Bacterial cadherin domains as carbohydrate binding modules: determination of affinity constants to insoluble complex polysaccharides.

Cadherin (CA) and cadherin-like (CADG) doublet domains from the complex polysaccharide-degrading marine bacterium, Saccharophagus degradans 2-40, demonstrated reversible calcium-dependent binding to different complex polysaccharides, which serve as growth substrates for the bacterium. Here we describe a procedure based on adsorption of CA and CADG doublet domains to different insoluble complex polysaccharides, followed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) for visualizing and quantifying the distribution of cadherins between the bound and unbound fractions. Scatchard plots were employed to determine the kinetics of interactions of CA and CADG with several complex carbohydrates.

Cadherin domains in the polysaccharide-degrading marine bacterium Saccharophagus degradans 2-40 are carbohydrate-binding modules.

The complex polysaccharide-degrading marine bacterium Saccharophagus degradans strain 2-40 produces putative proteins that contain numerous cadherin and cadherin-like domains involved in intercellular contact interactions. The current study reveals that both domain types exhibit reversible calcium-dependent binding to different complex polysaccharides which serve as growth substrates for the bacterium.

Structure of a polyisoprenoid binding domain from Saccharophagus degradans implicated in plant cell wall breakdown.

Saccharophagus degradans belongs to a recently discovered group of marine bacteria equipped with an arsenal of sugar cleaving enzymes coupled to carbohydrate-binding domains to degrade various insoluble complex polysaccharides. The modular Sde-1182 protein consists of a family 2 carbohydrate binding module linked to a X158 domain of unknown function. The 1.

Discovery and characterization of cadherin domains in Saccharophagus degradans 2-40.

Saccharophagus degradans strain 2-40 is a prominent member of newly discovered group of marine and estuarine bacteria that recycle complex polysaccharides. The S. degradans 2-40 genome codes for 15 extraordinary long polypeptides, ranging from 274 to 1,600 kDa.

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

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.

Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentus.

The dimorphic prosthecate bacteria (DPB) are alpha-proteobacteria that reproduce in an asymmetric manner rather than by binary fission and are of interest as simple models of development. Prior to this work, the only member of this group for which genome sequence was available was the model freshwater organism Caulobacter crescentus. Here we describe the genome sequence of Hyphomonas neptunium, a marine member of the DPB that differs from C.

Complete cellulase system in the marine bacterium Saccharophagus degradans strain 2-40T.

Saccharophagus degradans strain 2-40 is a representative of an emerging group of marine complex polysaccharide (CP)-degrading bacteria. It is unique in its metabolic versatility, being able to degrade at least 10 distinct CPs from diverse algal, plant and invertebrate sources. The S.

Genomic and proteomic analyses of the agarolytic system expressed by Saccharophagus degradans 2-40.

Saccharophagus degradans 2-40 (formerly Microbulbifer degradans 2-40) is a marine gamma-subgroup proteobacterium capable of degrading many complex polysaccharides, such as agar. While several agarolytic systems have been characterized biochemically, the genetics of agarolytic systems have been only partially determined. By use of genomic, proteomic, and genetic approaches, the components of the S.

Family 6 carbohydrate binding modules in beta-agarases display exquisite selectivity for the non-reducing termini of agarose chains.

Carbohydrate recognition is central to the biological and industrial exploitation of plant structural polysaccharides. These insoluble polymers are recalcitrant to microbial degradation, and enzymes that catalyze this process generally contain non-catalytic carbohydrate binding modules (CBMs) that potentiate activity by increasing substrate binding. Agarose, a repeat of the disaccharide 3,6-anhydro-alpha-L-galactose-(1,3)-beta-D-galactopyranose-(1,4), is the dominant matrix polysaccharide in marine algae, yet the role of CBMs in the hydrolysis of this important polymer has not previously been explored.

Saccharophagus degradans gen. nov., sp. nov., a versatile marine degrader of complex polysaccharides.

Gammaproteobacteria belonging and related to the genus Microbulbifer are an emerging group of complex carbohydrate-degrading marine bacteria. Previously, all of the representatives were placed within Microbulbifer or were unclassified. Recently, a new genus, Teredinibacter, represented by a single species, Teredinibacter turnerae, was formed to include an endosymbiotic branch of these organisms.

Identification and analysis of polyserine linker domains in prokaryotic proteins with emphasis on the marine bacterium Microbulbifer degradans.

Polyserine linkers (PSLs) are interdomain, serine-rich sequences found in modular proteins. Though common among eukaryotes, their presence in prokaryotic enzymes is limited. We identified 46 extracellular proteins involved in complex carbohydrate degradation from Microbulbifer degradans that contain PSLs that separate carbohydrate-binding domains or catalytic domains from other binding domains.

Chitinase B of "Microbulbifer degradans" 2-40 contains two catalytic domains with different chitinolytic activities.

Chitinase B of "Microbulbifer degradans" 2-40 is a modular protein that is predicted to contain two glycoside hydrolase family 18 (GH18) catalytic domains, two polyserine domains, and an acidic repeat domain. Each of the GH18 domains was shown to be catalytically active against chitin. Activity assays reveal that the amino-terminal catalytic domain (GH18(N)) releases methylumbelliferone from 4'-methylumbelliferyl-N,N'-diacetylchitobiose 13.

Detection and characterization of chitinases and other chitin-modifying enzymes.

Multiple industrial and medical uses of chitin and its derivatives have been developed in recent years. The demand for enzymes with new or desirable properties continues to grow as additional uses of chitin, chitooligosaccharides, and chitosan become apparent. Microorganisms, the primary degraders of chitin in the environment, are a rich source of valuable chitin-modifying enzymes.

Genomic analysis and initial characterization of the chitinolytic system of Microbulbifer degradans strain 2-40.

The marine bacterium Microbulbifer degradans strain 2-40 produces at least 10 enzyme systems for degrading insoluble complex polysaccharides (ICP). The draft sequence of the 2-40 genome allowed a genome-wide analysis of the chitinolytic system of strain 2-40. The chitinolytic system includes three secreted chitin depolymerases (ChiA, ChiB, and ChiC), a secreted chitin-binding protein (CbpA), periplasmic chitooligosaccharide-modifying enzymes, putative sugar transporters, and a cluster of genes encoding cytoplasmic proteins involved in N-acetyl-D-glucosamine (GlcNAc) metabolism.

Seasonal Concentration of Coliform Bacteria by Crassostrea virginica , the Eastern Oyster, in Chesapeake Bay.

Samples of water, sediment and oysters from actively harvested oyster beds located in Tolly Point and Eastern Bay of the Chesapeake Bay region were sampled over a 2-year period during which total coliforms remained at low densities. Under these conditions, there were times when total coliform densities in oysters significantly varied from those in overlying waters. The observed seasonal concentration of coliforms by oysters should be considered when assessing the efficacy of bacteriological quality standards.