TitleAbstractYear(sorted ascending)
the use of agarase from pseudomonas atlantica in the identification of agar in marine algae (rhodophyceae). 195713489548
enzymic hydrolysis of fucoidin by pseudomonas atlantica and pseudomonas carrageenovora. 195913644191
enzymatic hydrolysis of agar: purification and characterization of neoagarobiose hydrolase and p-nitrophenyl alpha-galactoside hydrolase.the mixture of polysaccharides in the gelling component of agar (agarose) is hydrolyzed to d-galactose and 3,6-anhydro-l-galactose by a series of hydrolytic enzymes obtained from pseudomonas atlantica. the final degradative step in the pathway of agarose decomposition is the hydrolysis of the alpha-linkage in the dissaccharide neoagarobiose yielding d-galactose and 3,6-anhydro-l-galactose. pseudomonas atlantica when grown on agar produces two specific enzymes, p-nitrophenyl alpha-galactose hydro ...1975137
a p-nitrophenyl alpha-galactoside hydrolase from pseudomonas atlantica. localization of the enzyme.a p-nitrophenyl alpha-galactoside hydrolase is partially released when whole cells of pseudomonas atlantica are converted to spheroplasts. the p-nitrophenyl alpha-glactoside hydrolase is completely inactivated by treatment of whole cells with diazonaphthalene -- disulfonic acid (nds), a reagent which does not penetrate the cytoplasmic membrane. under the conditions used no inactivation of lactic acid dehydrogenase was observed. a specific staining procedure for this enzyme for use in electron mi ...197553093
enzymatic hydrolysis of agar: purification and characterization of beta-neoagarotetraose hydrolase from pseudomonas atlantica.agarose is degraded by a beta-agarase from pseudomonas atlantica to neoagarooligosaccharides of degree of polymerization (dp), 4, 6, 8, and 10. a beta-neoagarotetraose hydrolase cleaves the central beta-linkage in neoagarotetraose and the beta-linkage near the nonreducing end in neoagarohexaose and -octaose to yield neoagarobiose. the beta-neoagarotetraose hydrolase was localized on or outside the cytoplasmic membrane, in the cell wall region. the enzyme was activated by nacl, kcl, cacl2, mncl2, ...197717463
beta-agarases i and ii from pseudomonas atlantica. purifications and some properties.the agarose-degrading system of pseudomonas atlantica has been re-examined. in addition to the previously reported extracellular endo-beta-agarase [yaphe, w. (1966) in proceedings 5th international seaweed symposium, pp. 333-335] a second, membrane-bound endo-enzyme activity, beta-agarase ii has been discovered. these two enzymes act in concert to degrade agarose to neoagarobiose [3,6-anhydro-alpha-l-galactopyranosyl-(1 leads to 3)-d-galactose] and also to degrade partially 6-o-methylated agaros ...19836617649
beta-agarases i and ii from pseudomonas atlantica. substrate specificities.beta-agarase i and ii were characterised by their action on agar-type polysaccharides and oligosaccharides. beta-agarase i, an endo-enzyme, was specific for regions containing a minimum of one unsubstituted neoagarobiose unit [3,6-anhydro-alpha-l-galactopyranosyl-(1 leads to 3)-d-galactose], hydrolysing at the reducing side of this moiety. yaphe demonstrated that agar was degraded by this enzyme to neoagaro-oligosaccharides limited by the disaccharide but with a predominance of the tetramer [yap ...19836653550
porphyran primary structure. an investigation using beta-agarase i from pseudomonas atlantica and 13c-nmr spectroscopy.porphyran, a highly substituted agarose from porphyra umbilicalis was degraded by highly purified beta-agarase i from pseudomonas atlantica. this enzyme cleaved at the reducing side of units of beta-neoagarobiose (3,6-anhydro-alpha-l-galactopyranosyl-(1 leads to 3)-beta-d-galactopyranose). the oligosaccharides were divided into fractions of low and high molecular weight by dialysis. the permeate (23% of total starting carbohydrate) was separated by ion-exchange into neutral and anionic fractions ...19836861749
relationship between physiological status and formation of extracellular polysaccharide glycocalyx in pseudomonas atlantica.marine pseudomonads, such as pseudomonas atlantica, are readily isolated from sediments. these organisms form extracellular polysaccharide polymers (glycocalyx). the factors affecting the composition and amount of glycocalyx in batch culture of these organisms were examined. the formation of glycocalyx was stimulated by the inclusion of galactose as the carbon source and by increased surface area resulting from addition of sand to the medium. the composition of the glycocalyx changed during the ...198316346183
bioreactor for the study of defined interactions of toxic metals and biofilms.a novel bioreactor system constructed for studies of the interactions of heavy metals and microbial cells at the solid-solution interface is described. the applicability of this experimental system to meet the severe constraints imposed on such an apparatus by the requirements for an unambiguous interpretation of data and for mathematical modeling of these interactions was explored with the trace metal lead and with the marine bacterium pseudomonas atlantica. a chemically defined medium composed ...19853911892
cloning and gene replacement mutagenesis of a pseudomonas atlantica agarase agarase gene (agra) was isolated by cloning genomic dna prepared from pseudomonas atlantica. the agarase activity in recombinant escherichia coli was found in cell-free culture supernatants and could pass through a 0.45-mum-pore-size membrane separating cells from agar, suggesting that the gene product was exported in e. coli. the enzyme was specific for agar and agarose and did not digest alginate or carrageenan. mutations generated by transposon mini-mu d1(lacz km) were used to define the a ...198816347536
variable expression of extracellular polysaccharide in the marine bacterium pseudomonas atlantica is controlled by genome rearrangement.production of extracellular polysaccharide by the marine bacterium pseudomonas atlantica is a variable trait. strains that produce extracellular polysaccharide (eps(+)) have a mucoid colony phenotype, but during cultivation in the laboratory nonmucoid, eps(-) variants arise that have a crenated colony morphology. this change is reversible since crenated variants rapidly switch to the original mucoid phenotype. we have cloned the locus (eps) controlling variable expression of eps production by sc ...198816593937
nucleotide sequence of is492, a novel insertion sequence causing variation in extracellular polysaccharide production in the marine bacterium pseudomonas atlantica.the complete nucleotide sequence of insertion element is492, which causes reversible inactivation of extracellular polysaccharide production in the marine bacterium pseudomonas atlantica, is presented. insertion of is492 results in the eps- phenotype, and excision results in restoration of eps+. dna sequencing of the site of insertion in the eps locus showed that insertion of is492 generates a 5-base-pair repeat and that its excision is precise. is492 is 1,202 nucleotides in length and contains ...19892537827
