From Corynebacterium glutamicum to Mycobacterium tuberculosis-towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet

Krawczyk J, Kohl TA, Goesmann A, Kalinowski J, Baumbach J (2009)
NUCLEIC ACIDS RESEARCH 37(14): e97.

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Abstract / Bemerkung
Year by year, approximately two million people die from tuberculosis, a disease caused by the bacterium Mycobacterium tuberculosis. There is a tremendous need for new anti-tuberculosis therapies (antituberculotica) and drugs to cope with the spread of tuberculosis. Despite many efforts to obtain a better understanding of M. tuberculosis' pathogenicity and its survival strategy in humans, many questions are still unresolved. Among other cellular processes in bacteria, pathogenicity is controlled by transcriptional regulation. Thus, various studies on M. tuberculosis concentrate on the analysis of transcriptional regulation in order to gain new insights on pathogenicity and other essential processes ensuring mycobacterial survival. We designed a bioinformatics pipeline for the reliable transfer of gene regulations between taxonomically closely related organisms that incorporates (i) a prediction of orthologous genes and (ii) the prediction of transcription factor binding sites. In total, 460 regulatory interactions were identified for M. tuberculosis using our comparative approach. Based on that, we designed a publicly available platform that aims to data integration, analysis, visualization and finally the reconstruction of mycobacterial transcriptional gene regulatory networks: MycoRegNet. It is a comprehensive database system and analysis platform that offers several methods for data exploration and the generation of novel hypotheses. MycoRegNet is publicly available at http://mycoregnet.cebitec.uni-bielefeld.de.
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NUCLEIC ACIDS RESEARCH
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37
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e97
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Krawczyk J, Kohl TA, Goesmann A, Kalinowski J, Baumbach J. From Corynebacterium glutamicum to Mycobacterium tuberculosis-towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet. NUCLEIC ACIDS RESEARCH. 2009;37(14):e97.
Krawczyk, J., Kohl, T. A., Goesmann, A., Kalinowski, J., & Baumbach, J. (2009). From Corynebacterium glutamicum to Mycobacterium tuberculosis-towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet. NUCLEIC ACIDS RESEARCH, 37(14), e97. doi:10.1093/nar/gkp453
Krawczyk, J., Kohl, T. A., Goesmann, A., Kalinowski, J., and Baumbach, J. (2009). From Corynebacterium glutamicum to Mycobacterium tuberculosis-towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet. NUCLEIC ACIDS RESEARCH 37, e97.
Krawczyk, J., et al., 2009. From Corynebacterium glutamicum to Mycobacterium tuberculosis-towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet. NUCLEIC ACIDS RESEARCH, 37(14), p e97.
J. Krawczyk, et al., “From Corynebacterium glutamicum to Mycobacterium tuberculosis-towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet”, NUCLEIC ACIDS RESEARCH, vol. 37, 2009, pp. e97.
Krawczyk, J., Kohl, T.A., Goesmann, A., Kalinowski, J., Baumbach, J.: From Corynebacterium glutamicum to Mycobacterium tuberculosis-towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet. NUCLEIC ACIDS RESEARCH. 37, e97 (2009).
Krawczyk, Justina, Kohl, Thomas A., Goesmann, Alexander, Kalinowski, Jörn, and Baumbach, Jan. “From Corynebacterium glutamicum to Mycobacterium tuberculosis-towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet”. NUCLEIC ACIDS RESEARCH 37.14 (2009): e97.

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Daten bereitgestellt von Europe PubMed Central.

PRODORIC2: the bacterial gene regulation database in 2018.
Eckweiler D, Dudek CA, Hartlich J, Brötje D, Jahn D., Nucleic Acids Res 46(d1), 2018
PMID: 29136200
Comparing Galactan Biosynthesis in Mycobacterium tuberculosis and Corynebacterium diphtheriae.
Wesener DA, Levengood MR, Kiessling LL., J Biol Chem 292(7), 2017
PMID: 28039359
Role of intragenic binding of cAMP responsive protein (CRP) in regulation of the succinate dehydrogenase genes Rv0249c-Rv0247c in TB complex mycobacteria.
Knapp GS, Lyubetskaya A, Peterson MW, Gomes AL, Ma Z, Galagan JE, McDonough KA., Nucleic Acids Res 43(11), 2015
PMID: 25940627
CMRegNet-An interspecies reference database for corynebacterial and mycobacterial regulatory networks.
