Team:Rice/Model/ExpressionMinimal

• Home
• Project
  • Overview
  • Design
  • Background
  • Modeling
  • Software
  • Notebook
  • Protocols
  • Results
  • Demonstration
  • Future Directions
  • Safety
  • InterLab
• Human Practices
  • Overview
  • Education & Engagement
  • Collaborations
  • Integrated Human Practices
• Achievements
  • Parts
  • Medal Requirements
• Team
  • Members
  • Advisors
  • Instructors
  • Attributions

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 dm_i/dt = w_i E_c/(E_c+o_i), where E_c is the cellular energy, w_i 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 o_i is the threshold for transcription. In addition, for m_H, the rate is multiplied by a regulatory constant 1/(1+(p_H/k_H)^h_H), where p_H 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 d_r. For translation to occur, functional host ribosomes need to be present. These are composed of ribosomal protein (p_R) and rRNA (r_R). Binding is a reversible process with binding constant b_r and unbinding constant u_r, but once bound, the functional ribosomes (R_h) can bind with an mRNA (m_i) to form a complex c_i. This second binding step is also reversible. Finally, translation can occur and the corresponding protein (p_i) is produced. Translation occurs at a rate of γ c_i/n_i, where γ is the global translation rate and equals γ_m E_c/(k_γ + E_c). Here γ_m is the maximum translation rate, k_γ is the energy threshold for translation, and n_i is the length of the protein to translation in amino acids.

Equations