PLoS Genet. 2008 May 30;4(5):e1000087. doi: 10.1371/journal.pgen.1000087.

Complete genome sequence of the complex carbohydrate-degrading marine bacterium, Saccharophagus degradans strain 2-40 T.

Weiner RM, Taylor LE 2nd, Henrissat B, Hauser L, Land M, Coutinho PM, Rancurel C, Saunders EH, Longmire AG, Zhang H, Bayer EA, Gilbert HJ, Larimer F, Zhulin IB, Ekborg NA, Lamed R, Richardson PM, Borovok I, Hutcheson S.

Source

Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA. RWeiner@umd.edu

Abstract

The marine bacterium Saccharophagus degradans strain 2-40 (Sde 2-40) is emerging as a vanguard of a recently discovered group of marine and estuarine bacteria that recycles complex polysaccharides. We report its complete genome sequence, analysis of which identifies an unusually large number of enzymes that degrade >10 complex polysaccharides. Not only is this an extraordinary range of catabolic capability, many of the enzymes exhibit unusual architecture including novel combinations of catalytic and substrate-binding modules. We hypothesize that many of these features are adaptations that facilitate depolymerization of complex polysaccharides in the marine environment. This is the first sequenced genome of a marine bacterium that can degrade plant cell walls, an important component of the carbon cycle that is not well-characterized in the marine environment.

PMID:: 18516288; [PubMed - indexed for MEDLINE]
PMCID:: PMC2386152

Free PMC Article

Images from this publication.See all images (3)Free text

Figure 2

Schematic organization of a typical Glycosyl Hydrolase catalyzing endo-cleavage of a polysaccharide shown within a generic cellulase system pathway.

Carbohydrate-binding modules (CBMs) specifically target enzymes to their substrates, initiating and maintaining prolonged contact with the insoluble polysaccharide. The catalytic module may be a glycosyl hydrolase (GH) polysachharide lysase (PL), glycosyl transferase or an esterase. The flexible linker affords the catalytic module a certain freedom of movement, which presumably allows it to adjust to conformational variations in the substrate while the CBM maintains contact with the substrate. Enzymes, representative of a typical cellulase system, are depicted depolymerizing a single cellulose chain. Exo-acting cellobiohydrolases and endoglucanase synergistically degrade polymeric cellulose to cellobiose and cellodextrins, respectively. At least part of the synergism is believed to result from the activity of endoglucanases creating additional ends for exoglucanases to act upon. Cellodextrins (soluble cello-oligomers) may be further processed to glucose and cellobiose by cellodextrinases. Depending on the organism cellobiose may be cleaved extracellularly by β-glucosidases (cellobiases) and imported as glucose, or imported directly and cleaved in the cytoplasm. Import generally occurs through phosphotransferase transport systems, resulting in cytoplasmic Glucose-6-Phosphate (G6P) and phosphorylated cellobiose. Certain organisms, such as Clostridium thermocellum, are also capable of importing cellodextrins for cytoplasmic cleavage. Systems that degrade other complex polysaccharides (e.g. chitin) share many of the features depicted for cellulose degradation, i.e. endo- and exo-acting enzymes and polymer-specific CBMs; however, there are substrate-specific variations in enzymatic composition, to include enzymes dedicated to the removal of side-chains such as xylose and/or arabinose oligomers or substituent groups, which may include acetate, sulfate and methyl, among others.

Complete Genome Sequence of the Complex Carbohydrate-Degrading Marine Bacterium, Saccharophagus degradans Strain 2-40T

PLoS Genet. 2008 May;4(5):e1000087.