Publications

cloning, sequencing, and expression of a xylanase gene from the extreme thermophile dictyoglomus thermophilum rt46b.1 and activity of the enzyme on fiber-bound substrate.	a genomic library of the dictyoglomus sp. strain rt46b.1 was constructed in the phage vector lambda zapii and screened for xylanase activity. a plaque expressing xylanase activity, designated b6-77, was isolated and shown to contain a genomic insert of 5.3 kb. subcloning revealed that the xylanase activity was restricted to a internal 1,507-bp psti-hindiii fragment which was subsequently sequenced and shown to contain a single complete open reading frame coding for a single-domain xylanase, xyna ...	1995	8534104
expression and secretion of a thermostable bacterial xylanase in kluyveromyces lactis.	the xyna structural gene from the extremely thermophilic anaerobe dictyoglomus thermophilum rt46b.1 was fused in frame with the secretion signal of the kluyveromyces lactis killer toxin in episomal expression vectors based on the kluyveromyces plasmid pkd1. xyna was secreted predominantly as an unglycosylated 35-kda protein which comprised up to 90% of the total extracellular proteins and reached a concentration of 130 micrograms/ml in shake-flask cultures grown under selective conditions.	1997	9251219
cloning, sequencing, and expression of the gene encoding amylopullulanase from pyrococcus furiosus and biochemical characterization of the recombinant enzyme.	the gene encoding the pyrococcus furiosus hyperthermophilic amylopullulanase (apu) was cloned, sequenced, and expressed in escherichia coli. the gene encoded a single 827-residue polypeptide with a 26-residue signal peptide. the protein sequence had very low homology (17 to 21% identity) with other apus and enzymes of the alpha-amylase family. in particular, none of the consensus regions present in the alpha-amylase family could be identified. p. furiosus apu showed similarity to three proteins, ...	1997	9293009
novel division level bacterial diversity in a yellowstone hot spring.	a culture-independent molecular phylogenetic survey was carried out for the bacterial community in obsidian pool (op), a yellowstone national park hot spring previously shown to contain remarkable archaeal diversity (s. m. barns, r. e. fundyga, m. w. jeffries, and n. r. page, proc. natl. acad. sci. usa 91:1609-1613, 1994). small-subunit rrna genes (rdna) were amplified directly from op sediment dna by pcr with universally conserved or bacteria-specific rdna primers and cloned. unique rdna types ...	1998	9440526
cloning of the xynb gene from dictyoglomus thermophilum rt46b.1 and action of the gene product on kraft pulp.	a two-step pcr protocol was used to identify and sequence a family 11 xylanase gene from dictyoglomus thermophilum rt46b.1. family 11 xylanase consensus fragments (gxcfs) were amplified from rt46b.1 genomic dna by using different sets of consensus pcr primers that exhibited broad specificity for conserved motifs within fungal and/or bacterial family 11 xylanase genes. on the basis of the sequences of a representative sample of the gxcfs a single family 11 xylanase gene (xynb) was identified. the ...	1998	9572948
sodium-dependent glutamate uptake by an alkaliphilic, thermophilic bacillus strain, ta2.a1.	a strain of bacillus designated ta2.a1, isolated from a thermal spring in te aroha, new zealand, grew optimally at ph 9.2 and 70 degrees c. bacillus strain ta2.a1 utilized glutamate as a sole carbon and energy source for growth, and sodium chloride (>5 mm) was an obligate requirement for growth. growth on glutamate was inhibited by monensin and amiloride, both inhibitors that collapse the sodium gradient (deltapna) across the cell membrane. n, n-dicyclohexylcarbodiimide inhibited the growth of b ...	1999	10322019
a gene encoding a novel multidomain beta-1,4-mannanase from caldibacillus cellulovorans and action of the recombinant enzyme on kraft pulp.	genomic walking pcr was used to obtained a 4,567-bp nucleotide sequence from caldibacillus cellulovorans. analysis of this sequence revealed that there were three open reading frames, designated orf1, orf2, and orf3. incomplete orf1 encoded a putative c-terminal cellulose-binding domain (cbd) homologous to members of cbd family iiib, while putative orf3 encoded a protein of unknown function. the putative mana protein encoded by complete mana orf2 was an enzyme with a novel multidomain structure ...	2000	10653733
