Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization
Figure 2
(A) Schematic representation of the network components and reactions is shown. In addition to the macromolecular synthesis of RNA and proteins, rRNA and tRNA processing reactions were included in the reconstruction. I: Transcription; II: mRNA degradation; III: translation; IV: protein maturation; V: protein folding; VI: metallo-ion binding; VII: protein complex formation; VIII: ribosome assembly; IX: RNA processing; X: rRNA modification; XI: tRNA modification; XII: tRNA charging (see Table 1 for complete list of subsystems and Figure S1 for a complete protein map). (B) The pentagram shows the five main data sources incorporated in the ‘E-matrix’: EcoCyc [36], CyberCell [70], and tRNA DB [71], the revised genome annotation [32], and the genome sequence (m56, [65]).