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a phenomenological model for predicting melting temperatures of dna sequences.we report here a novel method for predicting melting temperatures of dna sequences based on a molecular-level hypothesis on the phenomena underlying the thermal denaturation of dna. the model presented here attempts to quantify the energetic components stabilizing the structure of dna such as base pairing, stacking, and ionic environment which are partially disrupted during the process of thermal denaturation. the model gives a pearson product-moment correlation coefficient (r) of approximately ...201020865157
evolution of bacterial phosphoglycerate mutases: non-homologous isofunctional enzymes undergoing gene losses, gains and lateral transfers.the glycolytic phosphoglycerate mutases exist as non-homologous isofunctional enzymes (nise) having independent evolutionary origins and no similarity in primary sequence, 3d structure, or catalytic mechanism. cofactor-dependent pgm (dpgm) requires 2,3-bisphosphoglycerate for activity; cofactor-independent pgm (ipgm) does not. the pgm profile of any given bacterium is unpredictable and some organisms such as escherichia coli encode both forms.201021187861
a novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and dna viral systems.the use of nucleases as toxins for defense, offense or addiction of selfish elements is widely encountered across all life forms. using sensitive sequence profile analysis methods, we characterize a novel superfamily (the sukh superfamily) that unites a diverse group of proteins including smi1/knr4, pgs2, fbxo3, skip16, syd, herpesviral us22, irs1 and trs1, and their bacterial homologs. using contextual analysis we present evidence that the bacterial members of this superfamily are potential imm ...201121306995
search for hydrophilic marine fungal metabolites: a rational approach for their production and extraction in a bioactivity screening context.in the search for bioactive natural products, our lab screens hydrophobic extracts from marine fungal strains. while hydrophilic active substances were recently identified from marine macro-organisms, there was a lack of reported metabolites in the marine fungi area. as such, we decided to develop a general procedure for screening of hydrophobic metabolites. the aim of this study was to compare different processes of fermentation and extraction, using six representative marine fungal strains, in ...201121339948
purification and characterization of a bifunctional alginate lyase from pseudoalteromonas sp. sm0524.an alginate lyase-producing bacterial strain, pseudoalteromonas sp. sm0524, was screened from marine rotten kelp. in an optimized condition, the production of alginate lyase from pseudoalteromonas sp. sm0524 reached 62.6 u/ml, suggesting that strain sm0524 is a good producer of alginate lyases. the bifunctional alginate lyase aly-sj02 secreted by strain sm0524 was purified. aly-sj02 had an apparent molecular mass of 32 kda. the optimal temperature and ph of aly-sj02 toward sodium alginate was 50 ...201121339950
bioinformatic characterization of the trimeric intracellular cation-specific channel protein family.trimeric intracellular cation-specific (tric) channels are integral to muscle excitation-contraction coupling. tric channels provide counter-ionic flux when calcium is rapidly transported from intracellular stores to the cell cytoplasm. until recently, knowledge of the presence of these proteins was limited to animals. we analyzed the tric family and identified a profusion of prokaryotic family members with topologies and motifs similar to those of their eukaryotic counterparts. prokaryotic memb ...201121519847
carbohydrase systems of saccharophagus degradans degrading marine complex polysaccharides.saccharophagus degradans 2-40 is a +¦-subgroup proteobacterium capable of using many of the complex polysaccharides found in the marine environment for growth. to utilize these complex polysaccharides, this bacterium produces a plethora of carbohydrases dedicated to the processing of a carbohydrate class. aiding in the identification of the contributing genes and enzymes is the known genome sequence for this bacterium. this review catalogs the genes and enzymes of the s. degradans genome that ar ...201121731555
discovery of a cytokinin deaminase.an enzyme of unknown function within the amidohydrolase superfamily was discovered to catalyze the hydrolysis of n-6-substituted adenine derivatives, several of which are cytokinins. cytokinins are a common type of plant hormone and n-6-substituted adenines are also found as modifications to trna. patl2390, from pseudoalteromonas atlantica t6c, was shown to hydrolytically deaminate n-6-isopentenyladenine to hypoxanthine and isopentenylamine with a k(cat)/k(m) of 1.2 +ù 10(7) m(-1) s(-1). additio ...201121823622
long-chain n-acyl amino acid synthases are linked to the putative pep-cterm/exosortase protein-sorting system in gram-negative bacteria.clones that encode the biosynthesis of long-chain n-acyl amino acids are frequently recovered from activity-based screens of soil metagenomic libraries. members of a diverse set of enzymes referred to as n-acyl amino acid synthases are responsible for the production of all metagenome-derived n-acyl amino acids characterized to date. based on the frequency at which n-acyl amino acid synthase genes have been identified from metagenomic samples, related genes are expected to be common throughout th ...201121840974
bioactivities from marine algae of the genus gracilaria.seaweeds are an important source of bioactive metabolites for the pharmaceutical industry in drug development. many of these compounds are used to treat diseases like cancer, acquired immune-deficiency syndrome (aids), inflammation, pain, arthritis, as well as viral, bacterial, and fungal infections. this paper offers a survey of the literature for gracilaria algae extracts with biological activity, and identifies avenues for future research. nineteen species of this genus that were tested for a ...201121845096
