Process_Transcription – Transcription

WID Process_Transcription
Name Transcription
Initialization order 14 View in model
Chemical reactions View in model
Complex formation reactions DNA-directed RNA polymerase holoenzyme
View in model
Parameters View in model
Comments At the top level, each RNA polymerase is simulated as a Markov chain consisting of four states – free, non-specifically bound to the genome, bound to a specific transcription start site, and actively transcribing a transcription unit. First, the state of each RNA polymerase is updated according to experimentally measured state occupancies. Second, RNA polymerases which transition to the specifically bound state are bound to specific transcription start sites according to experimentally measured transcript abundances, half lives, and the active transcriptional regulation. Subject to the availability of initiation factors, specifically bound RNA polymerases next transition to the active state. Next, the available elongation factors and NTPs are allocated among the actively transcribing RNA polymerases. Finally, subject to the availability of termination factors, completed transcripts are released, and the corresponding RNA polymerases are released to the free state. Evolves the state of RNA polymerase using a markov chain model with four states actively translating specifically bound non-specifically bound free Transition probabilities are designed to maintain the occupancy of each state within a narrow window around their expected values. Transition probability are determined by four logistic control functions. These can be tuned with the constants rnaPolymeraseStateExpectations rnaPolymeraseStateLogisticConstants RNA polymerase are created in the free state. Actively translating state Release sigma factor if after first second of elongation Elongate transcript according to nucleic acid limits (transcriptionLimits) if elongation factors are available If transcription complete and termination factor available release transcript transition RNA polymerase to free state increment gene expression Otherwise remain in active state Specifically bound State Can transition to active, specifically bound, non-specifically bound, or free states Transition into state only if a free sigma factor is available Decrement number of free sigma factors Pick a transcription unit (tu) to bind to according to Expression transcription unit i~prob(ribosome releases tu i|ribosome active) =prob(ribosome within RNA polymerase elongation rate bases of length of tu i|ribosome active) =prob(ribosome within RNA polymerase elongation rate bases of length of tu i|ribosome active, bound to tu i)*prob(ribosome bound to tu i|ribosome active) =[(RNA polymerase transcription rate)/(length of tu i)] * [(length of tu i)*prob(binding tu i|binding)] prob(binding tu i | binding)~expression tu i Non-specifically bound state Can transition to specifically bound, non-specifically bound, or free states Free state Can transition to specifically bound, non-specifically bound, or free states Termination Transcription termination is currently not explicitly modeled. Transcription can be terminated intrinsically by a RNA stem loop followed by a short U-rich segement, or extrinsically by a ρ helicase and energy-dependent mechanism [PUB_0039].
  1. Nicholson AW. Function, mechanism and regulation of bacterial ribonucleases. FEMS Microbiol Rev 23, 371-90 (1999). WholeCell: PUB_0039, PubMed: 10371039

Created 2012-10-01 15:07:35
Last updated 2012-10-01 15:14:00