The Structural Bases of the Processive Degradation of ι-Carrageenan, a Main Cell Wall Polysaccharide of Red Algae

Michel, Gurvan; Helbert, William; Kahn, Richard; Dideberg, Otto; Kloareg, Bernard

doi:10.1016/j.jmb.2003.09.056

Cited by 61 publications

(62 citation statements)

References 63 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Electron microscopy analysis demonstrated that CgiA degrade ι-carrageenan fibres according to a processive mode of action, which is consistent with the tunnel topology of its active site [17]. ι-Carrageenan, which consists of only negatively charged sugars (DA2S and G4S) is recognized by CgiA essentially through ionic interactions between its sulfate groups and several conserved arginine residues of the protein [17].…”

Section: Introductionsupporting

confidence: 64%

See 1 more Smart Citation

Degradation of λ-carrageenan by Pseudoalteromonas carrageenovora λ-carrageenase: a new family of glycoside hydrolases unrelated to κ- and ι-carrageenases

Guibet¹,

Colin²,

Barbeyron³

et al. 2007

Biochem. J.

Self Cite

View full text Add to dashboard Cite

Carrageenans are sulfated galactans found in the cell walls of red seaweeds. They are classified according to the number and the position of sulfate ester groups. lambda-Carrageenan is the most sulfated carrageenan and carries at least three sulfates per disaccharide unit. The sole known depolymerizing enzyme of lambda-carrageenan, the lambda-carrageenase from Pseudoalteromonas carrageenovora, has been purified, cloned and sequenced. Sequence analyses have revealed that the lambda-carrageenase, referred to as CglA, is the first member of a new family of GHs (glycoside hydrolases), which is unrelated to families GH16, that contains kappa-carrageenases, and GH82, that contains iota-carrageenases. This large enzyme (105 kDa) features a low-complexity region, suggesting the presence of a linker connecting at least two independent modules. The N-terminal region is predicted to fold as a beta-propeller. The main degradation products have been purified and characterized as neo-lambda-carratetraose [DP (degree of polymerization) 4] and neo-lambda-carrahexaose (DP6), indicating that CglA hydrolyses the beta-(1-->4) linkage of lambda-carrageenan. LC-MALLS (liquid chromatography-multi-angle laser light scattering) and (1)H-NMR monitoring of the enzymatic degradation of lambda-carrageenan indicate that CglA proceeds according to an endolytic mode of action and a mechanism of inversion of the anomeric configuration. Using 2-aminoacridone-labelled neo-lambda-carrabiose oligosaccharides, in the present study we demonstrate that the active site of CglA comprises at least 8 subsites (-4 to +4) and that a DP6 oligosaccharide binds in the subsites -4 to +2 and can be hydrolysed into DP4 and DP2.

show abstract

Section: Introductionsupporting

confidence: 64%

“…Finally, the mode of action of P. carrageenovora λ-carrageenase is not processive, in contrast with that already demonstrated for the A. fortis ι-carrageenase [17] and strongly suggested for the…”

Section: Insights Into the Evolution Of Carrageenase Familiescontrasting

confidence: 54%

Degradation of λ-carrageenan by Pseudoalteromonas carrageenovora λ-carrageenase: a new family of glycoside hydrolases unrelated to κ- and ι-carrageenases

Guibet¹,

Colin²,

Barbeyron³

et al. 2007

Biochem. J.

Self Cite

View full text Add to dashboard Cite

show abstract

“…2 to 4). Consistent with its predicted role as a polysaccharide lyase, computational analyses revealed that RbmB contains six PbH1 domains with a right-handed parallel ␤-helix protein fold, commonly found in enzymes with polysaccharide substrates, including several bacterial pectate and pectin lyases (25,32,33), fungal and bacterial polygalacturonases and rhamnogalacturonases (32,33), and -carrageenase from Alteromonas fortis (45). The presence of putative N-acetylglucosamine-and mannose-binding sites in RbmB further reinforces the notion that RbmB may function as a polysaccharide lyase in V. cholerae, breaking down the VPS that is composed of glucose, galactose, N-acetylglucosamine, and mannose (71).…”

