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stepwise cloning and molecular characterization of the hgidi restriction-modification system from herpetosiphon giganteus hpa2.the restriction-modification system hgidi from herpetosiphon giganteus strain hpa2 has been cloned in e. coli in a two-step procedure. selection of the methyltransferase (m.hgidi) gene in vitro was performed using the heterologous restriction endonuclease ahaii, an isoschizomer of acyl and hgidi (grcgyc). cloning of the complete hgidi endonuclease (r.hgidi) gene could only be achieved in recipient cells harbouring a recombinant plasmid, which was expressing the corresponding methyltransferase an ...19912020544
isolation and genetic structure of the avaii isoschizomeric restriction-modification system hgibi from herpetosiphon giganteus hpg5: m.hgibi reveals high homology to m.bani.the complete type ii restriction-modification system hgibi of herpetosiphon giganteus strain hpg5 recognizing the avaii specific dna sequence ggwcc has been cloned and expressed functionally active in escherichia coli. a considerable acceleration in cloning could be achieved by preparing a size restricted library after application of a related hybridization probe. both methyltransferase (437 codons) and restriction endonuclease gene (274 codons) were found to be encoded on a 3.6 kilobases clai/h ...19912062638
restriction endonucleases from herpetosiphon giganteus: an example of the evolution of dna recognition specificity?we describe the partial purification and characterisation of five type ii restriction endonucleases from two strains of herpetosiphon giganteus. one of the activities, hgijii, was the first enzyme found that cleaves dna at the family of related sequences 5'-g-r-g-c-y/c-3'. this enzyme may be related to the enzyme hgiai from a different strain of the same species, and which cleaves at the sites 5'-g-w-g-c-w/c-3'. we have shown that dnas from the strains producing hgiai and hgijii are resistant to ...19863020503
distribution of multicopy single-stranded dna among myxobacteria and related species.multicopy single-stranded dna (msdna) is a short single-stranded linear dna originally discovered in myxococcus xanthus and subsequently found in stigmatella aurantiaca. it exists at an estimated 500 to 700 copies per chromosome (t. yee, t. furuichi, s. inouye, and m. inouye, cell 38:203-209, 1984). we found msdna in other myxobacteria, including myxococcus coralloides, cystobacter violaceus, cystobacter ferrugineus (cbfe17), nannocystis exedens, and nine independently isolated strains of m. xan ...19853932332
unusual sulfonolipids are characteristic of the cytophaga-flexibacter group.capnocytophaga spp. contain a group of unusual sulfonolipids, called capnoids (w. godchaux iii and e. r. leadbetter, j. bacteriol. 144:592-602, 1980). one of these lipids, capnine, is 2-amino-3-hydroxy-15-methylhexadecane-1-sulfonic acid; the others are, apparently, n-acylated versions of capnine. the lipids were found, in amounts ranging from 2.5 to 16 mumol of capnoid sulfur per g of cells (wet weight), in two cytophaga spp. and also in several closely related organisms: several capnocytophaga ...19836298180
eight new restriction endonucleases fröm herpetosiphon giganteus--divergent evolution in a family of enzymes.characterization of eight restriction endonucleases isolated from five strains of herpetosiphon giganteus is described. hgici from strain hpg9 recognizes and cleaves the degenerate sequence: ggpypucc, producing 5'-hexanucleotide protruding ends. endonucleases hgibi, hgicii and hgiei are isoschizomers of avaii; hgiciii and hgidii are isoschizomers of sali; and hgidi and hgigi are isoschizomers of acyi. based upon their closely related and in part overlapping recognition specificities a close evol ...19846326052
design and evaluation of useful bacterium-specific pcr primers that amplify genes coding for bacterial 16s rrna.we report the design and evaluation of pcr primers 63f and 1387r for amplification of 16s rrna genes from bacteria. their specificity and efficacy were tested systematically with a bacterial species and environmental samples. they were found to be more useful for 16s rrna gene amplification in ecological and systematic studies than pcr amplimers that are currently more generally used.19989464425
flow cytometric analysis of the in situ accessibility of escherichia coli 16s rrna for fluorescently labeled oligonucleotide probes.in situ identification of whole fixed bacterial cells by hybridization with fluorescently labeled, rrna-targeted oligonucleotide probes is often limited by low signal intensities. in addition to an impermeability of the cell periphery and a low cellular rrna content, the three-dimensional structure of the ribosome may hinder the access of oligonucleotides to their target sites. until now, a systematic study on the accessibility of 16s rrna target sites had not been done. here, we report fluoresc ...19989835591
combination of fluorescent in situ hybridization and microautoradiography-a new tool for structure-function analyses in microbial ecology.a new microscopic method for simultaneously determining in situ the identities, activities, and specific substrate uptake profiles of individual bacterial cells within complex microbial communities was developed by combining fluorescent in situ hybridization (fish) performed with rrna-targeted oligonucleotide probes and microautoradiography. this method was evaluated by using defined artificial mixtures of escherichia coli and herpetosiphon aurantiacus under aerobic incubation conditions with ad ...199910049895
identification of regions of the chromosome of neisseria meningitidis and neisseria gonorrhoeae which are specific to the pathogenic neisseria species.neisseria meningitidis and neisseria gonorrhoeae give rise to dramatically different diseases. their interactions with the host, however, do share common characteristics: they are both human pathogens which do not survive in the environment and which colonize and invade mucosa at their port of entry. it is therefore likely that they have common properties that might not be found in nonpathogenic bacteria belonging to the same genetically related group, such as neisseria lactamica. their common p ...199910531275
evidence of horizontal transfer of the ecoo109i restriction-modification gene to escherichia coli chromosomal dna.a dna fragment carrying the genes coding for ecoo109i endonuclease and ecoo109i methylase, which recognize the nucleotide sequence 5'-(a/g)ggncc(c/t)-3', was cloned from the chromosomal dna of escherichia coli h709c. the ecoo109i restriction-modification (r-m) system was found to be inserted between the int and psu genes from satellite bacteriophage p4, which were lysogenized in the chromosome at the p4 phage attachment site of the corresponding leux gene observed in e. coli k-12 chromosomal dna ...199910542186