Abreu VA, Almeida S, Tiwari S, Hassan SS, Mariano D, Silva A, Baumbach J, Azevedo V, Röttger R., BMC Genomics 16(), 2015
PMID: 26062809
Genomic mapping of cAMP receptor protein (CRP Mt) in Mycobacterium tuberculosis: relation to transcriptional start sites and the role of CRPMt as a transcription factor.
Kahramanoglou C, Cortes T, Matange N, Hunt DM, Visweswariah SS, Young DB, Buxton RS., Nucleic Acids Res 42(13), 2014
PMID: 24957601
Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models.
Faria JP, Overbeek R, Xia F, Rocha M, Rocha I, Henry CS., Brief Bioinform 15(4), 2014
PMID: 23422247
In silico analyses for the discovery of tuberculosis drug targets.
Chung BK, Dick T, Lee DY., J Antimicrob Chemother 68(12), 2013
PMID: 23838951
Immunological evaluation of a novel Mycobacterium tuberculosis antigen, Rv3117, absent in Mycobacterium bovis BCG.
Zhao J, Sun Z, Pei H, Ye J, Chen C, Samten B, Zhang S, Guo X., Mol Med Rep 8(5), 2013
PMID: 24045507
CoryneRegNet 6.0--Updated database content, new analysis methods and novel features focusing on community demands.
Pauling J, Röttger R, Tauch A, Azevedo V, Baumbach J., Nucleic Acids Res 40(database issue), 2012
PMID: 22080556
On the trail of EHEC/EAEC--unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria.
Pauling J, Röttger R, Neuner A, Salgado H, Collado-Vides J, Kalaghatgi P, Azevedo V, Tauch A, Pühler A, Baumbach J., Integr Biol (Camb) 4(7), 2012
PMID: 22318347
Efficient key pathway mining: combining networks and OMICS data.
Alcaraz N, Friedrich T, Kötzing T, Krohmer A, Müller J, Pauling J, Baumbach J., Integr Biol (Camb) 4(7), 2012
PMID: 22353882
Cyclic AMP signalling in mycobacteria: redirecting the conversation with a common currency.
Bai G, Knapp GS, McDonough KA., Cell Microbiol 13(3), 2011
PMID: 21199259
Mutations in the regulatory network underlie the recent clonal expansion of a dominant subclone of the Mycobacterium tuberculosis Beijing genotype.
Schürch AC, Kremer K, Warren RM, Hung NV, Zhao Y, Wan K, Boeree MJ, Siezen RJ, Smith NH, van Soolingen D., Infect Genet Evol 11(3), 2011
PMID: 21277396
Comparative genomics of NAD(P) biosynthesis and novel antibiotic drug targets.
Bi J, Wang H, Xie J., J Cell Physiol 226(2), 2011
PMID: 20857400
Diversity of metabolic shift in response to oxygen deprivation in Corynebacterium glutamicum and its close relatives.
Yamamoto S, Sakai M, Inui M, Yukawa H., Appl Microbiol Biotechnol 90(3), 2011
PMID: 21327408
Computational tools to study and understand the intricate biology of mycobacteria.
Sharma D, Surolia A., Tuberculosis (Edinb) 91(3), 2011
PMID: 21398182
The regulation of sulfur metabolism in Mycobacterium tuberculosis.
Hatzios SK, Bertozzi CR., PLoS Pathog 7(7), 2011
PMID: 21811406
RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes.
Novichkov PS, Laikova ON, Novichkova ES, Gelfand MS, Arkin AP, Dubchak I, Rodionov DA., Nucleic Acids Res 38(database issue), 2010
PMID: 19884135
Systems biology approaches to understanding mycobacterial survival mechanisms.
Boshoff HI, Lun DS., Drug Discov Today Dis Mech 7(1), 2010
PMID: 21072257
Structural and functional analysis of Rv0554 from Mycobacterium tuberculosis: testing a putative role in menaquinone biosynthesis.
Johnston JM, Jiang M, Guo Z, Baker EN., Acta Crystallogr D Biol Crystallogr 66(pt 8), 2010
PMID: 20693690
Tuberculosis: global approaches to a global disease.
Kirschner DE, Young D, Flynn JL., Curr Opin Biotechnol 21(4), 2010
PMID: 20637596
Role of the transcriptional regulator RamB (Rv0465c) in the control of the glyoxylate cycle in Mycobacterium tuberculosis.
