title: The kappa-carrageenase of the marine bacterium Cytophaga drobachiensis. Structural and phylogenetic relationships within family-16 glycoside hydrolases.
abstract: We report here cloning from the marine gliding bacterium Cytophaga drobachiensis of kappa-carrageenase, a glycoside hydrolase involved in the degradation of kappa-carrageenan. Structural features in the nucleotide sequence are pointed out, including the presence of an octameric omega sequence similar to the ribosome-binding sites of various eukaryotes and prokaryotes. The cgkA gene codes for a protein of 545 aa, with a signal peptide of 35 aa and a 229-aa-long posttranslationaly processed C-terminal domain. The enzyme displays the overall folding and catalytic domain characteristics of family 16 of glycoside hydrolases, which comprises other beta-1,4-alpha-1,3-D/L-galactan hydrolases, beta-1,3-D-glucan hydrolases (laminarinases), beta-1,4-1,3-D-glucan hydrolases (lichenases), and beta-1,4-D-xyloglucan endotransglycosylases. In order to address the origin and evolution of CgkA, a comprehensive phylogenetic tree of family 16 was built using parsimony analysis. Family-16 glycoside hydrolases cluster according to their substrate specificity, regardless of their phylogenetic distribution over eubacteria and eukaryotes. Such a topology suggests that the general homology between laminarinases, agarases, kappa-carrageenases, lichenases, and xyloglucan endotransglycosylases has arisen through gene duplication, likely from an ancestral protein with laminarinase activity.
authors.affiliation: Centre d'Etudes d'Océanologie et de Biologie Marine, CNRS, Roscoff, France.
authors.forename: T
authors.initials: T
authors.lastname: Barbeyron
authors.forename: A
authors.initials: A
authors.lastname: Gerard
authors.forename: P
authors.initials: P
authors.lastname: Potin
authors.forename: B
authors.initials: B
authors.lastname: Henrissat
authors.forename: B
authors.initials: B
authors.lastname: Kloareg
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins; D001483:Base Sequence; D003001:Cloning, Molecular; D003589:Cytophaga / Q000201:enzymology*; D019143:Evolution, Molecular; D006026:Glycoside Hydrolases / Q000737:chemistry* / Q000235:genetics / Q000502:physiology*; D008969:Molecular Sequence Data; D010802:Phylogeny; D017421:Sequence Analysis; D017386:Sequence Homology, Amino Acid; D013379:Substrate Specificity
chemical_list: D001426:Bacterial Proteins; D006026:Glycoside Hydrolases; C019846:kappa-carrageenase protein, Alteromonadaceae