the osmotic coefficients of the sodium form of some biopolymers.the osmotic coefficients phi p,na of dilute solutions of the sodium form of some weakly acidic polymers are theoretically predicted in this work. based on the measured value 0.73 of gamma na, the activity coefficient of free na+, of the completely ionized humic acid (sodium salt) in a salt-free solution, the effective interligand distance b is calculated to be 11.34 a by using manning's counterion condensation theory [manning, g. s. (1969) j. chem. phys. 51(3), 924]. the corresponding values of ...19892752102
sequence analysis of the agra gene encoding beta-agarase from pseudomonas atlantica.the nucleotide sequence of the agra gene encoding an extracellular beta-agarase of pseudomonas atlantica was determined. an open reading frame of 1,515 nucleotides which corresponded to agra was found. the nucleotide sequence predicts a primary translation product of 504 amino acids and mr 57,486. comparison of the deduced amino acid sequences of beta-agarase from p. atlantica and the extracellular beta-agarase from streptomyces coelicolor a3(2) suggests that these proteins share several domains ...19892914859
cloning and sequence of is1000, a putative insertion sequence from thermus thermophilus hb8.the complete nucleotide sequences of two copies of a putative insertion sequence is1000 from thermus thermophilus hb8 are presented. is1000 is 1196 base pairs long, contains a long open reading frame which could code for a protein of 317 amino acids, and has imperfect terminal inverted repeats of 6 base pairs (confirmed by the terminal sequencing of 4.5 copies of is1000), but does not cause a target site duplication. there are at least 6 copies of is1000 in the genome of t. thermophilus hb8. a s ...19902176725
cloning and sequencing of agaa, a unique agarase 0107 gene from a marine bacterium, vibrio sp. strain agarase gene (agaa) was cloned from genomic dna of vibrio sp. strain jt0107. an open reading frame of 2,985 nucleotides gave a primary translation product composed of the mature protein, agarase 0107 (975 amino acid residues, with a molecular weight of 105,271) and a signal peptide of 20 amino acid residues at the n terminus. comparison of the deduced amino acid sequence of agarase 0107 with those of streptomyces coelicolor and pseudomonas atlantica suggests that these enzymes share two regio ...19938285681
phylogenetic analysis of the genera alteromonas, shewanella, and moritella using genes coding for small-subunit rrna sequences and division of the genus alteromonas into two genera, alteromonas (emended) and pseudoalteromonas gen. nov., and proposal of twelve new species combinations.small-subunit ribosomal dna sequences were determined for 17 strains belonging to the genera alteromonas, shewanella, vibrio, and pseudomonas, and these sequences were analyzed by phylogenetic methods. the resulting data confirmed the existence of the genera shewanella and moritella, but suggested that the genus alteromonas should be split into two genera. we propose that a new genus, the genus pseudoalteromonas, should be created to accommodate 11 species that were previously alteromonas specie ...19957547295
pseudoalteromonas antarctica sp. nov., isolated from an antarctic coastal environment.the taxonomic characteristics of five bacterial strains which were isolated from antarctic coastal marine environments were studied. these bacteria were psychrotrophic, aerobic, and gram negative with polar flagella. the g + c contents of the dnas of these strains were 41 to 42 mol%. the antarctic strains were phenotypically distinct from the previously described pseudoalteromonas type species. dna-dna hybridization experiments revealed that the new strains were closely related to each other but ...19979103620
cloning and nucleotide sequence of the gyrb gene of vibrio parahaemolyticus and its application in detection of this pathogen in shrimp.because biochemical testing and 16s rrna sequence analysis have proven inadequate for the differentiation of vibrio parahaemolyticus from closely related species, we employed the gyrase b gene (gyrb) as a molecular diagnostic probe. the gyrb genes of v. parahaemolyticus and closely related vibrio alginolyticus were cloned and sequenced. oligonucleotide pcr primers were designed for the amplification of a 285-bp fragment from within gyrb specific for v. parahaemolyticus. these primers recognized ...19989464408
phenotypic diversity of pseudoalteromonas citrea from different marine habitats and emendation of the description.four strains of marine, aerobic, agar-decomposing bacteria with one polar flagellum and with dna g + c contents of 38.9-40.2 mol% were isolated from the far-eastern mussels crenomytilus grayanus and patinopecten yessoensis. these four strains were identified as pseudoalteromonas; however, they were phenotypically different from species described previously according to carbon compound utilization tests and the biolog identification system. high agar-decomposing activity was found in two strains, ...19989542094
an epimerase gene essential for capsule synthesis in vibrio vulnificus.the extracellular capsule polysaccharide (cps) of vibrio vulnificus is a primary virulence factor which allows survival of the bacteria in the human host. to study the genes involved in expression of the capsule, we generated mutants that lost the ability to produce cps following the insertion of a minitransposon into the genome of an encapsulated, clinical strain of v. vulnificus. a genomic region, from one nonencapsulated mutant, containing the transposon and flanking v. vulnificus dna was clo ...19989596722
algicidal effects of a novel marine pseudoalteromonas isolate (class proteobacteria, gamma subdivision) on harmful algal bloom species of the genera chattonella, gymnodinium, and heterosigma.during a bacterial survey of the huon estuary in southern tasmania, australia, we isolated a yellow-pigmented pseudoalteromonas strain (class proteobacteria, gamma subdivision), designated strain y, that had potent algicidal effects on harmful algal bloom species. this organism was identified by 16s rrna sequencing as a strain with close affinities to pseudoalteromonas peptidysin. this bacterium caused rapid cell lysis and death (within 3 h) of gymnodinoids (including gymnodinium catenatum) and ...19989687434
spatial and temporal deposition of hyphomonas strain vp-6 capsules involved in biofilm formationhyphomonas strain vp-6 is a prosthecate bacterium isolated from the guayamas vent region and is a member of a genus of primary and common colonizers of marine surfaces. it adheres to solid substrata as a first step in biofilm formation. fine-structure microscopy and the use of specific stains and lectins reveal that it synthesizes two different extracellular polymeric substances (eps). one is a temporally synthesized, polar holdfast eps, and the other is a capsular eps that is present during the ...19989687449
minimally invasive detection of piscirickettsia salmonis in cultivated salmonids via the pcr.the attributes of the pcr allowed implementation of an assay for specific detection of piscirickettsia salmonis from a few microliters of fish serum. this opens the way to less invasive modes of sampling for this microbial pathogen in salmonids.19989687475
