Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes

摘要

Schematic of modeling workflow and the hypothetical antioxidative properties of a protein. The genomes of 1764 strains of were gathered and orthologous genes were mapped to the reference K-12 MG1655 strain. External data sources were integrated to gather protein sequence and structure annotations with regards to susceptibility of oxidative damage, such as the locations of metal-binding sites [ ], known carbonylation sites [ ], and known cysteine damage sites [ ]. The structural proteome is further categorized into protein groups by their annotated localization and functionality (see Additional file : Table S1). We conducted gene deletions upon the genome-scale metabolic model of MG1655 integrated with ROS generating reactions ( ML1515-ROS [ , ]) for strain-specific predictions of basal ROS production levels, defining a strain’s “ROStype”. We utilized the GEM-PRO pipeline [ , ] to select representative protein structures for 95% of the MG1655 proteome. A hypothetical protein resistant to oxidative damage. Protein sequence and structure properties are highlighted based on previous studies finding enrichment of these properties in aerobes or long-living organisms. Structural properties defined by locations in 3D space, such as surface-exposed residues or those in a specified radius within a metal-binding site, are used to further divide a single protein into residue groups (see Additional file : Table S3)