| 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 ... | 1991 | 2020544 |
| 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 ... | 1991 | 2062638 |
| 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 ... | 1986 | 3020503 |
| 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 ... | 1985 | 3932332 |
| 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 ... | 1983 | 6298180 |
| 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 ... | 1984 | 6326052 |
| 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 ... | 1998 | 9835591 |
| 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 ... | 1999 | 10049895 |
| 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 ... | 1999 | 10531275 |
| 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 ... | 1999 | 10542186 |
| 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 ... | 2000 | 10671450 |
| 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 ... | 2001 | 11133943 |
| 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 ... | 2001 | 11526049 |
| 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 ... | 2002 | 11751814 |
| 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 ... | 2002 | 12379716 |
| 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 ... | 2004 | 14726454 |
| 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 ... | 2004 | 15337843 |
| 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. | 2004 | 15375151 |
| 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 ... | 2006 | 16672518 |
| 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 ... | 2006 | 16923888 |
| 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 ... | 2007 | 17538688 |
| social bacteria and asocial eukaryotes. | | 2008 | 18199122 |
| 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 ... | 2008 | 18502869 |
| 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 ... | 2008 | 18523684 |
| 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 ... | 2008 | 18588505 |
| 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 ... | 2008 | 18606739 |
| 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 ... | 2008 | 18658271 |
| 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 ... | 2008 | 18835983 |
| 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 ... | 2009 | 18988632 |
| 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 ... | 2009 | 18988632 |
| 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 ... | 2009 | 19101977 |
| 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 ... | 2009 | 19148287 |
| 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 ... | 2009 | 19561184 |
| 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 ... | 2009 | 19822745 |
| 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 ... | 2010 | 19857499 |
| 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 ... | 2010 | 19857499 |
| 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 ... | 2010 | 20007328 |
| 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 ... | 2010 | 20086163 |
| 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 ... | 2010 | 20382819 |
| 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. | 2010 | 20520734 |
| 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 ... | 2010 | 20525864 |
| 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 ... | 2010 | 20876533 |
| 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. | 2010 | 20889772 |
| 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 ... | 2010 | 20952389 |
| 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 ... | 2010 | 21255309 |
| 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 ... | 2010 | 21255309 |
| 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 ... | 2011 | 21306995 |
| 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 ... | 2011 | 21441348 |
| 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 ... | 2011 | 21503141 |
| 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 |
| 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 ... | 2011 | 21670566 |
| 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 ... | 2011 | 21752107 |
| 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 ... | 2011 | 21823229 |
| 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 ... | 2011 | 21733847 |
| 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 ... | 2012 | 22101035 |
| 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 ... | 2011 | 22045996 |
| 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 ... | 2011 | 22045996 |
| 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; ... | 2011 | 21892188 |
| 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 ... | 2011 | 21906287 |
| 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, ... | 2011 | 21926195 |
| 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 |
| multiple conversion between the genes encoding bacterial class-i release factors. | bacteria require two class-i release factors, rf1 and rf2, that recognize stop codons and promote peptide release from the ribosome. rf1 and rf2 were most likely established through gene duplication followed by altering their stop codon specificities in the common ancestor of extant bacteria. this scenario expects that the two rf gene families have taken independent evolutionary trajectories after the ancestral gene duplication event. however, we here report two independent cases of conversion b ... | 2015 | 26257102 |
| 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 |
| 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 ... | 2012 | 22638584 |
| distribution of protein poly(adp-ribosyl)ation systems across all domains of life. | poly(adp-ribosyl)ation is a post-translational modification of proteins involved in regulation of many cellular pathways. poly(adp-ribose) (par) consists of chains of repeating adp-ribose nucleotide units and is synthesized by the family of enzymes called poly(adp-ribose) polymerases (parps). this modification can be removed by the hydrolytic action of poly(adp-ribose) glycohydrolase (parg) and adp-ribosylhydrolase 3 (arh3). hydrolytic activity of macrodomain proteins (macrod1, macrod2 and targ1 ... | 2014 | 24865146 |
