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iota-carrageenases constitute a novel family of glycoside hydrolases, unrelated to that of kappa-carrageenases.iota-carrageenases are polysaccharide hydrolases that cleave the beta-1,4 linkages between the d-galactose-4-sulfate and 3, 6-anhydro-d-galactose-2-sulfate residues in the red algal galactans known as iota-carrageenans. we report here on the purification of iota-carrageenase activity from the marine bacterium zobellia galactanovorans and on the characterization of iota-carrageenase structural genes. genomic libraries from this latter bacterium as well as from alteromonas fortis were functionally ...200010934194
zobellia galactanovorans gen. nov., sp. nov., a marine species of flavobacteriaceae isolated from a red alga, and classification of [cytophaga] uliginosa (zobell and upham 1944) reichenbach 1989 as zobellia uliginosa gen. nov., comb. nov.a mesophilic, aerobic, non-flagellated, gliding bacterium, forming yellow colonies and designated dsijt, was isolated from a red alga on the sea-shore of roscoff, brittany, france. dsijt was selected for its ability to actively degrade both agars and carrageenans. the gram-negative cells occurred singly or in pairs as long rods. the temperature range for growth was 13-45 degrees c, with an optimum at 35 degrees c. the ph range for growth at 35 degrees c was from 6.0 to 8.5, with an optimum aroun ...200111411725
muricauda ruestringensis gen. nov., sp. nov., a facultatively anaerobic, appendaged bacterium from german north sea intertidal sediment.a gram-negative, facultatively anaerobic bacterium with appendages was isolated from continuous cultures with a seawater-sediment suspension containing hexadecane as the sole carbon source. although this organism was isolated from a hexadecane-degrading bacterial community, it was not able to degrade hexadecane. however, this bacterium was able to use different sugars and amino acids for growth, indicating that it probably profits from the lysis or from products like surfactants of other cells i ...200111760940
isolation and phylogenetic characterization of bacteria capable of inducing differentiation in the green alga monostroma oxyspermum.many green algae cannot develop normally when they are grown under axenic conditions. monostroma oxyspermum, for example, proliferates unicellularly in an aseptic culture, but develops into a normal foliaceous gametophyte in the presence of some marine bacteria. more than 1000 bacterial strains were isolated from marine algae and sponges and assayed for their ability to induce the morphogenesis of unicellular m. oxyspermum. fifty bacterial strains exhibiting morphogenesis-inducing activity again ...200312542710
the three-dimensional structures of two beta-agarases.agars are important gelifying agents for biochemical use and the food industry. to cleave the beta-1,4-linkages between beta-d-galactose and alpha-l-3,6-anhydro-galactose residues in the red algal galactans known as agars, marine bacteria produce polysaccharide hydrolases called beta-agarases. beta-agarases a and b from zobellia galactanivorans dsij have recently been biochemically characterized. here we report the first crystal structure of these two beta-agarases. the two proteins were overpro ...200312970344
parallel substrate binding sites in a beta-agarase suggest a novel mode of action on double-helical agarose.agarose is a gel-forming polysaccharide with an alpha-l(1,4)-3,6-anhydro-galactose, beta-d(1,3)-galactose repeat unit, from the cell walls of marine red algae. beta-agarase a, from the gram-negative bacterium zobellia galactanivorans, is secreted to the external medium and degrades agarose with an endo-mechanism. the structure of the inactive mutant beta-agarase a-e147s in complex with agaro-octaose has been solved at 1.7 a resolution. two oligosaccharide chains are bound to the protein. the fir ...200415062085
zobellia amurskyensis sp. nov., zobellia laminariae sp. nov. and zobellia russellii sp. nov., novel marine bacteria of the family flavobacteriaceae.the taxonomic position of four newly isolated marine, heterotrophic, gliding, gram-negative, aerobic, pigmented, agarolytic bacteria was established. 16s rrna gene sequence analysis indicated affiliation of the isolates to the genus zobellia in the family flavobacteriaceae. dna-dna hybridization experiments revealed that the strains studied represent three distinct and novel species, for which the names zobellia amurskyensis sp. nov., zobellia laminariae sp. nov. and zobellia russellii sp. nov. ...200415388723
