| role of extracellular polymeric substances in the surface chemical reactivity of hymenobacter aerophilus, a psychrotolerant bacterium. | bacterial surface layers, such as extracellular polymeric substances (eps), are known to play an important role in metal sorption and biomineralization; however, there have been very few studies investigating how environmentally induced changes in eps production affect the cell's surface chemistry and reactivity. acid-base titrations, cadmium adsorption assays, and fourier transform infrared spectroscopy (ft-ir) were used to characterize the surface reactivities of hymenobacter aerophilus cells ... | 2010 | 19915039 |
| microscope: a platform for microbial genome annotation and comparative genomics. | the initial outcome of genome sequencing is the creation of long text strings written in a four letter alphabet. the role of in silico sequence analysis is to assist biologists in the act of associating biological knowledge with these sequences, allowing investigators to make inferences and predictions that can be tested experimentally. a wide variety of software is available to the scientific community, and can be used to identify genomic objects, before predicting their biological functions. h ... | 2009 | 20157493 |
| structure and flexibility in cold-adapted iron superoxide dismutases: the case of the enzyme isolated from pseudoalteromonas haloplanktis. | superoxide dismutases (sods) are metalloenzymes catalysing the dismutation of superoxide anion radicals into molecular oxygen and hydrogen peroxide. here, we present the crystal structure of a cold-adapted fe-sod from the antarctic eubacterium pseudoalteromonas haloplanktis (phsod), and that of its complex with sodium azide. the structures were compared with those of the corresponding homologues having a high sequence identity with phsod, such as the mesophilic sod from escherichia coli (ecsod) ... | 2010 | 20732427 |
| cold adaptation in dead-box proteins. | spontaneous rearrangements of rna structures are usually characterized by large activation energies and thus become very slow at low temperatures, yet rna structure must remain dynamic even in cold-adapted (psychrophilic) organisms. dead-box proteins constitute a ubiquitous family of rna-dependent atpases that can often unwind short rna duplexes in vitro (helicase activity), hence the belief that one of their major (though not exclusive) roles in vivo is to assist in rna rearrangements. here, we ... | 2010 | 20166751 |
| the nana neuraminidase of streptococcus pneumoniae is involved in biofilm formation. | streptococcus pneumoniae remains a major cause of bacteremia, pneumonia, and otitis media despite vaccines and effective antibiotics. the neuraminidase of s. pneumoniae, which catalyzes the release of terminal sialic acid residues from glycoconjugates, is involved in host colonization in animal models of infection and may provide a novel target for preventing pneumococcal infection. we demonstrate that the s. pneumoniae neuraminidase (nana) cleaves sialic acid and show that it is involved in bio ... | 2009 | 19564377 |
| repulsion and metabolic switches in the collective behavior of bacterial colonies. | bacteria inoculated on surfaces create colonies that spread out, forming patterns shaped by their mutual interactions. here, by a combination of experiments and modeling, we address two striking phenomena observed when colonies spread out circularly, without dendritic instabilities. first, the velocity of spreading is generically found to decrease as levels of nutrients initially deposited on the surface increase. we demonstrate that the slowdown is due to phenomena of differentiation, leading t ... | 2009 | 19651027 |
| antifouling activities expressed by marine surface associated pseudoalteromonas species. | abstract members of the marine bacterial genus pseudoalteromonas have been found in association with living surfaces and are suggested to produce bioactive compounds against settlement of algal spores, invertebrate larvae, bacteria and fungi. to determine the extent by which these antifouling activities and the production of bioactive compounds are distributed amongst the members of the genus pseudoalteromonas, 10 different pseudoalteromonas species mostly derived from different host organisms w ... | 2002 | 19709238 |
| from the cover: bacterial flagellum as a propeller and as a rudder for efficient chemotaxis. | we investigate swimming and chemotactic behaviors of the polarly flagellated marine bacteria vibrio alginolyticus in an aqueous medium. our observations show that v. alginolyticus execute a cyclic, three-step (forward, reverse, and flick) swimming pattern that is distinctively different from the run-tumble pattern adopted by escherichia coli. specifically, the bacterium backtracks its forward swimming path when the motor reverses. however, upon resuming forward swimming, the flagellum flicks and ... | 2011 | 21205908 |
| plasmids with a chromosome-like role in rhizobia. | replicon architecture in bacteria is commonly comprised of one indispensable chromosome and several dispensable plasmids. this view has been enriched by the discovery of additional chromosomes, identified mainly by localization of rrna and/or trna genes, and also by experimental demonstration of their requirement for cell growth. the genome of rhizobium etli cfn42 is constituted by one chromosome and six large plasmids, ranging in size from 184 to 642 kb. five of the six plasmids are dispensable ... | 2011 | 21217003 |
| pseudoalteromonas bacteria are capable of degrading paralytic shellfish toxins. | marine bacterial isolates cultured from the digestive tracts of blue mussels (mytilus edulis) contaminated with paralytic shellfish toxins (psts) were screened for the ability to reduce the toxicity of a pst mixture. seven isolates reduced the overall toxicity of the algal extract by > or = 90% within 3 days. these isolates shared at least 99% 16s rrna gene sequence similarity with five pseudoalteromonas spp. phenotypic tests suggested that all are novel strains of pseudoalteromonas haloplanktis ... | 2009 | 19717625 |
| reverse and flick: hybrid locomotion in bacteria. | | 2011 | 21289282 |
| srmb, a dead-box helicase involved in escherichia coli ribosome assembly, is specifically targeted to 23s rrna in vivo. | dead-box proteins play specific roles in remodeling rna or ribonucleoprotein complexes. yet, in vitro, they generally behave as nonspecific rna-dependent atpases, raising the question of what determines their specificity in vivo. srmb, one of the five escherichia coli dead-box proteins, participates in the assembly of the large ribosomal subunit. moreover, when overexpressed, it compensates for a mutation in l24, the ribosomal protein (r-protein) thought to initiate assembly. here, using the tan ... | 2009 | 19734346 |
| molecular characterization of a novel n-acetylneuraminate lyase from lactobacillus plantarum wcfs1. | n-acetylneuraminate lyases (nals) or sialic acid aldolases catalyze the reversible aldol cleavage of n-acetylneuraminic acid (neu5ac) to form pyruvate and n-acetyl-d-mannosamine (mannac). in nature, n-acetylneuraminate lyase occurs mainly in pathogens. however, this paper describes how an n-acetylneuraminate lyase was cloned from the human gut commensal lactobacillus plantarum wcfs1 (lpnal), overexpressed, purified, and characterized for the first time. this novel enzyme, which reaches a high ex ... | 2011 | 21317263 |
