On the trail of EHEC/EAEC-unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria

Pauling J, Rottger R, Neuner A, Salgado H, Collado-Vides J, Kalaghatgi P, Azevedo V, Tauch A, Pühler A, Baumbach J (2012)
Integrative Biology 4(7): 728-733.

Download
Es wurde kein Volltext hochgeladen. Nur Publikationsnachweis!
Zeitschriftenaufsatz | Veröffentlicht | Englisch
Autor
; ; ; ; ; ; ; ; ;
Abstract / Bemerkung
Pathogenic Escherichia coli, such as Enterohemorrhagic E. coli (EHEC) and Enteroaggregative E. coli (EAEC), are globally widespread bacteria. Some may cause the hemolytic uremic syndrome (HUS). Varying strains cause epidemics all over the world. Recently, we observed an epidemic outbreak of a multi-resistant EHEC strain in Western Europe, mainly in Germany. The Robert Koch Institute reports >4300 infections and >50 deaths (July, 2011). Farmers lost several million EUR since the origin of infection was unclear. Here, we contribute to the currently ongoing research with a computer-aided study of EHEC transcriptional regulatory interactions, a network of genetic switches that control, for instance, pathogenicity, survival and reproduction of bacterial cells. Our strategy is to utilize knowledge of gene regulatory networks from the evolutionary relative E. coli K-12, a harmless strain mainly used for wet lab studies. In order to provide high-potential candidates for human pathogenic E. coli bacteria, such as EHEC, we developed the integrated online database and an analysis platform EhecRegNet. We utilize 3489 known regulations from E. coli K-12 for predictions of yet unknown gene regulatory interactions in 16 human pathogens. For these strains we predict 40913 regulatory interactions. EhecRegNet is based on the identification of evolutionarily conserved regulatory sites within the DNA of the harmless E. coli K-12 and the pathogens. Identifying and characterizing EHEC's genetic control mechanism network on a large scale will allow for a better understanding of its survival and infection strategies. This will support the development of urgently needed new treatments. EhecRegNet is online via.
Erscheinungsjahr
Zeitschriftentitel
Integrative Biology
Band
4
Ausgabe
7
Seite(n)
728-733
ISSN
eISSN
PUB-ID

Zitieren

Pauling J, Rottger R, Neuner A, et al. On the trail of EHEC/EAEC-unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria. Integrative Biology. 2012;4(7):728-733.
Pauling, J., Rottger, R., Neuner, A., Salgado, H., Collado-Vides, J., Kalaghatgi, P., Azevedo, V., et al. (2012). On the trail of EHEC/EAEC-unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria. Integrative Biology, 4(7), 728-733. doi:10.1039/c2ib00132b
Pauling, J., Rottger, R., Neuner, A., Salgado, H., Collado-Vides, J., Kalaghatgi, P., Azevedo, V., Tauch, A., Pühler, A., and Baumbach, J. (2012). On the trail of EHEC/EAEC-unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria. Integrative Biology 4, 728-733.
Pauling, J., et al., 2012. On the trail of EHEC/EAEC-unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria. Integrative Biology, 4(7), p 728-733.
J. Pauling, et al., “On the trail of EHEC/EAEC-unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria”, Integrative Biology, vol. 4, 2012, pp. 728-733.
Pauling, J., Rottger, R., Neuner, A., Salgado, H., Collado-Vides, J., Kalaghatgi, P., Azevedo, V., Tauch, A., Pühler, A., Baumbach, J.: On the trail of EHEC/EAEC-unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria. Integrative Biology. 4, 728-733 (2012).
Pauling, Josch, Rottger, Richard, Neuner, Andreas, Salgado, Heladia, Collado-Vides, Julio, Kalaghatgi, Prabhav, Azevedo, Vasco, Tauch, Andreas, Pühler, Alfred, and Baumbach, Jan. “On the trail of EHEC/EAEC-unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria”. Integrative Biology 4.7 (2012): 728-733.