Identification and Characterization of the Rhizobium sp. Strain GIN611 Glycoside Oxidoreductase Resulting in the Deglycosylation of Ginsenosides.Using enrichment culture, Rhizobium sp. strain GIN611 was isolated as having activity for deglycosylation of a ginsenoside, compound K (CK). The purified heterodimeric protein complex from Rhizobium sp. GIN611 consisted of two subunits with molecular masses of 63.5 kDa and 17.5 kDa. In the genome, the coding sequence for the small subunit was located right after the sequence for the large subunit, with one nucleotide overlapping. The large subunit showed CK oxidation activity, and the deglycosyl ...201222020506
glygly-cterm and rhombosortase: a c-terminal protein processing signal in a many-to-one pairing with a rhomboid family intramembrane serine protease.the rhomboid family of serine proteases occurs in all domains of life. its members contain at least six hydrophobic membrane-spanning helices, with an active site serine located deep within the hydrophobic interior of the plasma membrane. the model member glpg from escherichia coli is heavily studied through engineered mutant forms, varied model substrates, and multiple x-ray crystal studies, yet its relationship to endogenous substrates is not well understood. here we describe an apparent membr ...201122194940
latitudinal gradients in degradation of marine dissolved organic carbon.heterotrophic microbial communities cycle nearly half of net primary productivity in the ocean, and play a particularly important role in transformations of dissolved organic carbon (doc). the specific means by which these communities mediate the transformations of organic carbon are largely unknown, since the vast majority of marine bacteria have not been isolated in culture, and most measurements of doc degradation rates have focused on uptake and metabolism of either bulk doc or of simple mod ...201122216139
is histidine dissociation a critical component of the no/h-nox signaling mechanism? insights from x-ray absorption spectroscopy.the h-nox (heme-nitric oxide/oxygen binding) family of diatomic gas sensing hemoproteins has attracted great interest. soluble guanylate cyclase (sgc), the well-characterized eukaryotic nitric oxide (no) sensor is an h-nox family member. when no binds sgc at the ferrous histidine-ligated protoporphyrin-ix, the proximal histidine ligand dissociates, resulting in a 5-coordinate (5c) complex; formation of this 5c complex is viewed as necessary for activation of sgc. characterization of other h-nox ...201222430114
nitric oxide regulated two-component signaling in pseudoalteromonas atlantica.bacteria employ two-component signaling to detect and respond to environmental stimuli. in essence, two-component signaling relies on a protein called a response regulator that can elicit a change in gene expression or protein function in response to phosphoryl transfer from a histidine kinase. phosphorylation of the associated histidine kinase is regulated by detection of an environmental signal, thus linking sensing to cellular response. recently, it has been suggested that h-nox (heme-nitric ...201222521885
nitric oxide modulates bacterial biofilm formation through a multicomponent cyclic-di-gmp signaling network.nitric oxide (no) signaling in vertebrates is well characterized and involves the heme-nitric oxide/oxygen-binding (h-nox) domain of soluble guanylate cyclase as a selective no sensor. in contrast, little is known about the biological role or signaling output of bacterial h-nox proteins. here, we describe a molecular pathway for h-nox signaling in shewanella oneidensis. no stimulates biofilm formation by controlling the levels of the bacterial secondary messenger cyclic diguanosine monophosphate ...201222542454
cellular function and molecular structure of ecto-nucleotidases.ecto-nucleotidases play a pivotal role in purinergic signal transmission. they hydrolyze extracellular nucleotides and thus can control their availability at purinergic p2 receptors. they generate extracellular nucleosides for cellular reuptake and salvage via nucleoside transporters of the plasma membrane. the extracellular adenosine formed acts as an agonist of purinergic p1 receptors. they also can produce and hydrolyze extracellular inorganic pyrophosphate that is of major relevance in the c ...201222555564
characterization of bacteria in ballast water using maldi-tof mass spectrometry.to evaluate a rapid and cost-effective method for monitoring bacteria in ballast water, several marine bacterial isolates were characterized by matrix-assisted laser desorption ionization-time of flight mass spectrometry (maldi-tof ms). since international maritime organization (imo) regulations are concerned with the unintended transportation of pathogenic bacteria through ballast water, emphasis was placed on detecting species of vibrio, enterococci and coliforms. seawater samples collected fr ...201222685576
genome sequence of pseudoalteromonas flavipulchra jg1, a marine antagonistic bacterium with abundant antimicrobial metabolites.the marine bacterium pseudoalteromonas flavipulchra jg1 can synthesize various antibacterial metabolites, including protein and small molecules. the draft genome of jg1 is about 5.36 mb and harbors approximate 4,913 genes, which will provide further insight into the synthesis of antimicrobial agents and antagonistic mechanisms of p. flavipulchra against pathogens.201222740664
patterns and architecture of genomic islands in marine bacteria.genomic islands (gis) have key roles since they modulate the structure and size of bacterial genomes displaying a diverse set of laterally transferred genes. despite their importance, gis in marine bacterial genomes have not been explored systematically to uncover possible trends and to analyze their putative ecological significance.201222839777
controlling carrageenan structure using a novel formylglycine-dependent sulfatase, an endo-4s-iota-carrageenan sulfatase.carrageenans are sulfated polysaccharides that are found in the cell walls of red algae. these polysaccharides have gelling and texturizing properties that are widely appreciated in industrial applications. however, these functional properties depend strongly on the sulfation of the moieties of the carrabiose repetition unit. here we aimed to monitor the sulfate composition of gelling carrageenan. to do so, we screened and purified from pseudoalteromonas atlantica a 4s-iota carrageenan sulfatase ...201323011004
