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

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.

Structural insights into a unique cellulase fold and mechanism of cellulose hydrolysis

“…Thus, CBMs belonging to families 4, 17, and 28 recognize distinct amorphous or paracrystalline regions of cellulose (24,25), and CBM2a, CBM3a, and CBM1, which bind to crystalline cellulose, also display distinct specificities (26). Many cellulose-degrading bacteria express a large number of endo-β-1,4-glucanases (27,28), exemplified by C. thermocellum that has the potential to synthesize approximately 30 endoglucanases. The biological rationale for the expansion in this enzyme activity in C. thermocellum and other organisms is currently unclear.…”

Common biosynthetic origins for polycyclic tetramate macrolactams from phylogenetically diverse bacteria

“…3). Many of the genomes containing these clusters are from Streptomyces (10 out of 13), but others include the marine actinomycete Salinispora arenicola (17) and the γ-proteobacterium Saccharophagus degradans (18). Of the Streptomyces genomes searched (including both draft and complete sequences), almost half (10 out of 21) contained ftd clusters.…”

The Biochemistry and Structural Biology of Plant Cell Wall Deconstruction

“…Thus, biochemical and structural data indicate that GH6 cellobiohydrolases are not, exclusively, exo acting (Amano et al, 1996;Armand et al, 1997;Varrot et al, 1999). Furthermore, some highly active cellulase systems lack a classic pair of cellobiohydrolases that act from the reducing and nonreducing ends of cellulose chains, respectively (Xie et al, 2007;Weiner et al, 2008). Indeed, one of the most distinctive features of the cellulose-degrading bacterium, Cytophaga hutchinsonii, is the absence of GH6, GH48, or GH7 cellobiohydrolases (Xie et al, 2007), although it is possible that the bacterium contains novel cellobiohydrolases.…”