4 Zitationen in Europe PMC

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
Probiotic Enterococcus faecalis Symbioflor® down regulates virulence genes of EHEC in vitro and decrease pathogenicity in a Caenorhabditis elegans model.
Neuhaus K, Lamparter MC, Zölch B, Landstorfer R, Simon S, Spanier B, Ehrmann MA, Vogel RF., Arch Microbiol 199(2), 2017
PMID: 27655246
Improving Gene Regulatory Network Inference by Incorporating Rates of Transcriptional Changes.
Desai JS, Sartor RC, Lawas LM, Jagadish SVK, Doherty CJ., Sci Rep 7(1), 2017
PMID: 29222512

21 References

Daten bereitgestellt von Europe PubMed Central.

The continuing evolution of a bacterial pathogen.
Kaper JB, Karmali MA., Proc. Natl. Acad. Sci. U.S.A. 105(12), 2008
PMID: 18353979

Karch, Semin. Thromb. Hemostasis 27(3), 2001
Enteropathogenic and enterohemorrhagic Escherichia coli virulence gene regulation.
Mellies JL, Barron AM, Carmona AM., Infect. Immun. 75(9), 2007
PMID: 17576759
Genome sequence analyses of two isolates from the recent Escherichia coli outbreak in Germany reveal the emergence of a new pathotype: Entero-Aggregative-Haemorrhagic Escherichia coli (EAHEC).
Brzuszkiewicz E, Thurmer A, Schuldes J, Leimbach A, Liesegang H, Meyer FD, Boelter J, Petersen H, Gottschalk G, Daniel R., Arch. Microbiol. 193(12), 2011
PMID: 21713444
GenBank.
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL., Nucleic Acids Res. 36(Database issue), 2007
PMID: 18073190
MicrobesOnline: an integrated portal for comparative and functional genomics.
Dehal PS, Joachimiak MP, Price MN, Bates JT, Baumohl JK, Chivian D, Friedland GD, Huang KH, Keller K, Novichkov PS, Dubchak IL, Alm EJ, Arkin AP., Nucleic Acids Res. 38(Database issue), 2009
PMID: 19906701
OperonDB: a comprehensive database of predicted operons in microbial genomes.
Pertea M, Ayanbule K, Smedinghoff M, Salzberg SL., Nucleic Acids Res. 37(Database issue), 2008
PMID: 18948284
RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units).
Gama-Castro S, Salgado H, Peralta-Gil M, Santos-Zavaleta A, Muniz-Rascado L, Solano-Lira H, Jimenez-Jacinto V, Weiss V, Garcia-Sotelo JS, Lopez-Fuentes A, Porron-Sotelo L, Alquicira-Hernandez S, Medina-Rivera A, Martinez-Flores I, Alquicira-Hernandez K, Martinez-Adame R, Bonavides-Martinez C, Miranda-Rios J, Huerta AM, Mendoza-Vargas A, Collado-Torres L, Taboada B, Vega-Alvarado L, Olvera M, Olvera L, Grande R, Morett E, Collado-Vides J., Nucleic Acids Res. 39(Database issue), 2010
PMID: 21051347

Wittkop, J. Integr. Bioinf. 7(3), 2010
BLAST+: architecture and applications.
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL., BMC Bioinformatics 10(), 2009
PMID: 20003500
Partitioning biological data with transitivity clustering.
Wittkop T, Emig D, Lange S, Rahmann S, Albrecht M, Morris JH, Bocker S, Stoye J, Baumbach J., Nat. Methods 7(6), 2010
PMID: 20508635
Comprehensive cluster analysis with Transitivity Clustering.
Wittkop T, Emig D, Truss A, Albrecht M, Bocker S, Baumbach J., Nat Protoc 6(3), 2011
PMID: 21372810

Wittkop, Interact. Math. 7(), 2011
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
CoryneRegNet 6.0--Updated database content, new analysis methods and novel features focusing on community demands.
Pauling J, Rottger R, Tauch A, Azevedo V, Baumbach J., Nucleic Acids Res. 40(Database issue), 2011
PMID: 22080556
Linking Cytoscape and the corynebacterial reference database CoryneRegNet.
Baumbach J, Apeltsin L., BMC Genomics 9(), 2008
PMID: 18426593

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 22318347
PubMed | Europe PMC

Suchen in

Google Scholar