genomes of surface isolates of alteromonas macleodii: the life of a widespread marine opportunistic copiotroph.alteromonas macleodii is a marine gammaproteobacterium with widespread distribution in temperate or tropical waters. we describe three genomes of isolates from surface waters around europe (atlantic, mediterranean and black sea) and compare them with a previously described deep mediterranean isolate (altde) that belongs to a widely divergent clade. the surface isolates are quite similar, the most divergent being the black sea (bs11) isolate. the genomes contain several genomic islands with diffe ...201223019517
qsdh, a novel ahl lactonase in the rnd-type inner membrane of marine pseudoalteromonas byunsanensis strain 1a01261.n-acyl-homoserine lactones (ahls) are the main quorum-sensing (qs) signals in gram-negative bacteria. ahls trigger the expression of genes for particular biological functions when their density reaches a threshold. in this study, we identified and cloned the qsdh gene by screening a genomic library of pseudoalteromonas byunsanensis strain 1a01261, which has ahl-degrading activity. the qsdh gene encoded a gdsl hydrolase found to be located in the n-terminus of a multidrug efflux transporter prote ...201223056356
mobile genetic elements in the bacterial phylum acidobacteria.analysis of the genome of candidatus solibacter usitatus ellin6076, a member of the phylum acidobacteria, revealed a large number of genes associated with mobile genetic elements. these genes encoded transposases, insertion sequence elements and phage integrases. when the amino acid sequences of the mobile element-associated genes were compared, many of them had high (90-100%) amino acid sequence identities, suggesting that these genes may have recently duplicated and dispersed throughout the ge ...201223087842
contrasting life strategies of viruses that infect photo- and heterotrophic bacteria, as revealed by viral tagging.ocean viruses are ubiquitous and abundant and play important roles in global biogeochemical cycles by means of their mortality, horizontal gene transfer, and manipulation of host metabolism. however, the obstacles involved in linking viruses to their hosts in a high-throughput manner bottlenecks our ability to understand virus-host interactions in complex communities. we have developed a method called viral tagging (vt), which combines mixtures of host cells and fluorescent viruses with flow cyt ...201223111870
analysis of extracellular alginate lyase (alya) expression and its regulatory region in a marine bacterial strain, pseudoalteromonas atlantica ar06, using a gfp gene reporter system.extracellular alginate lyase (alya) has an important role in the use of alginate in the marine bacterial strain pseudoalteromonas atlantica ar06. green fluorescent protein (gfp) is a convenient, useful tool for visualization of gene expression, and here we introduced the gfp gene at the end of alya by homologous recombination in ar06. the gfp gene was expressed as a polycistronic transcript in reporter strain arag (ar06 alya-gfp). the analysis of gfp fluorescence of arag in minimal medium contai ...201323179456
polyclonality of concurrent natural populations of alteromonas macleodii.we have analyzed a natural population of the marine bacterium, alteromonas macleodii, from a single sample of seawater to evaluate the genomic diversity present. we performed full genome sequencing of four isolates and 161 metagenomic fosmid clones, all of which were assigned to a. macleodii by sequence similarity. out of the four strain genomes, a. macleodii deep ecotype (altde1) represented a different genome, whereas altde2 and altde3 were identical to the previously described altde. although ...201223212172
discovery of an l-fucono-1,5-lactonase from cog3618 of the amidohydrolase superfamily.a member of the amidohydrolase superfamily, bmulj_04915 from burkholderia multivorans, of unknown function was determined to hydrolyze a series of sugar lactones: l-fucono-1,4-lactone, d-arabino-1,4-lactone, l-xylono-1,4-lactone, d-lyxono-1,4-lactone, and l-galactono-1,4-lactone. the highest activity was shown for l-fucono-1,4-lactone with a k(cat) value of 140 s(-1) and a k(cat)/k(m) value of 1.0 × 10(5) m(-1) s(-1) at ph 8.3. the enzymatic product of an adjacent l-fucose dehydrogenase, bmulj_0 ...201223214453
discovery of an l-fucono-1,5-lactonase from cog3618 of the amidohydrolase superfamily.a member of the amidohydrolase superfamily, bmulj_04915 from burkholderia multivorans, of unknown function was determined to hydrolyze a series of sugar lactones: l-fucono-1,4-lactone, d-arabino-1,4-lactone, l-xylono-1,4-lactone, d-lyxono-1,4-lactone, and l-galactono-1,4-lactone. the highest activity was shown for l-fucono-1,4-lactone with a k(cat) value of 140 s(-1) and a k(cat)/k(m) value of 1.0 × 10(5) m(-1) s(-1) at ph 8.3. the enzymatic product of an adjacent l-fucose dehydrogenase, bmulj_0 ...201223214453
ethanolamine utilization in vibrio alginolyticus.ethanolamine is used as an energy source by phylogenetically diverse bacteria including pathogens, by the concerted action of proteins from the eut-operon. previous studies have revealed the presence of eutbc genes encoding ethanolamine-ammonia lyase, a key enzyme that breaks ethanolamine into acetaldehyde and ammonia, in about 100 bacterial genomes including members of gamma-proteobacteria. however, ethanolamine utilization has not been reported for any member of the vibrio genus. our comparati ...201223234435
characterization of the 5-hydroxymethylcytosine-specific dna restriction endonucleases.in t4 bacteriophage, 5-hydroxymethylcytosine (5hmc) is incorporated into dna during replication. in response, bacteria may have developed modification-dependent type iv restriction enzymes to defend the cell from t4-like infection. pvurts1i was the first identified restriction enzyme to exhibit specificity toward hmc over 5-methylcytosine (5mc) and cytosine. by using pvurts1i as the original member, we identified and characterized a number of homologous proteins. most enzymes exhibited similar c ...201323482393
