Proteomic analysis of carbohydrate catabolism and regulation in the marine bacterium Rhodopirellula baltica

The marine bacterium Rhodopirellula baltica is a model organism for aerobic carbohydrate degradation in marine systems, where polysaccharides represent the dominant components of biomass. On the basis of the genome sequence and a 2-D map of soluble proteins, the central catabolic routes of R. baltica were reconstructed. Almost all enzymes of glycolysis and TCA cycle were identified. In addition, almost all enzymes of the oxidative branch of the pentose phosphate cycle were detected. This proteomic reconstruction was corroborated by determination of selected enzymatic activities. To study substrate-dependent regulation in R. baltica, cells were adapted to growth with eight different carbohydrates and profiled with 2-DE for changes in protein patterns. Relative abundances of regulated proteins were determined using the 2-D DIGE technology and protein identification was achieved by PMF. Most of the up-regulated proteins were either dehydrogenases/oxidoreductases or proteins of unknown function which are unique for R. baltica. For only some of the regulated proteins, the coding genes are located in a physiologically meaningful genomic context. e.g., a ribose-induced alcohol dehydrogenase is encoded within an operon-like structure together with genes coding for a ribose-specific ABC-transporter. However, most of the regulated genes are randomly distributed across the genome.