Section: Discussionmentioning

confidence: 68%

“…Computational analyses using the Simple Modular Architecture Research tool (SMART) revealed that RbmB contains six domains composed of parallel ␤-helix repeats (PbH1; T116-S147, S181-G210, T234-Y256, Y257-P279, W289-S310, and I321-S342), which are often found in enzymes with polysaccharide substrates (25,32,33,45). ModBase software (for threedimensional protein models calculated by comparative modeling) also predicted a right-handed parallel ␤-helix protein fold for RbmB, with an E-value of 6e-19 to rhamnogalacturonase A from Aspergillus aculeatus (52).…”

Section: Resultsmentioning

confidence: 99%

The rbmBCDEF Gene Cluster Modulates Development of Rugose Colony Morphology and Biofilm Formation in Vibrio cholerae

2007

View full text Add to dashboard Cite

Vibrio cholerae, the causative agent of cholera, can undergo phenotypic variation generating rugose and smooth variants. The rugose variant forms corrugated colonies and well-developed biofilms and exhibits increased levels of resistance to several environmental stresses. Many of these phenotypes are mediated in part by increased expression of the vps genes, which are organized into vps-I and vps-II coding regions, separated by an intergenic region. In this study, we generated in-frame deletions of the five genes located in the vps intergenic region, termed rbmB to -F (rugosity and biofilm structure modulators B to F) in the rugose genetic background, and characterized the mutants for rugose colony development and biofilm formation. Deletion of rbmB, which encodes a protein with low sequence similarity to polysaccharide hydrolases, resulted in an increase in colony corrugation and accumulation of exopolysaccharides relative to the rugose variant. RbmC and its homolog Bap1 are predicted to encode proteins with carbohydrate-binding domains. The colonies of the rbmC bap1 double deletion mutant and bap1 single deletion mutant exhibited a decrease in colony corrugation. Furthermore, the rbmC bap1 double deletion mutant was unable to form biofilms at the air-liquid interface after 2 days, while the biofilms formed on solid surfaces detached readily. Although the colony morphology of rbmDEF mutants was similar to that of the rugose variant, their biofilm structure and cell aggregation phenotypes were different than those of the rugose variant. Taken together, these results indicate that vps intergenic region genes encode proteins that are involved in biofilm matrix production and maintenance of biofilm structure and stability.

show abstract

“…These include cellulose (31), chitin-/chitosan-like molecules (32), hemicelluloses (33), pectins (34), fucans (35), alginates (24), ulvans (36), carrageenans (37), and lichenins (38). The polysaccharides in marine algae are frequently sulfated (22).…”

mentioning

confidence: 99%

Ultrastructure and Composition of the Nannochloropsis gaditana Cell Wall

et al. 2014

View full text Add to dashboard Cite

e Marine algae of the genus Nannochloropsis are promising producers of biofuel precursors and nutraceuticals and are also harvested commercially for aquaculture feed. We have used quick-freeze, deep-etch electron microscopy, Fourier transform infrared spectroscopy, and carbohydrate analyses to characterize the architecture of the Nannochloropsis gaditana (strain CCMP 526) cell wall, whose recalcitrance presents a significant barrier to biocommodity extraction. The data indicate a bilayer structure consisting of a cellulosic inner wall (ϳ75% of the mass balance) protected by an outer hydrophobic algaenan layer. Cellulase treatment of walls purified after cell lysis generates highly enriched algaenan preparations without using the harsh chemical treatments typically used in algaenan isolation and characterization. Nannochloropsis algaenan was determined to comprise long, straight-chain, saturated aliphatics with ether cross-links, which closely resembles the cutan of vascular plants. Chemical identification of >85% of the isolated cell wall mass is detailed, and genome analysis is used to identify candidate biosynthetic enzymes.

show abstract

The Structural Bases of the Processive Degradation of ι-Carrageenan, a Main Cell Wall Polysaccharide of Red Algae

Cited by 61 publications

References 63 publications

Degradation of λ-carrageenan by Pseudoalteromonas carrageenovora λ-carrageenase: a new family of glycoside hydrolases unrelated to κ- and ι-carrageenases

Degradation of λ-carrageenan by Pseudoalteromonas carrageenovora λ-carrageenase: a new family of glycoside hydrolases unrelated to κ- and ι-carrageenases

The rbmBCDEF Gene Cluster Modulates Development of Rugose Colony Morphology and Biofilm Formation in Vibrio cholerae

Ultrastructure and Composition of the Nannochloropsis gaditana Cell Wall

Contact Info

Product

Resources

About