title: Model-based inference of gene expression dynamics from sequence information.
abstract: A dynamic model of prokaryotic gene expression is developed that makes considerable use of gene sequence information. The main contribution arises from the fact that the combined gene expression model allows us to access the impact of altering a nucleotide sequence on the dynamics of gene expression rates mechanistically. The high level of detail of the mathematical model is considered as an important step towards bringing together the tremendous amount of biological in-depth knowledge that has been accumulated at the molecular level, using a systems level analysis (in the sense of a bottom-up, inductive approach). This enables to the model to provide highly detailed insights into the various steps of the protein expression process and it allows us to access possible targets for model-based design. Taken as a whole, the mathematical gene expression model presented in this study provides a comprehensive framework for a thorough analysis of sequence-related effects on the stages of mRNA synthesis, mRNA degradation and ribosomal translation, as well as their nonlinear interconnectedness. Therefore, it may be useful in the rational design of recombinant bacterial protein synthesis systems, the modulation of enzyme activities in pathway design, in vitro protein biosynthesis, and RNA-based vaccination.
authors.affiliation: Biotechnology R&D, DSM Nutritional Products Ltd., Bldg. 203/113A, 4002 Basel, Switzerland.
authors.forename: Sabine
authors.initials: S
authors.lastname: Arnold
authors.forename: Martin
authors.initials: M
authors.lastname: Siemann-Herzberg
authors.forename: Joachim
authors.initials: J
authors.lastname: Schmid
authors.forename: Matthias
authors.initials: M
authors.lastname: Reuss
mesh_terms: D001483:Base Sequence; D003198:Computer Simulation; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation / Q000235:genetics*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D014176:Protein Biosynthesis / Q000235:genetics*; D020543:Proteome / Q000502:physiology*; D012333:RNA, Messenger / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D020543:Proteome; D012333:RNA, Messenger