title: Piecewise linear approximations to model the dynamics of adaptation to osmotic stress by food-borne pathogens.
abstract: Addition of salt to food is one of the most ancient and most common methods of food preservation. However, little is known of how bacterial cells adapt to such conditions. We propose to use piecewise linear approximations to model the regulatory adaptation of Escherichiacoli to osmotic stress. We apply the method to eight selected genes representing the functions known to be at play during osmotic adaptation. The network is centred on the general stress response factor, sigma S, and also includes a module representing the catabolic repressor CRP-cAMP. Glutamate, potassium and supercoiling are combined to represent the intracellular regulatory signal during osmotic stress induced by salt. The output is a module where growth is represented by the concentration of stable RNAs and the transcription of the osmotic gene osmY. The time course of gene expression of transport of osmoprotectant represented by the symporter proP and of the osmY is successfully reproduced by the network. The behaviour of the rpoS mutant predicted by the model is in agreement with experimental data. We discuss the application of the model to food-borne pathogens such as Salmonella; although the genes considered have orthologs, it seems that supercoiling is not regulated in the same way. The model is limited to a few selected genes, but the regulatory interactions are numerous and span different time scales. In addition, they seem to be condition specific: the links that are important during the transition from exponential to stationary phase are not all needed during osmotic stress. This model is one of the first steps towards modelling adaptation to stress in food safety and has scope to be extended to other genes and pathways, other stresses relevant to the food industry, and food-borne pathogens. The method offers a good compromise between systems of ordinary differential equations, which would be unmanageable because of the size of the system and for which insufficient data are available, and the more abstract Boolean methods.
authors.affiliation: Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK. Electronic address: aline.metris@ifr.ac.uk.
authors.forename: Aline
authors.initials: A
authors.lastname: Métris
authors.affiliation: Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK. Electronic address: susie.george@ifr.ac.uk.
authors.forename: Susie M
authors.initials: SM
authors.lastname: George
authors.affiliation: Inria Grenoble - Rhône-Alpes Research Center, Saint Ismier, France. Electronic address: delphine.ropers@inria.fr.
authors.forename: Delphine
authors.initials: D
authors.lastname: Ropers
mesh_terms: D000222:Adaptation, Physiological / Q000502:physiology*; D001426:Bacterial Proteins / Q000096:biosynthesis / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000096:biosynthesis / Q000235:genetics; D005516:Food Microbiology; D005519:Food Preservation / Q000379:methods*; D059022:Food Safety; D005517:Foodborne Diseases / Q000382:microbiology; D015964:Gene Expression Regulation, Bacterial; D018698:Glutamic Acid / Q000378:metabolism; D008954:Models, Biological; D009997:Osmotic Pressure / Q000502:physiology*; D033902:Periplasmic Binding Proteins / Q000096:biosynthesis / Q000235:genetics; D011188:Potassium / Q000378:metabolism; D012475:Salmonella / Q000235:genetics / Q000378:metabolism*; D012808:Sigma Factor / Q000096:biosynthesis / Q000235:genetics; D012965:Sodium Chloride / Q000494:pharmacology*; D027981:Symporters / Q000096:biosynthesis / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; D033902:Periplasmic Binding Proteins; C079244:ProP protein, E coli; D012808:Sigma Factor; D027981:Symporters; C069567:sigma factor KatF protein, Bacteria; C074783:osmY protein, E coli; D018698:Glutamic Acid; D012965:Sodium Chloride; D011188:Potassium
keywords: Dynamic modelling; Osmotic stress; Piecewise linear approximations; Systems biology