Dandekar T. Salmonella Project
Metabolism of intracellular Salmonella enterica: One lifestyle in intra-cellular infections
The intracellular lifestyle of Salmonella enterica relies on the adaptation to nutritional conditions within the Salmonella-containing vacuole (SCV) in host cells. Based on previous results, metabolic requirements for Salmonella in the SCV shall be characterized further. This includes (i) prediction of intracellular phenotypes of mutant strains based on metabolic modeling and experimental tests, (ii) isotopologue profiling using 13C compounds in intracellular Salmonella, and (iii) complementation of metabolic defects for attenuated mutant strains. The collaborative work between the Dandekar and Hensel groups proposed for the second funding period should lead to a comprehensive understanding of the metabolic requirements of the intracellular lifestyle of Salmonella. Further analyses of intracellular phenotypes will be based on improved metabolic predictions. Vice versa, based on analyses of mutant phenotypes and isotopologue analyses, iterative refinement of metabolic flux models will be achieved. Our vision is a comprehensive understanding of the adaptation of Salmonella to its lifestyle in a membrane-bound compartment in mammalian cells. Towards an integrated model and profiting from SPP1316, we will do comparisons of the Salmonella lifestyle with other pathogens and their metabolic requirements during infection such as cytoplasmic lifestyle found in Listeria or within a membrane compartment as for Legionella.
Mitarbeiter
Prof. Thomas Dandekar
Dr. Muhammed Naseem, Dr. Ahmed Zeeshan (Z-Projekt)
Astrid Fieselmann (Salmonella Projekt)
Dr. Tobias Müller
Dr. Beate Krüger
Stefan Obermeyer
Bioinformatik, Biozentrum,
Universitaet Wuerzburg
Am Hubland, D-97074
Tel.: +49 (0)931 31-84551,
Fax: +49 (0)931 31-84552
Email: dandekar@biozentrum.uni-wuerzburg.de
Infection-related publications
Dandekar,T. and Xiao,K. (2010) New bioinformaic strategies against apicomplexan parasites pp. 21-33. In: Katja Becker (Ed.), Apicomplexan Parasites: Molecular Approaches toward Targeted Drug Development. Wiley-VCH, Weinheim.
Eisenreich, W., Dandekar, T., Heesemann,J., and Goebel,W. (2010). Carbon metabolism of intracellular bacterial pathogens and possible links to virulence. Nature Reviews Microbiology 8, 401-412.
Vainshtein, Y.*, Sanchez,M., Brazma,A., Hentze,M.W., Dandekar T* and Martina U. Muckenthaler* (2010) The IronChip Evaluation Package: A package of Perl modules for robust analysis of custom microarrays. BMC Bioinformatics 11:112.
Beisser D, Klau GW, Dandekar T, Mueller T, Dittrich M. BioNet: an R-Package for the Functional Analysis of Biological Networks. Bioinformatics 2010 Apr 15;26(8):1129-30.
Friedrich T, Rahmann S, Weigel W, Rabsch W, Fruth A, Ron E, Gunzer F, Dandekar T, Hacker J, Müller T, Dobrindt U. High-throughput microarray technology in diagnostics of enterobacteria based on genome-wide probe selection and regression analysis. BMC Genomics. 2010 Oct 21;11:591. PubMed PMID: 20964857;
Schauer K, Geginat G, Liang C, Goebel W, Dandekar T, Fuchs TM. Deciphering the intracellular metabolism of Listeria monocytogenes by mutant screening and modelling. BMC Genomics. 2010 Oct 18;11:573. PubMed PMID: 20955543; PubMed Central PMCID: PMC3091722.
Fuchs S, Mehlan H, Kusch H, Teumer A, Zühlke D, Berth M, Wolf C, Dandekar T, Hecker M, Engelmann S, Bernhardt J. Protecs, a comprehensive and powerful storage and analysis system for OMICS data, applied for profiling the anaerobiosis response of Staphylococcus aureus COL. Proteomics. 2010 Aug;10(16):2982-3000. PubMed PMID: 20662099.
Siegl A, Kamke J, Hochmuth T, Piel J, Richter M, Liang C, Dandekar T, Hentschel U. Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges. ISME J. 2011 Jan;5(1):61-70. Epub 2010 Jul 8. PubMed PMID: 20613790.
Ratzka C, Liang C, Dandekar T, Gross R, Feldhaar H. Immune response of the ant Camponotus floridanus against pathogens and its obligate mutualistic endosymbiont. Insect Biochem Mol Biol. 2011 Aug;41(8):529-36. doi: 10.1016/j.ibmb.2011.03.002.
Cecil A, Rikanovic C, Ohlsen K, Liang C, Bernhardt J, Oelschlaeger TA, Gulder T, Bringmann G, Holzgrabe U, Unger M, Dandekar T. Modeling antibiotic and cytotoxic effects of the dimeric isoquinoline IQ-143 on metabolism and its regulation in Staphylococcus aureus, Staphylococcus epidermidis and human cells. Genome Biol. 2011 Mar 21;12(3):R24. [Epub ahead of print] PubMed PMID: 21418624.
