiniosis. II: The pathogenesis of Yersinia infections.
Koornhof HJ, Smego RA Jr, Nicol M., Eur. J. Clin. Microbiol. Infect. Dis. 18(2), 1999
PMID: 10219574
Yersiniosis I: microbiological and clinicoepidemiological aspects of plague and non-plague Yersinia infections.
Smego RA, Frean J, Koornhof HJ., Eur. J. Clin. Microbiol. Infect. Dis. 18(1), 1999
PMID: 10192708
Environmental modulation of gene expression and pathogenesis in Yersinia.
Straley SC, Perry RD., Trends Microbiol. 3(8), 1995
PMID: 8528615
Multiple mechanisms controlling carbon metabolism in bacteria.
Saier MH Jr., Biotechnol. Bioeng. 58(2-3), 1998
PMID: 10191387
Identification of the CRP regulon using in vitro and in vivo transcriptional profiling.
Zheng D, Constantinidou C, Hobman JL, Minchin SD., Nucleic Acids Res. 32(19), 2004
PMID: 15520470
The cyclic AMP receptor protein, CRP, is required for both virulence and expression of the minimal CRP regulon in Yersinia pestis biovar microtus.
Zhan L, Han Y, Yang L, Geng J, Li Y, Gao H, Guo Z, Fan W, Li G, Zhang L, Qin C, Zhou D, Yang R., Infect. Immun. 76(11), 2008
PMID: 18710863
Crp induces switching of the CsrB and CsrC RNAs in Yersinia pseudotuberculosis and links nutritional status to virulence.
Heroven AK, Sest M, Pisano F, Scheb-Wetzel M, Steinmann R, Bohme K, Klein J, Munch R, Schomburg D, Dersch P., Front Cell Infect Microbiol 2(), 2012
PMID: 23251905
Reprogramming of Yersinia from virulent to persistent mode revealed by complex in vivo RNA-seq analysis.
Avican K, Fahlgren A, Huss M, Heroven AK, Beckstette M, Dersch P, Fallman M., PLoS Pathog. 11(1), 2015
PMID: 25590628
Posttranscriptional regulation of the Yersinia pestis cyclic AMP receptor protein Crp and impact on virulence.
Lathem WW, Schroeder JA, Bellows LE, Ritzert JT, Koo JT, Price PA, Caulfield AJ, Goldman WE., MBio 5(1), 2014
PMID: 24520064
Direct and negative regulation of the sycO-ypkA-ypoJ operon by cyclic AMP receptor protein (CRP) in Yersinia pestis.
Zhan L, Yang L, Zhou L, Li Y, Gao H, Guo Z, Zhang L, Qin C, Zhou D, Yang R., BMC Microbiol. 9(), 2009
PMID: 19703315
Direct transcriptional control of the plasminogen activator gene of Yersinia pestis by the cyclic AMP receptor protein.
Kim TJ, Chauhan S, Motin VL, Goh EB, Igo MM, Young GM., J. Bacteriol. 189(24), 2007
PMID: 17933899
The pyruvate-tricarboxylic acid cycle node: a focal point of virulence control in the enteric pathogen Yersinia pseudotuberculosis.
Bucker R, Heroven AK, Becker J, Dersch P, Wittmann C., J. Biol. Chem. 289(43), 2014
PMID: 25164818
A direct link between the global regulator PhoP and the Csr regulon in Y. pseudotuberculosis through the small regulatory RNA CsrC.
Nuss AM, Schuster F, Kathrin Heroven A, Heine W, Pisano F, Dersch P., RNA Biol 11(5), 2014
PMID: 24786463
Colonization of cecum is important for development of persistent infection by Yersinia pseudotuberculosis.
Fahlgren A, Avican K, Westermark L, Nordfelth R, Fallman M., Infect. Immun. 82(8), 2014
PMID: 24891107
The presence of professional phagocytes dictates the number of host cells targeted for Yop translocation during infection.
Durand EA, Maldonado-Arocho FJ, Castillo C, Walsh RL, Mecsas J., Cell. Microbiol. 12(8), 2010
PMID: 20148898
Autoproteolysis and intramolecular dissociation of Yersinia YscU precedes secretion of its C-terminal polypeptide YscU(CC).
Frost S, Ho O, Login FH, Weise CF, Wolf-Watz H, Wolf-Watz M., PLoS ONE 7(11), 2012
PMID: 23185318
Expression of the temperature-inducible outer membrane proteins of yersiniae.
Bolin I, Portnoy DA, Wolf-Watz H., Infect. Immun. 48(1), 1985
PMID: 3980086
Differential RNA-seq: the approach behind and the biological insight gained.
Sharma CM, Vogel J., Curr. Opin. Microbiol. 19(), 2014
PMID: 25024085
Riboswitch discovery by combining RNA-seq and genome-wide identification of transcriptional start sites.
Rosinski-Chupin I, Soutourina O, Martin-Verstraete I., Meth. Enzymol. 549(), 2014
PMID: 25432742
Genome-wide identification of regulatory RNAs in the human pathogen Clostridium difficile.
Soutourina OA, Monot M, Boudry P, Saujet L, Pichon C, Sismeiro O, Semenova E, Severinov K, Le Bouguenec C, Coppee JY, Dupuy B, Martin-Verstraete I., PLoS Genet. 9(5), 2013
PMID: 23675309
Temperature sensing in Yersinia pestis: regulation of yopE transcription by lcrF.
Hoe NP, Minion FC, Goguen JD., J. Bacteriol. 174(13), 1992
PMID: 1624422
Concerted actions of a thermo-labile regulator and a unique intergenic RNA thermosensor control Yersinia virulence.