differential distribution of novel restriction-modification systems in clonal lineages of neisseria meningitidis.using representational difference analysis, we isolated novel meningococcal restriction-modification (r-m) systems. nmebi, which is a homologue of the r-m system hgai of pasteurella volantium, was present in meningococci of the et-5 complex and of lineage iii. nmeai was found in serogroup a, et-37 complex, and cluster a4 meningococci. nmedi was harbored by meningococci of the et-37 complex and of cluster a4, but not by serogroup a meningococci. two of the r-m systems, nmebi and nmedi, were locat ...200010671450
evidence for horizontal transfer of ssudat1i restriction-modification genes to the streptococcus suis genome.different strains of streptococcus suis serotypes 1 and 2 isolated from pigs either contained a restriction-modification (r-m) system or lacked it. the r-m system was an isoschizomer of streptococcus pneumoniae dpnii, which recognizes nucleotide sequence 5'-gatc-3'. the nucleotide sequencing of the genes encoding the r-m system in s. suis dat1, designated ssudat1i, showed that the ssudat1i gene region contained two methyltransferase genes, designated ssuma and ssumb, as does the dpnii system. th ...200111133943
diversity and distribution in hypersaline microbial mats of bacteria related to chloroflexus spp.filamentous bacteria containing bacteriochlorophylls c and a were enriched from hypersaline microbial mats. based on phylogenetic analyses of 16s rrna gene sequences, these organisms form a previously undescribed lineage distantly related to chloroflexus spp. we developed and tested a set of pcr primers for the specific amplification of 16s rrna genes from filamentous phototrophic bacteria within the kingdom of "green nonsulfur bacteria." pcr products recovered from microbial mats in a saltern i ...200111526049
molecular organization of intrinsic restriction and modification genes bsum of bacillus subtilis marburg.transcriptional analysis and disruption of five open reading frames (orfs), ydio, ydip, ydir, ydis, and ydja, in the prophage 3 region of the chromosome of bacillus subtilis marburg revealed that they are component genes of the intrinsic bsum restriction and modification system of this organism. the classical mutant strain rm125, which lacks the restriction and modification system of b. subtilis marburg, lacks the prophage 3 region carrying these five orfs. these orfs constitute two operons, the ...200211751814
genetic structure and distribution of four pathogenicity islands (pai i(536) to pai iv(536)) of uropathogenic escherichia coli strain 536.for the uropathogenic escherichia coli strain 536 (o6:k15:h31), the dna sequences of three pathogenicity islands (pais) (pai i(536) to pai iii(536)) and their flanking regions (about 270 kb) were determined to further characterize the virulence potential of this strain. pai i(536) to pai iii(536) exhibit features typical of pais, such as (i) association with trna-encoding genes; (ii) g+c content differing from that of the host genome; (iii) flanking repeat structures; (iv) a mosaic-like structur ...200212379716
pathogenicity islands in bacterial pathogenesis.in this review, we focus on a group of mobile genetic elements designated pathogenicity islands (pai). these elements play a pivotal role in the virulence of bacterial pathogens of humans and are also essential for virulence in pathogens of animals and plants. characteristic molecular features of pai of important human pathogens and their role in pathogenesis are described. the availability of a large number of genome sequences of pathogenic bacteria and their benign relatives currently offers a ...200414726454
biofilms 2003: emerging themes and challenges in studies of surface-associated microbial life. 200415231774
in search of rnase p rna from microbial genomes.a simple procedure has been developed to quickly retrieve and validate the dna sequence encoding the rna subunit of ribonuclease p (rnase p rna) from microbial genomes. rnase p rna sequences were identified from 94% of bacterial and archaeal complete genomes where previously no rnase p rna was annotated. a sequence was found in camelpox virus, highly conserved in all orthopoxviruses (including smallpox virus), which could fold into a putative rnase p rna in terms of conserved primary features an ...200415337843
channel-forming (porin) activity in herpetosiphon aurantiacus hp a2.detergent extracts of cell envelopes of the gliding bacterium herpetosiphon aurantiacus formed channels in lipid bilayers. fast protein liquid chromatography across a hitrap-q cation-exchange column demonstrated that a 45-kda protein forms the channel. the observation of a channel-forming protein suggests that herpetosiphon aurantiacus hp a2 has a permeability barrier on its surface.200415375151
unexpected diversity and complexity of the guerrero negro hypersaline microbial mat.we applied nucleic acid-based molecular methods, combined with estimates of biomass (atp), pigments, and microelectrode measurements of chemical gradients, to map microbial diversity vertically on a millimeter scale in a hypersaline microbial mat from guerrero negro, baja california sur, mexico. to identify the constituents of the mat, small-subunit rrna genes were amplified by pcr from community genomic dna extracted from layers, cloned, and sequenced. bacteria dominated the mat and displayed u ...200616672518
two genes encoding new carotenoid-modifying enzymes in the green sulfur bacterium chlorobium tepidum.the green sulfur bacterium chlorobium tepidum produces chlorobactene as its primary carotenoid. small amounts of chlorobactene are hydroxylated by the enzyme crtc and then glucosylated and acylated to produce chlorobactene glucoside laurate. the genes encoding the enzymes responsible for these modifications of chlorobactene, ct1987, and ct0967, have been identified by comparative genomics, and these genes were insertionally inactivated in c. tepidum to verify their predicted function. the gene e ...200616923888
rice non-yellow coloring1 is involved in light-harvesting complex ii and grana degradation during leaf senescence.chlorophyll degradation is an aspect of leaf senescence, which is an active process to salvage nutrients from old tissues. non-yellow coloring1 (nyc1) is a rice (oryza sativa) stay-green mutant in which chlorophyll degradation during senescence is impaired. pigment analysis revealed that degradation of not only chlorophylls but also light-harvesting complex ii (lhcii)-bound carotenoids was repressed in nyc1, in which most lhcii isoforms were selectively retained during senescence. ultrastructura ...200717416733
identification and analysis of novel amino-acid sequence repeats in bacillus anthracis str. ames proteome using computational tools.we have identified four repeats and ten domains that are novel in proteins encoded by the bacillus anthracis str. ames proteome using automated in silico methods. a "repeat" corresponds to a region comprising less than 55-amino-acid residues that occur more than once in the protein sequence and sometimes present in tandem. a "domain" corresponds to a conserved region with greater than 55-amino-acid residues and may be present as single or multiple copies in the protein sequence. these correspond ...200717538688
social bacteria and asocial eukaryotes. 200818199122