Liebeke M, Dörries K, Zühlke D, Bernhardt J, Fuchs S, Pané-Farré J, Engelmann S, Völker U, Bode R, Dandekar T, Lindequist U, Hecker M, Lalk M. A metabolomics and proteomics study of the adaptation of Staphylococcus aureus to glucose starvation. Mol Biosyst. 2011 Apr 1;7(4):1241-53. Epub 2011 Feb 16. PubMed PMID: 21327190.
Agarwal S, Kern S, Halbert J, Przyborski JM, Baumeister S, Dandekar T, Doerig C, Pradel G. Two nucleus-localized CDK-like kinases with crucial roles for malaria parasite erythrocytic replication are involved in phosphorylation of splicing factor. J Cell Biochem. 2011 Feb 10. doi: 10.1002/jcb.23034. [Epub ahead of print] PubMed PMID: 21312235.
Liang C, Liebeke M, Schwarz R, Zühlke D, Fuchs S, Menschner L, Engelmann S, Wolz C, Jaglitz S, Bernhardt J, Hecker M, Lalk M, Dandekar T. Staphylococcus aureus physiological growth limitations: Insights from flux calculations built on proteomics and external metabolite data. Proteomics. 2011 May;11(10):1915-35.
Zeeshan A, Dandekar T, Majeed S (2012) Semantic Web; Ontology Specific Languages for Web Application Development. International Journal of Web applications 4 (1), pp. 42-50.
Naseem M, Philippi N, Hussain A, Wangorsch G, Ahmed N, and Dandekar T (2012) Integrated Systems View on Networking by Hormones in Arabidopsis Immunity Reveals Multiple Crosstalk for Cytokinin. Plant Cell 24, 1793-814.
Krueger B, Friedrich T, Förster F, Bernhardt J, Gross R, Dandekar T. (2012) Different evolutionary modifications as a guide to rewire two-component systems. Bioinform Biol Insights. 6, 97-128.
Beisser D, Brunkhorst S, Dandekar T, Klau GW, Dittrich MT, Müller T. Robustness and accuracy of functional modules in integrated network analysis. Bioinformatics. 2012 May 11. [Epub ahead of print] PubMed PMID: 22581175.
Dandekar T, Astrid F, Jasmin P, Hensel M. Salmonella enterica: a surprisingly well-adapted intracellular lifestyle. Front Microbiol. 2012;3:164. Epub 2012 May 3. PubMed PMID: 22563326; PubMed Central PMCID: PMC3342586.
Fuchs TM, Eisenreich W, Kern T, Dandekar T. Toward a Systemic Understanding of Listeria monocytogenes Metabolism during Infection. Front Microbiol. 2012;3:23. Epub 2012 Feb 3. PubMed PMID: 22347216; PubMed Central PMCID: PMC3271275.
Ratzka C, Förster F, Liang C, Kupper M, Dandekar T, Feldhaar H, Gross R. (2012) Molecular characterization of antimicrobial peptide genes of the carpenter ant Camponotus floridanus. PLoS One 7(8):e43036.
Beisser D, Grohme MA, Kopka J, Frohme M, Schill RO, Hengherr S, Dandekar T, Klau GW, Dittrich M, Müller T. (2012) Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum. BMC Syst Biol. 6(1):72.
Zirkel J, Cecil A, Schäfer F, Rahlfs S, Ouedraogo A, Xiao K, Sawadogo S, Coulibaly B, Becker K, Dandekar T. Analyzing Thiol-Dependent Redox Networks in the Presence of Methylene Blue and Other Antimalarial Agents with RT-PCR-Supported in silico Modeling. Bioinform Biol Insights. 2012;6:287-302. doi: 10.4137/BBI.S10193.
Zeeshan A., Saman M., Dandekar T. (2012) Unified Modeling and HCI Mockup Designing towards MIDA. International Journal of Emerging Sciences, Vol. 2, No. 3, Pages: 361-382.
Zeeshan A., Saman M., Dandekar T. (2012) Formal UML Modelling of Isotopo, Bioinformatical Software for Mass Isotopomers Distribution Analysis. Software Engineering Journal, SAP Publishing, 2(4): 147-159.
Dandekar T, Fieselmann A, Majeed S, Ahmed Z. Software applications toward quantitative metabolic flux analysis and modeling. Brief Bioinform. 2012 Nov 9. [Epub ahead of print] PMID: 23142828.
Naseem M and Dandekar T. The role of auxin-cytokinin antagonism in plant-pathogen interactions. PLoS Pathog. 2012 Nov;8(11):e1003026.
Krüger B, Liang C, Prell F, Fieselmann A, Moya A, Schuster S, Voelker U, Dandekar T (2012) Metabolic Adaptation and Protein Complexes in Prokaryotes Metabolites 2(4), 940-958; doi:10.3390/metabo2040940
