title: Protein distributions from a stochastic model of the lac operon of E. coli with DNA looping: analytical solution and comparison with experiments.
abstract: Although noisy gene expression is widely accepted, its mechanisms are subjects of debate, stimulated largely by single-molecule experiments. This work is concerned with one such study, in which Choi et al., 2008, obtained real-time data and distributions of Lac permease in E. coli. They observed small and large protein bursts in strains with and without auxiliary operators. They also estimated the size and frequency of these bursts, but these were based on a stochastic model of a constitutive promoter. Here, we formulate and solve a stochastic model accounting for the existence of auxiliary operators and DNA loops. We find that DNA loop formation is so fast that small bursts are averaged out, making it impossible to extract their size and frequency from the data. In contrast, we can extract not only the size and frequency of the large bursts, but also the fraction of proteins derived from them. Finally, the proteins follow not the negative binomial distribution, but a mixture of two distributions, which reflect the existence of proteins derived from small and large bursts.
authors: Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology, Delhi, India.
authors: Krishna
authors: K
authors: Choudhary
authors: Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology, Delhi, India.
authors: Stefan
authors: S
authors: Oehler
authors: Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology, Delhi, India.
authors: Atul
authors: A
authors: Narang
mesh_terms: D000465:Algorithms; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics*; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000235:genetics* / Q000378:metabolism; D025461:Feedback, Physiological; D015964:Gene Expression Regulation, Bacterial; D007763:Lac Operon; D056968:Lac Repressors / Q000235:genetics / Q000378:metabolism; D008957:Models, Genetic; D009690:Nucleic Acid Conformation; D009875:Operator Regions, Genetic / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D013269:Stochastic Processes
chemical_list: D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; D056968:Lac Repressors; D012333:RNA, Messenger