genetic diversity of the biofilm covering montacuta ferruginosa (mollusca, bivalvia) as evaluated by denaturing gradient gel electrophoresis analysis and cloning of pcr-amplified gene fragments coding for 16s rrna.the shell of the bivalve montacuta ferruginosa, a symbiont living in the burrow of an echinoid, is covered with a rust-colored biofilm. this biofilm includes different morphotypes of bacteria that are encrusted with a mineral rich in ferric ion and phosphate. the aim of this research was to determine the genetic diversity and phylogenetic affiliation of the biofilm bacteria. also, the possible roles of the microorganisms in the processes of mineral deposition within the biofilm, as well as their ...19989726898
identification of a marine agarolytic pseudoalteromonas isolate and characterization of its extracellular agarasethe phenotypic and agarolytic features of an unidentified marine bacteria that was isolated from the southern pacific coast was investigated. the strain was gram negative, obligately aerobic, and polarly flagellated. on the basis of several phenotypic characters and a phylogenetic analysis of the genes coding for the 16s rrna, this strain was identified as pseudoalteromonas antarctica strain n-1. in solid agar, this isolate produced a diffusible agarase that caused agar softening around the colo ...19989797294
insertion sequences.insertion sequences (iss) constitute an important component of most bacterial genomes. over 500 individual iss have been described in the literature to date, and many more are being discovered in the ongoing prokaryotic and eukaryotic genome-sequencing projects. the last 10 years have also seen some striking advances in our understanding of the transposition process itself. not least of these has been the development of various in vitro transposition systems for both prokaryotic and eukaryotic e ...19989729608
kinetic bias in estimates of coastal picoplankton community structure obtained by measurements of small-subunit rrna gene pcr amplicon length heterogeneitymarine bacterioplankton diversity was examined by quantifying natural length variation in the 5' domain of small-subunit (ssu) rrna genes (rdna) amplified by pcr from a dna sample from the oregon coast. this new technique, length heterogeneity analysis by pcr (lh-pcr), determines the relative proportions of amplicons originating from different organisms by measuring the fluorescence emission of a labeled primer used in the amplification reaction. relationships between the sizes of amplicons and ...19989797317
new sulfated oligosaccharides produced by pseudomonas β-agarase from gracilaria verrucosa polysaccharide.polysaccharide (partially sulfated agarose) with macrophage-stimulation activity, derived from gracilaria verrucosa, was decomposed by two types of β-agarase (agarases ii and iv) from pseudomonas sp. o-148. the hydrolysates were fractionated with ethanol precipitation and anion-exchange chromatography. the resulting anionic oligosaccharides with sulfate groups were investigated by (13)c-nmr spectroscopy. while the spectra of oligosaccharides produced by agarase iv showed identical patterns with ...199827388645
diversity of free-living and attached bacteria in offshore western mediterranean waters as depicted by analysis of genes encoding 16s a previous study (s. g. acinas, f. rodríguez-valera, and c. pedrós-alió, fems microbiol. ecol. 24:27-40, 1997), community fingerprinting by 16s rdna restriction analysis applied to mediterranean offshore waters showed that the free-living pelagic bacterial community was very different from the bacterial cells aggregated or attached to particles of more than about 8 micrometer. here we have studied both assemblages at three depths (5, 50, and 400 m) by cloning and sequencing the 16s rdna obtai ...19999925576
determination of total protein content of bacterial cells by sypro staining and flow assay has been developed for measuring protein biomass of marine planktonic bacteria by flow cytometry. the method was calibrated by using five species of bacteria (an arcobacter sp., a cytophaga sp., an oceanospirillum sp., a pseudoalteromonas sp., and a vibrio sp.) recently isolated from seawater samples and grown in culture at different temperatures. the intensity of sypro-protein fluorescence of these bacteria strongly correlated with their total protein content, measured by the bicinchon ...199910388732
excision of is492 requires flanking target sequences and results in circle formation in pseudoalteromonas atlantica.the gram-negative marine bacterium pseudoalteromonas atlantica produces extracellular polysaccharide (eps) that is important in biofilm formation by this bacterium. insertion and precise excision of is492 at a locus essential for extracellular polysaccharide production (eps) controls phase variation of eps production in p. atlantica. examination of is492 transposition in p. atlantica by using a pcr-based assay revealed a circular form of is492 that may be an intermediate in transposition or a te ...199910438765
reactivation of insertionally inactivated shiga toxin 2 genes of escherichia coli o157:h7 caused by nonreplicative transposition of the insertion sequence.is1203v is an insertion sequence which has been found in inactivated shiga toxin 2 genes of escherichia coli o157:h7. we analyzed the transpositional mechanism of is1203v in order to investigate whether the shiga toxin 2 genes inactivated by is1203v could revert to the wild type. when the transposase activity of is1203v was enhanced by artificial frameshifting, is1203v was obviously excised from the shiga toxin 2 gene in a circular form. the is1203v circle consisted of the entire is1203v, but an ...200010698782
curli loci of shigella unstable chromosomal element encoding multiple antibiotic resistance in shigella flexneri serotype 2a was found to include sequences homologous to the csg genes encoding curli in escherichia coli and salmonella enterica serovar typhimurium. as curli have been implicated in the virulence of serovar typhimurium, we investigated the csg loci in all four species of shigella. dna sequencing and pcr analysis showed that the csg loci of a wide range of shigella strains, of diverse serotypes and diff ...200010816548
complete genome sequence of caulobacter crescentus.the complete genome sequence of caulobacter crescentus was determined to be 4,016,942 base pairs in a single circular chromosome encoding 3,767 genes. this organism, which grows in a dilute aquatic environment, coordinates the cell division cycle and multiple cell differentiation events. with the annotated genome sequence, a full description of the genetic network that controls bacterial differentiation, cell growth, and cell cycle progression is within reach. two-component signal transduction p ...200111259647
growth patterns of two marine isolates: adaptations to substrate patchiness?during bottle incubations of heterotrophic marine picoplankton, some bacterial groups are conspicuously favored. in an earlier investigation bacteria of the genus pseudoalteromonas rapidly multiplied in substrate-amended north sea water, whereas the densities of oceanospirillum changed little (h. eilers, j. pernthaler, and r. amann, appl. environ. microbiol. 66:4634-4640, 2000). we therefore studied the growth patterns of two isolates affiliating with pseudoalteromonas and oceanospirillum in bat ...200111526008
