Stochasticity in Protein Levels Drives Colinearity of Gene Order in Metabolic Operons of Escherichia coli

Reaction scheme for modelling gene expression of a polycistronic operon. We constructed a model of a four-gene operon and a linear metabolic pathway, containing 5 metabolites and 4 enzymes encoded by the operonic genes. Operon expression was modelled following the “read-through” operon model of Swain . Transcription is modelled as reversible binding of RNAP to promoter (D) with rates: f 0 (association) and b 0 (dissociation). Isomerization from closed to open complex and initiation of transcription are approximated as a first-order process (with rate k 0). Only the leader region of the mRNA, M, is tracked in the model, which is made by transcribing polymerase, T, at rate v 0. mRNA molecules are degraded with rate mf 0, and diluted with rate D. Ribosomes compete with degradosomes for leader mRNA and bind reversibly (rates mf 1 for association and mb 1 for dissociation). Translation is started from the mC 2 state with rate k 1, which then frees M for further ribosome or degradasome binding. Enzymes are translated in the mT state with rate v 1, and decay and dilute with rate α (α = D+kdegr). In case of a “read-through” operon, only the first cistron has a ribosome binding site; thus, a translating ribosome, mT 2, releases enzyme E 1 before translating the next protein (in the state mT 3). The translation rate parameter was fine tuned to achieve realistic time delays between the appearances of consecutive gene products (approximately 60 s, on average). See for parameter values and constants.

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Stochasticity in Protein Levels Drives Colinearity of Gene Order in Metabolic Operons of Escherichia coli . (2009) Károly Kovács, et al. PLoS Biol. 2009 May;7(5):e1000115. Figure: F2. All organisms Homo sapiens Drosophila melanogaster

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