Publications

a thermostable bilirubin-oxidizing enzyme from activated sludge isolated by a metagenomic approach.	a gene coding for a multicopper oxidase (bopa) was identified through the screening of a metagenomic library constructed from wastewater treatment activated sludge. the recombinant bopa protein produced in escherichia coli exhibited oxidation activity toward 2,2'-azino-bis-(3-ethylbenzothiazoline-6-sulfonate) (abts) in the presence of copper, suggesting that bopa is laccase. a bioinformatic analysis of the bopa gene sequence indicated that it has a phylogenetically bacterial origin, possibly der ...	2016	27885197
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
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
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
marine and giant viruses as indicators of a marine microbial community in a riverine system.	viral communities are important for ecosystem function as they are involved in critical biogeochemical cycles and controlling host abundance. this study investigates riverine viral communities around a small rural town that influences local water inputs. myoviridae, siphoviridae, phycodnaviridae, mimiviridae, herpesviridae, and podoviridae were the most abundant families. viral species upstream and downstream of the town were similar, with synechoccocus phage, salinus, prochlorococcus phage, mim ...	2016	27506856
tatypa, a ribosome-binding gtpase protein, positively regulates wheat resistance to the stripe rust fungus.	tyrosine phosphorylation protein a (typa/bipa) belongs to the ribosome-binding gtpase superfamily. in many bacterial species, typa acts as a global stress and virulence regulator and also mediates resistance to the antimicrobial peptide bactericidal permeability-increasing protein. however, the function of typa in plants under biotic stresses is not known. in this study, we isolated and functionally characterized a stress-responsive typa gene (tatypa) from wheat, with three copies located on chr ...	2016	27446108
genome sequence of the organohalide-respiring dehalogenimonas alkenigignens type strain (ip3-3(t)).	dehalogenimonas alkenigignens ip3-3(t) is a strictly anaerobic, mesophilic, gram negative staining bacterium that grows by organohalide respiration, coupling the oxidation of h2 to the reductive dehalogenation of polychlorinated alkanes. growth has not been observed with any non-polyhalogenated alkane electron acceptors. here we describe the features of strain ip3-3(t) together with genome sequence information and its annotation. the 1,849,792 bp high-quality-draft genome contains 1936 predicted ...	2016	27340512
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
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
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
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
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
expanding the landscape of diterpene structural diversity through stereochemically controlled combinatorial biosynthesis.	plant-derived diterpenoids serve as important pharmaceuticals, food additives, and fragrances, yet their low natural abundance and high structural complexity limits their broader industrial utilization. by mimicking the modularity of diterpene biosynthesis in plants, we constructed 51 functional combinations of class i and ii diterpene synthases, 41 of which are "new-to-nature". stereoselective biosynthesis of over 50 diterpene skeletons was demonstrated, including natural variants and novel ena ...	2016	26749264
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
draft genome sequence of herpetosiphon geysericola gc-42, a nonphototrophic member of the chloroflexi class chloroflexia.	we report here the draft genome sequence of herpetosiphon geysericola gc-42, a predatory nonphototrophic member of the class chloroflexia in the phylum chloroflexi. this genome provides insight into the evolution of phototrophy and aerobic respiration within the chloroflexi.	2015	26586889
bacterial calpains and the evolution of the calpain (c2) family of peptidases.	homologues of calpain, often thought to be an essential, cytoplasmic, calcium-dependent cysteine endopeptidase found exclusively in eukaryotes, have been found in bacterial proteomes. the homologues lack calcium-binding sites, have differing domain architectures, and can be secreted or membrane-associated. homologues are rare and occur in a minority of bacterial phyla and often in a minority of species in a genus. however, the differences in domain architecture argue against a recent, horizontal ...	2015	26527411
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
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
spontaneous deletion of an "orfanage" region facilitates host adaptation in a "photosynthetic" cyanophage.	viruses have been suggested to be the largest source of genetic diversity on earth. genome sequencing and metagenomic surveys reveal that novel genes with unknown functions are abundant in viral genomes. yet few observations exist for the processes and frequency by which these genes are gained and lost. the surface waters of marine environments are dominated by marine picocyanobacteria and their co-existing viruses (cyanophages). recent genome sequencing of cyanophages has revealed a vast array ...	2015	26177354
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
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
active site and laminarin binding in glycoside hydrolase family 55.	the carbohydrate active enzyme (cazy) database indicates that glycoside hydrolase family 55 (gh55) contains both endo- and exo-β-1,3-glucanases. the founding structure in the gh55 is pclam55a from the white rot fungus phanerochaete chrysosporium (ishida, t., fushinobu, s., kawai, r., kitaoka, m., igarashi, k., and samejima, m. (2009) crystal structure of glycoside hydrolase family 55 β-1,3-glucanase from the basidiomycete phanerochaete chrysosporium. j. biol. chem. 284, 10100-10109). here, we pr ...	2015	25752603
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
insight into biases and sequencing errors for amplicon sequencing with the illumina miseq platform.	with read lengths of currently up to 2 × 300 bp, high throughput and low sequencing costs illumina's miseq is becoming one of the most utilized sequencing platforms worldwide. the platform is manageable and affordable even for smaller labs. this enables quick turnaround on a broad range of applications such as targeted gene sequencing, metagenomics, small genome sequencing and clinical molecular diagnostics. however, illumina error profiles are still poorly understood and programs are therefore ...	2015	25586220
cellulolytic potential under environmental changes in microbial communities from grassland litter.	in many ecosystems, global changes are likely to profoundly affect microorganisms. in southern california, changes in precipitation and nitrogen deposition may influence the composition and functional potential of microbial communities and their resulting ability to degrade plant material. to test whether such environmental changes impact the distribution of functional groups involved in leaf litter degradation, we determined how the genomic diversity of microbial communities in a semi-arid gras ...	2014	25505459
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
structure- and context-based analysis of the gxgyxyp family reveals a new putative class of glycoside hydrolase.	gut microbiome metagenomics has revealed many protein families and domains found largely or exclusively in that environment. proteins containing the gxgyxyp domain are over-represented in the gut microbiota, and are found in polysaccharide utilization loci in the gut symbiont bacteroides thetaiotaomicron, suggesting their involvement in polysaccharide metabolism, but little else is known of the function of this domain.	2014	24938123