Bohme K, Steinmann R, Kortmann J, Seekircher S, Heroven AK, Berger E, Pisano F, Thiermann T, Wolf-Watz H, Narberhaus F, Dersch P., PLoS Pathog. 8(2), 2012
PMID: 22359501
Hfq and its constellation of RNA.
Vogel J, Luisi BF., Nat. Rev. Microbiol. 9(8), 2011
PMID: 21760622
Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid.
Ali Azam T, Iwata A, Nishimura A, Ueda S, Ishihama A., J. Bacteriol. 181(20), 1999
PMID: 10515926
Molecular characterization of KatY (antigen 5), a thermoregulated chromosomally encoded catalase-peroxidase of Yersinia pestis.
Garcia E, Nedialkov YA, Elliott J, Motin VL, Brubaker RR., J. Bacteriol. 181(10), 1999
PMID: 10322012
Comparative analysis of the regulation of rovA from the pathogenic yersiniae.
Lawrenz MB, Miller VL., J. Bacteriol. 189(16), 2007
PMID: 17573476
WebLogo: a sequence logo generator.
Crooks GE, Hon G, Chandonia JM, Brenner SE., Genome Res. 14(6), 2004
PMID: 15173120
Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling.
Kim D, Hong JS, Qiu Y, Nagarajan H, Seo JH, Cho BK, Tsai SF, Palsson BO., PLoS Genet. 8(8), 2012
PMID: 22912590
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
Fitting a mixture model by expectation maximization to discover motifs in biopolymers.
Bailey TL, Elkan C., Proc Int Conf Intell Syst Mol Biol 2(), 1994
PMID: 7584402
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
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
The single-nucleotide resolution transcriptome of Pseudomonas aeruginosa grown in body temperature.
Wurtzel O, Yoder-Himes DR, Han K, Dandekar AA, Edelheit S, Greenberg EP, Sorek R, Lory S., PLoS Pathog. 8(9), 2012
PMID: 23028334
RibEx: a web server for locating riboswitches and other conserved bacterial regulatory elements.
Abreu-Goodger C, Merino E., Nucleic Acids Res. 33(Web Server issue), 2005
PMID: 15980564
A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism.
Regulski EE, Moy RH, Weinberg Z, Barrick JE, Yao Z, Ruzzo WL, Breaker RR., Mol. Microbiol. 68(4), 2008
PMID: 18363797
An RNA sensor for intracellular Mg(2+).
Cromie MJ, Shi Y, Latifi T, Groisman EA., Cell 125(1), 2006
PMID: 16615891
A Mg2+-responding RNA that controls the expression of a Mg2+ transporter.
Groisman EA, Cromie MJ, Shi Y, Latifi T., Cold Spring Harb. Symp. Quant. Biol. 71(), 2006
PMID: 17381304
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
Differential expression analysis for sequence count data.
Anders S, Huber W., Genome Biol. 11(10), 2010
PMID: 20979621
Temperature-dependent regulation of Yersinia enterocolitica Class III flagellar genes.
Kapatral V, Olson JW, Pepe JC, Miller VL, Minnich SA., Mol. Microbiol. 19(5), 1996
PMID: 8830263
Temporal global changes in gene expression during temperature transition in Yersinia pestis.
Motin VL, Georgescu AM, Fitch JP, Gu PP, Nelson DO, Mabery SL, Garnham JB, Sokhansanj BA, Ott LL, Coleman MA, Elliott JM, Kegelmeyer LM, Wyrobek AJ, Slezak TR, Brubaker RR, Garcia E., J. Bacteriol. 186(18), 2004
PMID: 15342600
The acetate switch.
Wolfe AJ., Microbiol. Mol. Biol. Rev. 69(1), 2005
PMID: 15755952
Short chain fatty acids in human large intestine, portal, hepatic and venous blood.
Cummings JH, Pomare EW, Branch WJ, Naylor CP, Macfarlane GT., Gut 28(10), 1987
PMID: 3678950
The small RNA chaperone Hfq is required for the virulence of Yersinia pseudotuberculosis.
Schiano CA, Bellows LE, Lathem WW., Infect. Immun. 78(5), 2010
PMID: 20231416
Intrinsic thermal sensing controls proteolysis of Yersinia virulence regulator RovA.
Herbst K, Bujara M, Heroven AK, Opitz W, Weichert M, Zimmermann A, Dersch P., PLoS Pathog. 5(5), 2009
PMID: 19468295
Function and regulation of the transcriptional activator RovA of Yersinia pseudotuberculosis.
Nagel G, Heroven AK, Eitel J, Dersch P., Adv. Exp. Med. Biol. 529(), 2003
PMID: 12756772
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
Sigma E controls biogenesis of the antisense RNA MicA.
Udekwu KI, Wagner EG., Nucleic Acids Res. 35(4), 2007
PMID: 17267407
Conserved small non-coding RNAs that belong to the sigmaE regulon: role in down-regulation of outer membrane proteins.
Johansen J, Rasmussen AA, Overgaard M, Valentin-Hansen P., J. Mol. Biol. 364(1), 2006
PMID: 17007876
The pyruvate-tricarboxylic acid cycle node: a focal point of virulence control in the enteric pathogen Yersinia pseudotuberculosis.
Bucker R, Heroven AK, Becker J, Dersch P, Wittmann C., J. Biol. Chem. 289(43), 2014
PMID: 25164818