| diversity takes shape: understanding the mechanistic and adaptive basis of bacterial morphology. | the modern age of metagenomics has delivered unprecedented volumes of data describing the genetic and metabolic diversity of bacterial communities, but it has failed to provide information about coincident cellular morphologies. much like metabolic and biosynthetic capabilities, morphology comprises a critical component of bacterial fitness, molded by natural selection into the many elaborate shapes observed across the bacterial domain. in this essay, we discuss the diversity of bacterial morpho ... | 2016 | 27695035 |
| metagenomic analysis of microbial consortia enriched from compost: new insights into the role of actinobacteria in lignocellulose decomposition. | compost habitats sustain a vast ensemble of microbes specializing in the degradation of lignocellulosic plant materials and are thus important both for their roles in the global carbon cycle and as potential sources of biochemical catalysts for advanced biofuels production. studies have revealed substantial diversity in compost microbiomes, yet how this diversity relates to functions and even to the genes encoding lignocellulolytic enzymes remains obscure. here, we used a metagenomic analysis of ... | 2016 | 26834834 |
| c/n ratio drives soil actinobacterial cellobiohydrolase gene diversity. | cellulose accounts for approximately half of photosynthesis-fixed carbon; however, the ecology of its degradation in soil is still relatively poorly understood. the role of actinobacteria in cellulose degradation has not been extensively investigated despite their abundance in soil and known cellulose degradation capability. here, the diversity and abundance of the actinobacterial glycoside hydrolase family 48 (cellobiohydrolase) gene in soils from three paired pasture-woodland sites were determ ... | 2015 | 25710367 |
| highly diverse nirk genes comprise two major clades that harbour ammonium-producing denitrifiers. | copper dependent nitrite reductase, nirk, catalyses the key step in denitrification, i.e. nitrite reduction to nitric oxide. distinct structural nirk classes and phylogenetic clades of nirk-type denitrifiers have previously been observed based on a limited set of nirk sequences, however, their environmental distribution or ecological strategies are currently unknown. in addition, environmental nirk-type denitrifiers are currently underestimated in pcr-dependent surveys due to primer coverage lim ... | 2016 | 26923558 |
| genomics of biological wastewater treatment. | | 2008 | 21261852 |
| 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 ... | 2010 | 20591188 |
| dcia is an ancestral replicative helicase operator essential for bacterial replication initiation. | delivery of the replicative helicase onto dna is an essential step in the initiation of replication. in bacteria, dnac (in escherichia coli) and dnai (in bacillus subtilis) are representative of the two known mechanisms that assist the replicative helicase at this stage. here, we establish that these two strategies cannot be regarded as prototypical of the bacterial domain since dnac and dnai (dna[ci]) are present in only a few bacterial phyla. we show that dna[ci] was domesticated at least seve ... | 2016 | 27830752 |
| 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 ... | 2012 | 22798450 |
| 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, ... | 2012 | 22389377 |
| cold shock induction of recombinant arctic environmental genes. | heterologous expression of psychrophilic enzymes in e. coli is particularly challenging due to their intrinsic instability. the low stability is regarded as a consequence of adaptation that allow them to function at low temperatures. recombinant production presents a significant barrier to their exploitation for commercial applications in industry. | 2015 | 26286037 |
| the eukaryotic translation initiation regulator cdc123 defines a divergent clade of atp-grasp enzymes with a predicted role in novel protein modifications. | deciphering the origin of uniquely eukaryotic features of sub-cellular systems, such as the translation apparatus, is critical in reconstructing eukaryogenesis. one such feature is the highly conserved, but poorly understood, eukaryotic protein cdc123, which regulates the abundance of the eukaryotic translation initiation eif2 complex and binds one of its components eif2γ. we show that the eukaryotic protein cdc123 defines a novel clade of atp-grasp enzymes distinguished from all other members o ... | 2015 | 25976611 |
| 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 ... | 2009 | 19089947 |
| 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 ... | 2009 | 19909532 |
| 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. | 1998 | 9464425 |
| biofilms 2003: emerging themes and challenges in studies of surface-associated microbial life. | | 2004 | 15231774 |
| gingipains from porphyromonas gingivalis - complex domain structures confer diverse functions. | gingipains, a group of arginine or lysine specific cysteine proteinases (also known as rgpa, rgpb and kgp), have been recognized as major virulence factors in porphyromonas gingivalis. this bacterium is one of a handful of pathogens that cause chronic periodontitis. gingipains are involved in adherence to and colonization of epithelial cells, haemagglutination and haemolysis of erythrocytes, disruption and manipulation of the inflammatory response, and the degradation of host proteins and tissue ... | 2011 | 24466435 |
| gbtools: interactive visualization of metagenome bins in r. | improvements in dna sequencing technology have increased the amount and quality of sequences that can be obtained from metagenomic samples, making it practical to extract individual microbial genomes from metagenomic assemblies ("binning"). however, while many tools and methods exist for unsupervised binning with various statistical algorithms, there are few options for visualizing the results, even though visualization is vital to exploratory data analysis. we have developed gbtools, a software ... | 2015 | 26732662 |
| a comprehensive benchmarking study of protocols and sequencing platforms for 16s rrna community profiling. | in the last 5 years, the rapid pace of innovations and improvements in sequencing technologies has completely changed the landscape of metagenomic and metagenetic experiments. therefore, it is critical to benchmark the various methodologies for interrogating the composition of microbial communities, so that we can assess their strengths and limitations. the most common phylogenetic marker for microbial community diversity studies is the 16s ribosomal rna gene and in the last 10 years the field h ... | 2016 | 26763898 |