sequencing and expression of additional xylanase genes from the hyperthermophile thermotoga maritima fjss3b.1.	two genes, xynb and xync, coding for xylanases were isolated from thermotoga maritima fjss3b.1 by a genomic-walking-pcr technique. sequencing of the genes showed that they encode multidomain family 10 xylanases. only xynb exhibited activity against xylan substrates. the temperature optimum (87 degrees c) and ph optimum (ph 6.5) of xynb are different from the previously reported xylanase, xyna (also a family 10 enzyme), from this organism. the catalytic domain expressed without other domains has ...	2000	10742238
sequencing, cloning, and high-level expression of the pfp gene, encoding a pp(i)-dependent phosphofructokinase from the extremely thermophilic eubacterium dictyoglomus thermophilum.	the sequencing, cloning, and expression of the pfp gene from dictyoglomus thermophilum, which consists of 1,041 bp and encodes a pyrophosphate-dependent phosphofructokinase, are described. a phylogenetic analysis indicates that the enzyme is closely related to the pyrophosphate-dependent enzyme from thermoproteus tenax. the recombinant and native enzymes share a high degree of similarity for most properties examined.	2000	10913106
thermotoga maritima phosphofructokinases: expression and characterization of two unique enzymes.	a pyrophosphate-dependent phosphofructokinase (pp(i)-pfk) and an atp-dependent phosphofructokinase (atp-pfk) from thermotoga maritima have been cloned and characterized. the pp(i)-pfk is unique in that the k(m) and v(max) values indicate that polyphosphate is the preferred substrate over pyrophosphate; the enzyme in reality is a polyphosphate-dependent pfk. the atp-pfk was not significantly affected by common allosteric effectors (e.g., phosphoenolpyruvate) but was strongly inhibited by pp(i) an ...	2001	11133978
different physiological roles of atp- and pp(i)-dependent phosphofructokinase isoenzymes in the methylotrophic actinomycete amycolatopsis methanolica.	cells of the actinomycete amycolatopsis methanolica grown on glucose possess only a single, exclusively pp(i)-dependent phosphofructokinase (pp(i)-pfk) (a. m. c. r. alves, g. j. w. euverink, h. j. hektor, j. van der vlag, w. vrijbloed, d.h.a. hondmann, j. visser, and l. dijkhuizen, j. bacteriol. 176:6827-6835, 1994). when this methylotrophic bacterium is grown on one-carbon (c(1)) compounds (e.g., methanol), an atp-dependent phosphofructokinase (atp-pfk) activity is specifically induced, complet ...	2001	11717283
hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability.	enzymes synthesized by hyperthermophiles (bacteria and archaea with optimal growth temperatures of > 80 degrees c), also called hyperthermophilic enzymes, are typically thermostable (i.e., resistant to irreversible inactivation at high temperatures) and are optimally active at high temperatures. these enzymes share the same catalytic mechanisms with their mesophilic counterparts. when cloned and expressed in mesophilic hosts, hyperthermophilic enzymes usually retain their thermal properties, ind ...	2001	11238984
lamprey lymphocyte-like cells express homologs of genes involved in immunologically relevant activities of mammalian lymphocytes.	to shed light on the origin of adaptive immunity, a cdna library was prepared from purified lymphocyte-like cells of a jawless vertebrate, the sea lamprey (petromyzon marinus). randomly selected cdna clones were sequenced, and their homologies to proteins in the databases were determined. of the sequences homologous to proteins involved in immune responses, five were selected for further characterization. their encoding genes corresponded to loci that in jawed vertebrates are essential for activ ...	2002	12391333
novel carbohydrate-binding module of beta-1,3-xylanase from a marine bacterium, alcaligenes sp. strain xy-234.	a beta-1,3-xylanase gene (txya) from a marine bacterium, alcaligenes sp. strain xy-234, has been cloned and sequenced. txya consists of a 1,410-bp open reading frame that encodes 469 amino acid residues with a calculated molecular mass of 52,256 da. the domain structure of the beta-1,3-xylanase (txya) consists of a signal peptide of 22 amino acid residues, followed by a catalytic domain which belongs to family 26 of the glycosyl hydrolases, a linker region with one array of dgg and six repeats o ...	2002	11948152