| engineering of a psychrophilic bacterium for the bioremediation of aromatic compounds. | microbial degradation of aromatic hydrocarbons has been studied with the aim of developing applications for the removal of toxic compounds. efforts have been directed toward the genetic manipulation of mesophilic bacteria to improve their ability to degrade pollutants, even though many pollution problems occur in sea waters and in effluents of industrial processes which are characterized by low temperatures. from these considerations the idea of engineering a psychrophilic microorganism for the ... | 2010 | 21326928 |
| structure and dynamics of cold-adapted enzymes as investigated by phosphorescence spectroscopy and molecular dynamics studies. 2. the case of an esterase from pseudoalteromonas haloplanktis. | enzymes from psychrophiles display high catalytic efficiency at low temperatures. as a consequence, there is a lot of academic and industrial interest in investigating the molecular strategies adopted from these enzymes to work in conditions where other enzymes are almost inactive. recently, a novel esterase activity was identified and isolated from the cold-adapted organism pseudoalteromonas haloplanktis. the enzyme, named phest, is a dimer with a molecular mass of 60 kda composed of two identi ... | 2009 | 19754077 |
| heterogeneous electron transfer of a two-centered heme protein: redox and electrocatalytic properties of surface-immobilized cytochrome c(4). | the recombinant diheme cytochrome c(4) from the psycrophilic bacterium pseudoalteromonas haloplanktis tac 125 and its met64ala and met164ala variants, which feature a hydroxide ion axially bound to the heme iron at the n- and c-terminal domains, respectively, were found to exchange electrons efficiently with a gold electrode coated with a sam of 11-mercapto-1-undecanoic acid. the mutation-induced removal of the redox equivalence of the two heme groups and changes in the net charge of the protein ... | 2009 | 19764800 |
| structural properties of 2/2 hemoglobins: the group iii protein from helicobacter hepaticus. | the e-proteobacterium helicobacter hepaticus (hh) contains a gene coding for a hemoglobin (hb). the protein belongs to the 2/2 hb lineage and is representative of group iii, a set of hbs about which little is known. an expression and purification procedure was developed for hh hb. electronic absorption and nuclear magnetic resonance (nmr) spectra were used to characterize ligation states of the ferric and ferrous protein. the pk(a) of the acid/alkaline transition of ferric hh hb was 7.3, an unus ... | 2011 | 21445851 |
| pssa is required for alpha-amylase secretion in antarctic pseudoalteromonas haloplanktis. | extracellular protein secretion is an essential feature in bacterial physiology. the ability to efficiently secrete diverse hydrolytic enzymes represents a key nutritional strategy for all bacteria, including micro-organisms living in extreme and hostile habitats, such as cold environments. however, little is known about protein secretion mechanisms in psychrophilic bacteria. in this study, the recombinant secretion of a cold-adapted alpha-amylase in the antarctic gram-negative pseudoalteromonas ... | 2010 | 19778966 |
| a natural plasmid uniquely encodes two biosynthetic pathways creating a potent anti-mrsa antibiotic. | understanding how complex antibiotics are synthesised by their producer bacteria is essential for creation of new families of bioactive compounds. thiomarinols, produced by marine bacteria belonging to the genus pseudoalteromonas, are hybrids of two independently active species: the pseudomonic acid mixture, mupirocin, which is used clinically against mrsa, and the pyrrothine core of holomycin. | 2011 | 21483852 |
| 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 ... | 2011 | 21519847 |
| characterization of a cryptic plasmid psm429 and its application for heterologous expression in psychrophilic pseudoalteromonas. | abstract: background: pseudoalteromonas is an important genus widespread in marine environment, and a lot of psychrophilic pseudoalteromonas strains thrive in deep sea and polar sea. by now, there are only a few genetic systems for pseudoalteromonas reported and no commercial pseudoalteromonas genetic system is available, which impedes the study of pseudoalteromonas, especially for psychrophilic strains. the aim of this study is to develop a heterologous expression system for psychrophilic pseud ... | 2011 | 21542941 |
| engineering microbial biofuel tolerance and export using efflux pumps. | many compounds being considered as candidates for advanced biofuels are toxic to microorganisms. this introduces an undesirable trade-off when engineering metabolic pathways for biofuel production because the engineered microbes must balance production against survival. cellular export systems, such as efflux pumps, provide a direct mechanism for reducing biofuel toxicity. to identify novel biofuel pumps, we used bioinformatics to generate a list of all efflux pumps from sequenced bacterial geno ... | 2011 | 21556065 |
| neurotoxic alkaloids: saxitoxin and its analogs. | saxitoxin (stx) and its 57 analogs are a broad group of natural neurotoxic alkaloids, commonly known as the paralytic shellfish toxins (psts). psts are the causative agents of paralytic shellfish poisoning (psp) and are mostly associated with marine dinoflagellates (eukaryotes) and freshwater cyanobacteria (prokaryotes), which form extensive blooms around the world. pst producing dinoflagellates belong to the genera alexandrium, gymnodinium and pyrodinium whilst production has been identified in ... | 2010 | 20714432 |
| characterization of the rna degradosome of pseudoalteromonas haloplanktis: conservation of the rnase e-rhlb interaction in the gammaproteobacteria. | the degradosome is a multienzyme complex involved in mrna degradation in escherichia coli. the essential endoribonuclease rnase e contains a large noncatalytic region necessary for protein-protein interactions with other components of the rna degradosome. interacting proteins include the dead-box rna helicase rhlb, the glycolytic enzyme enolase, and the exoribonuclease pnpase. pseudoalteromonas haloplanktis, a psychrotolerant gammaproteobacterium distantly related to e. coli, encodes homologs of ... | 2010 | 20729366 |
| fed-batch process for the psychrotolerant marine bacterium pseudoalteromonas haloplanktis. | pseudoalteromonas haloplanktis is a cold-adapted γ-proteobacterium isolated from antarctic sea ice. it is characterized by remarkably high growth rates at low temperatures. p. haloplanktis is one of the model organisms of cold-adapted bacteria and has been suggested as an alternative host for the soluble overproduction of heterologous proteins which tend to form inclusion bodies in established expression hosts. despite the progress in establishing p. haloplanktis as an alternative expression hos ... | 2010 | 20858251 |