| 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 |
| highly active and specific tyrosine ammonia-lyases from diverse origins enable enhanced production of aromatic compounds in bacteria and saccharomyces cerevisiae. | phenylalanine and tyrosine ammonia-lyases form cinnamic acid and p-coumaric acid, which are precursors of a wide range of aromatic compounds of biotechnological interest. lack of highly active and specific tyrosine ammonia-lyases has previously been a limitation in metabolic engineering approaches. we therefore identified 22 sequences in silico using synteny information and aiming for sequence divergence. we performed a comparative in vivo study, expressing the genes intracellularly in bacteria ... | 2015 | 25911487 |
| 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 ... | 2008 | 18322033 |
| veillonella, firmicutes: microbes disguised as gram negatives. | the firmicutes represent a major component of the intestinal microflora. the intestinal firmicutes are a large, diverse group of organisms, many of which are poorly characterized due to their anaerobic growth requirements. although most firmicutes are gram positive, members of the class negativicutes, including the genus veillonella, stain gram negative. veillonella are among the most abundant organisms of the oral and intestinal microflora of animals and humans, in spite of being strict anaerob ... | 2013 | 24976898 |
| 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 ... | 2010 | 20981284 |
| unpublished but public microbial genomes with biotechnological relevance. | | 2008 | 21261839 |
| metagenomic analyses reveal phylogenetic diversity of carboxypeptidase gene sequences in activated sludge of a wastewater treatment plant in shanghai, china. | activated sludge of wastewater treatment plants carries a diverse microflora. however, up to 80-90 % of microorganisms in activated sludge cannot be cultured by current laboratory techniques, leaving an enzyme reservoir largely unexplored. in this study, we investigated carboxypeptidase diversity in activated sludge of a wastewater treatment plant in shanghai, china, by a culture-independent metagenomic approach. three sets of consensus degenerate hybrid oligonucleotide primers (codehops) target ... | 2013 | 24860282 |
| metagenomic analyses reveal phylogenetic diversity of carboxypeptidase gene sequences in activated sludge of a wastewater treatment plant in shanghai, china. | activated sludge of wastewater treatment plants carries a diverse microflora. however, up to 80-90 % of microorganisms in activated sludge cannot be cultured by current laboratory techniques, leaving an enzyme reservoir largely unexplored. in this study, we investigated carboxypeptidase diversity in activated sludge of a wastewater treatment plant in shanghai, china, by a culture-independent metagenomic approach. three sets of consensus degenerate hybrid oligonucleotide primers (codehops) target ... | 2013 | 24860282 |
| novel lant associated lantibiotic clusters identified by genome database mining. | frequent use of antibiotics has led to the emergence of antibiotic resistance in bacteria. lantibiotic compounds are ribosomally synthesized antimicrobial peptides against which bacteria are not able to produce resistance, hence making them a good alternative to antibiotics. nisin is the oldest and the most widely used lantibiotic, in food preservation, without having developed any significant resistance against it. having their antimicrobial potential and a limited number, there is a need to id ... | 2014 | 24621781 |
| disruption of macrodomain protein sco6735 increases antibiotic production in streptomyces coelicolor. | adp-ribosylation is a post-translational modification that can alter the physical and chemical properties of target proteins and that controls many important cellular processes. macrodomains are evolutionarily conserved structural domains that bind adp-ribose derivatives and are found in proteins with diverse cellular functions. some proteins from the macrodomain family can hydrolyze adp-ribosylated substrates and therefore reverse this post-translational modification. bacteria and streptomyces, ... | 2016 | 27634042 |
| a comprehensive curation shows the dynamic evolutionary patterns of prokaryotic crisprs. | motivation. clustered regularly interspaced short palindromic repeat (crispr) is a genetic element with active regulation roles for foreign invasive genes in the prokaryotic genomes and has been engineered to work with the crispr-associated sequence (cas) gene cas9 as one of the modern genome editing technologies. due to inconsistent definitions, the existing crispr detection programs seem to have missed some weak crispr signals. results. this study manually curates all the currently annotated c ... | 2016 | 27195295 |
| antibiotics from predatory bacteria. | bacteria, which prey on other microorganisms, are commonly found in the environment. while some of these organisms act as solitary hunters, others band together in large consortia before they attack their prey. anecdotal reports suggest that bacteria practicing such a wolfpack strategy utilize antibiotics as predatory weapons. consistent with this hypothesis, genome sequencing revealed that these micropredators possess impressive capacities for natural product biosynthesis. here, we will present ... | 2016 | 27340451 |
| 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 ... | 2011 | 22675585 |
| ethanolamine utilization in vibrio alginolyticus. | ethanolamine is used as an energy source by phylogenetically diverse bacteria including pathogens, by the concerted action of proteins from the eut-operon. previous studies have revealed the presence of eutbc genes encoding ethanolamine-ammonia lyase, a key enzyme that breaks ethanolamine into acetaldehyde and ammonia, in about 100 bacterial genomes including members of gamma-proteobacteria. however, ethanolamine utilization has not been reported for any member of the vibrio genus. our comparati ... | 2012 | 23234435 |
| 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. ... | 2012 | 23185476 |
| 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 ... | 2012 | 23029318 |
| 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 ... | 2012 | 22865886 |