cohesion group approach for evolutionary analysis of tyra, a protein family with wide-ranging substrate specificities.many enzymes and other proteins are difficult subjects for bioinformatic analysis because they exhibit variant catalytic, structural, regulatory, and fusion mode features within a protein family whose sequences are not highly conserved. however, such features reflect dynamic and interesting scenarios of evolutionary importance. the value of experimental data obtained from individual organisms is instantly magnified to the extent that given features of the experimental organism can be projected u ...200818322033
the dawn of synthetic genomics. 200818353151
hydrogen peroxide linked to lysine oxidase activity facilitates biofilm differentiation and dispersal in several gram-negative bacteria.the marine bacterium pseudoalteromonas tunicata produces an antibacterial and autolytic protein, alpp, which causes death of a subpopulation of cells during biofilm formation and mediates differentiation, dispersal, and phenotypic variation among dispersal cells. the alpp homologue (loda) in the marine bacterium marinomonas mediterranea was recently identified as a lysine oxidase which mediates cell death through the production of hydrogen peroxide. here we show that alpp in p. tunicata also act ...200818502869
comparative genome analysis of filamentous fungi reveals gene family expansions associated with fungal pathogenesis.fungi and oomycetes are the causal agents of many of the most serious diseases of plants. here we report a detailed comparative analysis of the genome sequences of thirty-six species of fungi and oomycetes, including seven plant pathogenic species, that aims to explore the common genetic features associated with plant disease-causing species. the predicted translational products of each genome have been clustered into groups of potential orthologues using markov chain clustering and the data int ...200818523684
structure and function of sirc from bacillus megaterium: a metal-binding precorrin-2 dehydrogenase.in bacillus megaterium, the synthesis of vitamin b(12) (cobalamin) and sirohaem diverges at sirohydrochlorin along the branched modified tetrapyrrole biosynthetic pathway. this key intermediate is made by the action of sirc, a precorrin-2 dehydrogenase that requires nad(+) as a cofactor. the structure of sirc has now been solved by x-ray crystallography to 2.8 a (1 a = 0.1 nm) resolution. the protein is shown to consist of three domains and has a similar topology to the multifunctional sirohaem ...200818588505
toxic introns and parasitic intein in coxiella burnetii: legacies of a promiscuous past.the genome of the obligate intracellular pathogen coxiella burnetii contains a large number of selfish genetic elements, including two group i introns (cbu.l1917 and cbu.l1951) and an intervening sequence that interrupts the 23s rrna gene, an intein (cbu.dnab) within dnab and 29 insertion sequences. here, we describe the ability of the intron-encoded rnas (ribozymes) to retard bacterial growth rate (toxicity) and examine the functionality and phylogenetic history of cbu.dnab. when expressed in e ...200818606739
identification of sesquiterpene synthases from nostoc punctiforme pcc 73102 and nostoc sp. strain pcc 7120.cyanobacteria are a rich source of natural products and are known to produce terpenoids. these bacteria are the major source of the musty-smelling terpenes geosmin and 2-methylisoborneol, which are found in many natural water supplies; however, no terpene synthases have been characterized from these organisms to date. here, we describe the characterization of three sesquiterpene synthases identified in nostoc sp. strain pcc 7120 (terpene synthase ns1) and nostoc punctiforme pcc 73102 (terpene sy ...200818658271
a unique combination of genetic systems for the synthesis of trehalose in rubrobacter xylanophilus: properties of a rare actinobacterial tret.trehalose is the primary organic solute in rubrobacter xylanophilus under all conditions tested, including those for optimal growth. we detected genes of four different pathways for trehalose synthesis in the genome of this organism, namely, the trehalose-6-phosphate synthase (tps)/trehalose-6-phosphate phosphatase (tpp), tres, trey/trez, and tret pathways. moreover, r. xylanophilus is the only known member of the phylum actinobacteria to harbor tret. the tps sequence is typically bacterial, but ...200818835983
using shotgun sequence data to find active restriction enzyme genes.whole genome shotgun sequence analysis has become the standard method for beginning to determine a genome sequence. the preparation of the shotgun sequence clones is, in fact, a biological experiment. it determines which segments of the genome can be cloned into escherichia coli and which cannot. by analyzing the complete set of sequences from such an experiment, it is possible to identify genes lethal to e. coli. among this set are genes encoding restriction enzymes which, when active in e. col ...200918988632
using shotgun sequence data to find active restriction enzyme genes.whole genome shotgun sequence analysis has become the standard method for beginning to determine a genome sequence. the preparation of the shotgun sequence clones is, in fact, a biological experiment. it determines which segments of the genome can be cloned into escherichia coli and which cannot. by analyzing the complete set of sequences from such an experiment, it is possible to identify genes lethal to e. coli. among this set are genes encoding restriction enzymes which, when active in e. col ...200918988632
natural history of the e1-like superfamily: implication for adenylation, sulfur transfer, and ubiquitin conjugation.the e1-like superfamily is central to ubiquitin (ub) conjugation, biosynthesis of cysteine, thiamine, and moco, and several secondary metabolites. yet, its functional diversity and evolutionary history is not well understood. we develop a natural classification of this superfamily and use it to decipher the major adaptive trends occurring in the evolution of the e1-like superfamily. within the rossmann fold, e1-like proteins are closest to nad(p)/fad-dependent dehydrogenases and s-adomet-depende ...200919089947
biosynthetic gene cluster of cetoniacytone a, an unusual aminocyclitol from the endosymbiotic bacterium actinomyces sp. lu 9419.a gene cluster responsible for the biosynthesis of the antitumor agent cetoniacytone a was identified in actinomyces sp. strain lu 9419, an endosymbiotic bacterium isolated from the intestines of the rose chafer beetle (cetonia aurata). the nucleotide sequence analysis of the 46 kb dna region revealed the presence of 31 complete orfs, including genes predicted to encode a 2-epi-5-epi-valiolone synthase (ceta), a glyoxalase/bleomycin resistance protein (cetb), an acyltransferase (cetd), an fad-de ...200919101977