| the peculiar heme pocket of the 2/2 hemoglobin of cold-adapted pseudoalteromonas haloplanktis tac125. | the genome of the cold-adapted bacterium pseudoalteromonas haloplanktis tac125 contains multiple genes encoding three distinct monomeric hemoglobins exhibiting a 2/2 α-helical fold. in the present work, one of these hemoglobins is studied by resonance raman, electronic absorption and electronic paramagnetic resonance spectroscopies, kinetic measurements, and different bioinformatic approaches. it is the first cold-adapted bacterial hemoglobin to be characterized. the results indicate that this p ... | 2010 | 21076847 |
| proteomics of life at low temperatures: trigger factor is the primary chaperone in the antarctic bacterium pseudoalteromonas haloplanktis tac125. | the proteomes expressed at 4 degrees c and 18 degrees c by the psychrophilic antarctic bacterium pseudoalteromonas haloplanktis have been compared using two-dimensional differential in-gel electrophoresis, showing that translation, protein folding, membrane integrity and anti-oxidant activities are upregulated at 4 degrees c. this proteomic analysis revealed that the trigger factor is the main upregulated protein at low temperature. the trigger factor is the first molecular chaperone interacting ... | 2010 | 20199592 |
| crystal structure of an s-formylglutathione hydrolase from pseudoalteromonas haloplanktis tac125. | s-formylglutathione hydrolases (fghs) constitute a family of ubiquitous enzymes which play a key role in formaldehyde detoxification both in prokaryotes and eukaryotes, catalyzing the hydrolysis of s-formylglutathione to formic acid and glutathione. while a large number of functional studies have been reported on these enzymes, few structural studies have so far been carried out. in this article we report on the functional and structural characterization of phest, a fgh isolated from the psychro ... | 2010 | 20209484 |
| three feruloyl esterases in cellulosilyticum ruminocola h1 act synergistically to hydrolyze esterified polysaccharides. | feruloyl esterases (faes) constitute a subclass of carboxyl esterases that specially hydrolyze the ester linkages between ferulate and polysaccharides in plant cell walls. until now, the described microbial faes were mainly from fungi. in this study, we reported that cellulosilyticum ruminocola h1, a previously described fibrolytic rumen bacterium, possesses three differing active feruloyl esterases, faei, faeii, and faeiii. phylogenetic analysis classified the described bacterial faes into two ... | 2011 | 21764976 |
| general secretory pathway from marine antarctic pseudoalteromonas haloplanktis tac125. | in gram-negative bacteria type ii secretion system (t2ss) is one of six protein secretion machineries that permit the export of proteins from within the bacterial cell to the extra-cellular milieu and/or into target host cells. the ability to secrete proteins in the extra-cellular medium is a key aspect of the physiology of gram-negative bacteria. indeed, secreted proteins provide the means, among others, by which microorganisms interact and modify the surrounding environment. this is a crucial ... | 2009 | 21798163 |
| influence of production process design on inclusion bodies protein: the case of an antarctic flavohemoglobin. | protein over-production in escherichia coli often results in formation of inclusion bodies (ibs). some recent reports have shown that the aggregation into ibs does not necessarily mean that the target protein is inactivated and that ibs may contain a high proportion of correctly folded protein. this proportion is variable depending on the protein itself, the genetic background of the producing cells and the expression temperature. in this paper we have evaluated the influence of other production ... | 2010 | 20334669 |
| finding new enzymes from bacterial physiology: a successful approach illustrated by the detection of novel oxidases in marinomonas mediterranea. | the identification and study of marine microorganisms with unique physiological traits can be a very powerful tool discovering novel enzymes of possible biotechnological interest. this approach can complement the enormous amount of data concerning gene diversity in marine environments offered by metagenomic analysis, and can help to place the activities associated with those sequences in the context of microbial cellular metabolism and physiology. accordingly, the detection and isolation of micr ... | 2010 | 20411113 |
| 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 ... | 2011 | 22194940 |
| cytoplasmic and periplasmic proteomic signatures of exponentially growing cells of the psychrophilic bacterium pseudoalteromonas haloplanktis tac125. | the psychrophilic model bacterium pseudoalteromonas haloplanktis is characterized by remarkably fast growth rates under low-temperature conditions in a range from 5°c to 20°c. in this study the proteome of cellular compartments, the cytoplasm and periplasm, of p. haloplanktis strain tac125 was analyzed under exponential growth conditions at a permissive temperature of 16°c. by means of two-dimensional protein gel electrophoresis and mass spectrometry, a first inventory of the most abundant cytop ... | 2010 | 21183643 |
| a novel cold-active beta-d-galactosidase from the paracoccus sp. 32d - gene cloning, purification and characterization. | abstract: background: beta-d-galactosidases (ec 3.2.1.23) catalyze the hydrolysis of terminal non-reducing beta-d-galactose residues in beta-d-galactosides. cold-active beta-d-galactosidases have recently become a focus of attention of researchers and dairy product manufactures owing to theirs ability to: (i) eliminate of lactose from refrigerated milk for people afflicted with lactose intolerance, (ii) convert lactose to glucose and galactose which increase the sweetness of milk and decreases ... | 2011 | 22166118 |
| FK506-Binding Protein 22 from a Psychrophilic Bacterium, a Cold Shock-Inducible Peptidyl Prolyl Isomerase with the Ability to Assist in Protein Folding. | Adaptation of microorganisms to low temperatures remains to be fully elucidated. It has been previously reported that peptidyl prolyl cis-trans isomerases (PPIases) are involved in cold adaptation of various microorganisms whether they are hyperthermophiles, mesophiles or phsycrophiles. The rate of cis-trans isomerization at low temperatures is much slower than that at higher temperatures and may cause problems in protein folding. However, the mechanisms by which PPIases are involved in cold ada ... | 2011 | 21954357 |
| cytoplasmic and periplasmic proteomic signatures of exponentially growing cells of the psychrophilic bacterium pseudoalteromonas haloplanktis tac125. | the psychrophilic model bacterium pseudoalteromonas haloplanktis is characterized by remarkably fast growth rates under low-temperature conditions in a range from 5°c to 20°c. in this study the proteome of cellular compartments, the cytoplasm and periplasm, of p. haloplanktis strain tac125 was analyzed under exponential growth conditions at a permissive temperature of 16°c. by means of two-dimensional protein gel electrophoresis and mass spectrometry, a first inventory of the most abundant cytop ... | 2010 | 21183643 |
