In silico method for modelling metabolism andgene product expression at genome scale

摘要

Transcription and translation use raw materials and energy generated metabolically to createthe macromolecular machinery responsible for all cellular functions, including metabolism.A biochemically accurate model of molecular biology and metabolism will facilitatecomprehensive and quantitative computations of an organism’s molecular constitution as afunction of genetic and environmental parameters. Here we formulate a model of metabolismand macromolecular expression. Prototyping it using the simple microorganism Thermotogamaritima, we show our model accurately simulates variations in cellular composition andgene expression. moreover, through in silico comparative transcriptomics, the model allowsthe discovery of new regulons and improving the genome and transcription unit annotations.our method presents a framework for investigating molecular biology and cellular physiologyin silico and may allow quantitative interpretation of multi-omics data sets in the context of anintegrated biochemical description of an organism.