AUTHOR UNKNOWN, 2001
The Pseudomonas aeruginosa transcriptome in planktonic cultures and static biofilms using RNA sequencing.
Dotsch A, Eckweiler D, Schniederjans M, Zimmermann A, Jensen V, Scharfe M, Geffers R, Haussler S., PLoS ONE 7(2), 2012
PMID: 22319605

AUTHOR UNKNOWN, 0
Fast gapped-read alignment with Bowtie 2.
Langmead B, Salzberg SL., Nat. Methods 9(4), 2012
PMID: 22388286
The Sequence Alignment/Map format and SAMtools.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup., Bioinformatics 25(16), 2009
PMID: 19505943
Global mapping of transcription start sites and promoter motifs in the symbiotic α-proteobacterium Sinorhizobium meliloti 1021.
Schluter JP, Reinkensmeier J, Barnett MJ, Lang C, Krol E, Giegerich R, Long SR, Becker A., BMC Genomics 14(), 2013
PMID: 23497287
Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions.
Schmidtke C, Findeiss S, Sharma CM, Kuhfuss J, Hoffmann S, Vogel J, Stadler PF, Bonas U., Nucleic Acids Res. 40(5), 2011
PMID: 22080557
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
Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®
Quellen

PMID: 25816203
PubMed | Europe PMC

Suchen in

Google Scholar