sequence analysis of a 101-kilobase plasmid required for agar degradation by a microscilla agar-degrading marine bacterium identified as a microscilla species was isolated from coastal california marine sediment. this organism harbored a single 101-kb circular dna plasmid designated psd15. the complete nucleotide sequence of psd15 was obtained, and sequence analysis indicated a number of genes putatively encoding a variety of enzymes involved in polysaccharide utilization. the most striking feature was the occurrence of five putative agarase genes. loss of the plasmid, which occurr ...200111722934
[diversity in the monosaccharide composition of antigenic polysaccharides from proteobacteria pseudoalteromonas and marinomonas genera].the sugar analysis of the glycans of the type strains of marine proteobacteria of the genera pseudoalteromonas and marinomonas--pseudoalteromonas atlantica iam12927t, p. aurantia ncimb 2033t, p. citrea atcc 29719t, p. elyakovii kmm 162t, p. espejiana atcc 29659t, p. piscicida ncimb 645t, p. tetraodonis iam 14160t, marinomonas communis atcc 27118t, and m. vaga atcc 27119t--showed that they contain glucose, galactose, galactosamine, glucosamine, fucose, rhamnose, mannose, heptose, 2-keto-3-deoxyoc ...200111763785
phylogenetic composition of bacterioplankton assemblages from the arctic ocean.we analyzed the phylogenetic composition of bacterioplankton assemblages in 11 arctic ocean samples collected over three seasons (winter-spring 1995, summer 1996, and summer-fall 1997) by sequencing cloned fragments of 16s rrna genes. the sequencing effort was directed by denaturing gradient gel electrophoresis (dgge) screening of samples and the clone libraries. sequences of 88 clones fell into seven major lineages of the domain bacteria: alpha(36%)-, gamma(32%)-, delta(14%)-, and epsilon(1%)-p ...200211823184
a luxr homolog controls production of symbiotically active extracellular polysaccharide ii by sinorhizobium meliloti.production of complex extracellular polysaccharides (epss) by the nitrogen-fixing soil bacterium sinorhizobium meliloti is required for efficient invasion of root nodules on the host plant alfalfa. any one of three s. meliloti polysaccharides, succinoglycan, eps ii, or k antigen, can mediate infection thread initiation and extension (root nodule invasion) on alfalfa. of these three polysaccharides, the only symbiotically active polysaccharide produced by s. meliloti wild-type strain rm1021 is su ...200212193623
identification of dna-synthesizing bacterial cells in coastal north sea plankton.we describe a method for microscopic identification of dna-synthesizing cells in bacterioplankton samples. after incubation with the halogenated thymidine analogue bromodeoxyuridine (brdu), environmental bacteria were identified by fluorescence in situ hybridization (fish) with horseradish peroxidase (hrp)-linked oligonucleotide probes. tyramide signal amplification was used to preserve the fish staining during the subsequent immunocytochemical detection of brdu incorporation. dna-synthesizing c ...200212406771
identification of genetic loci required for capsular expression in vibrio vulnificus.transposon mutagenesis of an encapsulated, virulent strain of vibrio vulnificus 1003(o) led to the identification of four genetic regions that are essential to capsular polysaccharide (cps) expression and virulence. of the four regions, three are believed to be part of a capsule gene locus comprised of biosynthesis, polymerization, and transport genes clustered on a single chromosomal fragment. genes indicating a wzy-dependent system of polymerization and transmembrane export are present, sugges ...200312595419
pseudoalteromonas agarivorans sp. nov., a novel marine agarolytic bacterium.the phenotypic, genomic and phylogenetic characteristics of four aerobic, gram-negative, non-fermentative, motile, non-pigmented, agarolytic pseudoalteromonas-like bacteria, isolated from marine environments, have been investigated. these bacteria share dna-dna similarities above 86%. comparative 16s rdna sequence analysis of strain kmm 255t revealed its membership of the genus pseudoalteromonas; it shares 99.9% sequence similarity with pseudoalteromonas distincta, pseudoalteromonas elyakovii, p ...200312656163
a novel is element, is621, of the is110/is492 family transposes to a specific site in repetitive extragenic palindromic sequences in escherichia escherichia coli strain, ecor28, was found to have insertions of an identical sequence (1,279 bp in length) at 10 loci in its genome. this insertion sequence (named is621) has one large open reading frame encoding a putative protein that is 326 amino acids in length. a computer-aided homology search using the dna sequence as the query revealed that is621 was homologous to the piv genes, encoding pilin gene invertase (piv). a homology search using the amino acid sequence of the putative protei ...200312897009
positive and negative cis-acting regulatory sequences control expression of leukotoxin in actinobacillus actinomycetemcomitans 652.integration of is1301 into an at-rich inverted repeat located upstream of the ltx operon was previously shown to confer a hyperleukotoxic phenotype in actinobacillus actinomycetemcomitans is1 (t. he, t. nishihara, d. r. demuth, and i. ishikawa, j. periodontol. 70:1261-1268, 1999), but the mechanism leading to increased leukotoxin production was not determined. we show that an is1 ltx promoter::lacz reporter construct expresses 12-fold higher levels of beta-galactosidase activity than a reporter ...200314500484
investigation of the role of a beta(1-4) agarase produced by pseudoalteromonas gracilis b9 in eliciting disease symptoms in the red alga gracilaria gracilis.gracilaria species are an important source of agar. the south african gracilaria industry has experienced a number of setbacks over the last decade in the form of complete or partial die-offs of the agarophyte growing in saldanha bay, which may be attributed to bacterial infection. since a positive correlation was observed between the presence of agarolytic epiphytes and bacterial pathogenicity, we investigated the role of an agarase in the virulence mechanism employed by a bacterium that elicit ...200314523124
prospecting for novel biocatalysts in a soil metagenome.the metagenomes of complex microbial communities are rich sources of novel biocatalysts. we exploited the metagenome of a mixed microbial population for isolation of more than 15 different genes encoding novel biocatalysts by using a combined cultivation and direct cloning strategy. a 16s rrna sequence analysis revealed the presence of hitherto uncultured microbes closely related to the genera pseudomonas, agrobacterium, xanthomonas, microbulbifer, and janthinobacterium. total genomic dna from t ...200314532085
effect of extracellular products of pseudoalteromonas atlantica on the edible crab cancer pagurus.previous studies have shown that injection of extracellular products (ecp) of pseudoalteromononas atlantica isolated from shell disease-infected edible crabs (cancer pagurus) into healthy crabs causes rapid death. in this study we examined the nature of the active lethal factor(s) in ecp. injection of ecp into crabs caused a rapid decline in the total number of circulating hemocytes (blood cells), and the crabs died within 60 to 90 min. the individuals that died showed eyestalk retraction, limb ...200414766548