| comprehensive prediction of chromosome dimer resolution sites in bacterial genomes. | during the replication process of bacteria with circular chromosomes, an odd number of homologous recombination events results in concatenated dimer chromosomes that cannot be partitioned into daughter cells. however, many bacteria harbor a conserved dimer resolution machinery consisting of one or two tyrosine recombinases, xerc and xerd, and their 28-bp target site, dif. | 2011 | 21223577 |
| influence of growth temperature on the production of antibody fab fragments in different microbes: a host comparative analysis. | microorganisms encounter diverse stress conditions in their native habitats but also during fermentation processes, which have an impact on industrial process performance. these environmental stresses and the physiological reactions they trigger, including changes in the protein folding/secretion machinery, are highly interrelated. thus, the investigation of environmental factors, which influence protein expression and secretion is still of great importance. among all the possible stresses, temp ... | 2010 | 21312353 |
| structure and function of an arabinoxylan-specific xylanase. | the enzymatic degradation of plant cell walls plays a central role in the carbon cycle and is of increasing environmental and industrial significance. the enzymes that catalyze this process include xylanases that degrade xylan, a ß-1,4-xylose polymer that is decorated with various sugars. although xylanases efficiently hydrolyze unsubstituted xylans, these enzymes are unable to access highly decorated forms of the polysaccharide, such as arabinoxylans that contain arabinofuranose decorations. he ... | 2011 | 21378160 |
| Heterologous production of bisucaberin using a biosynthetic gene cluster cloned from a deep sea metagenome. | A siderophore biosynthetic gene cluster was cloned from a metagenomic library generated from deep sea sediment. The gene cluster was successfully expressed in Escherichia coli to produce bisucaberin, a siderophore originally reported from the marine bacterium Alteromonas haloplanktis. The cloned bisucaberin biosynthetic gene cluster was moderately similar to that of the known bisucaberin producer Vibrio salmonicida. However, the cloned gene cluster consists of four genes rather than three genes ... | 2011 | 22051782 |
| suitability of different β-galactosidases as reporter enzymes in bacillus subtilis. | the suitability of three β-galactosidases as reporter enzymes for promoter expression analyses was investigated in bacillus subtilis with respect to various temperature conditions during cultivation and assay procedures. starting from the hypothesis that proteins derived from diverse habitats have different advantages as reporters at different growth temperatures, the beta-galactosidases from the thermophilic organism bacillus stearothermophilus, from the mesophilic bacterium escherichia coli an ... | 2011 | 22052389 |
| the metj regulon in gammaproteobacteria determined by comparative genomics methods. | whole-genome sequencing of bacteria has proceeded at an exponential pace but annotation validation has lagged behind. for instance, the metj regulon, which controls methionine biosynthesis and transport, has been studied almost exclusively in e. coli and salmonella, but homologs of metj exist in a variety of other species. these include some that are pathogenic (e.g. yersinia) and some that are important for environmental remediation (e.g. shewanella) but many of which have not been extensively ... | 2011 | 22082356 |
| production of metabolites as bacterial responses to the marine environment. | bacteria in marine environments are often under extreme conditions of e.g., pressure, temperature, salinity, and depletion of micronutrients, with survival and proliferation often depending on the ability to produce biologically active compounds. some marine bacteria produce biosurfactants, which help to transport hydrophobic low water soluble substrates by increasing their bioavailability. however, other functions related to heavy metal binding, quorum sensing and biofilm formation have been de ... | 2010 | 20411122 |
| composition and conservation of the mrna-degrading machinery in bacteria. | rna synthesis and decay counteract each other and therefore inversely regulate gene expression in pro- and eukaryotic cells by controlling the steady-state level of individual transcripts. genetic and biochemical data together with recent in depth annotation of bacterial genomes indicate that many components of the bacterial rna decay machinery are evolutionarily conserved and that their functional analogues exist in organisms belonging to all kingdoms of life. here we briefly review biological ... | 2011 | 21418661 |
| the role of a 2-on-2 haemoglobin in oxidative and nitrosative stress resistance of antarctic pseudoalteromonas haloplanktis tac125. | the 2-on-2 haemoglobins, previously named truncated, are monomeric, low-molecular weight oxygen-binding proteins that share the overall topology with vertebrate haemoglobins. although several studies on 2-on-2 haemoglobins have been reported, their physiological and biochemical functions are not yet well defined, and various roles have been suggested. the genome of the psychrophilic antarctic marine bacterium pseudoalteromonas haloplanktis tac125 (phtac125) is endowed with three genes encoding 2 ... | 2010 | 20434514 |
| backbone and side chain 1h, 15n and 13c assignments for a thiol-disulphide oxidoreductase from the antarctic bacterium pseudoalteromonas haloplanktis tac125. | enzymes produced by psychrophilic organisms have successfully overcome the low temperature challenge and evolved to maintain high catalytic rates in their permanently cold environments. as an initial step in our attempt to elucidate the cold-adaptation strategies used by these enzymes we report here the (1)h, (15)n and (13)c assignments for the reduced form of a thiol-disulphide oxidoreductase from the antarctic bacterium pseudoalteromonas haloplanktis tac125. | 2010 | 20455034 |
| ecogenomics and genome landscapes of marine pseudoalteromonas phage h105/1. | marine phages have an astounding global abundance and ecological impact. however, little knowledge is derived from phage genomes, as most of the open reading frames in their small genomes are unknown, novel proteins. to infer potential functional and ecological relevance of sequenced marine pseudoalteromonas phage h105/1, two strategies were used. first, similarity searches were extended to include six viral and bacterial metagenomes paired with their respective environmental contextual data. th ... | 2011 | 20613791 |
| ecogenomics and genome landscapes of marine pseudoalteromonas phage h105/1. | marine phages have an astounding global abundance and ecological impact. however, little knowledge is derived from phage genomes, as most of the open reading frames in their small genomes are unknown, novel proteins. to infer potential functional and ecological relevance of sequenced marine pseudoalteromonas phage h105/1, two strategies were used. first, similarity searches were extended to include six viral and bacterial metagenomes paired with their respective environmental contextual data. th ... | 2011 | 20613791 |
