Team:Rice/Model/ExpressionMinimal

Host Expression

Overview

Expression begins when mRNAs are transcribed at an energy-dependent rate and then form complexes with ribosomes. Since most of the energy in a bacterial cell is used in translation [4], our model assumes that transcriptional energy use is negligible. Ribosome complexes translate mRNAs into protein molecules, using up cellular energy in the process. After translation, the complexes unbind and can be reused. rRNAs are also transcribed, though at a higher rate, and they bind to ribosomal proteins to form functional ribosomes.

Explanation

Expression starts with transcription; in our model, transcription is a spontaneous, energy-dependent process. Each mRNA is produced at a rate of dmi/dt = wi Ec/(Ec+oi), where Ec is the cellular energy, wi is the maximum transcription rate for mRNA (with i = E,T,R,H for the metabolic enzymes, transport enzymes, ribosomal proteins, or other host proteins respectively), and oi is the threshold for transcription. In addition, for mH, the rate is multiplied by a regulatory constant 1/(1+(pH/kH)^hH), where pH is the number of other host proteins in the cell and the remaining values are constants. This factor approximates the normal host regulation of its own proteins. All RNAs slowly degrade in the cell, with a degradation constant of dr. For translation to occur, functional host ribosomes need to be present. These are composed of ribosomal protein (pR) and rRNA (rR). Binding is a reversible process with binding constant br and unbinding constant ur, but once bound, the functional ribosomes (Rh) can bind with an mRNA (mi) to form a complex ci. This second binding step is also reversible. Finally, translation can occur and the corresponding protein (pi) is produced. Translation occurs at a rate of γ ci/ni, where γ is the global translation rate and equals γm Ec/(kγ + Ec). Here γm is the maximum translation rate, kγ is the energy threshold for translation, and ni is the length of the protein to translation in amino acids.

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