Micklinghoff JC, Breitinger KJ, Schmidt M, Geffers R, Eikmanns BJ, Bange FC., J Bacteriol 191(23), 2009
PMID: 19767422

69 References

Daten bereitgestellt von Europe PubMed Central.

Tuberculosis.
Frieden TR, Sterling TR, Munsiff SS, Watt CJ, Dye C., Lancet 362(9387), 2003
PMID: 13678977
XDR tuberculosis--implications for global public health.
Raviglione MC, Smith IM., N. Engl. J. Med. 356(7), 2007
PMID: 17301295
Exploring drug-induced alterations in gene expression in Mycobacterium tuberculosis by microarray hybridization.
Wilson M, DeRisi J, Kristensen HH, Imboden P, Rane S, Brown PO, Schoolnik GK., Proc. Natl. Acad. Sci. U.S.A. 96(22), 1999
PMID: 10536008
XDR-TB in South Africa: no time for denial or complacency.
Singh JA, Upshur R, Padayatchi N., PLoS Med. 4(1), 2007
PMID: 17253901
Rv3133c/dosR is a transcription factor that mediates the hypoxic response of Mycobacterium tuberculosis.
Park HD, Guinn KM, Harrell MI, Liao R, Voskuil MI, Tompa M, Schoolnik GK, Sherman DR., Mol. Microbiol. 48(3), 2003
PMID: 12694625
Overexpression of heat-shock proteins reduces survival of Mycobacterium tuberculosis in the chronic phase of infection.
Stewart GR, Snewin VA, Walzl G, Hussell T, Tormay P, O'Gaora P, Goyal M, Betts J, Brown IN, Young DB., Nat. Med. 7(6), 2001
PMID: 11385512
RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation.
Gama-Castro S, Jimenez-Jacinto V, Peralta-Gil M, Santos-Zavaleta A, Penaloza-Spinola MI, Contreras-Moreira B, Segura-Salazar J, Muniz-Rascado L, Martinez-Flores I, Salgado H, Bonavides-Martinez C, Abreu-Goodger C, Rodriguez-Penagos C, Miranda-Rios J, Morett E, Merino E, Huerta AM, Trevino-Quintanilla L, Collado-Vides J., Nucleic Acids Res. 36(Database issue), 2007
PMID: 18158297
MtbRegList, a database dedicated to the analysis of transcriptional regulation in Mycobacterium tuberculosis.
Jacques PE, Gervais AL, Cantin M, Lucier JF, Dallaire G, Drouin G, Gaudreau L, Goulet J, Brzezinski R., Bioinformatics 21(10), 2005
PMID: 15722376
TB database: an integrated platform for tuberculosis research.
Reddy TB, Riley R, Wymore F, Montgomery P, DeCaprio D, Engels R, Gellesch M, Hubble J, Jen D, Jin H, Koehrsen M, Larson L, Mao M, Nitzberg M, Sisk P, Stolte C, Weiner B, White J, Zachariah ZK, Sherlock G, Galagan JE, Ball CA, Schoolnik GK., Nucleic Acids Res. 37(Database issue), 2008
PMID: 18835847
Evolution of transcription factors and the gene regulatory network in Escherichia coli.
Madan Babu M, Teichmann SA., Nucleic Acids Res. 31(4), 2003
PMID: 12582243
Structure and evolution of transcriptional regulatory networks.
Babu MM, Luscombe NM, Aravind L, Gerstein M, Teichmann SA., Curr. Opin. Struct. Biol. 14(3), 2004
PMID: 15193307
Evolutionary dynamics of prokaryotic transcriptional regulatory networks.
Madan Babu M, Teichmann SA, Aravind L., J. Mol. Biol. 358(2), 2006
PMID: 16530225
Proposal for a new hierarchic classification system, Actionbacteria classis nov
Stackebrandt E, Rainey FA, Ward-Rainey NL., 1997
Structure and synthesis of the cell wall
Eggeling L, Besra GS, Alderwick L., 2008
A polyketide synthase catalyzes the last condensation step of mycolic acid biosynthesis in mycobacteria and related organisms.
Portevin D, De Sousa-D'Auria C, Houssin C, Grimaldi C, Chami M, Daffe M, Guilhot C., Proc. Natl. Acad. Sci. U.S.A. 101(1), 2003
PMID: 14695899
The transcriptional regulatory network of the amino acid producer Corynebacterium glutamicum.