complete genome sequence of the aerobic co-oxidizing thermophile thermomicrobium roseum.in order to enrich the phylogenetic diversity represented in the available sequenced bacterial genomes and as part of an "assembling the tree of life" project, we determined the genome sequence of thermomicrobium roseum dsm 5159. t. roseum dsm 5159 is a red-pigmented, rod-shaped, gram-negative extreme thermophile isolated from a hot spring that possesses both an atypical cell wall composition and an unusual cell membrane that is composed entirely of long-chain 1,2-diols. its genome is composed o ...200919148287
methods for comparative metagenomics.metagenomics is a rapidly growing field of research that aims at studying uncultured organisms to understand the true diversity of microbes, their functions, cooperation and evolution, in environments such as soil, water, ancient remains of animals, or the digestive system of animals and humans. the recent development of ultra-high throughput sequencing technologies, which do not require cloning or pcr amplification, and can produce huge numbers of dna reads at an affordable cost, has boosted th ...200919208111
a horizontal gene transfer at the origin of phenylpropanoid metabolism: a key adaptation of plants to land.the pioneering ancestor of land plants that conquered terrestrial habitats around 500 million years ago had to face dramatic stresses including uv radiation, desiccation, and microbial attack. this drove a number of adaptations, among which the emergence of the phenylpropanoid pathway was crucial, leading to essential compounds such as flavonoids and lignin. however, the origin of this specific land plant secondary metabolism has not been clarified.200919220881
identification of a novel two-peptide lantibiotic, lichenicidin, following rational genome mining for lanm proteins.lantibiotics are ribosomally synthesized peptide antimicrobials which contain considerable posttranslational modifications. given their usually broad host range and their highly stable structures, there have been renewed attempts to identify and characterize novel members of the lantibiotic family in recent years. the increasing availability of bacterial genome sequences means that in addition to traditional microbiological approaches, in silico screening strategies may now be employed to the sa ...200919561184
a subset of the diverse cog0523 family of putative metal chaperones is linked to zinc homeostasis in all kingdoms of life.cog0523 proteins are, like the nickel chaperones of the ureg family, part of the g3e family of gtpases linking them to metallocenter biosynthesis. even though the first cog0523-encoding gene, cobw, was identified almost 20 years ago, little is known concerning the function of other members belonging to this ubiquitous family.200919822009
structural and biochemical insights into 2'-o-methylation at the 3'-terminal nucleotide of rna by hen1.small rnas of approximately 20-30 nt have diverse and important biological roles in eukaryotic organisms. after being generated by dicer or piwi proteins, all small rnas in plants and a subset of small rnas in animals are further modified at their 3'-terminal nucleotides via 2'-o-methylation, carried out by the s-adenosylmethionine-dependent methyltransferase (mtase) hen1. methylation at the 3' terminus is vital for biological functions of these small rnas. here, we report four crystal structure ...200919822745
the crystal structure of the novobiocin biosynthetic enzyme novp: the first representative structure for the tylf o-methyltransferase superfamily.novp is an s-adenosyl-l-methionine-dependent o-methyltransferase that catalyzes the penultimate step in the biosynthesis of the aminocoumarin antibiotic novobiocin. specifically, it methylates at 4-oh of the noviose moiety, and the resultant methoxy group is important for the potency of the mature antibiotic: previous crystallographic studies have shown that this group interacts directly with the target enzyme dna gyrase, which is a validated drug target. we have determined the high-resolution c ...201019857499
the crystal structure of the novobiocin biosynthetic enzyme novp: the first representative structure for the tylf o-methyltransferase superfamily.novp is an s-adenosyl-l-methionine-dependent o-methyltransferase that catalyzes the penultimate step in the biosynthesis of the aminocoumarin antibiotic novobiocin. specifically, it methylates at 4-oh of the noviose moiety, and the resultant methoxy group is important for the potency of the mature antibiotic: previous crystallographic studies have shown that this group interacts directly with the target enzyme dna gyrase, which is a validated drug target. we have determined the high-resolution c ...201019857499
the effect of sequencing errors on metagenomic gene prediction.gene prediction is an essential step in the annotation of metagenomic sequencing reads. since most metagenomic reads cannot be assembled into long contigs, specialized statistical gene prediction tools have been developed for short and anonymous dna fragments, e.g. metageneannotator and orphelia. while conventional gene prediction methods have been subject to a benchmark study on real sequencing reads with typical errors, such a comparison has not been conducted for specialized tools, yet. their ...200919909532
bacterial hen1 is a 3' terminal rna ribose 2'-o-methyltransferase component of a bacterial rna repair cassette.hen1 is an rna ribose 2'-o-methyltransferase that modifies the 3' terminal nucleoside of eukaryal small regulatory rnas. here, we report that hen1 homologs are present in bacterial proteomes from eight different phyla. bacterial hen1 is encoded by the proximal orf of a two-gene operon that also encodes polynucleotide kinase-phosphatase (pnkp), an rna repair enzyme. purified recombinant clostridium thermocellum hen1 is a homodimer of a 465-amino acid polypeptide. cthhen1 catalyzes methyl transfer ...201020007328
molecular cloning and heterologous expression of a biosynthetic gene cluster for the antitubercular agent d-cycloserine produced by streptomyces lavendulae.in the present study, we successfully cloned a 21-kb dna fragment containing a d-cycloserine (dcs) biosynthetic gene cluster from a dcs-producing streptomyces lavendulae strain, atcc 11924. the putative gene cluster consists of 10 open reading frames (orfs), designated dcsa to dcsj. this cluster includes two orfs encoding d-alanyl-d-alanine ligase (dcsi) and a putative membrane protein (dcsj) as the self-resistance determinants of the producer organism, indicated by our previous work. when the 1 ...201020086163
detection and quantification of functional genes of cellulose- degrading, fermentative, and sulfate-reducing bacteria and methanogenic archaea.cellulose degradation, fermentation, sulfate reduction, and methanogenesis are microbial processes that coexist in a variety of natural and engineered anaerobic environments. compared to the study of 16s rrna genes, the study of the genes encoding the enzymes responsible for these phylogenetically diverse functions is advantageous because it provides direct functional information. however, no methods are available for the broad quantification of these genes from uncultured microbes characteristi ...201020139321