the structure of a streptomyces avermitilis α-l-rhamnosidase reveals a novel carbohydrate-binding module cbm67 within the six-domain arrangement.α-l-rhamnosidases hydrolyze α-linked l-rhamnosides from oligosaccharides or polysaccharides. we determined the crystal structure of the glycoside hydrolase family 78 streptomyces avermitilis α-l-rhamnosidase (sarha78a) in its free and l-rhamnose complexed forms, which revealed the presence of six domains n, d, e, f, a, and c. in the ligand complex, l-rhamnose was bound in the proposed active site of the catalytic module, revealing the likely catalytic mechanism of sarha78a. glu(636) is predicted ...201323486481
gene cloning, expression and characterization of a novel xylanase from the marine bacterium, glaciecola mesophila kmm241.marine xylanases are rather less studied compared to terrestrial xylanases. in this study, a new xylanase gene, xynb, was cloned from the marine bacterium, glaciecola mesophila kmm241, and expressed in escherichia coli. xynb encodes a multi-domain xylanase xynb of glycoside hydrolase (gh) family 8. the recombinant xynb comprises an n-terminal domain (ntd) with unknown function and a catalytic domain, which is structurally novel among the characterized xylanases of gh family 8. xynb has the highe ...201323567318
bringing the ocean into the laboratory to probe the chemical complexity of sea spray aerosol.the production, size, and chemical composition of sea spray aerosol (ssa) particles strongly depend on seawater chemistry, which is controlled by physical, chemical, and biological processes. despite decades of studies in marine environments, a direct relationship has yet to be established between ocean biology and the physicochemical properties of ssa. the ability to establish such relationships is hindered by the fact that ssa measurements are typically dominated by overwhelming background aer ...201323620519
morphology, physiological characteristics, and complete sequence of marine bacteriophage ϕrio-1 infecting pseudoalteromonas marina.bacteria of the genus pseudoalteromonas are ubiquitous in the world's oceans. marine bacteria have been posited to be associated with a major ancient branch of podoviruses related to t7. yet, although pseudoalteromonas phages belonging to the corticoviridae and the siphoviridae and prophages belonging to the myoviridae have been reported, no pseudoalteromonas podovirus was previously known. here, a new lytic pseudoalteromonas marina phage, ϕrio-1, belonging to the podoviridae was isolated and ch ...201323760254
thermophilic and halophilic β-agarase from a halophilic archaeon halococcus sp. 197a.an agar-degrading archaeon halococcus sp. 197a was isolated from a solar salt sample. the agarase was purified by hydrophobic column chromatography using a column of toyopearl phenyl-650 m. the molecular mass of the purified enzyme, designated as aga-hc, was ~55 kda on both sds-page and gel-filtration chromatography. aga-hc released degradation products in the order of neoagarohexose, neoagarotetraose and small quantity of neoagarobiose, indicating that aga-hc was a β-type agarase. aga-hc showed ...201323949137
molecular cloning, characterization and enzymatic properties of a novel βeta-agarase from a marine isolate psudoalteromonas sp. ag52.an 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
diversity and evolution of bacterial twin arginine translocase protein, tatc, reveals a protein secretion system that is evolving to fit its environmental niche.the twin-arginine translocation (tat) protein export system enables the transport of fully folded proteins across a membrane. this system is composed of two integral membrane proteins belonging to tata and tatc protein families and in some systems a third component, tatb, a homolog of tata. tatc participates in substrate protein recognition through its interaction with a twin arginine leader peptide sequence.201324236045
regulatory and functional diversity of methylmercaptopropionate coenzyme a ligases from the dimethylsulfoniopropionate demethylation pathway in ruegeria pomeroyi dss-3 and other proteobacteria.the organosulfur compound dimethylsulfoniopropionate (dmsp) is produced by phytoplankton and is ubiquitous in the surface ocean. once released from phytoplankton, marine bacteria degrade dmsp by either the cleavage pathway to form the volatile gas dimethylsulfide (dms) or the demethylation pathway, yielding methanethiol (mesh), which is readily assimilated or oxidized. the enzyme dmdb, a methylmercaptopropionate (mmpa)-coenzyme a (coa) ligase, catalyzes the second step in the demethylation pathw ...201424443527
identification, cloning, and expression of l-amino acid oxidase from marine pseudoalteromonas sp. b3.l-amino acid oxidase (laao) is attracting more attentions due to its broad and important biological functions. recently, an laao-producing marine microorganism (strain b3) was isolated from the intertidal zone of dinghai sea area, china. physiological, biochemical, and molecular identifications together with phylogenetic analysis congruously suggested that it belonged to the genus pseudoalteromonas. therefore, it was designated as pseudoalteromonas sp. b3. its capability of laao production was c ...201424526926
bacterial genome instability.bacterial genomes are remarkably stable from one generation to the next but are plastic on an evolutionary time scale, substantially shaped by horizontal gene transfer, genome rearrangement, and the activities of mobile dna elements. this implies the existence of a delicate balance between the maintenance of genome stability and the tolerance of genome instability. in this review, we describe the specialized genetic elements and the endogenous processes that contribute to genome instability. we ...201424600039
annotation of protein domains reveals remarkable conservation in the functional make up of proteomes across superkingdoms.the functional repertoire of a cell is largely embodied in its proteome, the collection of proteins encoded in the genome of an organism. the molecular functions of proteins are the direct consequence of their structure and structure can be inferred from sequence using hidden markov models of structural recognition. here we analyze the functional annotation of protein domain structures in almost a thousand sequenced genomes, exploring the functional and structural diversity of proteomes. we find ...201124710297