| life in the cold: a proteomic study of cold-repressed proteins in the antarctic bacterium pseudoalteromonas haloplanktis tac125. | the proteomes expressed at 4°c and 18°c by the psychrophilic antarctic bacterium pseudoalteromonas haloplanktis were compared using two-dimensional differential in-gel electrophoresis with special reference to proteins repressed by low temperatures. remarkably, the major cold-repressed proteins, almost undetectable at 4°c, were heat shock proteins involved in folding assistance. | 2011 | 21478318 |
| comparative metagenomics of bathypelagic plankton and bottom sediment from the sea of marmara. | to extend comparative metagenomic analyses of the deep-sea, we produced metagenomic data by direct 454 pyrosequencing from bathypelagic plankton (1000 m depth) and bottom sediment of the sea of marmara, the gateway between the eastern mediterranean and the black seas. data from small subunit ribosomal rna (ssu rrna) gene libraries and direct pyrosequencing of the same samples indicated that gamma- and alpha-proteobacteria, followed by bacteroidetes, dominated the bacterial fraction in marmara d ... | 2011 | 20668488 |
| 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 ... | 2011 | 24710297 |
| comparative metagenomics of bathypelagic plankton and bottom sediment from the sea of marmara. | to extend comparative metagenomic analyses of the deep-sea, we produced metagenomic data by direct 454 pyrosequencing from bathypelagic plankton (1000 m depth) and bottom sediment of the sea of marmara, the gateway between the eastern mediterranean and the black seas. data from small subunit ribosomal rna (ssu rrna) gene libraries and direct pyrosequencing of the same samples indicated that gamma- and alpha-proteobacteria, followed by bacteroidetes, dominated the bacterial fraction in marmara d ... | 2011 | 20668488 |
| 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 ... | 2015 | 25607991 |
| bioinformatic analyses of integral membrane transport proteins encoded within the genome of the planctomycetes species, rhodopirellula baltica. | rhodopirellula baltica (r. baltica) is a planctomycete, known to have intracellular membranes. because of its unusual cell structure and ecological significance, we have conducted comprehensive analyses of its transmembrane transport proteins. the complete proteome of r. baltica was screened against the transporter classification database (tcdb) to identify recognizable integral membrane transport proteins. 342 proteins were identified with a high degree of confidence, and these fell into severa ... | 2013 | 23969110 |
| bioinformatic analyses of integral membrane transport proteins encoded within the genome of the planctomycetes species, rhodopirellula baltica. | rhodopirellula baltica (r. baltica) is a planctomycete, known to have intracellular membranes. because of its unusual cell structure and ecological significance, we have conducted comprehensive analyses of its transmembrane transport proteins. the complete proteome of r. baltica was screened against the transporter classification database (tcdb) to identify recognizable integral membrane transport proteins. 342 proteins were identified with a high degree of confidence, and these fell into severa ... | 2013 | 23969110 |
| the selective value of bacterial shape. | why do bacteria have shape? is morphology valuable or just a trivial secondary characteristic? why should bacteria have one shape instead of another? three broad considerations suggest that bacterial shapes are not accidental but are biologically important: cells adopt uniform morphologies from among a wide variety of possibilities, some cells modify their shape as conditions demand, and morphology can be tracked through evolutionary lineages. all of these imply that shape is a selectable featur ... | 2006 | 16959965 |
| comparative genomics reveals a deep-sea sediment-adapted life style of pseudoalteromonas sp. sm9913. | deep-sea sediment is one of the most important microbial-driven ecosystems, yet it is not well characterized. genome sequence analyses of deep-sea sedimentary bacteria would shed light on the understanding of this ecosystem. in this study, the complete genome of deep-sea sedimentary bacterium pseudoalteromonas sp. sm9913 (sm9913) is described and compared with that of the closely related antarctic surface sea-water ecotype pseudoalteromonas haloplanktis tac125 (tac125). sm9913 has fewer dioxygen ... | 2011 | 20703316 |
| comparative genomics reveals a deep-sea sediment-adapted life style of pseudoalteromonas sp. sm9913. | deep-sea sediment is one of the most important microbial-driven ecosystems, yet it is not well characterized. genome sequence analyses of deep-sea sedimentary bacteria would shed light on the understanding of this ecosystem. in this study, the complete genome of deep-sea sedimentary bacterium pseudoalteromonas sp. sm9913 (sm9913) is described and compared with that of the closely related antarctic surface sea-water ecotype pseudoalteromonas haloplanktis tac125 (tac125). sm9913 has fewer dioxygen ... | 2011 | 20703316 |
| thalassospira sp. isolated from the oligotrophic eastern mediterranean sea exhibits chemotaxis toward inorganic phosphate during starvation. | the eastern mediterranean sea represents an ultraoligotrophic environment where soluble phosphate limits the growth of bacterioplankton. correspondingly, genes coding for high affinity phosphate uptake systems and for organophosphonate utilization are highly prevalent in the plankton metagenome. chemotaxis toward inorganic phosphate constitutes an alternative strategy to cope with phosphate limitation, but so far has only been demonstrated for two bacterial pathogens and an archaeon, and not in ... | 2011 | 21602377 |
| genomic and proteomic analysis of invertebrate iridovirus type 9. | iridoviruses are nuclear cytoplasmic large dna viruses that are receiving increasing attention as sublethal pathogens of a range of insects. invertebrate iridovirus type 9 (iiv-9; wiseana iridovirus) is a member of the major phylogenetic group of iridoviruses for which there is very limited genomic and proteomic information. the genome is 205,791 bp with a %g+c content of 31% encoding 191 predicted genes with approximately 20% repeat sequences located predominantly within coding regions. the rep ... | 2011 | 21632757 |
| the secondary substrate binding site of the pseudoalteromonas haloplanktis gh8 xylanase is relevant for activity on insoluble but not soluble substrates. | previously, it has been demonstrated that the glycoside hydrolase family 8 xylanase from the psychrophylic bacterium pseudoalteromonas haloplanktis (xph) can bind substrate non-catalytically on the surface of its catalytic module. in the present study, the functional relevance of this secondary binding site (sbs) for the enzyme is investigated by site-directed mutagenesis and evaluation of activity and binding properties of mutant variants on a range of structurally different homoxylan and heter ... | 2011 | 21656141 |