diversity of bacteria and glycosyl hydrolase family 48 genes in cellulolytic consortia enriched from thermophilic biocompost.the enrichment from nature of novel microbial communities with high cellulolytic activity is useful in the identification of novel organisms and novel functions that enhance the fundamental understanding of microbial cellulose degradation. in this work we identify predominant organisms in three cellulolytic enrichment cultures with thermophilic compost as an inoculum. community structure based on 16s rrna gene clone libraries featured extensive representation of clostridia from cluster iii, with ...201020382819
phylogenetic evidence for lateral gene transfer in the intestine of marine iguanas.lateral gene transfer (lgt) appears to promote genotypic and phenotypic variation in microbial communities in a range of environments, including the mammalian intestine. however, the extent and mechanisms of lgt in intestinal microbial communities of non-mammalian hosts remains poorly understood.201020520734
biosynthesis of cylindrospermopsin and 7-epicylindrospermopsin in oscillatoria sp. strain pcc 6506: identification of the cyr gene cluster and toxin analysis.cylindrospermopsin is a cytotoxin produced by cylindrospermopsis raciborskii and other cyanobacteria that has been implicated in human intoxications. we report here the complete sequence of the gene cluster responsible for the biosynthesis of this toxin in oscillatoria sp. strain pcc 6506. this cluster of genes was found to be homologous with that of c. raciborskii but with a different gene organization. using an enzyme-linked immunosorbent assay and an optimized liquid chromatography analytical ...201020525864
presence of a classical rrm-fold palm domain in thg1-type 3'- 5'nucleic acid polymerases and the origin of the ggdef and crispr polymerase domains.almost all known nucleic acid polymerases catalyze 5'-3' polymerization by mediating the attack on an incoming nucleotide 5' triphosphate by the 3'oh from the growing polynucleotide chain in a template dependent or independent manner. the only known exception to this rule is the thg1 rna polymerase that catalyzes 3'-5' polymerization in vitro and also in vivo as a part of the maturation process of histidinyl trna. while the initial reaction catalyzed by thg1 has been compared to adenylation cata ...201020591188
evolution and multiplicity of arginine decarboxylases in polyamine biosynthesis and essential role in bacillus subtilis biofilm formation.arginine decarboxylases (adcs; ec 4.1.1.19) from four different protein fold families are important for polyamine biosynthesis in bacteria, archaea, and plants. biosynthetic alanine racemase fold (ar-fold) adc is widespread in bacteria and plants. we report the discovery and characterization of an ancestral form of the ar-fold adc in the bacterial chloroflexi and bacteroidetes phyla. the ancestral ar-fold adc lacks a large insertion found in escherichia coli and plant ar-fold adc and is more sim ...201020876533
nutrient-regulated transcriptional responses in the brown tide-forming alga aureococcus anophagefferens.long-sage (serial analysis of gene expression) was used to profile the transcriptome of the brown tide-forming alga, aureococcus anophagefferens, under nutrient replete (control), and nitrogen (n) and phosphorus (p) deficiency to understand how this organism responds at the transcriptional level to varying nutrient conditions. this approach has aided a. anophagefferens genome annotation efforts and identified a suite of genes upregulated by n and p deficiency, some of which have known roles in n ...201020880332
nutrient-regulated transcriptional responses in the brown tide-forming alga aureococcus anophagefferens.long-sage (serial analysis of gene expression) was used to profile the transcriptome of the brown tide-forming alga, aureococcus anophagefferens, under nutrient replete (control), and nitrogen (n) and phosphorus (p) deficiency to understand how this organism responds at the transcriptional level to varying nutrient conditions. this approach has aided a. anophagefferens genome annotation efforts and identified a suite of genes upregulated by n and p deficiency, some of which have known roles in n ...201020880332
genome analysis of deep-sea thermophilic phage d6e.in deep-sea hydrothermal vent communities, viruses play very important roles. however vent thermophilic bacteriophages remain largely unexplored. in this investigation, a novel vent geobacillus bacteriophage, d6e, was characterized. based on comparative genomics and proteomics analyses, the results showed an extensive mosaicism of d6e genome with other mesophilic or thermophilic phages.201020889772
moonlighting glutamate formiminotransferases can functionally replace 5-formyltetrahydrofolate cycloligase.5-formyltetrahydrofolate (5-cho-thf) is formed by a side reaction of serine hydroxymethyltransferase. unlike other folates, it is not a one-carbon donor but a potent inhibitor of folate enzymes and must therefore be metabolized. only 5-cho-thf cycloligase (5-fcl) is generally considered to do this. however, comparative genomic analysis indicated (i) that certain prokaryotes lack 5-fcl, implying that they have an alternative 5-cho-thf-metabolizing enzyme, and (ii) that the histidine breakdown enz ...201020952389
functional promiscuity of homologues of the bacterial arsa atpases.the arsa atpase of e. coli plays an essential role in arsenic detoxification. published evidence implicates arsa in the energization of as(iii) efflux via the formation of an oxyanion-translocating complex with arsb. in addition, eukaryotic arsa homologues have several recognized functions unrelated to arsenic resistance. by aligning arsa homologues, constructing phylogenetic trees, examining arsa encoding operons, and estimating the probable coevolution of these homologues with putative transpo ...201020981284
hyperthermostable acetyl xylan esterase.an esterase which is encoded within a thermotoga maritima chromosomal gene cluster for xylan degradation and utilization was characterized after heterologous expression of the corresponding gene in escherichia coli and purification of the enzyme. the enzyme, designated axea, shares amino acid sequence similarity and its broad substrate specificity with the acetyl xylan esterase from bacillus pumilus, the cephalosporin c deacetylase from bacillus subtilis, and other (putative) esterases, allowing ...201021255309
hyperthermostable acetyl xylan esterase.an esterase which is encoded within a thermotoga maritima chromosomal gene cluster for xylan degradation and utilization was characterized after heterologous expression of the corresponding gene in escherichia coli and purification of the enzyme. the enzyme, designated axea, shares amino acid sequence similarity and its broad substrate specificity with the acetyl xylan esterase from bacillus pumilus, the cephalosporin c deacetylase from bacillus subtilis, and other (putative) esterases, allowing ...201021255309
unpublished but public microbial genomes with biotechnological relevance. 200821261839
natural products genomics. 200821261848
genomics of biological wastewater treatment. 200821261852
a novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and dna viral systems.the use of nucleases as toxins for defense, offense or addiction of selfish elements is widely encountered across all life forms. using sensitive sequence profile analysis methods, we characterize a novel superfamily (the sukh superfamily) that unites a diverse group of proteins including smi1/knr4, pgs2, fbxo3, skip16, syd, herpesviral us22, irs1 and trs1, and their bacterial homologs. using contextual analysis we present evidence that the bacterial members of this superfamily are potential imm ...201121306995
a transmembrane inner nuclear membrane protein in the mitotic spindle.we have recently characterized a novel transmembrane protein of the inner nuclear membrane of mammalian cells. the protein has two very interesting features. first, despite being an integral membrane protein it is able to concentrate in the membranes colocalizing with the mitotic spindle in metaphase and anaphase. hence, the protein was named samp1, spindle associated membrane protein 1. secondly, it displays a functional connection to centrosomes. this article discusses various aspects of samp1 ...201021327071
prp8, the pivotal protein of the spliceosomal catalytic center, evolved from a retroelement-encoded reverse transcriptase.prp8 is the largest and most highly conserved protein of the spliceosome, encoded by all sequenced eukaryotic genomes but missing from prokaryotes and viruses. despite all evidence that prp8 is an integral part of the spliceosomal catalytic center, much remains to be learned about its molecular functions and evolutionary origin. by analyzing sequence and structure similarities between prp8 and other protein domains, we show that its n-terminal region contains a putative bromodomain. the central ...201121441348
the human postsynaptic density shares conserved elements with proteomes of unicellular eukaryotes and prokaryotes.the animal nervous system processes information from the environment and mediates learning and memory using molecular signaling pathways in the postsynaptic terminal of synapses. postsynaptic neurotransmitter receptors assemble to form multiprotein complexes that drive signal transduction pathways to downstream cell biological processes. studies of mouse and drosophila postsynaptic proteins have identified key roles in synaptic physiology and behavior for a wide range of proteins including recep ...201121503141
bioinformatic characterization of the trimeric intracellular cation-specific channel protein family.trimeric intracellular cation-specific (tric) channels are integral to muscle excitation-contraction coupling. tric channels provide counter-ionic flux when calcium is rapidly transported from intracellular stores to the cell cytoplasm. until recently, knowledge of the presence of these proteins was limited to animals. we analyzed the tric family and identified a profusion of prokaryotic family members with topologies and motifs similar to those of their eukaryotic counterparts. prokaryotic memb ...201121519847
calpain chronicle--an enzyme family under multidisciplinary characterization.calpain is an intracellular ca2+-dependent cysteine protease (ec 3.4.22.17; clan ca, family c02) discovered in 1964. it was also called canp (ca2+-activated neutral protease) as well as casf, cdp, kaf, etc. until 1990. calpains are found in almost all eukaryotes and a few bacteria, but not in archaebacteria. calpains have a limited proteolytic activity, and function to transform or modulate their substrates' structures and activities; they are therefore called, "modulator proteases." in the huma ...201121670566
structural and functional insights into dr2231 protein, the mazg-like nucleoside triphosphate pyrophosphohydrolase from deinococcus radiodurans.deinococcus radiodurans is among the very few bacterial species extremely resistant to ionizing radiation, uv light, oxidizing agents, and cycles of prolonged desiccation. the proteome of d. radiodurans reflects the evolutionary pressure exerted by chronic exposure to (nonradioactive) forms of dna and protein damage. a clear example of this adaptation is the overrepresentation of protein families involved in the removal of non-canonical nucleoside triphosphates (ntps) whose incorporation into na ...201121733847
a new family of bacterial condensins.condensins play a central role in global chromatin organization. in bacteria, two families of condensins have been identified, the mukbef and smc-scpab complexes. only one of the two complexes is usually found in a given species, giving rise to a paradigm that a single condensin organizes bacterial chromosomes. using sequence analysis, we identified a third family of condensins, mksbef (mukbef-like smc proteins), which is broadly present in diverse bacteria. the proteins appear distantly related ...201121752107
emerging roles for the ro 60-kda autoantigen in noncoding rna metabolism.all cells contain an enormous variety of ribonucleoprotein (rnp) complexes that function in diverse processes. although the mechanisms by which many of these rnps contribute to cell metabolism are well understood, the roles of others are only now beginning to be revealed. a member of this latter category, the ro 60-kda protein and its associated noncoding y rnas, was discovered because the protein component is a frequent target of the autoimmune response in patients with the rheumatic diseases s ...201121823229
a widespread class of reverse transcriptase-related cellular genes.reverse transcriptases (rts) polymerize dna on rna templates. they fall into several structurally related but distinct classes and form an assemblage of rt-like enzymes that, in addition to rts, also includes certain viral rna-dependent rna polymerases (rdrp) synthesizing rna on rna templates. it is generally believed that most rt-like enzymes originate from retrotransposons or viruses and have no specific function in the host cell, with telomerases being the only notable exception. here we repo ...201121876125
the structure and catalytic mechanism of a poly(adp-ribose) glycohydrolase.post-translational modification of proteins by poly(adp-ribosyl)ation regulates many cellular pathways that are critical for genome stability, including dna repair, chromatin structure, mitosis and apoptosis. poly(adp-ribose) (par) is composed of repeating adp-ribose units linked via a unique glycosidic ribose-ribose bond, and is synthesized from nad by par polymerases. par glycohydrolase (parg) is the only protein capable of specific hydrolysis of the ribose-ribose bonds present in par chains; ...201121892188
mutation of l-2,3-diaminopropionic acid synthase genes blocks staphyloferrin b synthesis in staphylococcus aureus.staphylococcus aureus synthesizes two siderophores, staphyloferrin a and staphyloferrin b, that promote iron-restricted growth. previous work on the biosynthesis of staphyloferrin b has focused on the role of the synthetase enzymes, encoded from within the sbna-i operon, which build the siderophore from the precursor molecules citrate, alpha-ketoglutarate and l-2,3-diaminopropionic acid. however, no information yet exists on several other enzymes, expressed from the biosynthetic cluster, that ar ...201121906287