Brinkrolf K, Brune I, Tauch A., J. Biotechnol. 129(2), 2006
PMID: 17227685
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
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
Regulation of the expression of whiB1 in Mycobacterium tuberculosis: role of cAMP receptor protein.
Agarwal N, Raghunand TR, Bishai WR., Microbiology (Reading, Engl.) 152(Pt 9), 2006
PMID: 16946269
The Mycobacterium tuberculosis ECF sigma factor sigmaE: role in global gene expression and survival in macrophages.
Manganelli R, Voskuil MI, Schoolnik GK, Smith I., Mol. Microbiol. 41(2), 2001
PMID: 11489128
Role of the extracytoplasmic-function sigma factor sigma(H) in Mycobacterium tuberculosis global gene expression.
Manganelli R, Voskuil MI, Schoolnik GK, Dubnau E, Gomez M, Smith I., Mol. Microbiol. 45(2), 2002
PMID: 12123450
Dissection of the heat-shock response in Mycobacterium tuberculosis using mutants and microarrays.
Stewart GR, Wernisch L, Stabler R, Mangan JA, Hinds J, Laing KG, Young DB, Butcher PD., Microbiology (Reading, Engl.) 148(Pt 10), 2002
PMID: 12368446
The senX3-regX3 two-component regulatory system of Mycobacterium tuberculosis is required for virulence.
Parish T, Smith DA, Roberts G, Betts J, Stoker NG., Microbiology (Reading, Engl.) 149(Pt 6), 2003
PMID: 12777483
The Mycobacterium tuberculosis dosRS two-component system is induced by multiple stresses.
Kendall SL, Movahedzadeh F, Rison SC, Wernisch L, Parish T, Duncan K, Betts JC, Stoker NG., Tuberculosis (Edinb) 84(3-4), 2004
PMID: 15207494
A highly conserved transcriptional repressor controls a large regulon involved in lipid degradation in Mycobacterium smegmatis and Mycobacterium tuberculosis.
Kendall SL, Withers M, Soffair CN, Moreland NJ, Gurcha S, Sidders B, Frita R, Ten Bokum A, Besra GS, Lott JS, Stoker NG., Mol. Microbiol. 65(3), 2007
PMID: 17635188
A family of acr-coregulated Mycobacterium tuberculosis genes shares a common DNA motif and requires Rv3133c (dosR or devR) for expression.
Florczyk MA, McCue LA, Purkayastha A, Currenti E, Wolin MJ, McDonough KA., Infect. Immun. 71(9), 2003
PMID: 12933881
GenBank.
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW., Nucleic Acids Res. 37(Database issue), 2008
PMID: 18940867
The MicrobesOnline Web site for comparative genomics.
Alm EJ, Huang KH, Price MN, Koche RP, Keller K, Dubchak IL, Arkin AP., Genome Res. 15(7), 2005
PMID: 15998914
Unraveling the web services web: an introduction to SOAP, WSDL, and UDDI
Curbera F, Duftler M, Khalaf R, Nagy W, Mukhi N, Weerawarana S., 2002
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
EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data.
Dondrup M, Albaum SP, Griebel T, Henckel K, Junemann S, Kahlke T, Kleindt CK, Kuster H, Linke B, Mertens D, Mittard-Runte V, Neuweger H, Runte KJ, Tauch A, Tille F, Puhler A, Goesmann A., BMC Bioinformatics 10(), 2009
PMID: 19200358
From genomics to chemical genomics: new developments in KEGG.
Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M., Nucleic Acids Res. 34(Database issue), 2006
PMID: 16381885
The COG database: an updated version includes eukaryotes.
Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA., BMC Bioinformatics 4(), 2003
PMID: 12969510
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G., Nat. Genet. 25(1), 2000
PMID: 10802651
CoryneRegNet 2: an integrative bioinformatics approach for reconstruction and comparison of transcriptional regulatory networks in prokaryotes
Baumbach J, Brinkrolf K, Wittkop T, Tauch A, Rahmann S., 2006
SOAP-based services provided by the European Bioinformatics Institute.
Pillai S, Silventoinen V, Kallio K, Senger M, Sobhany S, Tate J, Velankar S, Golovin A, Henrick K, Rice P, Stoehr P, Lopez R., Nucleic Acids Res. 33(Web Server issue), 2005
PMID: 15980463
BRENDA, AMENDA and FRENDA: the enzyme information system in 2007.