the endo-beta-agarases agaa and agab from the marine bacterium zobellia galactanivorans: two paralogue enzymes with different molecular organizations and catalytic behaviours.two beta-agarase genes, agaa and agab, were functionally cloned from the marine bacterium zobellia galactanivorans. the agaa and agab genes encode proteins of 539 and 353 amino acids respectively, with theoretical masses of 60 and 40 kda. these two beta-agarases feature homologous catalytic domains belonging to family gh-16. however, agaa displays a modular architecture, consisting of the catalytic domain (agaac) and two c-terminal domains of unknown function which are processed during secretion ...200515456406
costertonia aggregata gen. nov., sp. nov., a mesophilic marine bacterium of the family flavobacteriaceae, isolated from a mature biofilm.a marine bacterium, strain kopri 13342(t), was isolated from a mature marine biofilm, including various marine algae, covering a rock-bed of the east sea, korea (also known as the sea of japan). colonies of the isolate were orange-coloured on marine agar 2216. the isolate showed relatively high 16s rrna gene sequence similarities to members of the genera maribacter (91.2-92.4 % similarity), zobellia (90.7-91.5 %) and muricauda (90.7-91.4 %). phylogenetic analysis based on the nearly complete 16s ...200616738113
kriegella aquimaris gen. nov., sp. nov., isolated from marine environments.two novel marine, heterotrophic, gliding, gram-negative, aerobic and orange-pigmented strains were investigated by using a polyphasic approach. 16s rrna gene sequence analysis indicated an affiliation of the novel isolates to the family flavobacteriaceae of the phylum bacteroidetes. the level of sequence similarity between the strains studied and their closest relatives, the recognized zobellia species, ranged from 93.2 to 93.9 %. phylogenetic evidence, supported by several differences in phenot ...200818984704
pseudozobellia thermophila gen. nov., sp. nov., a bacterium of the family flavobacteriaceae, isolated from the green alga ulva fenestrata.two novel aerobic, dark-orange-pigmented, gram-negative bacterial strains, designated kmm 3531(t) and kmm 3953, were isolated from the green alga ulva fenestrata. analysis of the 16s rrna gene sequences showed that the strains represented a novel lineage within the family flavobacteriaceae. the most closely related genera with validly published names were costertonia, flagellimonas, kriegella, maribacter, muricauda and zobellia, with 16s rrna gene sequence similarities of 93.3-91.8 %. cells of s ...200919329611
euzebyella saccharophila gen. nov., sp. nov., a marine bacterium of the family flavobacteriaceae.strain 7sm30(t)(,) an aerobic marine, gram-negative, heterotrophic and yellow- to orange-pigmented bacterium isolated from seawater from castellón, spain, was characterized using a polyphasic approach. analysis of the 16s rrna gene sequence showed that the isolate represented a novel lineage within the family flavobacteriaceae. the most closely related genera were pseudozobellia, zobellia and kriegella. cells of strain 7sm30(t) were non-motile rods that required sea salts for growth, used a wide ...201020081010
enhancement of the thermostability of a recombinant beta-agarase, agab, from zobellia galactanivorans by random mutagenesis.random mutagenesis was performed on beta-agarase, agab, from zobellia galactanivorans to improve its catalytic activity and thermostability. the activities of three mutants e99k, t307i and e99k-t307i were approx. 140, 190 and 200%, respectively, of wild type beta-agarase (661 u/mg) at 40 degrees c. all three mutant enzymes were stable up to 50 degrees c and e99k-t307i had the highest thermostability. the melting temperature (tm) of e99k-t307i, determined by cd spectra, was increased by 5.2 degre ...201020213521