overexpression and characterization of a novel thermostable β-agarase ym01-3, from marine bacterium catenovulum agarivorans ym01(t).genome sequencing of catenovulum agarivorans ym01t reveals 15 open-reading frames (orfs) encoding various agarases. in this study, extracellular proteins of ym01t were precipitated by ammonium sulfate and separated by one-dimensional gel electrophoresis. the results of in-gel agarase activity assay and mass spectrometry analysis revealed that the protein, ym01-3, was an agarase with the most evident agarolytic activity. agarase ym01-3, encoded by the ym01-3 gene, consisted of 420 amino acids wit ...201424824021
structural features of the pseudomonas fluorescens biofilm adhesin lapa required for lapg-dependent cleavage, biofilm formation, and cell surface localization.the localization of the lapa protein to the cell surface is a key step required by pseudomonas fluorescens pf0-1 to irreversibly attach to a surface and form a biofilm. lapa is a member of a diverse family of predicted bacterial adhesins, and although lacking a high degree of sequence similarity, family members do share common predicted domains. here, using mutational analysis, we determine the significance of each domain feature of lapa in relation to its export and localization to the cell sur ...201424837291
production and characterization of a novel thermostable extracellular agarase from pseudoalteromonas hodoensis newly isolated from the west sea of south korea.a gram-negative, aerobic, motile, rod-shaped, agarolytic bacterium, designated as h7, was isolated from a coastal seawater sample. this strain grows at ph 6.0-8.0, temperature of 15-40 °c, and at an nacl concentration of 1-7% (w/v). ubiquinone-8 was the predominant respiratory quinone, and the dna g+c content was 45.82 mol%. analysis of the 16s rrna sequence suggests that strain h7 belongs to the genus pseudoalteromonas. dna-dna hybridization analysis showed dna relatedness of as low as 55.42 an ...201424879592
genomes of alteromonas australica, a world apart.alteromonas is a genus of marine bacteria that is very easy to isolate and grow in the laboratory. there are genomes available of the species alteromonas macleodii from different locations around the world and an alteromonas sp. isolated from a sediment in korea. we have analyzed the genomes of two strains classified by 16s rrna (>99% similarity) as the recently described species alteromonas australica, and isolated from opposite ends of the world; a. australica de170 was isolated in the south a ...201424942065
microbiota from litopenaeus vannamei: digestive tract microbial community of pacific white shrimp (litopenaeus vannamei).bacteria capable of producing different extracellular enzymes of potential relevance in digestive processes were isolated from the stomach, hepatopancreas and intestine of pacific white shrimp litopenaeus vannamei. a total of 64 strains with proteolytic activity were isolated and grouped into 16 clusters based on morphological characteristics: 4 groups were isolated from the intestine; 5 from the hepatopancreas; and 7 from the stomach. molecular methods (16s rrna gene amplification and sequencin ...201424955302
molecular insight into the role of the n-terminal extension in the maturation, substrate recognition, and catalysis of a bacterial alginate lyase from polysaccharide lyase family 18.bacterial alginate lyases, which are members of several polysaccharide lyase (pl) families, have important biological roles and biotechnological applications. the mechanisms for maturation, substrate recognition, and catalysis of pl18 alginate lyases are still largely unknown. a pl18 alginate lyase, aly-sj02, from pseudoalteromonas sp. 0524 displays a β-jelly roll scaffold. structural and biochemical analyses indicated that the n-terminal extension in the aly-sj02 precursor may act as an intramo ...201425210041
conservation analysis of the cydx protein yields insights into small protein identification and evolution.the reliable identification of proteins containing 50 or fewer amino acids is difficult due to the limited information content in short sequences. the 37 amino acid cydx protein in escherichia coli is a member of the cytochrome bd oxidase complex, an enzyme found throughout eubacteria. to investigate the extent of cydx conservation and prevalence and evaluate different methods of small protein homologue identification, we surveyed 1095 eubacteria species for the presence of the small protein.201425475368
alkane hydroxylase genes in psychrophile genomes and the potential for cold active catalysis.psychrophiles are presumed to play a large role in the catabolism of alkanes and other components of crude oil in natural low temperature environments. in this study we analyzed the functional diversity of genes for alkane hydroxylases, the enzymes responsible for converting alkanes to more labile alcohols, as found in the genomes of nineteen psychrophiles for which alkane degradation has not been reported. to identify possible mechanisms of low temperature optimization we compared putative alka ...201425515036
marine-derived quorum-sensing inhibitory activities enhance the antibacterial efficacy of tobramycin against pseudomonas aeruginosa.bacterial epiphytes isolated from marine eukaryotes were screened for the production of quorum sensing inhibitory compounds (qsis). marine isolate ks8, identified as a pseudoalteromonas sp., was found to display strong quorum sensing inhibitory (qsi) activity against acyl homoserine lactone (ahl)-based reporter strains chromobacterium violaceum atcc 12472 and cv026. ks8 supernatant significantly reduced biofilm biomass during biofilm formation (-63%) and in pre-established, mature p. aeruginosa ...201425546516