| use of psychrophilic xylanases provides insight into the xylanase functionality in bread making. | the bread improving potential of three psychrophilic xylanases from pseudoalteromonas haloplanktis tah3a (xph), flavobacterium sp. msy-2 (rxfh) and unknown bacterial origin (rxyn8) was compared to that of the mesophilic xylanases from bacillus subtilis (xbs) and aspergillus aculeatus (xaa). xph, rxfh and rxyn8 increased specific bread volumes up to 28%, 18% and 18%, respectively, while xbs and xaa gave increases of 23% and 12%, respectively. this could be related to their substrate hydrolysis be ... | 2011 | 21806059 |
| metaproteomics reveals major microbial players and their biodegradation functions in a large-scale aerobic composting plant. | composting is an appropriate management alternative for municipal solid waste; however, our knowledge about the microbial regulation of this process is still scare. we employed metaproteomics to elucidate the main biodegradation pathways in municipal solid waste composting system across the main phases in a large-scale composting plant. the investigation of microbial succession revealed that bacillales, actinobacteria and saccharomyces increased significantly with respect to abundance in compost ... | 2015 | 25989417 |
| structural prediction and comparative docking studies of psychrophilic ß- galactosidase with lactose, onpg and pnpg against its counter parts of mesophilic and thermophilic enzymes. | enzymes from psychrophiles catalyze the reactions at low temperatures with higher specific activity. among all the psychrophilic enzymes produced, cold active ß-galactosidase from marine psychrophiles revalorizes a new arena in numerous areas at industrial level. the hydrolysis of lactose in to glucose and galactose by cold active ß-galactosidase offers a new promising approach in removal of lactose from milk to overcome the problem of lactose intolerance. herein we propose, a 3d structure of co ... | 2011 | 21769193 |
| functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter. | targeting sequencing to genes involved in key environmental processes, i.e., ecofunctional genes, provides an opportunity to sample nature's gene guilds to greater depth and help link community structure to process-level outcomes. vastly different approaches have been implemented for sequence processing and, ultimately, for taxonomic placement of these gene reads. the overall quality of next generation sequence analysis of functional genes is dependent on multiple steps and assumptions of unknow ... | 2013 | 24062736 |
| cold-adapted bacteria and the globin case study in the antarctic bacterium pseudoalteromonas haloplanktis tac125. | environmental oxygen availability may play an important role in the evolution of polar marine organisms, as suggested by the physiological and biochemical strategies adopted by these organisms to acquire, deliver and scavenge oxygen. stress conditions such as extreme temperatures increase the production of reactive oxygen species (ros) in cells. thus, in order to prevent cellular damage, adjustments in antioxidant defences are needed to maintain the steady-state concentration of ros. cold-adapte ... | 2010 | 21798206 |
| reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes. | the increasing number of sequenced prokaryotic genomes contains a wealth of genomic data that needs to be effectively analysed. a set of statistical tools exists for such analysis, but their strengths and weaknesses have not been fully explored. the statistical methods we are concerned with here are mainly used to examine similarities between archaeal and bacterial dna from different genomes. these methods compare observed genomic frequencies of fixed-sized oligonucleotides with expected values, ... | 2008 | 18307761 |
| a persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations. | acute exacerbations of chronic obstructive pulmonary disease (copd) are a major source of morbidity and contribute significantly to healthcare costs. although bacterial infections are implicated in nearly 50% of exacerbations, only a handful of pathogens have been consistently identified in copd airways, primarily by culture-based methods, and the bacterial microbiota in acute exacerbations remains largely uncharacterized. the aim of this study was to comprehensively profile airway bacterial com ... | 2010 | 20141328 |
| ligand- and proton-linked conformational changes of the ferrous 2/2 hemoglobin of pseudoalteromonas haloplanktis tac125. | the spectroscopic and ligand-binding properties of a 2/2 globin from the antarctic bacterium pseudoalteromonas haloplanktis tac125 have been studied in the ferrous state. it displays two major conformations characterized by co-association rates that differ by a factor of 20, with relative fractions that depend on ph. a dynamic equilibrium is found between the two conformations, as indicated by an enhanced slower phase when lower co levels were used to allow a longer time to facilitate the transi ... | 2011 | 21698762 |
| Identification of the antibacterial compound produced by the marine epiphytic bacterium Pseudovibrio sp. D323 and related sponge-associated bacteria. | Surface-associated marine bacteria often produce secondary metabolites with antagonistic activities. In this study, tropodithietic acid (TDA) was identified to be responsible for the antibacterial activity of the marine epiphytic bacterium Pseudovibrio sp. D323 and related strains. Phenol was also produced by these bacteria but was not directly related to the antibacterial activity. TDA was shown to effectively inhibit a range of marine bacteria from various phylogenetic groups. However TDA-prod ... | 2011 | 21892353 |
| Distinct Roles of ß-Galactosidase Paralogues of the Rumen Bacterium Mannheimia succiniciproducens. | Mannheimia succiniciproducens, a rumen bacterium belonging to the family Pasteurellaceae, has two putative ß-galactosidase genes, bgaA and bgaB, encoding polypeptides whose deduced amino acid sequences share 56% identity with each other and show approximately 30% identity to the Escherichia coli gene for LacZ. The M. succiniciproducens bgaA (MsbgaA) gene-deletion mutant was not able to grow on lactose as the sole carbon source, suggesting its essential role in lactose metabolism, whereas the Msb ... | 2012 | 22081396 |
| evolution of the chaperone/usher assembly pathway: fimbrial classification goes greek. | many proteobacteria use the chaperone/usher pathway to assemble proteinaceous filaments on the bacterial surface. these filaments can curl into fimbrial or nonfimbrial surface structures (e.g., a capsule or spore coat). this article reviews the phylogeny of operons belonging to the chaperone/usher assembly class to explore the utility of establishing a scheme for subdividing them into clades of phylogenetically related gene clusters. based on usher amino acid sequence comparisons, our analysis s ... | 2007 | 18063717 |
| 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 |
