title: In Silico Knockout Studies of Xenophagic Capturing of Salmonella.
abstract: The degradation of cytosol-invading pathogens by autophagy, a process known as xenophagy, is an important mechanism of the innate immune system. Inside the host, Salmonella Typhimurium invades epithelial cells and resides within a specialized intracellular compartment, the Salmonella-containing vacuole. A fraction of these bacteria does not persist inside the vacuole and enters the host cytosol. Salmonella Typhimurium that invades the host cytosol becomes a target of the autophagy machinery for degradation. The xenophagy pathway has recently been discovered, and the exact molecular processes are not entirely characterized. Complete kinetic data for each molecular process is not available, so far. We developed a mathematical model of the xenophagy pathway to investigate this key defense mechanism. In this paper, we present a Petri net model of Salmonella xenophagy in epithelial cells. The model is based on functional information derived from literature data. It comprises the molecular mechanism of galectin-8-dependent and ubiquitin-dependent autophagy, including regulatory processes, like nutrient-dependent regulation of autophagy and TBK1-dependent activation of the autophagy receptor, OPTN. To model the activation of TBK1, we proposed a new mechanism of TBK1 activation, suggesting a spatial and temporal regulation of this process. Using standard Petri net analysis techniques, we found basic functional modules, which describe different pathways of the autophagic capture of Salmonella and reflect the basic dynamics of the system. To verify the model, we performed in silico knockout experiments. We introduced a new concept of knockout analysis to systematically compute and visualize the results, using an in silico knockout matrix. The results of the in silico knockout analyses were consistent with published experimental results and provide a basis for future investigations of the Salmonella xenophagy pathway.
authors.affiliation: Molecular Bioinformatics, Institute of Computer Science, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Scheidel
authors.affiliation: Molecular Bioinformatics, Institute of Computer Science, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany.
authors.forename: Leonie
authors.initials: L
authors.lastname: Amstein
authors.affiliation: Molecular Bioinformatics, Institute of Computer Science, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany.
authors.forename: Jörg
authors.initials: J
authors.lastname: Ackermann
authors.affiliation: Institute of Biochemistry II, Johann Wolfgang Goethe-University Hospital Frankfurt am Main, Frankfurt am Main, Germany.|Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany.
authors.forename: Ivan
authors.initials: I
authors.lastname: Dikic
authors.affiliation: Molecular Bioinformatics, Institute of Computer Science, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany.
authors.forename: Ina
authors.initials: I
authors.lastname: Koch
mesh_terms: D000818:Animals; D001343:Autophagy / Q000502:physiology*; D003198:Computer Simulation; D003600:Cytosol; D037161:Galectins / Q000378:metabolism; D007413:Intestinal Mucosa / Q000166:cytology / Q000382:microbiology; D007421:Intestine, Small / Q000166:cytology; D008322:Mammals; D008954:Models, Biological; D017346:Protein Serine-Threonine Kinases / Q000378:metabolism; D012486:Salmonella typhimurium / Q000166:cytology / Q000472:pathogenicity / Q000502:physiology; D025801:Ubiquitin / Q000378:metabolism
chemical_list: D037161:Galectins; D025801:Ubiquitin; D017346:Protein Serine-Threonine Kinases