marine-derived quorum-sensing inhibitory activities enhance the antibacterial efficacy of tobramycin against pseudomonas aeruginosa.bacterial epiphytes isolated from marine eukaryotes were screened for the production of quorum sensing inhibitory compounds (qsis). marine isolate ks8, identified as a pseudoalteromonas sp., was found to display strong quorum sensing inhibitory (qsi) activity against acyl homoserine lactone (ahl)-based reporter strains chromobacterium violaceum atcc 12472 and cv026. ks8 supernatant significantly reduced biofilm biomass during biofilm formation (-63%) and in pre-established, mature p. aeruginosa ...201425546516
life-style and genome structure of marine pseudoalteromonas siphovirus b8b isolated from the northwestern mediterranean sea.marine viruses (phages) alter bacterial diversity and evolution with impacts on marine biogeochemical cycles, and yet few well-developed model systems limit opportunities for hypothesis testing. here we isolate phage b8b from the mediterranean sea using pseudoalteromonas sp. qc-44 as a host and characterize it using myriad techniques. morphologically, phage b8b was classified as a member of the siphoviridae family. one-step growth analyses showed that this siphovirus had a latent period of 70 mi ...201525587991
comparative genomic and phylogenetic analyses of gammaproteobacterial glg genes traced the origin of the escherichia coli glycogen glgbxcap operon to the last common ancestor of the sister orders enterobacteriales and pasteurellales.production of branched α-glucan, glycogen-like polymers is widely spread in the bacteria domain. the glycogen pathway of synthesis and degradation has been fairly well characterized in the model enterobacterial species escherichia coli (order enterobacteriales, class gammaproteobacteria), in which the cognate genes (branching enzyme glgb, debranching enzyme glgx, adp-glucose pyrophosphorylase glgc, glycogen synthase glga, and glycogen phosphorylase glgp) are clustered in a glgbxcap operon arrang ...201525607991
alginate lyase: review of major sources and classification, properties, structure-function analysis and applications.alginate lyases catalyze the degradation of alginate, a complex copolymer of α-l-guluronate and its c5 epimer β-d-mannuronate. the enzymes have been isolated from various kinds of organisms with different substrate specificities, including algae, marine mollusks, marine and terrestrial bacteria, and some viruses and fungi. with the progress of structural biology, many kinds of alginate lyases of different polysaccharide lyases families have been characterized by obtaining crystal structures, and ...201525831216
from broad-spectrum biocides to quorum sensing disruptors and mussel repellents: antifouling profile of alkyl triphenylphosphonium salts.'onium' compounds, including ammonium and phosphonium salts, have been employed as antiseptics and disinfectants. these cationic biocides have been incorporated into multiple materials, principally to avoid bacterial attachment. in this work, we selected 20 alkyl-triphenylphosphonium salts, differing mainly in the length and functionalization of their alkyl chains, in fulfilment of two main objectives: 1) to provide a comprehensive evaluation of the antifouling profile of these molecules with re ...201525897858
coral symbiotic algae calcify ex hospite in partnership with bacteria.dinoflagellates of the genus symbiodinium are commonly recognized as invertebrate endosymbionts that are of central importance for the functioning of coral reef ecosystems. however, the endosymbiotic phase within symbiodinium life history is inherently tied to a more cryptic free-living (ex hospite) phase that remains largely unexplored. here we show that free-living symbiodinium spp. in culture commonly form calcifying bacterial-algal communities that produce aragonitic spherulites and encase t ...201525918367
structural and functional analysis of betaine aldehyde dehydrogenase from staphylococcus aureus.when exposed to high osmolarity, methicillin-resistant staphylococcus aureus (mrsa) restores its growth and establishes a new steady state by accumulating the osmoprotectant metabolite betaine. effective osmoregulation has also been implicated in the acquirement of a profound antibiotic resistance by mrsa. betaine can be obtained from the bacterial habitat or produced intracellularly from choline via the toxic betaine aldehyde (ba) employing the choline dehydrogenase and betaine aldehyde dehydro ...201525945581
seaweed hydrocolloid production: an update on enzyme assisted extraction and modification technologies.agar, alginate, and carrageenans are high-value seaweed hydrocolloids, which are used as gelation and thickening agents in different food, pharmaceutical, and biotechnological applications. the annual global production of these hydrocolloids has recently reached 100,000 tons with a gross market value just above us$ 1.1 billion. the techno-functional properties of the seaweed polysaccharides depend strictly on their unique structural make-up, notably degree and position of sulfation and presence ...201526023840
specific proteins in nontuberculous mycobacteria: new potential tools.nontuberculous mycobacteria (ntm) have been isolated from water, soil, air, food, protozoa, plants, animals, and humans. although most ntm are saprophytes, approximately one-third of ntm have been associated with human diseases. in this study, we did a comparative proteomic analysis among five ntm strains isolated from several sources. there were different numbers of protein spots from m. gordonae (1,264), m. nonchromogenicum type i (894), m. nonchromogenicum type ii (935), m. peregrinum (806), ...201526106621
biotechnological applications of functional metagenomics in the food and pharmaceutical industries.microorganisms are found throughout nature, thriving in a vast range of environmental conditions. the majority of them are unculturable or difficult to culture by traditional methods. metagenomics enables the study of all microorganisms, regardless of whether they can be cultured or not, through the analysis of genomic data obtained directly from an environmental sample, providing knowledge of the species present, and allowing the extraction of information regarding the functionality of microbia ...201526175729