high-yield production of a bacterial xylanase in the filamentous fungus trichoderma reesei requires a carrier polypeptide with an intact domain structure.	a bacterial xylanase gene, nonomuraea flexuosa xyn11a, was expressed in the filamentous fungus trichoderma reesei from the strong cellobiohydrolase 1 promoter as fusions to a variety of carrier polypeptides. by using single-copy isogenic transformants, it was shown that production of this xylanase was clearly increased (up to 820 mg/liter) when it was produced as a fusion protein with a carrier polypeptide having an intact domain structure compared to the production (150 to 300 mg/liter) of fusi ...	2003	14660351
targeted disruption of the alpha-amylase gene in the hyperthermophilic archaeon sulfolobus solfataricus.	sulfolobus solfataricus secretes an acid-resistant alpha-amylase (amya) during growth on starch as the sole carbon and energy source. synthesis of this activity is subject to catabolite repression. to better understand alpha-amylase function and regulation, the structural gene was identified and disrupted and the resulting mutant was characterized. internal alpha-amylase peptide sequences obtained by tandem mass spectroscopy were used to identify the amya coding sequence. anti-alpha-amylase anti ...	2003	12511494
differences in hyporheic-zone microbial community structure along a heavy-metal contamination gradient.	the hyporheic zone of a river is nonphotic, has steep chemical and redox gradients, and has a heterotrophic food web based on the consumption of organic carbon entrained from downwelling surface water or from upwelling groundwater. the microbial communities in the hyporheic zone are an important component of these heterotrophic food webs and perform essential functions in lotic ecosystems. using a suite of methods (denaturing gradient gel electrophoresis, 16s rrna phylogeny, phospholipid fatty a ...	2003	12957946
prospecting for novel biocatalysts in a soil metagenome.	the metagenomes of complex microbial communities are rich sources of novel biocatalysts. we exploited the metagenome of a mixed microbial population for isolation of more than 15 different genes encoding novel biocatalysts by using a combined cultivation and direct cloning strategy. a 16s rrna sequence analysis revealed the presence of hitherto uncultured microbes closely related to the genera pseudomonas, agrobacterium, xanthomonas, microbulbifer, and janthinobacterium. total genomic dna from t ...	2003	14532085
molecular characterization of community structures and sulfur metabolism within microbial streamers in japanese hot springs.	community structures of submerged microbial slime streamers (smss) in sulfide-containing hot springs at 72 to 80 degrees c at nakabusa and yumata, japan, were investigated by molecular analysis based on the 16s rrna gene. the smss were classified into two consortia; consortium i occurred at lower levels of sulfide in the hot springs (less than 0.1 mm), and consortium ii dominated when the sulfide levels were higher (more than 0.1 mm). the dominant cell morphotypes in consortium i were filamentou ...	2003	14660348
characterization of a novel amylolytic enzyme encoded by a gene from a soil-derived metagenomic library.	it has been estimated that less than 1% of the microorganisms in nature can be cultivated by conventional techniques. thus, the classical approach of isolating enzymes from pure cultures allows the analysis of only a subset of the total naturally occurring microbiota in environmental samples enriched in microorganisms. to isolate useful microbial enzymes from uncultured soil microorganisms, a metagenome was isolated from soil samples, and a metagenomic library was constructed by using the puc19 ...	2004	15574921
