Subproject A1 – Physiological proteomics of relevant enzymes and transporters in marine polysaccharide-degrading Bacteroidetes

Responsible: Thomas Schweder, Greifswald University

The individual role of abundant bacterial clades during algae blooms and the molecular mechanisms of polysaccharide degradation in marine habitats are not well understood. Subproject A1 aims to characterize the physiology of marine Bacteroidetes that specialize in polysaccharide degradation. We will functionally analyze mechanisms that determine substrate specificity of polysaccharide utilization loci (PULs). Comparative quantitative analyses of proteome fractions of cultivable, polysaccharide-degrading marine key-bacteria under defined substrate conditions will be used to deduce specific functions of selected PULs and their encoded CAZymes and transporters. In the focus of this project are bacterial isolates, which have been identified as relevant during spring phytoplankton blooms in the North Sea. This project will investigate the cellular localization and putative interlinkages of PUL-specific proteins in marine Bacteriodetes. It will identify polysaccharide-specific marker proteins, which will be used to functionally analyze in situ metaproteome data. The planned correlation of defined laboratory cultivations and environmental data will help to define ecological niches of these key bacteria in marine polysaccharide turnover.

Differential expression (A) and genomic structure (B) of the alginate utilization cluster of ‘Gramella forsetii’ KT0803 (Kabisch et al., 2014 ISME J, 8(7):1492-502).

(A) Shown are protein expression ratios of the intracellular and of the membrane protein fractions of cultures grown on alginate compared to laminarin. The grey background marks clustering of protein patterns in corresponding cultures. Error bars indicate the standard deviation of the biological replicates (n=3). (B) Homologous gene equivalents are present in related marine Flavobacteriaceae. Dotted lines mark genes that belong to a separate operon, but were considered in this overview, because of their orthology to corresponding genes in ‘G. forsetii’.