purification and characterization of a fucoidanase (fnase s) from a marine bacterium sphingomonas paucimobilis pf-1.the search for enzyme activities that efficiently degrade marine polysaccharides is becoming an increasingly important area for both structural analysis and production of lower-molecular weight oligosaccharides. in this study, an endo-acting fucoidanase that degrades miyeokgui fucoidan (mf), a sulfated galactofucan isolated from the sporophyll (called miyeokgui in korean) of undaria pinnatifida, into smaller-sized galactofuco-oligosaccharides (1000-4000 da) was purified from a marine bacterium, ...201526193285
environmental pressure may change the composition protein disorder in prokaryotes.many prokaryotic organisms have adapted to incredibly extreme habitats. the genomes of such extremophiles differ from their non-extremophile relatives. for example, some proteins in thermophiles sustain high temperatures by being more compact than homologs in non-extremophiles. conversely, some proteins have increased volumes to compensate for freezing effects in psychrophiles that survive in the cold. here, we revealed that some differences in organisms surviving in extreme habitats correlate w ...201526252577
progress in the development of gelling agents for improved culturability of microorganisms.gelling agents are required for formulating both solid and semisolid media, vital for the isolation of microorganisms. gelatin was the first gelling agent to be discovered but it soon paved the way for agar, which has far superior material qualities. source depletion, issues with polymerase-chain-reaction and inability to sustain extermophiles etc., necessitate the need of other gelling agents. many new gelling agents, such as xantham gum, gellan gum, carrageenan, isubgol, and guar gum have been ...201526257708
the spot 42 rna: a regulatory small rna with roles in the central metabolism.the spot 42 rna is a 109 nucleotide long (in escherichia coli) noncoding small regulatory rna (srna) encoded by the spf (spot fourty-two) gene. spf is found in gamma-proteobacteria and the majority of experimental work on spot 42 rna has been performed using e. coli, and recently aliivibrio salmonicida. in the cell spot 42 rna plays essential roles as a regulator in carbohydrate metabolism and uptake, and its expression is activated by glucose, and inhibited by the camp-crp complex. here we summ ...201526327359
biochemical characterization of putative adenylate dimethylallyltransferase and cytokinin dehydrogenase from nostoc sp. pcc 7120.cytokinins, a class of phytohormones, are adenine derivatives common to many different organisms. in plants, these play a crucial role as regulators of plant development and the reaction to abiotic and biotic stress. key enzymes in the cytokinin synthesis and degradation in modern land plants are the isopentyl transferases and the cytokinin dehydrogenases, respectively. their encoding genes have been probably introduced into the plant lineage during the primary endosymbiosis. to shed light on th ...201526376297
impaired performance of pressure-retarded osmosis due to irreversible biofouling.next-generation pressure-retarded osmosis (pro) approaches aim to harness the energy potential of streams with high salinity differences, such as wastewater effluent and seawater desalination plant brine. in this study, we evaluated biofouling propensity in pro. bench-scale experiments were carried out for 24 h using a model wastewater effluent feed solution and simulated seawater desalination brine pressurized to 24 bar. for biofouling tests, wastewater effluent was inoculated with pseudomonas ...201526426100
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
enzyme-assisted preparation of furcellaran-like κ-/β-carrageenan.carrageenans are sulfated galactans that are widely used in industrial applications for their thickening and gelling properties, which vary according to the amount and distribution of ester sulfate groups along the galactan backbone. to determine and direct the sulfation of κ-carrageenan moieties, we purified an endo-κ-carrageenan sulfatase (q15xh1 accession in uniprotkb) from pseudoalteromonas atlantica t6c extracts. based on sequence analyses and exploration of the genomic environment of q15xh ...201626585588
biogenesis and growth phase-dependent alteration of 5-methoxycarbonylmethoxyuridine in trna anticodons.post-transcriptional modifications at the anticodon first (wobble) position of trna play critical roles in precise decoding of genetic codes. 5-carboxymethoxyuridine (cmo(5)u) and its methyl ester derivative 5-methoxycarbonylmethoxyuridine (mcmo(5)u) are modified nucleosides found at the anticodon wobble position in several trnas from gram-negative bacteria. cmo(5)u and mcmo(5)u facilitate non-watson-crick base pairing with guanosine and pyrimidines at the third positions of codons, thereby expa ...201526681692
biogenesis and growth phase-dependent alteration of 5-methoxycarbonylmethoxyuridine in trna anticodons.post-transcriptional modifications at the anticodon first (wobble) position of trna play critical roles in precise decoding of genetic codes. 5-carboxymethoxyuridine (cmo(5)u) and its methyl ester derivative 5-methoxycarbonylmethoxyuridine (mcmo(5)u) are modified nucleosides found at the anticodon wobble position in several trnas from gram-negative bacteria. cmo(5)u and mcmo(5)u facilitate non-watson-crick base pairing with guanosine and pyrimidines at the third positions of codons, thereby expa ...201526681692
mechanistic insights into c-di-gmp-dependent control of the biofilm regulator fleq from pseudomonas aeruginosa.bacterial biofilm formation during chronic infections confers increased fitness, antibiotic tolerance, and cytotoxicity. in many pathogens, the transition from a planktonic lifestyle to collaborative, sessile biofilms represents a regulated process orchestrated by the intracellular second-messenger c-di-gmp. a main effector for c-di-gmp signaling in the opportunistic pathogen pseudomonas aeruginosa is the transcription regulator fleq. fleq is a bacterial enhancer-binding protein (bebp) with a ce ...201626712005