amya, an alpha-amylase with beta-cyclodextrin-forming activity, and amyb from the thermoalkaliphilic organism anaerobranca gottschalkii: two alpha-amylases adapted to their different cellular localizations.	two alpha-amylase genes from the thermophilic alkaliphile anaerobranca gottschalkii were cloned, and the corresponding enzymes, amya and amyb, were investigated after purification of the recombinant proteins. based on their amino acid sequences, amya is proposed to be a lipoprotein with extracellular localization and thus is exposed to the alkaline milieu, while amyb apparently represents a cytoplasmic enzyme. the amino acid sequences of both enzymes bear high similarity to those of ghf13 protei ...	2005	16000780
improving the alkalophilic performances of the xyl1 xylanase from streptomyces sp. s38: structural comparison and mutational analysis.	endo-beta-1,4-xylanases of the family 11 glycosyl-hydrolases are catalytically active over a wide range of ph. xyl1 from streptomyces sp. s38 belongs to this family, and its optimum ph for enzymatic activity is 6. xyn11 from bacillus agaradhaerens and xylj from bacillus sp. 41m-1 share 85% sequence identity and have been described as highly alkalophilic enzymes. in an attempt to better understand the alkalophilic adaptation of xylanases, the three-dimensional structures of xyn11 and xyl1 were co ...	2005	15659364
identification and characterization of a novel intracellular alkaline alpha-amylase from the hyperthermophilic bacterium thermotoga maritima msb8.	the gene for a novel alpha-amylase, designated amyc, from the hyperthermophilic bacterium thermotoga maritima was cloned and heterologously overexpressed in escherichia coli. the putative intracellular enzyme had no amino acid sequence similarity to glycoside hydrolase family (ghf) 13 alpha-amylases, yet the range of substrate hydrolysis and the product profile clearly define the protein as an alpha-amylase. based on sequence similarity amyc belongs to a subgroup within ghf 57. on the basis of a ...	2006	16517673
the genome of deep-sea vent chemolithoautotroph thiomicrospira crunogena xcl-2.	presented here is the complete genome sequence of thiomicrospira crunogena xcl-2, representative of ubiquitous chemolithoautotrophic sulfur-oxidizing bacteria isolated from deep-sea hydrothermal vents. this gammaproteobacterium has a single chromosome (2,427,734 base pairs), and its genome illustrates many of the adaptations that have enabled it to thrive at vents globally. it has 14 methyl-accepting chemotaxis protein genes, including four that may assist in positioning it in the redoxcline. a ...	2006	17105352
the tmrdb and srpdb resources.	maintained at the university of texas health science center at tyler, texas, the tmrna database (tmrdb) is accessible at the url http://psyche.uthct.edu/dbs/tmrdb/tmrdb.html with mirror sites located at auburn university, auburn, alabama (http://www.ag.auburn.edu/mirror/tmrdb/) and the royal veterinary and agricultural university, denmark (http://tmrdb.kvl.dk/). the signal recognition particle database (srpdb) at http://psyche.uthct.edu/dbs/srpdb/srpdb.html is mirrored at http://srpdb.kvl.dk/ an ...	2006	16381838
the tmrdb and srpdb resources.	maintained at the university of texas health science center at tyler, texas, the tmrna database (tmrdb) is accessible at the url http://psyche.uthct.edu/dbs/tmrdb/tmrdb.html with mirror sites located at auburn university, auburn, alabama (http://www.ag.auburn.edu/mirror/tmrdb/) and the royal veterinary and agricultural university, denmark (http://tmrdb.kvl.dk/). the signal recognition particle database (srpdb) at http://psyche.uthct.edu/dbs/srpdb/srpdb.html is mirrored at http://srpdb.kvl.dk/ an ...	2006	16381838
the streptomyces nrdr transcriptional regulator is a zn ribbon/atp cone protein that binds to the promoter regions of class ia and class ii ribonucleotide reductase operons.	ribonucleotide reductases (rnrs) catalyze the conversion of ribonucleotides to deoxyribonucleotides and are essential for de novo dna synthesis and repair. streptomyces spp. contain genes coding for two rnrs, either of which is sufficient for vegetative growth. the class ia rnr is encoded by the nrdab genes, and the class ii rnr is encoded by nrdj, which is coexpressed with nrdr. we previously showed that the streptomyces coelicolor nrdr gene encodes a protein, nrdr, which represses transcriptio ...	2006	16950922