transfer of carbohydrate-active enzymes from marine bacteria to japanese gut microbiota.gut microbes supply the human body with energy from dietary polysaccharides through carbohydrate active enzymes, or cazymes, which are absent in the human genome. these enzymes target polysaccharides from terrestrial plants that dominated diet throughout human evolution. the array of cazymes in gut microbes is highly diverse, exemplified by the human gut symbiont bacteroides thetaiotaomicron, which contains 261 glycoside hydrolases and polysaccharide lyases, as well as 208 homologues of susc and ...201020376150
expression, purification and preliminary x-ray diffraction analysis of the catalytic module of a beta-agarase from the flavobacterium zobellia galactanivorans.marine bacteria secrete specific glycoside hydrolases such as agarases to access polysaccharides from algal cell walls as a carbon and energy source. in an attempt to identify agarases with variable degradation patterns, a novel family gh16 beta-agarase from the marine bacterium zobellia galactanivorans was expressed, purified and crystallized. the purified enzyme crystallized in two distinct forms that were grown by the hanging-drop vapour-diffusion method using polyethylene glycol as a precipi ...201020383011
hyper-production and characterization of the ι-carrageenase useful for ι-carrageenan oligosaccharide production from a deep-sea bacterium, microbulbifer thermotolerans jamb-a94(t), and insight into the unusual catalytic mechanism.a gene of unknown function from the genome of the agar-degrading deep-sea bacterium microbulbifer thermotolerans jamb-a94(t) was functionally identified as a ι-carrageenase gene. this gene, designated as cgia, is located together with two β-agarase genes, agaa and agao in a cluster. the cgia gene product is 569 amino acids and shares 29% identity over 185 amino acids with the ι-carrageenase from zobellia galactanivorans dsij dsm 12802. recombinant, cgia-encoded ι-carrageenase (55 kda) was hyper- ...201020686828
evaluation of reference genes for real-time quantitative pcr in the marine flavobacterium zobellia galactanivorans.the marine bacteria zobellia galactanivorans is an emerging model microorganism for the bioconversion of algal polysaccharides. the sequence analysis of its genome opens the way to in-depth gene expression analysis, such as reverse transcription quantitative pcr (rt-qpcr) studies. the selection and validation of reference genes are a mandatory first step for the accurate quantification of transcripts. we selected fourteen candidate reference genes belonging to distinct pathways, namely replicati ...201021047531
discovery and structural characterization of a novel glycosidase family of marine origin.the genomic data on heterotrophic marine bacteria suggest the crucial role that microbes play in the global carbon cycle. however, the massive presence of hypothetical proteins hampers our understanding of the mechanisms by which this carbon cycle is carried out. moreover, genomic data from marine microorganisms are essentially annotated in the light of the biochemical knowledge accumulated on bacteria and fungi which decompose terrestrial plants. however marine algal polysaccharides clearly dif ...201121332624
improvement in the catalytic activity of β-agarase agaa from zobellia galactanivorans by site-directed mutagenesis.in this study, site-directed mutagenesis was performed on the β-agarase agaa gene from zobellia galactanivorans to improve its catalytic activity and thermostability. the activities of three mutant enzymes, s63k, c253i, and s63k-c253i, were 126% (1,757.78 u/mg), 2.4% (33.47 u/mg), and 0.57% (8.01 u/mg), respectively, relative to the wildtype beta-agarase agaa (1,392.61 u/mg) at 40°c. the stability of the mutant s63k enzyme was 125% of the wild-type up to 45°c, where agar is in a sol state. the m ...201122127121
identification of catalytic residues and mechanistic analysis of family gh82 iota-carrageenases.marine polysaccharide degrading enzymes, and iota-carrageenases in particular, have received little attention in the past, although their substrate specificity is of interest for biotechnological applications. this is mostly a consequence of the lack of data about their occurrence in the marine environment. recent metagenomic data mining and the genome sequencing of a marine bacterium, zobellia galactanivorans, led to the identification of three new iota-carrageenase genes belonging to the glyco ...201020681629
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