Barthelmes J, Ebeling C, Chang A, Schomburg I, Schomburg D., Nucleic Acids Res. 35(Database issue), 2007
PMID: 17202167
Novel biochemical properties of a CRP/FNR family transcription factor from Mycobacterium tuberculosis.
Akhter Y, Tundup S, Hasnain SE., Int. J. Med. Microbiol. 297(6), 2007
PMID: 17702648
The mechanisms of carbon catabolite repression in bacteria.
Deutscher J., Curr. Opin. Microbiol. 11(2), 2008
PMID: 18359269
Structural and biochemical analysis of the Rv0805 cyclic nucleotide phosphodiesterase from Mycobacterium tuberculosis.
Shenoy AR, Capuder M, Draskovic P, Lamba D, Visweswariah SS, Podobnik M., J. Mol. Biol. 365(1), 2006
PMID: 17059828
New messages from old messengers: cAMP and mycobacteria.
Shenoy AR, Visweswariah SS., Trends Microbiol. 14(12), 2006
PMID: 17055275
Mycobacterial adenylyl cyclases: biochemical diversity and structural plasticity.
Shenoy AR, Visweswariah SS., FEBS Lett. 580(14), 2006
PMID: 16730005
Expression of Corynebacterium glutamicum glycolytic genes varies with carbon source and growth phase.
Han SO, Inui M, Yukawa H., Microbiology (Reading, Engl.) 153(Pt 7), 2007
PMID: 17600063
Characterization and use of catabolite-repressed promoters from gluconate genes in Corynebacterium glutamicum.
Letek M, Valbuena N, Ramos A, Ordonez E, Gil JA, Mateos LM., J. Bacteriol. 188(2), 2006
PMID: 16385030
Genome scale portrait of cAMP-receptor protein (CRP) regulons in mycobacteria points to their role in pathogenesis.
Akhter Y, Yellaboina S, Farhana A, Ranjan A, Ahmed N, Hasnain SE., Gene 407(1-2), 2007
PMID: 18022770
WebLogo: a sequence logo generator.
Crooks GE, Hon G, Chandonia JM, Brenner SE., Genome Res. 14(6), 2004
PMID: 15173120
Macro-array and bioinformatic analyses reveal mycobacterial 'core' genes, variation in the ESAT-6 gene family and new phylogenetic markers for the Mycobacterium tuberculosis complex.
Marmiesse M, Brodin P, Buchrieser C, Gutierrez C, Simoes N, Vincent V, Glaser P, Cole ST, Brosch R., Microbiology (Reading, Engl.) 150(Pt 2), 2004
PMID: 14766927
Genes required for mycobacterial growth defined by high density mutagenesis.
Sassetti CM, Boyd DH, Rubin EJ., Mol. Microbiol. 48(1), 2003
PMID: 12657046
A postgenomic method for predicting essential genes at subsaturation levels of mutagenesis: application to Mycobacterium tuberculosis.
Lamichhane G, Zignol M, Blades NJ, Geiman DE, Dougherty A, Grosset J, Broman KW, Bishai WR., Proc. Natl. Acad. Sci. U.S.A. 100(12), 2003
PMID: 12775759
Genome-wide requirements for Mycobacterium tuberculosis adaptation and survival in macrophages.
Rengarajan J, Bloom BR, Rubin EJ., Proc. Natl. Acad. Sci. U.S.A. 102(23), 2005
PMID: 15928073
Characterization of a Mycobacterium tuberculosis H37Rv transposon library reveals insertions in 351 ORFs and mutants with altered virulence.
McAdam RA, Quan S, Smith DA, Bardarov S, Betts JC, Cook FC, Hooker EU, Lewis AP, Woollard P, Everett MJ, Lukey PT, Bancroft GJ, Jacobs WR Jr, Duncan K., Microbiology (Reading, Engl.) 148(Pt 10), 2002
PMID: 12368431
Persistence of Mycobacterium tuberculosis in macrophages and mice requires the glyoxylate shunt enzyme isocitrate lyase.
McKinney JD, Honer zu Bentrup K, Munoz-Elias EJ, Miczak A, Chen B, Chan WT, Swenson D, Sacchettini JC, Jacobs WR Jr, Russell DG., Nature 406(6797), 2000
PMID: 10963599

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