widespread distribution of archaeal reverse gyrase in thermophilic bacteria suggests a complex history of vertical inheritance and lateral gene transfers.	reverse gyrase, an enzyme of uncertain funtion, is present in all hyperthermophilic archaea and bacteria. previous phylogenetic studies have suggested that the gene for reverse gyrase has an archaeal origin and was transferred laterally (lgt) to the ancestors of the two bacterial hyperthermophilic phyla, thermotogales and aquificales. here, we performed an in-depth analysis of the evolutionary history of reverse gyrase in light of genomic progress. we found genes coding for reverse gyrase in the ...	2007	17350929
widespread distribution of archaeal reverse gyrase in thermophilic bacteria suggests a complex history of vertical inheritance and lateral gene transfers.	reverse gyrase, an enzyme of uncertain funtion, is present in all hyperthermophilic archaea and bacteria. previous phylogenetic studies have suggested that the gene for reverse gyrase has an archaeal origin and was transferred laterally (lgt) to the ancestors of the two bacterial hyperthermophilic phyla, thermotogales and aquificales. here, we performed an in-depth analysis of the evolutionary history of reverse gyrase in light of genomic progress. we found genes coding for reverse gyrase in the ...	2007	17350929
increased production of xylanase by expression of a truncated version of the xyn11a gene from nonomuraea flexuosa in trichoderma reesei.	we have previously shown that the nonomuraea flexuosa xyn11a polypeptides devoid of the carbohydrate binding module (cbm) have better thermostability than the full-length xylanase and are effective in bleaching of pulp. to produce an enzyme preparation useful for industrial applications requiring high temperature, the region encoding the cbm was deleted from the n. flexuosa xyn11a gene and the truncated gene was expressed in trichoderma reesei. the xylanase sequence was fused to the t. reesei ma ...	2007	17384308
potential and utilization of thermophiles and thermostable enzymes in biorefining.	in today's world, there is an increasing trend towards the use of renewable, cheap and readily available biomass in the production of a wide variety of fine and bulk chemicals in different biorefineries. biorefineries utilize the activities of microbial cells and their enzymes to convert biomass into target products. many of these processes require enzymes which are operationally stable at high temperature thus allowing e.g. easy mixing, better substrate solubility, high mass transfer rate, and ...	2007	17359551
a simple, fast, and accurate method of phylogenomic inference.	the explosive growth of genomic data provides an opportunity to make increased use of protein markers for phylogenetic inference. we have developed an automated pipeline for phylogenomic analysis (amphora) that overcomes the existing bottlenecks limiting large-scale protein phylogenetic inference. we demonstrated its high throughput capabilities and high quality results by constructing a genome tree of 578 bacterial species and by assigning phylotypes to 18,607 protein markers identified in meta ...	2008	18851752
sorting out the mix in microbial genomics.		2008	19025554
comparative genomic analysis of t-box regulatory systems in bacteria.	t-box antitermination is one of the main mechanisms of regulation of genes involved in amino acid metabolism in gram-positive bacteria. t-box regulatory sites consist of conserved sequence and rna secondary structure elements. using a set of known t-box sites, we constructed the common pattern and used it to scan available bacterial genomes. new t-boxes were found in various gram-positive bacteria, some gram-negative bacteria (delta-proteobacteria), and some other bacterial groups (deinococcales ...	2008	18359782
profilegrids as a new visual representation of large multiple sequence alignments: a case study of the reca protein family.	multiple sequence alignments are a fundamental tool for the comparative analysis of proteins and nucleic acids. however, large data sets are no longer manageable for visualization and investigation using the traditional stacked sequence alignment representation.	2008	19102758