cloning, expression, and characterization of a glycoside hydrolase family 86 beta-agarase from a deep-sea microbulbifer-like isolate.the gene for a novel beta-agarase from a deep-sea microbulbifer-like isolate was cloned and sequenced. it encoded a mature protein of 126,921 da (1146 amino acids), which was a modular protein including two tandem carbohydrate-binding module (cbm)-like sequences and a catalytic module. the catalytic module resembled a glycoside hydrolase family 86 beta-agarase, agra, from pseudoalteromonas atlantica t6c with 31% amino acid identity. its recombinant agarase was hyper-produced extracellularly usin ...200415490156
molecular modeling of family gh16 glycoside hydrolases: potential roles for xyloglucan transglucosylases/hydrolases in cell wall modification in the gh16 glycoside hydrolases can be assigned to five subgroups according to their substrate specificities, including xyloglucan transglucosylases/hydrolases (xths), (1,3)-beta-galactanases, (1,4)-beta-galactanases/kappa-carrageenases, "nonspecific" (1,3/1,3;1,4)-beta-d-glucan endohydrolases, and (1,3;1,4)-beta-d-glucan endohydrolases. a structured family gh16 glycoside hydrolase database has been constructed ( and provides multiple sequence alignments with fu ...200415557263
phase and antigenic variation in bacteria.phase and antigenic variation result in a heterogenic phenotype of a clonal bacterial population, in which individual cells either express the phase-variable protein(s) or not, or express one of multiple antigenic forms of the protein, respectively. this form of regulation has been identified mainly, but by no means exclusively, for a wide variety of surface structures in animal pathogens and is implicated as a virulence strategy. this review provides an overview of the many bacterial proteins a ...200415258095
structure of an acidic polysaccharide from the agar-decomposing marine bacterium pseudoalteromonas atlantica strain iam 14165 containing 5,7-diacetamido-3,5,7,9-tetradeoxy-l-glycero-l-manno-non-2-ulosonic acid.the structure of an acidic polysaccharide from pseudoalteromonas atlantica strain 14165 containing 5,7-diacetamido-3,5,7,9-tetradeoxy-l-glycero-l-manno-non-2-ulosonic acid (di-n-acetylpseudaminic acid, pse5ac7ac) has been elucidated. the polysaccharide was studied by 1h and 13c nmr spectroscopy, including 2d experiments, along with sugar and methylation analyses. after a selective hydrolysis a modified polysaccharide devoid of its side chain could be isolated. it was found that the polysaccharid ...200515620668
analysis of the piv recombinase-related gene family of neisseria gonorrhoeae.neisseria gonorrhoeae (the gonococcus) is an obligate human pathogen and the causative agent of the disease gonorrhea. the gonococcal pilus undergoes antigenic variation through high-frequency recombination events between unexpressed pils silent copies and the pilin expression locus pile. the machinery involved in pilin antigenic variation identified to date is composed primarily of genes involved in homologous recombination. however, a number of characteristics of antigenic variation suggest th ...200515687191
resistance of marine bacterioneuston to solar radiation.a total of 90 bacterial strains were isolated from the sea surface microlayer (i.e., bacterioneuston) and underlying waters (i.e., bacterioplankton) from two sites of the northwestern mediterranean sea. the strains were identified by sequence analysis, and growth recovery was investigated after exposure to simulated solar radiation. bacterioneuston and bacterioplankton isolates were subjected to six different exposure times, ranging from 0.5 to 7 h of simulated noontime solar radiation. followin ...200516151115
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
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. degradans 2-40 agarolytic system were identified. five agarases were identified in the s. degradans ...200616672483
concurrence of cat and tet genes in multiple antibiotic-resistant bacteria isolated from a sea cucumber and sea urchin mariculture farm in china.a basic understanding of abundance and diversity of antibiotic-resistant microbes and their genetic determinants is necessary for finding a way to prevent and control the spread of antibiotic resistance. for this purpose, chloramphenicol and multiple antibiotic-resistant bacteria were screened from a mariculture farm in northern china. both sea cucumber and sea urchin rearing ponds were populated with abundant antibiotic-resistant bacteria, especially marine vibrios. sixty-five percent chloramph ...200616909348
exopolysaccharide-associated protein sorting in environmental organisms: the pep-cterm/epsh system. application of a novel phylogenetic profiling heuristic.protein translocation to the proper cellular destination may be guided by various classes of sorting signals recognizable in the primary sequence. detection in some genomes, but not others, may reveal sorting system components by comparison of the phylogenetic profile of the class of sorting signal to that of various protein families.200616930487
antioxidant activity and hepatoprotective potential of agaro-oligosaccharides in vitro and in vivo.agaro-oligosaccharides derived from red seaweed polysaccharide have been reported to possess antioxidant activity. in order to assess the live protective effects of agar-oligosaccharides, we did both in vitro and in vivo studies based on own-made agaro-oligosaccharides, and the structural information of this oligosaccharide was also determined.200617140450
the rbmbcdef gene cluster modulates development of rugose colony morphology and biofilm formation in vibrio cholerae.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 ...200717220218
chromosomal context directs high-frequency precise excision of is492 in pseudoalteromonas atlantica.dna rearrangements, including insertions, deletions, and inversions, control gene expression in numerous prokaryotic and eukaryotic systems, ranging from phase variation of surface antigens in pathogenic bacteria to generation of ig diversity in human b cells. we report here that precise excision of the mobile element is492 from one site on the pseudoalteromonas atlantica chromosome directly correlates with phase variation of peripheral extracellular polysaccharide ((p)eps) production from off ( ...200717264213
surprising arginine biosynthesis: a reappraisal of the enzymology and evolution of the pathway in microorganisms.major aspects of the pathway of de novo arginine biosynthesis via acetylated intermediates in microorganisms must be revised in light of recent enzymatic and genomic investigations. the enzyme n-acetylglutamate synthase (nags), which used to be considered responsible for the first committed step of the pathway, is present in a limited number of bacterial phyla only and is absent from archaea. in many bacteria, shorter proteins related to the gcn5-related n-acetyltransferase family appear to acet ...200717347518
