genome-scale reconstruction of escherichia colis transcriptional and translational machinery a knowledge base, its mathematical formulation, and its functional characterization公司重建大肠杆菌的转录和转译机械知识库,它的数学公式,其功能特性.pdfVIP

Genome-Scale Reconstruction of Escherichia coli’s Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization 1,2 2 2 2 Ines Thiele , Neema Jamshidi , Ronan M. T. Fleming , Bernhard Ø. Palsson * 1 Ph.D. Program in Bioinformatics, University of California San Diego, La Jolla, California, United States of America, 2 Systems Biology Research Group, Bioengineering Department, University of California San Diego, La Jolla, California, United States of America Abstract Metabolic network reconstructions represent valuable scaffolds for ‘-omics’ data integration and are used to computationally interrogate network properties. However, they do not explicitly account for the synthesis of macromolecules (i.e., proteins and RNA). Here, we present the first genome-scale, fine-grained reconstruction of Escherichia coli’s transcriptional and translational machinery, which produces 423 functional gene products in a sequence-specific manner and accounts for all necessary chemical transformations. Legacy data from over 500 publications and three databases were reviewed, and many pathways were considered, including stable RNA maturation and modification, protein complex formation, and iron–sulfur cluster biogenesis. This reconstruction represents the most comprehensive knowledge base for these important cellular functions in E. coli and is unique in its scope. Furthermore, it was converted into a mathematical model and used to: (1) quantitatively integrate gene expression data as reaction constraints and (2) compute functional network states, which were compared