mechanistic insights into c-di-gmp-dependent control of the biofilm regulator fleq from pseudomonas aeruginosa.bacterial biofilm formation during chronic infections confers increased fitness, antibiotic tolerance, and cytotoxicity. in many pathogens, the transition from a planktonic lifestyle to collaborative, sessile biofilms represents a regulated process orchestrated by the intracellular second-messenger c-di-gmp. a main effector for c-di-gmp signaling in the opportunistic pathogen pseudomonas aeruginosa is the transcription regulator fleq. fleq is a bacterial enhancer-binding protein (bebp) with a ce ...201626712005
metabolic pathway of 3,6-anhydro-d-galactose in carrageenan-degrading microorganisms.complete hydrolysis of κ-carrageenan produces two sugars, d-galactose and 3,6-anhydro-d-galactose (d-ang). at present, however, we do not know how carrageenan-degrading microorganisms metabolize d-ang. in this study, we investigated the metabolic pathway of d-ang degradation by comparative genomic analysis of cellulophaga lytica lim-21, pseudoalteromonas atlantica t6c, and epulopiscium sp. n.t. morphotype b, which represent the classes flavobacteria, gammaproteobacteria, and clostridia, respecti ...201626875872
pangenome evolution in the marine bacterium alteromonas.we have examined a collection of the free-living marine bacterium alteromonas genomes with cores diverging in average nucleotide identities ranging from 99.98% to 73.35%, i.e., from microbes that can be considered members of a natural clone (like in a clinical epidemiological outbreak) to borderline genus level. the genomes were largely syntenic allowing a precise delimitation of the core and flexible regions in each. the core was 1.4 mb (ca. 30% of the typical strain genome size). recombination ...201627189983
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
functional exploration of the polysaccharide lyase family pl6.alginate, the main cell-wall polysaccharide of brown algae, is composed of two residues: mannuronic acid (m-residues) and, its c5-epimer, guluronic acid (g-residues). alginate lyases define a class of enzymes that cleave the glycosidic bond of alginate by β-elimination. they are classified according to their ability to recognize the distribution of m- and g-residues and are named m-, g- or mg-lyases. in the cazy database, alginate lyases have been grouped by sequence similarity into seven distin ...201627438604
preliminary characterization of a novel β-agarase from thalassospira profundimonas.the objective of this study was to characterize the agarase from a newly isolated agarolytic bacterium thalassospira profundimaris fst-13007.201627468386
nitric oxide regulation of h-nox signaling pathways in bacteria.nitric oxide (no) is a freely diffusible, radical gas that has now been established as an integral signaling molecule in eukaryotes and bacteria. it has been demonstrated that no signaling is initiated upon ligation to the heme iron of an h-nox domain in mammals and in some bacteria. bacterial h-nox proteins have been found to interact with enzymes that participate in signaling pathways and regulate bacterial processes such as quorum sensing, biofilm formation, and symbiosis. here, we review the ...201627479081
bioprospecting red sea coastal ecosystems for culturable microorganisms and their antimicrobial potential.microorganisms that inhabit unchartered unique soil such as in the highly saline and hot red sea lagoons on the saudi arabian coastline, represent untapped sources of potentially new bioactive compounds. in this study, a culture-dependent approach was applied to three types of sediments: mangrove mud (mn), microbial mat (mm), and barren soil (bs), collected from rabigh harbor lagoon (rhl) and al-kharrar lagoon (akl). the isolated bacteria were evaluated for their potential to produce bioactive c ...201627626430
marine microbiological enzymes: studies with multiple strategies and prospects.marine microorganisms produce a series of promising enzymes that have been widely used or are potentially valuable for our daily life. both classic and newly developed biochemistry technologies have been broadly used to study marine and terrestrial microbiological enzymes. in this brief review, we provide a research update and prospects regarding regulatory mechanisms and related strategies of acyl-homoserine lactones (ahl) lactonase, which is an important but largely unexplored enzyme. we also ...201627669268
extremophiles in an antarctic marine ecosystem.recent attempts to explore marine microbial diversity and the global marine microbiome have indicated a large proportion of previously unknown diversity. however, sequencing alone does not tell the whole story, as it relies heavily upon information that is already contained within sequence databases. in addition, microorganisms have been shown to present small-to-large scale biogeographical patterns worldwide, potentially making regional combinations of selection pressures unique. here, we focus ...201627681902
matching the diversity of sulfated biomolecules: creation of a classification database for sulfatases reflecting their substrate specificity.sulfatases cleave sulfate groups from various molecules and constitute a biologically and industrially important group of enzymes. however, the number of sulfatases whose substrate has been characterized is limited in comparison to the huge diversity of sulfated compounds, yielding functional annotations of sulfatases particularly prone to flaws and misinterpretations. in the context of the explosion of genomic data, a classification system allowing a better prediction of substrate specificity a ...201627749924
networking in microbes: conjugative elements and plasmids in the genus alteromonas.to develop evolutionary models for the free living bacterium alteromonas the genome sequences of isolates of the genus have been extensively analyzed. however, the main genetic exchange drivers in these microbes, conjugative elements (ces), have not been considered in detail thus far. in this work, ces have been searched in several complete alteromonas genomes and their sequence studied to understand their role in the evolution of this genus. six genomes are reported here for the first time.201728056800
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