combinatorial materials research applied to the development of new surface coatings iii. utilisation of a high-throughput multiwell plate screening method to rapidly assess bacterial biofilm retention on antifouling surfaces.the authors recently reported on the development of a novel multiwell plate screening method for the high-throughput assessment of bacterial biofilm retention on surfaces. two series of biocide containing coatings were prepared to assess the ability of the developed assay to adequately discern differences in antifouling performance: i) a commercially available poly(methyl methacrylate) (pmma) and silicone elastomer (dc) physically blended with an organic antifouling biocide sea-nine 211 (sn211) ...200717453727
gene cloning and characterization of the very large nad-dependent l-glutamate dehydrogenase from the psychrophile janthinobacterium lividum, isolated from cold soil.nad-dependent l-glutamate dehydrogenase (nad-gdh) activity was detected in cell extract from the psychrophile janthinobacterium lividum utb1302, which was isolated from cold soil and purified to homogeneity. the native enzyme (1,065 kda, determined by gel filtration) is a homohexamer composed of 170-kda subunits (determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis). consistent with these findings, gene cloning and sequencing enabled deduction of the amino acid sequence of the ...200717526698
ecological genomics of marine roseobacters.bacterioplankton of the marine roseobacter clade have genomes that reflect a dynamic environment and diverse interactions with marine plankton. comparative genome sequence analysis of three cultured representatives suggests that cellular requirements for nitrogen are largely provided by regenerated ammonium and organic compounds (polyamines, allophanate, and urea), while typical sources of carbon include amino acids, glyoxylate, and aromatic metabolites. an unexpectedly large number of genes are ...200717526795
atomic force microscopy study of the effect of lipopolysaccharides and extracellular polymers on adhesion of pseudomonas aeruginosa.the roles of lipopolysaccharides (lps) and extracellular polymers (ecp) on the adhesion of pseudomonas aeruginosa pao1 (expresses the a-band and b-band of o antigen) and ak1401 (expresses the a-band but not the b-band) to silicon were investigated with atomic force microscopy (afm) and related to biopolymer physical properties. measurement of macroscopic properties showed that strain ak1401 is more negatively charged and slightly more hydrophobic than strain pao1 is. microscopic afm investigatio ...200717905997
seven dictyostelium discoideum phosphodiesterases degrade three pools of camp and cgmp.the dictyostelium discoideum genome uncovers seven cyclic nucleotide pdes (phosphodiesterases), of which six have been characterized previously and the seventh is characterized in the present paper. three enzymes belong to the ubiquitous class i pdes, common in all eukaryotes, whereas four enzymes belong to the rare class ii pdes that are present in bacteria and lower eukaryotes. since all d. discoideum pdes are now characterized we have calculated the contribution of each enzyme in the degradat ...200717040207
molecular structure of endotoxins from gram-negative marine bacteria: an update.marine bacteria are microrganisms that have adapted, through millions of years, to survival in environments often characterized by one or more extreme physical or chemical parameters, namely pressure, temperature and salinity. the main interest in the research on marine bacteria is due to their ability to produce several biologically active molecules, such as antibiotics, toxins and antitoxins, antitumor and antimicrobial agents. nonetheless, lipopolysaccharides (lpss), or their portions, from g ...200718463721
bioactive compound synthetic capacity and ecological significance of marine bacterial genus pseudoalteromonas.the genus pseudoalteromonas is a marine group of bacteria belonging to the class gammaproteobacteria that has come to attention in the natural product and microbial ecology science fields in the last decade. pigmented species of the genus have been shown to produce an array of low and high molecular weight compounds with antimicrobial, anti-fouling, algicidal and various pharmaceutically-relevant activities. compounds formed include toxic proteins, polyanionic exopolymers, substituted phenolic a ...200718463726
evolution of ribonuclease h genes in prokaryotes to avoid inheritance of redundant genes.a theoretical model of genetic redundancy has proposed that the fates of redundant genes depend on the degree of functional redundancy, and that functionally redundant genes will not be inherited together. however, no example of actual gene evolution has been reported that can be used to test this model. here, we analyzed the molecular evolution of the ribonuclease h (rnase h) family in prokaryotes and used the results to examine the implications of functional redundancy for gene evolution.200717663799
transcriptional regulation of nad metabolism in bacteria: nrtr family of nudix-related regulators.a novel family of transcription factors responsible for regulation of various aspects of nad synthesis in a broad range of bacteria was identified by comparative genomics approach. regulators of this family (here termed nrtr for nudix-related transcriptional regulators), currently annotated as adp-ribose pyrophosphatases from the nudix family, are composed of an n-terminal nudix-like effector domain and a c-terminal dna-binding hth-like domain. nrtr regulons were reconstructed in diverse bacteri ...200818276643
bacterial heme-transport proteins and their heme-coordination modes.efficient iron acquisition is critical for an invading microbe's survival and virulence. most of the iron in mammals is incorporated into heme, which can be plundered by certain bacterial pathogens as a nutritional iron source. utilization of exogenous heme by bacteria involves the binding of heme or hemoproteins to the cell surface receptors, followed by the transport of heme into cells. once taken into the cytosol, heme is presented to heme oxygenases where the tetrapyrrole ring is cleaved in ...200818977196
bacterial heme-transport proteins and their heme-coordination modes.efficient iron acquisition is critical for an invading microbe's survival and virulence. most of the iron in mammals is incorporated into heme, which can be plundered by certain bacterial pathogens as a nutritional iron source. utilization of exogenous heme by bacteria involves the binding of heme or hemoproteins to the cell surface receptors, followed by the transport of heme into cells. once taken into the cytosol, heme is presented to heme oxygenases where the tetrapyrrole ring is cleaved in ...200818977196
veillonella rogosae sp. nov., an anaerobic, gram-negative coccus isolated from dental plaque.strains of a novel anaerobic, gram-negative coccus were isolated from the supra-gingival plaque of children. independent strains from each of six subjects were shown, at a phenotypic level and based on 16s rrna gene sequencing, to be members of the genus veillonella. analysis revealed that the six strains shared 99.7 % similarity in their 16s rrna gene sequences and 99.0 % similarity in their rpob gene sequences. the six novel strains formed a distinct group and could be clearly separated from r ...200818319459