the anabaena sensory rhodopsin transducer defines a novel superfamily of prokaryotic small-molecule binding domains.	the anabaena sensory rhodopsin transducer (asrt) is a small protein that has been claimed to function as a signaling molecule downstream of the cyanobacterial sensory rhodopsin. however, orthologs of asrt have been detected in several bacteria that lack rhodopsin, raising questions about the generality of this function. using sequence profile searches we show that asrt defines a novel superfamily of beta-sandwich fold domains. through contextual inference based on domain architectures and predic ...	2009	19682383
biodiversity of thermophilic prokaryotes with hydrolytic activities in hot springs of uzon caldera, kamchatka (russia).	samples of water from the hot springs of uzon caldera with temperatures from 68 to 87 degrees c and phs of 4.1 to 7.0, supplemented with proteinaceous (albumin, casein, or alpha- or beta-keratin) or carbohydrate (cellulose, carboxymethyl cellulose, chitin, or agarose) biological polymers, were filled with thermal water and incubated at the same sites, with the contents of the tubes freely accessible to the hydrothermal fluid. as a result, several enrichment cultures growing in situ on different ...	2009	18978089
biodiversity of thermophilic prokaryotes with hydrolytic activities in hot springs of uzon caldera, kamchatka (russia).	samples of water from the hot springs of uzon caldera with temperatures from 68 to 87 degrees c and phs of 4.1 to 7.0, supplemented with proteinaceous (albumin, casein, or alpha- or beta-keratin) or carbohydrate (cellulose, carboxymethyl cellulose, chitin, or agarose) biological polymers, were filled with thermal water and incubated at the same sites, with the contents of the tubes freely accessible to the hydrothermal fluid. as a result, several enrichment cultures growing in situ on different ...	2009	18978089
the prospects of cellulase-producing bacteria for the bioconversion of lignocellulosic biomass.	lignocellulosic biomass is a renewable and abundant resource with great potential for bioconversion to value-added bioproducts. however, the biorefining process remains economically unfeasible due to a lack of biocatalysts that can overcome costly hurdles such as cooling from high temperature, pumping of oxygen/stirring, and, neutralization from acidic or basic ph. the extreme environmental resistance of bacteria permits screening and isolation of novel cellulases to help overcome these challeng ...	2009	19680472
identification of functional lsrb-like autoinducer-2 receptors.	although a variety of bacterial species have been reported to use the interspecies communication signal autoinducer-2 (ai-2) to regulate multiple behaviors, the molecular mechanisms of ai-2 recognition and signal transduction remain poorly understood. to date, two types of ai-2 receptors have been identified: luxp, present in vibrio spp., and lsrb, first identified in salmonella enterica serovar typhimurium. in s. typhimurium, lsrb is the ligand binding protein of a transport system that enables ...	2009	19749048
comparative characterization of commercially important xylanase enzymes.	xylanase is an industrially important enzyme having wide range of applications especially in paper industry. it is crucial to gain an understanding about the structure and functional aspects of various xylanases produced from diverse sources. in this study, a bioinformatics and molecular modeling approach was adopted to explore properties and structure of xylanases. physico-chemical properties were predicted and prediction of motifs, disulfide bridges and secondary structure was performed for fu ...	2009	19759868
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
characterization of camh from methanosarcina thermophila, founding member of a subclass of the {gamma} class of carbonic anhydrases.	the homotrimeric enzyme mt-cam from methanosarcina thermophila is the archetype of the gamma class of carbonic anhydrases. a search of databases queried with mt-cam revealed that a majority of the homologs comprise a putative subclass (camh) in which there is major conservation of all of the residues essential for the archetype mt-cam except glu62 and an acidic loop containing the essential proton shuttle residue glu84. the camh homolog from m. thermophila (mt-camh) was overproduced in escherich ...	2010	20023030
