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

Josch Pauling, Richard Röttger, Andreas Neuner, Heladia Salgado, Julio Collado-Vides, Prabhav Kalaghatgi, Vasco Azevedo, Andreas Tauch, Alfred Pühler, Jan Baumbach

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

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 40,913 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 http://www.ehecregnet.de.
Original languageEnglish
JournalIntegrative Biology
Volume4
Issue number7
Pages (from-to)728-33
ISSN1757-9694
DOIs
Publication statusPublished - 2012
Externally publishedYes

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Escherichia coli
Bacteria
Genes
Pathogens
Disease Outbreaks
Germany
Virulence
Databases
DNA
Research
Switches

Cite this

Pauling, Josch ; Röttger, Richard ; Neuner, Andreas ; Salgado, Heladia ; Collado-Vides, Julio ; Kalaghatgi, Prabhav ; Azevedo, Vasco ; Tauch, Andreas ; Pühler, Alfred ; Baumbach, Jan. / On the trail of EHEC/EAEC--unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria. In: Integrative Biology. 2012 ; Vol. 4, No. 7. pp. 728-33.
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Pauling, J, Röttger, R, Neuner, A, Salgado, H, Collado-Vides, J, Kalaghatgi, P, Azevedo, V, Tauch, A, Pühler, A & Baumbach, J 2012, 'On the trail of EHEC/EAEC--unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria' Integrative Biology, vol. 4, no. 7, pp. 728-33. https://doi.org/10.1039/c2ib00132b

On the trail of EHEC/EAEC--unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria. / Pauling, Josch; Röttger, Richard; Neuner, Andreas; Salgado, Heladia; Collado-Vides, Julio; Kalaghatgi, Prabhav; Azevedo, Vasco; Tauch, Andreas; Pühler, Alfred; Baumbach, Jan.

In: Integrative Biology, Vol. 4, No. 7, 2012, p. 728-33.

Research output: Contribution to journalJournal articleResearchpeer-review

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T1 - On the trail of EHEC/EAEC--unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria

AU - Pauling, Josch

AU - Röttger, Richard

AU - Neuner, Andreas

AU - Salgado, Heladia

AU - Collado-Vides, Julio

AU - Kalaghatgi, Prabhav

AU - Azevedo, Vasco

AU - Tauch, Andreas

AU - Pühler, Alfred

AU - Baumbach, Jan

PY - 2012

Y1 - 2012

N2 - 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 40,913 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 http://www.ehecregnet.de.

AB - 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 40,913 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 http://www.ehecregnet.de.

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DO - 10.1039/c2ib00132b

M3 - Journal article

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SP - 728

EP - 733

JO - Integrative Biology

JF - Integrative Biology

SN - 1757-9694

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