| 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 ... | 2008 | 18276643 |
| 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 ... | 2004 | 15258095 |
| 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. | 2007 | 17663799 |
| 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 ... | 2012 | 22555564 |
| 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 ... | 2009 | 20023723 |
| 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 ... | 1998 | 9729608 |
| 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. | 2014 | 25475368 |
| 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 ... | 2014 | 24600039 |
| 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 ... | 2016 | 26712005 |
| 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 ... | 2016 | 26712005 |
| 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 ... | 2008 | 18977196 |
| 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 ... | 2008 | 18977196 |
| kinetic bias in estimates of coastal picoplankton community structure obtained by measurements of small-subunit rrna gene pcr amplicon length heterogeneity | marine 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 ... | 1998 | 9797317 |
| 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. | 2010 | 20230630 |
| 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 ... | 2012 | 23234435 |
| 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 ... | 2014 | 24443527 |
| 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 ... | 2013 | 23486481 |
| molecular modeling of family gh16 glycoside hydrolases: potential roles for xyloglucan transglucosylases/hydrolases in cell wall modification in the poaceae. | family 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 (http://www.ghdb.uni-stuttgart.de) and provides multiple sequence alignments with fu ... | 2004 | 15557263 |
| 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 ... | 2010 | 20631875 |
| 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 ... | 2012 | 22685576 |
| 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 ... | 2015 | 26257708 |
| 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 ... | 2015 | 26023840 |
| 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. | 2009 | 19133128 |
| 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. | 2012 | 22740664 |
| 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 ... | 2013 | 23567318 |
| 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 ... | 2014 | 25515036 |
| 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 ... | 2014 | 24526926 |
| 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 ... | 2015 | 25587991 |
| 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 ... | 2016 | 27669268 |
| 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 ... | 2016 | 27189983 |
| 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 ... | 2016 | 27479081 |
| 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 ... | 2009 | 26443758 |
| 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- ... | 2010 | 24031567 |
| 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 ... | 2010 | 20454581 |
| 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. 3.2.1.158) and beta-agarase (e.c. 3.2.1.81) 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 ... | 2010 | 20161978 |
| 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 ... | 2011 | 22216139 |
| 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 ... | 2011 | 21840974 |
| 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 ... | 2011 | 21845096 |
| 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 ... | 2011 | 21339948 |
| 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 ... | 2012 | 23214453 |
| 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 ... | 2012 | 23214453 |
| 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 ... | 2012 | 23212172 |
| 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 ... | 2012 | 23111870 |
| 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 ... | 2012 | 23056356 |
| 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 ... | 2012 | 23019517 |
| 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. | 2012 | 22839777 |
| 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 ... | 2012 | 23087842 |
| 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 ... | 2012 | 22542454 |
| 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 ... | 2012 | 22430114 |
| 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. | 2013 | 24236045 |
| 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 ... | 2013 | 23949137 |
| 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 ... | 2013 | 23760254 |
| 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 ... | 2013 | 23620519 |
| 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 ... | 2013 | 23482393 |
| 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 ... | 2014 | 25546516 |
| 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 ... | 2014 | 25546516 |
| 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 ... | 2014 | 25210041 |
| 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 ... | 2014 | 24837291 |
| 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 ... | 2014 | 24942065 |
| 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 ... | 2014 | 24955302 |
| 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 ... | 2014 | 24824021 |
| 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 ... | 2015 | 26681692 |
| 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 ... | 2015 | 26681692 |
| 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 ... | 2015 | 26376297 |
| 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 ... | 2015 | 26327359 |
| 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 ... | 2015 | 26252577 |
| 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, ... | 2015 | 26193285 |
| 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), ... | 2015 | 26106621 |
| 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 ... | 2015 | 25918367 |
| 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 ... | 2015 | 25945581 |
| 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 ... | 2015 | 25897858 |
| 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 ... | 2015 | 25831216 |
| 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 ... | 2016 | 27438604 |
| 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. | 2016 | 27468386 |
| 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 ... | 2016 | 27681902 |
| 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. | 2017 | 28056800 |
| 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 ... | 2016 | 26875872 |
| 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 ... | 2016 | 26585588 |
| 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 ... | 2015 | 26426100 |
| 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 ... | 2014 | 24879592 |
| 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 ... | 2013 | 23179456 |
| 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 ... | 2013 | 23011004 |
| 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 ... | 2012 | 22521885 |
| 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 ... | 1998 | 27388645 |