piggybac can bypass dna synthesis during cut and paste transposition.dna synthesis is considered a defining feature in the movement of transposable elements. in determining the mechanism of piggybac transposition, an insect transposon that is being increasingly used for genome manipulation in a variety of systems including mammalian cells, we have found that dna synthesis can be avoided during piggybac transposition, both at the donor site following transposon excision and at the insertion site following transposon integration. we demonstrate that piggybac transp ...200818354502
analysis of the pseudoalteromonas tunicata genome reveals properties of a surface-associated life style in the marine environment.colonisation of sessile eukaryotic host surfaces (e.g. invertebrates and seaweeds) by bacteria is common in the marine environment and is expected to create significant inter-species competition and other interactions. the bacterium pseudoalteromonas tunicata is a successful competitor on marine surfaces owing primarily to its ability to produce a number of inhibitory molecules. as such p. tunicata has become a model organism for the studies into processes of surface colonisation and eukaryotic ...200818813346
identification and characterization of sigma, a novel component of the staphylococcus aureus stress and virulence responses.s. aureus is a highly successful pathogen that is speculated to be the most common cause of human disease. the progression of disease in s. aureus is subject to multi-factorial regulation, in response to the environments encountered during growth. this adaptive nature is thought to be central to pathogenesis, and is the result of multiple regulatory mechanisms employed in gene regulation. in this work we describe the existence of a novel s. aureus regulator, an as yet uncharacterized ecf-sigma f ...200819050758
possible effects of microbial ecto-nucleoside triphosphate diphosphohydrolases on host-pathogen humans, purinergic signaling plays an important role in the modulation of immune responses through specific receptors that recognize nucleoside tri- and diphosphates as signaling molecules. ecto-nucleoside triphosphate diphosphohydrolases (ecto-ntpdases) have important roles in the regulation of purinergic signaling by controlling levels of extracellular nucleotides. this process is key to pathophysiological protective responses such as hemostasis and inflammation. ecto-ntpdases are found in ...200819052327
repulsion and metabolic switches in the collective behavior of bacterial colonies.bacteria inoculated on surfaces create colonies that spread out, forming patterns shaped by their mutual interactions. here, by a combination of experiments and modeling, we address two striking phenomena observed when colonies spread out circularly, without dendritic instabilities. first, the velocity of spreading is generically found to decrease as levels of nutrients initially deposited on the surface increase. we demonstrate that the slowdown is due to phenomena of differentiation, leading t ...200919651027
innovations in host and microbial sialic acid biosynthesis revealed by phylogenomic prediction of nonulosonic acid structure.sialic acids (sias) are nonulosonic acid (nulo) sugars prominently displayed on vertebrate cells and occasionally mimicked by bacterial pathogens using homologous biosynthetic pathways. it has been suggested that sias were an animal innovation and later emerged in pathogens by convergent evolution or horizontal gene transfer. to better illuminate the evolutionary processes underlying the phenomenon of sia molecular mimicry, we performed phylogenomic analyses of biosynthetic pathways for sias and ...200919666579
site-specific insertion of is492 in pseudoalteromonas atlantica.reversible insertion of is492 at a site within epsg on the pseudoalteromonas atlantica chromosome controls peripheral extracellular polysaccharide production and biofilm formation by p. atlantica. high-frequency precise excision of is492 from epsg requires 5 and 7 bp of flanking dna, suggesting that is492 transposition involves a site-specific recombination mechanism. the site specificity of is492 insertion was examined in p. atlantica and shown to be specific for a 7-bp target, 5'-cttgtta-3'. c ...200919684137
zinc-independent folate biosynthesis: genetic, biochemical, and structural investigations reveal new metal dependence for gtp cyclohydrolase ib.gtp cyclohydrolase i (gcyh-i) is an essential zn(2+)-dependent enzyme that catalyzes the first step of the de novo folate biosynthetic pathway in bacteria and plants, the 7-deazapurine biosynthetic pathway in bacteria and archaea, and the biopterin pathway in mammals. we recently reported the discovery of a new prokaryotic-specific gcyh-i (gcyh-ib) that displays no sequence identity to the canonical enzyme and is present in approximately 25% of bacteria, the majority of which lack the canonical ...200919767425
scaffold degradation elevates the collagen content and dynamic compressive modulus in engineered articular was hypothesized that controlled, scaffold removal in engineered cartilage constructs would improve their collagen content and mechanical properties over time in culture.200918801665
scaffold degradation elevates the collagen content and dynamic compressive modulus in engineered articular was hypothesized that controlled, scaffold removal in engineered cartilage constructs would improve their collagen content and mechanical properties over time in culture.200918801665
amidoligases with atp-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteins.recent studies have shown that the ubiquitin system had its origins in ancient cofactor/amino acid biosynthesis pathways. preliminary studies also indicated that conjugation systems for other peptide tags on proteins, such as pupylation, have evolutionary links to cofactor/amino acid biosynthesis pathways. following up on these observations, we systematically investigated the non-ribosomal amidoligases of the atp-grasp, glutamine synthetase-like and acetyltransferase folds by classifying the kno ...200920023723
noncellulosomal cohesin- and dockerin-like modules in the three domains of life.the high-affinity cohesin-dockerin interaction was originally discovered as modular components, which mediate the assembly of the various subunits of the multienzyme cellulosome complex that characterizes some cellulolytic bacteria. until recently, the presence of cohesins and dockerins within a bacterial proteome was considered a definitive signature of a cellulosome-producing bacterium. widespread genome sequencing has since revealed a wealth of putative cohesin- and dockerin-containing protei ...200919025568
noncellulosomal cohesin- and dockerin-like modules in the three domains of life.the high-affinity cohesin-dockerin interaction was originally discovered as modular components, which mediate the assembly of the various subunits of the multienzyme cellulosome complex that characterizes some cellulolytic bacteria. until recently, the presence of cohesins and dockerins within a bacterial proteome was considered a definitive signature of a cellulosome-producing bacterium. widespread genome sequencing has since revealed a wealth of putative cohesin- and dockerin-containing protei ...200919025568
