title: Markov Chain modeling of pyelonephritis-associated pili expression in uropathogenic Escherichia coli.
abstract: Pyelonephritis-associated pili (Pap) expression in uropathogenic Escherichia coli is regulated by a complex phase variation mechanism involving the competition between leucine-responsive regulatory protein (Lrp) and DNA adenine methylase (Dam). Population dynamics of pap gene expression has been studied extensively and the detailed molecular mechanism has been largely elucidated, providing sufficient information for mathematical modeling. Although the Gillespie algorithm is suited for modeling of stochastic systems such as the pap operon, it becomes computationally expensive when detailed molecular steps are explicitly modeled in a population. Here we developed a Markov Chain model to simplify the computation. Our model is analytically derived from the molecular mechanism. The model presented here is able to reproduce results presented using the Gillespie method, but since the regulatory information is incorporated before simulation, our model runs more efficiently and allows investigation of additional regulatory features. The model predictions are consistent with experimental data obtained in this work and in the literature. The results show that pap expression in uropathogenic E. coli is initial-state-dependent, as previously reported. However, without environment stimuli, the pap-expressing fraction in a population will reach an equilibrium level after approximately 50-100 generations. The transient time before reaching equilibrium is determined by PapI stability and Lrp and Dam copy numbers per cell. This work demonstrates that the Markov Chain model captures the essence of the complex molecular mechanism and greatly simplifies the computation.
authors.affiliation: Department of Chemical Engineering, University of California at Los Angeles, California 90095, USA.
authors.forename: Baiyu
authors.initials: B
authors.lastname: Zhou
authors.forename: David
authors.initials: D
authors.lastname: Beckwith
authors.forename: Laura R
authors.initials: LR
authors.lastname: Jarboe
authors.forename: James C
authors.initials: JC
authors.lastname: Liao
mesh_terms: D000465:Algorithms; D001703:Biophysics / Q000379:methods*; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000096:biosynthesis* / Q000737:chemistry; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism* / Q000502:physiology*; D029968:Escherichia coli Proteins / Q000502:physiology; D010861:Fimbriae, Bacterial / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial; D051756:Leucine-Responsive Regulatory Protein; D008390:Markov Chains; D008954:Models, Biological; D008962:Models, Theoretical; D009876:Operon; D011401:Promoter Regions, Genetic; D021381:Protein Transport; D011704:Pyelonephritis / Q000382:microbiology* / Q000473:pathology*; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific) / Q000096:biosynthesis* / Q000737:chemistry; D013269:Stochastic Processes; D013696:Temperature; D014157:Transcription Factors / Q000096:biosynthesis* / Q000737:chemistry / Q000502:physiology; D014158:Transcription, Genetic
chemical_list: D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; C497278:Lrp protein, E coli; D014157:Transcription Factors; D051756:Leucine-Responsive Regulatory Protein; C058693:Dam methyltransferase; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific); C499294:dam protein, E coli