| a score of the ability of a three-dimensional protein model to retrieve its own sequence as a quantitative measure of its quality and appropriateness. | despite the remarkable progress of bioinformatics, how the primary structure of a protein leads to a three-dimensional fold, and in turn determines its function remains an elusive question. alignments of sequences with known function can be used to identify proteins with the same or similar function with high success. however, identification of function-related and structure-related amino acid positions is only possible after a detailed study of every protein. folding pattern diversity seems to ... | 2010 | 20830209 |
| crystal structure of hyperthermophilic endo-β-1,4-glucanase: implications for catalytic mechanism and thermostability. | endo-β-1,4-glucanase from thermophilic fervidobacterium nodosum rt17-b1 (fncel5a), a new member of glycosyl hydrolase family 5, is highly thermostable and exhibits the highest activity on carboxymethylcellulose among the reported homologues. to understand the structural basis for the thermostability and catalytic mechanism, we report here the crystal structures of fncel5a and the complex with glucose at atomic resolution. fncel5a exhibited a (β/α)8-barrel structure typical of clan gh-a of glycos ... | 2011 | 22128157 |
| crystal structure of hyperthermophilic endo-β-1,4-glucanase: implications for catalytic mechanism and thermostability. | endo-β-1,4-glucanase from thermophilic fervidobacterium nodosum rt17-b1 (fncel5a), a new member of glycosyl hydrolase family 5, is highly thermostable and exhibits the highest activity on carboxymethylcellulose among the reported homologues. to understand the structural basis for the thermostability and catalytic mechanism, we report here the crystal structures of fncel5a and the complex with glucose at atomic resolution. fncel5a exhibited a (β/α)8-barrel structure typical of clan gh-a of glycos ... | 2011 | 22128157 |
| recombinant antibody production evolves into multiple options aimed at yielding reagents suitable for application-specific needs. | antibodies have been a pillar of basic research, while their relevance in clinical diagnostics and therapy is constantly growing. consequently, the production of both conventional and fragment antibodies constantly faces more demanding challenges for the improvement of their quantity and quality. the answer to such an increasing need has been the development of a wide array of formats and alternative production platforms. this review offers a critical comparison and evaluation of the different o ... | 2015 | 26330219 |
| a functional-phylogenetic classification system for transmembrane solute transporters. | a comprehensive classification system for transmembrane molecular transporters has been developed and recently approved by the transport panel of the nomenclature committee of the international union of biochemistry and molecular biology. this system is based on (i) transporter class and subclass (mode of transport and energy coupling mechanism), (ii) protein phylogenetic family and subfamily, and (iii) substrate specificity. almost all of the more than 250 identified families of transporters in ... | 2000 | 10839820 |
| 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 |
| comparative void-volume analysis of psychrophilic and mesophilic enzymes: structural bioinformatics of psychrophilic enzymes reveals sources of core flexibility. | psychrophiles, cold-adapted organisms, have adapted to live at low temperatures by using a variety of mechanisms. their enzymes are active at cold temperatures by being structurally more flexible than mesophilic enzymes. even though, there are some indications of the possible structural mechanisms by which psychrophilic enzymes are catalytic active at cold temperatures, there is not a generalized structural property common to all psychrophilic enzymes. | 2011 | 22013889 |
| A Novel Strategy for the Construction of Genomic Mutants of the Antarctic Bacterium Pseudoalteromonas haloplanktis TAC125. | The sequencing and the annotation of the marine Antarctic Pseudoalteromonas haloplanktis TAC125 genome has paved the way to investigate on the molecular mechanisms involved in adaptation to cold conditions. The growing interest in this unique bacterium prompted the developing of several genetic tools for studying it at the molecular level. To allow a deeper understanding of the PhTAC125 physiology a genetic system for the reverse genetics in this bacterium was developed. In the present work, we ... | 2012 | 22160901 |
| Improving Protein Crystal Quality by the Without-Oil Microbatch Method: Crystallization and Preliminary X-ray Diffraction Analysis of Glutathione Synthetase from Pseudoalteromonas haloplanktis. | Glutathione synthetases catalyze the ATP-dependent synthesis of glutathione from l-?-glutamyl- l-cysteine and glycine. Although these enzymes have been sequenced and characterized from a variety of biological sources, their exact catalytic mechanism is not fully understood and nothing is known about their adaptation at extremophilic environments. Glutathione synthetase from the Antarctic eubacterium Pseudoalteromonas haloplanktis (PhGshB) has been expressed, purified and successfully crystallize ... | 2011 | 22016660 |
| Rational disruption of the oligomerization of the mini-ferritin E. coli DPS through protein-protein interface mutation. | DNA-binding protein from starved cells (DPS), a mini-ferritin capable of self-assembling into a 12-meric nano-cage, was chosen as the basis for an alanine-shaving mutagenesis study to investigate the importance of key amino acid residues, located at symmetry-related protein-protein interfaces, in controlling protein stability and self-assembly. Nine mutants were designed through simple inspection, synthesized, and subjected to transmission electron microscopy, circular dichroism, size exclusion ... | 2011 | 21898653 |
| interactions between diatoms and bacteria. | diatoms and bacteria have cooccurred in common habitats for hundreds of millions of years, thus fostering specific associations and interactions with global biogeochemical consequences. diatoms are responsible for one-fifth of the photosynthesis on earth, while bacteria remineralize a large portion of this fixed carbon in the oceans. through their coexistence, diatoms and bacteria cycle nutrients between oxidized and reduced states, impacting bioavailability and ultimately feeding higher trophic ... | 2012 | 22933565 |
| Regulated Recombinant Protein Production in the Antarctic Bacterium Pseudoalteromonas haloplanktis TAC125. | This review reports results from our laboratory on the development of an effective inducible expression system for the homologous/heterologous protein production in cold-adapted bacteria. Recently, we isolated and characterized a regulative genomic region from Pseudoalteromonas haloplanktis TAC125; in particular, a two-component regulatory system was identified. It is involved in the transcriptional regulation of the gene coding for an outer membrane porin (PSHAb0363) that is strongly induced by ... | 2012 | 22160900 |
| lateral transfers of insertion sequences between wolbachia, cardinium and rickettsia bacterial endosymbionts. | various bacteria live exclusively within arthropod cells and collectively act as an important driver of arthropod evolutionary ecology. whereas rampant intra-generic dna transfers were recently shown to have a pivotal role in the evolution of the most common of these endosymbionts, wolbachia, the present study show that inter-generic dna transfers also commonly take place, constituting a potent source of rapid genomic change. bioinformatic, molecular and phylogenetic data provide evidence that a ... | 2013 | 23759724 |