Dynamics of microbial community structure of and enhanced biological phosphorus removal by aerobic granules cultivated on propionate or acetate.Aerobic granules are dense microbial aggregates with the potential to replace floccular sludge for the treatment of wastewaters. In bubble-column sequencing batch reactors, distinct microbial populations dominated propionate- and acetate-cultivated aerobic granules after 50 days of reactor operation when only carbon removal was detected. Propionate granules were dominated by Zoogloea (40%), Acidovorax, and Thiothrix, whereas acetate granules were mainly dominated by Thiothrix (60%). Thereafter, ...201121926195
Phylogenetic Analysis of the Teneurins: Conserved Features and Premetazoan Ancestry.Teneurins are type II transmembrane proteins expressed during pattern formation and neurogenesis with an intracellular domain that can be transported to the nucleus and an extracellular domain that can be shed into the extracellular milieu. In Drosophila melanogaster, Caenorhabditis elegans and mouse the knockdown or knockout of teneurin expression can lead to abnormal patterning, defasciculation and abnormal pathfinding of neurites, and the disruption of basement membranes. Here we have identif ...201122045996
Phylogenetic Analysis of the Teneurins: Conserved Features and Premetazoan Ancestry.Teneurins are type II transmembrane proteins expressed during pattern formation and neurogenesis with an intracellular domain that can be transported to the nucleus and an extracellular domain that can be shed into the extracellular milieu. In Drosophila melanogaster, Caenorhabditis elegans and mouse the knockdown or knockout of teneurin expression can lead to abnormal patterning, defasciculation and abnormal pathfinding of neurites, and the disruption of basement membranes. Here we have identif ...201122045996
Natural niche for organohalide-respiring chloroflexi.The phylum Chloroflexi contains several isolated bacteria that have been found to respire a diverse array of halogenated anthropogenic chemicals. The distribution and role of these Chloroflexi in uncontaminated terrestrial environments, where abundant natural organohalogens could function as potential electron acceptors, have not been studied. Soil samples (116 total, including 6 sectioned cores) from a range of uncontaminated sites were analyzed for the number of Dehalococcoides-like Chloroflex ...201222101035
improved thermostability of clostridium thermocellum endoglucanase cel8a by using consensus-guided mutagenesis.the use of thermostable cellulases is advantageous for the breakdown of lignocellulosic biomass toward the commercial production of biofuels. previously, we have demonstrated the engineering of an enhanced thermostable family 8 cellulosomal endoglucanase (ec 3.2.1.4), cel8a, from clostridium thermocellum, using random error-prone pcr and a combination of three beneficial mutations, dominated by an intriguing serine-to-glycine substitution (m. anbar, r. lamed, e. a. bayer, chemcatchem 2:997-1003, ...201222389377
homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily.the rapid advance in genome sequencing presents substantial challenges for protein functional assignment, with half or more of new protein sequences inferred from these genomes having uncertain assignments. the assignment of enzyme function in functionally diverse superfamilies represents a particular challenge, which we address through a combination of computational predictions, enzymology, and structural biology. here we describe the results of a focused investigation of a group of enzymes in ...201222392983
sequence, structure and functional diversity of pd-(d/e)xk phosphodiesterase superfamily.proteins belonging to pd-(d/e)xk phosphodiesterases constitute a functionally diverse superfamily with representatives involved in replication, restriction, dna repair and trna-intron splicing. their malfunction in humans triggers severe diseases, such as fanconi anemia and xeroderma pigmentosum. to date there have been several attempts to identify and classify new pd-(d/e)kk phosphodiesterases using remote homology detection methods. such efforts are complicated, because the superfamily exhibit ...201222638584
complete genome sequence of the filamentous gliding predatory bacterium herpetosiphon aurantiacus type strain (114-95(t)).herpetosiphon aurantiacus holt and lewin 1968 is the type species of the genus herpetosiphon, which in turn is the type genus of the family herpetosiphonaceae, type family of the order herpetosiphonales in the phylum chloroflexi. h. aurantiacus cells are organized in filaments which can rapidly glide. the species is of interest not only because of its rather isolated position in the tree of life, but also because herpetosiphon ssp. were identified as predators capable of facultative predation by ...201122675585
complete genome sequence of dehalogenimonas lykanthroporepellens type strain (bl-dc-9(t)) and comparison to "dehalococcoides" strains.dehalogenimonas lykanthroporepellens is the type species of the genus dehalogenimonas, which belongs to a deeply branching lineage within the phylum chloroflexi. this strictly anaerobic, mesophilic, non spore-forming, gram-negative staining bacterium was first isolated from chlorinated solvent contaminated groundwater at a superfund site located near baton rouge, louisiana, usa. d. lykanthroporepellens was of interest for genome sequencing for two reasons: (a) an unusual ability to couple growth ...201222768368
phylogeny of rieske/cytb complexes with a special focus on the haloarchaeal enzymes.rieske/cytochrome b (rieske/cytb) complexes are proton pumping quinol oxidases that are present in most bacteria and archaea. the phylogeny of their subunits follows closely the 16s-rrna phylogeny, indicating that chemiosmotic coupling was already present in the last universal common ancestor of archaea and bacteria. haloarchaea are the only organisms found so far that acquired rieske/cytb complexes via interdomain lateral gene transfer. they encode two rieske/cytb complexes in their genomes; on ...201222798450
structural insights into the anti-hiv activity of the oscillatoria agardhii agglutinin homolog lectin family.oscillatoria agardhii agglutinin homolog (oaah) proteins belong to a recently discovered lectin family. all members contain a sequence repeat of ~66 amino acids, with the number of repeats varying among different family members. apart from data for the founding member oaa, neither three-dimensional structures, information about carbohydrate binding specificities, nor antiviral activity data have been available up to now for any other members of the oaah family. to elucidate the structural basis ...201222865886
promoter propagation in prokaryotes.transcriptional activation or 'rewiring' of silent genes is an important, yet poorly understood, phenomenon in prokaryotic genomes. anecdotal evidence coming from experimental evolution studies in bacterial systems has shown the promptness of adaptation upon appropriate selective pressure. in many cases, a partial or complete promoter is mobilized to silent genes from elsewhere in the genome. we term hereafter such recruited regulatory sequences as putative mobile promoters (pmps) and we hypothe ...201222933716