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
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
a noncellulosomal mannanase26e contains a cbm59 in clostridium cellulovorans.	a multicomponent enzyme-complex prevents efficient degradation of the plant cell wall for biorefinery. in this study, the method of identifying glycoside hydrolases (ghs) to degrade hemicelluloses was demonstrated. the competence of c. cellulovorans, which changes to be suitable for degradation of each carbon source, was used for the method. c. cellulovorans was cultivated into locust bean gum (lbg) that is composed of galactomannan. the proteins produced by c. cellulovorans were separated into ...	2014	24795881
compositional biases among synonymous substitutions cause conflict between gene and protein trees for plastid origins.	archaeplastida (=kingdom plantae) are primary plastid-bearing organisms that evolved via the endosymbiotic association of a heterotrophic eukaryote host cell and a cyanobacterial endosymbiont approximately 1,400 ma. here, we present analyses of cyanobacterial and plastid genomes that show strongly conflicting phylogenies based on 75 plastid (or nuclear plastid-targeted) protein-coding genes and their direct translations to proteins. the conflict between genes and proteins is largely robust to th ...	2014	24795089
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
microbial community functional structures in wastewater treatment plants as characterized by geochip.	biological wwtps must be functionally stable to continuously and steadily remove contaminants which rely upon the activity of complex microbial communities. however, knowledge is still lacking in regard to microbial community functional structures and their linkages to environmental variables.	2014	24671164
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
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
discovery of a metabolic alternative to the classical mevalonate pathway.	eukarya, archaea, and some bacteria encode all or part of the essential mevalonate (mva) metabolic pathway clinically modulated using statins. curiously, two components of the mva pathway are often absent from archaeal genomes. the search for these missing elements led to the discovery of isopentenyl phosphate kinase (ipk), one of two activities necessary to furnish the universal five-carbon isoprenoid building block, isopentenyl diphosphate (ipp). unexpectedly, we now report functional ipks als ...	2013	24327557
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
comparative genomics of metabolic capacities of regulons controlled by cis-regulatory rna motifs in bacteria.	in silico comparative genomics approaches have been efficiently used for functional prediction and reconstruction of metabolic and regulatory networks. riboswitches are metabolite-sensing structures often found in bacterial mrna leaders controlling gene expression on transcriptional or translational levels.an increasing number of riboswitches and other cis-regulatory rnas have been recently classified into numerous rna families in the rfam database. high conservation of these rna motifs provides ...	2013	24060102
the crystal structure of the core domain of a cellulose induced protein (cip1) from hypocrea jecorina, at 1.5 å resolution.	in an effort to characterise the whole transcriptome of the fungus hypocrea jecorina, cdna clones of this fungus were identified that encode for previously unknown proteins that are likely to function in biomass degradation. one of these newly identified proteins, found to be co-regulated with the major h. jecorina cellulases, is a protein that was denoted cellulose induced protein 1 (cip1). this protein consists of a glycoside hydrolase family 1 carbohydrate binding module connected via a linke ...	2013	24039705
a tribute to disorder in the genome of the bloom-forming freshwater cyanobacterium microcystis aeruginosa.	microcystis aeruginosa is one of the most common bloom-forming cyanobacteria in freshwater ecosystems worldwide. this species produces numerous secondary metabolites, including microcystins, which are harmful to human health. we sequenced the genomes of ten strains of m. aeruginosa in order to explore the genomic basis of their ability to occupy varied environments and proliferate. our findings show that m. aeruginosa genomes are characterized by having a large open pangenome, and that each geno ...	2013	23950996
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 ...	2013	23894099
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 ...	2013	23887922
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 ...	2013	23718284
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 ...	2013	23671590
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
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 ...	2013	23258841
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 ...	2013	23258841
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
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 ...	2012	23145189
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
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 ...	2012	23019363
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 ...	2012	22933716
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
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
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 ...	2012	22768368
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
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
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 ...	2012	22392983
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
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
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
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
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
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 ...	2011	21876125
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
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
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
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
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
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
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
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 ...	2010	21327071
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
genomics of biological wastewater treatment.		2008	21261852
natural products genomics.		2008	21261848
unpublished but public microbial genomes with biotechnological relevance.		2008	21261839
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
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
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
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
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 ...	2010	20880332
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 ...	2010	20880332
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
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
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
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
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
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 ...	2010	20139321
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
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
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
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
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
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.	2009	19822009