cohesion group approach for evolutionary analysis of aspartokinase, an enzyme that feeds a branched network of many biochemical pathways.aspartokinase (ask) exists within a variable network that supports the synthesis of 9 amino acids and a number of other important metabolites. lysine, isoleucine, aromatic amino acids, and dipicolinate may arise from the ask network or from alternative pathways. ask proteins were subjected to cohesion group analysis, a methodology that sorts a given protein assemblage into groups in which evolutionary continuity is assured. two subhomology divisions, ask(alpha) and ask(beta), have been recognize ...200919946135
biogenesis and homeostasis of nicotinamide adenine dinucleotide cofactor.universal and ubiquitous redox cofactors, nicotinamide adenine dinucleotide (nad) and its phosphorylated analog (nadp), collectively contribute to approximately 12% of all biochemical reactions included in the metabolic model of escherichia coli k-12. a homeostasis of the nad pool faithfully maintained by the cells results from a dynamic balance in a network of nad biosynthesis, utilization, decomposition, and recycling pathways that is subject to tight regulation at various levels. a brief over ...200926443758
comparative proteome analysis of psychrophilic versus mesophilic bacterial species: insights into the molecular basis of cold adaptation of proteins.cold adapted or psychrophilic organisms grow at low temperatures, where most of other organisms cannot grow. this adaptation requires a vast array of sequence, structural and physiological adjustments. to understand the molecular basis of cold adaptation of proteins, we analyzed proteomes of psychrophilic and mesophilic bacterial species and compared the differences in amino acid composition and substitution patterns to investigate their likely association with growth temperatures.200919133128
molecular cloning, characterization and enzymatic properties of a novel βeta-agarase from a marine isolate psudoalteromonas sp. agar-degrading pseudoalteromonas sp. ag52 bacterial strain was identified from the red seaweed gelidium amansii collected from jeju island, korea. a β-agarase gene which has 96.8% nucleotide identity to aeromonas β-agarase was cloned from this strain, and was designated as agaa. the coding region is 870 bp, encoding 290 amino acids and possesses characteristic features of the glycoside hydrolase family (ghf)-16. the predicted molecular mass of the mature protein was 32 kda. the recombinant β- ...201024031567
analysis of transcripts expressed in one-day-old larvae and fifth instar silk glands of tasar silkworm, antheraea mylitta.antheraea mylitta is one of the wild nonmulberry silkworms, which produces tasar silk. an est project has been undertaken to understand the gene expression profile of a. mylitta silk gland. two cdna libraries, one from the whole bodies of one-day-old larvae and the other from the silkglands of fifth instar larvae, were constructed and sequenced. a total of 2476 good-quality ests (1239 clones) were obtained and grouped into 648 clusters containing 390 contigs and 258 singletons to represent 467 p ...201020454581
agarase: review of major sources, categories, purification method, enzyme characteristics and applications.agarases are the enzymes which catalyze the hydrolysis of agar. they are classified into alpha-agarase (e.c. and beta-agarase (e.c. according to the cleavage pattern. several agarases have been isolated from different genera of bacteria found in seawater and marine sediments, as well as engineered microorganisms. agarases have wide applications in food industry, cosmetics, and medical fields because they produce oligosaccharides with remarkable activities. they are also used ...201020161978
cloning, purification and biochemical characterization of beta agarase from the marine bacterium pseudoalteromonas sp. ag4.a gene (agrp) encoding a beta-agarase from pseudoalteromonas sp. ag4 was cloned and expressed in escherichia coli. the agrp primary structure consists of an 870-bp open reading frame (orf) encoding 290 amino acids (aa). the predicted molecular mass and isoelectric point were determined at 33 kda and 5.9, respectively. the signal peptide was predicted to be 21 aa. the deduced aa sequence showed 98.6% identity to beta-agarase from pseudoalteromonas atlantica. the recombinant protein was purified a ...201020213114
the hp0256 gene product is involved in motility and cell envelope architecture of helicobacter pylori.helicobacter pylori is the causative agent for gastritis, and peptic and duodenal ulcers. the bacterium displays 5-6 polar sheathed flagella that are essential for colonisation and persistence in the gastric mucosa. the biochemistry and genetics of flagellar biogenesis in h. pylori has not been fully elucidated. bioinformatics analysis suggested that the gene hp0256, annotated as hypothetical, was a flij homologue. in salmonella, flij is a chaperone escort protein for flgn and flit, two proteins ...201020377912
characterization of the o-antigen polymerase (wzy) of francisella tularensis.the o-antigen polymerase of gram-negative bacteria has been difficult to characterize. herein we report the biochemical and functional characterization of the protein product (wzy) of the gene annotated as the putative o-antigen polymerase, which is located in the o-antigen biosynthetic locus of francisella tularensis. in silico analysis (homology searching, hydropathy plotting, and codon usage assessment) strongly suggested that wzy is an o-antigen polymerase whose function is to catalyze the a ...201020605777
research and application of marine microbial enzymes: status and prospects.over billions of years, the ocean has been regarded as the origin of life on earth. the ocean includes the largest range of habitats, hosting the most life-forms. competition amongst microorganisms for space and nutrients in the marine environment is a powerful selective force, which has led to evolution. the evolution prompted the marine microorganisms to generate multifarious enzyme systems to adapt to the complicated marine environments. therefore, marine microbial enzymes can offer novel bio ...201020631875
missing genes in the annotation of prokaryotic genomes.protein-coding gene detection in prokaryotic genomes is considered a much simpler problem than in intron-containing eukaryotic genomes. however there have been reports that prokaryotic gene finder programs have problems with small genes (either over-predicting or under-predicting). therefore the question arises as to whether current genome annotations have systematically missing, small genes.201020230630
analysis of extracellular alginate lyase and its gene from a marine bacterial strain, pseudoalteromonas atlantica ar06.pseudoalteromonas atlantica ar06 is a marine bacterial strain that can utilize alginate as a sole source of carbon and energy. the extracellular protein fraction prepared from the ar06 cultivation media exhibited alginate lyase activity to depolymerize the alginate molecules having homopolymeric and heteropolymeric forms of mannuronate and guluronate so as to mainly convert into the dimer to tetramer. a dna fragment encoding a portion of alginate lyase was amplified from ar06 genomic dna by pcr ...201019844705
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