dinoflagellate tandem array gene transcripts are highly conserved and not polycistronic.dinoflagellates are an important component of the marine biota, but a large genome with high-copy number (up to 5,000) tandem gene arrays has made genomic sequencing problematic. more importantly, little is known about the expression and conservation of these unusual gene arrays. we assembled de novo a gene catalog of 74,655 contigs for the dinoflagellate lingulodinium polyedrum from rna-seq (illumina) reads. the catalog contains 93% of a lingulodinium est dataset deposited in genbank and 94% of ...201223019363
high mannose-binding antiviral lectin pfl from pseudomonas fluorescens pf0-1 promotes cell death of gastric cancer cell mkn28 via interaction with α2-integrin.novel anti-hiv lectin family which shows a strict binding specificity for high mannose glycans has been found in lower organisms. the bacterial orthologue has been identified in the genome of pseudomonas fluorescens pf0-1 and the gene coding a putative lectin was cloned, expressed in escherichia coli and purified by one step gel filtration. glycan array screening of the recombinant lectin, termed pfl, has revealed that pfl preferentially recognizes high mannose glycans with α1-3 man that was hig ...201223029318
whole genome analysis of leptospira licerasiae provides insight into leptospiral evolution and pathogenicity.the whole genome analysis of two strains of the first intermediately pathogenic leptospiral species to be sequenced (leptospira licerasiae strains var010 and mmd0835) provides insight into their pathogenic potential and deepens our understanding of leptospiral evolution. comparative analysis of eight leptospiral genomes shows the existence of a core leptospiral genome comprising 1547 genes and 452 conserved genes restricted to infectious species (including l. licerasiae) that are likely to be pa ...201223145189
prokaryotic caspase homologs: phylogenetic patterns and functional characteristics reveal considerable diversity.caspases accomplish initiation and execution of apoptosis, a programmed cell death process specific to metazoans. the existence of prokaryotic caspase homologs, termed metacaspases, has been known for slightly more than a decade. despite their potential connection to the evolution of programmed cell death in eukaryotes, the phylogenetic distribution and functions of these prokaryotic metacaspase sequences are largely uncharted, while a few experiments imply involvement in programmed cell death. ...201223185476
ethanolamine utilization in vibrio alginolyticus.ethanolamine is used as an energy source by phylogenetically diverse bacteria including pathogens, by the concerted action of proteins from the eut-operon. previous studies have revealed the presence of eutbc genes encoding ethanolamine-ammonia lyase, a key enzyme that breaks ethanolamine into acetaldehyde and ammonia, in about 100 bacterial genomes including members of gamma-proteobacteria. however, ethanolamine utilization has not been reported for any member of the vibrio genus. our comparati ...201223234435
chlorophyll biosynthesis gene evolution indicates photosystem gene duplication, not photosystem merger, at the origin of oxygenic photosynthesis.an open question regarding the evolution of photosynthesis is how cyanobacteria came to possess the two reaction center (rc) types, type i reaction center (rci) and type ii reaction center (rcii). the two main competing theories in the foreground of current thinking on this issue are that either 1) rci and rcii are related via lineage divergence among anoxygenic photosynthetic bacteria and became merged in cyanobacteria via an event of large-scale lateral gene transfer (also called "fusion" theo ...201323258841
chlorophyll biosynthesis gene evolution indicates photosystem gene duplication, not photosystem merger, at the origin of oxygenic photosynthesis.an open question regarding the evolution of photosynthesis is how cyanobacteria came to possess the two reaction center (rc) types, type i reaction center (rci) and type ii reaction center (rcii). the two main competing theories in the foreground of current thinking on this issue are that either 1) rci and rcii are related via lineage divergence among anoxygenic photosynthetic bacteria and became merged in cyanobacteria via an event of large-scale lateral gene transfer (also called "fusion" theo ...201323258841
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.201223282134
clcas - a family of metalloproteases of intriguing phylogenetic distribution and with cases of substituted catalytic sites.the zinc-dependent metalloproteases with his-glu-x-x-his (hexxh) active site motif, zincins, are a broad group of proteins involved in many metabolic and regulatory functions, and found in all forms of life. human genome contains more than 100 genes encoding proteins with known zincin-like domains. a survey of all proteins containing the hexxh motif shows that approximately 52% of hexxh occurrences fall within known protein structural domains (as defined in the pfam database). domain families wi ...201323671590
elevated co₂ influences microbial carbon and nitrogen cycling.elevated atmospheric co₂ (eco₂) has been shown to have significant effects on terrestrial ecosystems. however, little is known about its influence on the structure, composition, and functional potential of soil microbial communities, especially carbon (c) and nitrogen (n) cycling. a high-throughput functional gene array (geochip 3.0) was used to examine the composition, structure, and metabolic potential of soil microbial communities from a grassland field experiment after ten-year field exposur ...201323718284
in silico resurrection of the major vault protein suggests it is ancestral in modern eukaryotes.vaults are very large oligomeric ribonucleoproteins conserved among a variety of species. the rat vault 3d structure shows an ovoid oligomeric particle, consisting of 78 major vault protein monomers, each of approximately 861 amino acids. vaults are probably the largest ribonucleoprotein structures in eukaryote cells, being approximately 70 nm in length with a diameter of 40 nm--the size of three ribosomes and with a lumen capacity of 50 million å(3). we use both protein sequences and inferred a ...201323887922
characterization of mineral phosphate solubilization traits from a barley rhizosphere soil functional metagenome.mineral phosphate solubilization (mps) microorganisms are important for their provision of orthophosphate anions for plant growth promotion activity in soil. in this study, we applied a functional metagenomic approach to identify this trait directly from the microbiome in barley rhizosphere soil that had not received p fertilizer over a 15-year period. a fosmid system was used to clone the metagenome of which 18,000 clones (~666 mb of dna) was screened for mps. functional assays and high perform ...201323894099
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