PNNL

Abstract

To address a practically and fundamentally important challenge of reconstruction of carbohydrate utilization machinery in any microorganism directly from its genomic sequence, we have established a subsystems-based comparative approach and applied it to 19 genomes from the Shewanella genus. The key stages of our approach include: (i) a homology-based identification of gene candidates using a genomic compilation of ~500 known components of sugar catabolic pathways; (ii) functional assignment of orthologs and prediction of alternative genes and pathway variants based on genomic (operons, regulons) and functional (subsystems, pathways) context analysis; (iii) validation of bioinformatic predictions by a combination of biochemical, genetic and physiological experiments. The obtained genomic encyclopedia of sugar utilization includes ~170 protein families (mostly metabolic enzymes, transporters and transcriptional regulators) spanning 17 distinct pathways with a mosaic distribution across Shewanella species providing insights into their ecophysiology and adaptive evolution. The reconstructed catabolic pathways are significantly enriched by nonorthologous gene replacements and alternative biochemical routes. Phenotypic assays revealed a remarkable consistency between predicted and observed phenotype, an ability to utilize an individual sugar as a sole source of carbon and energy, over the entire matrix of tested strains and sugars. In addition to improving our knowledge of genomics, functional organization and evolution of the sugar catabolome, this study confirmed the efficiency of the established approach, which is scalable and applicable to other groups of microorganisms.