| Stepwise adaptations to low temperature as revealed by multiple mutants of psychrophilic a-amylase from Antarctic Bacterium. | The mutants Mut5 and Mut5CC from a psychrophilic a-amylase bear representative stabilizing interactions found in the heat-stable porcine pancreatic a-amylase but lacking in the cold-active enzyme from an Antarctic bacterium. From an evolutionary perspective, these mutants can be regarded as structural intermediates between the psychrophilic and the mesophilic enzymes. We found that these engineered interactions improve all the investigated parameters related to protein stability as follows: comp ... | 2011 | 21900238 |
| characterization of halomonas sp. h11 α-glucosidase activated by monovalent cations and its application for efficient synthesis of α-d-glucosylglycerol. | an α-glucosidase (hag) with the following unique properties was isolated from halomonas sp. h11 strain: 1) high transglucosylation activity; 2) activation by monovalent cations; and 3) very narrow substrate specificity. the molecular mass of the purified hag was estimated at 58 kda by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (sds-page). hag showed high hydrolytic activities toward maltose, sucrose, and p-nitrophenyl α-d-glucoside (pnpg), but to almost no other disaccharides or m ... | 2012 | 22226947 |
| molecular adaptations in antarctic fish and marine microorganisms. | the antarctic marine environment is one of the most extreme on earth due to its stably low temperature and high oxygen content. here we discuss various aspects of the molecular adaptations evolved by antarctic fish and marine microorganisms living in this environment. this review will in particular focus on: (i) the genetic/genomic bases of adaptation in antarctic notothenioid fish; (ii) the role of neuroglobin recently identified in the brain of antarctic icefish; (iii) the structural and funct ... | 2011 | 22578653 |
| metagenomic profiles of free-living archaea, bacteria and small eukaryotes in coastal areas of sichang island, thailand. | tha wang and tham phang coasts, though situated at similar oceanographic positions on sichang island, chonburi province, thailand, are different in bay geography and amount of municipal disturbances. these affect the marine ecosystems. the study used metagenomics combined with 16s and 18s rdna pyrosequencing to identify types and distributions of archaea, bacteria, fungi and small eukaryotes of sizes ranges 0.45 and ~30 μm. | 2012 | 23282134 |
| plasmids of psychrophilic and psychrotolerant bacteria and their role in adaptation to cold environments. | extremely cold environments are a challenge for all organisms. they are mostly inhabited by psychrophilic and psychrotolerant bacteria, which employ various strategies to cope with the cold. such harsh environments are often highly vulnerable to the influence of external factors and may undergo frequent dynamic changes. the rapid adjustment of bacteria to changing environmental conditions is crucial for their survival. such "short-term" evolution is often enabled by plasmids-extrachromosomal rep ... | 2014 | 25426110 |
| two new xylanases with different substrate specificities from the human gut bacterium bacteroides intestinalis dsm 17393. | xylan is an abundant plant cell wall polysaccharide and is a dominant component of dietary fiber. bacteria in the distal human gastrointestinal tract produce xylanase enzymes to initiate the degradation of this complex heteropolymer. these xylanases typically derive from glycoside hydrolase (gh) families 10 and 11; however, analysis of the genome sequence of the xylan-degrading human gut bacterium bacteroides intestinalis dsm 17393 revealed the presence of two putative gh8 xylanases. in the curr ... | 2014 | 24463968 |
| structural investigation and biological activity of the lipooligosaccharide from the psychrophilic bacterium pseudoalteromonas haloplanktis tab 23. | pseudoalteromonas haloplanktis tab 23 is a gram-negative psychrophilic bacterium isolated from the antarctic coastal sea. to survive in these conditions psychrophilic bacteria have evolved typical membrane lipids and "antifreeze" proteins to protect the inner side of the microorganism. as for gram-negative bacteria, the outer membrane is mainly constituted by lipopoly- or lipooligosaccharides (lps or los, respectively), which lean towards the external environment. despite this, very little is kn ... | 2011 | 21557359 |
| quantitative analysis of replication-related mutation and selection pressures in bacterial chromosomes and plasmids using generalised gc skew index. | due to their bi-directional replication machinery starting from a single finite origin, bacterial genomes show characteristic nucleotide compositional bias between the two replichores, which can be visualised through gc skew or (c-g)/(c+g). although this polarisation is used for computational prediction of replication origins in many bacterial genomes, the degree of gc skew visibility varies widely among different species, necessitating a quantitative measurement of gc skew strength in order to ... | 2009 | 20042086 |
| ligand-modulated parallel mechanical unfolding pathways of maltose-binding proteins. | protein folding and unfolding are complex phenomena, and it is accepted that multidomain proteins generally follow multiple pathways. maltose-binding protein (mbp) is a large (a two-domain, 370-amino acid residue) bacterial periplasmic protein involved in maltose uptake. despite the large size, it has been shown to exhibit an apparent two-state equilibrium unfolding in bulk experiments. single-molecule studies can uncover rare events that are masked by averaging in bulk studies. here, we use sin ... | 2011 | 21659518 |
| superoxide dismutases and superoxide reductases. | | 2014 | 24684599 |
| search and discovery strategies for biotechnology: the paradigm shift. | profound changes are occurring in the strategies that biotechnology-based industries are deploying in the search for exploitable biology and to discover new products and develop new or improved processes. the advances that have been made in the past decade in areas such as combinatorial chemistry, combinatorial biosynthesis, metabolic pathway engineering, gene shuffling, and directed evolution of proteins have caused some companies to consider withdrawing from natural product screening. in this ... | 2000 | 10974127 |
| microfluidics expanding the frontiers of microbial ecology. | microfluidics has significantly contributed to the expansion of the frontiers of microbial ecology over the past decade by allowing researchers to observe the behaviors of microbes in highly controlled microenvironments, across scales from a single cell to mixed communities. spatially and temporally varying distributions of organisms and chemical cues that mimic natural microbial habitats can now be established by exploiting physics at the micrometer scale and by incorporating structures with sp ... | 2014 | 24773019 |