characterization of camh from methanosarcina thermophila, founding member of a subclass of the {gamma} class of carbonic anhydrases.	the homotrimeric enzyme mt-cam from methanosarcina thermophila is the archetype of the gamma class of carbonic anhydrases. a search of databases queried with mt-cam revealed that a majority of the homologs comprise a putative subclass (camh) in which there is major conservation of all of the residues essential for the archetype mt-cam except glu62 and an acidic loop containing the essential proton shuttle residue glu84. the camh homolog from m. thermophila (mt-camh) was overproduced in escherich ...	2010	20023030
the amazing world of bacterial structured rnas.	the discovery of several new structured non-coding rnas in bacterial and archaeal genomes and metagenomes raises burning questions about their biological and biochemical functions.	2010	20236470
tertiary structure and characterization of a glycoside hydrolase family 44 endoglucanase from clostridium acetobutylicum.	a gene encoding a glycoside hydrolase family 44 (gh44) protein from clostridium acetobutylicum atcc 824 was synthesized and transformed into escherichia coli. the previously uncharacterized protein was expressed with a c-terminal his tag and purified by nickel-nitrilotriacetic acid affinity chromatography. crystallization and x-ray diffraction to a 2.2-a resolution revealed a triose phosphate isomerase (tim) barrel-like structure with additional greek key and beta-sandwich folds, similar to othe ...	2010	19915043
tertiary structure and characterization of a glycoside hydrolase family 44 endoglucanase from clostridium acetobutylicum.	a gene encoding a glycoside hydrolase family 44 (gh44) protein from clostridium acetobutylicum atcc 824 was synthesized and transformed into escherichia coli. the previously uncharacterized protein was expressed with a c-terminal his tag and purified by nickel-nitrilotriacetic acid affinity chromatography. crystallization and x-ray diffraction to a 2.2-a resolution revealed a triose phosphate isomerase (tim) barrel-like structure with additional greek key and beta-sandwich folds, similar to othe ...	2010	19915043
heat resistance mediated by a new plasmid encoded clp atpase, clpk, as a possible novel mechanism for nosocomial persistence of klebsiella pneumoniae.	klebsiella pneumoniae is an important opportunistic pathogen and a frequent cause of nosocomial infections. we have characterized a k. pneumoniae strain responsible for a series of critical infections in an intensive care unit over a two-year period. the strain was found to be remarkably thermotolerant providing a conceivable explanation of its persistence in the hospital environment. this marked phenotype is mediated by a novel type of clp atpase, designated clpk. the clpk gene is encoded by a ...	2010	21085699
distinguishing microbial genome fragments based on their composition: evolutionary and comparative genomic perspectives.	it is well known that patterns of nucleotide composition vary within and among genomes, although the reasons why these variations exist are not completely understood. between-genome compositional variation has been exploited to assign environmental shotgun sequences to their most likely originating genomes, whereas within-genome variation has been used to identify recently acquired genetic material such as pathogenicity islands. recent sequence assignment techniques have achieved high levels of ...	2010	20333228
representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation.	the accelerating growth in the number of protein sequences taxes both the computational and manual resources needed to analyze them. one approach to dealing with this problem is to minimize the number of proteins subjected to such analysis in a way that minimizes loss of information. to this end we have developed a set of representative proteomes (rps), each selected from a representative proteome group (rpg) containing similar proteomes calculated based on co-membership in uniref50 clusters. a ...	2011	21556138
insights into plant biomass conversion from the genome of the anaerobic thermophilic bacterium caldicellulosiruptor bescii dsm 6725.	caldicellulosiruptor bescii dsm 6725 utilizes various polysaccharides and grows efficiently on untreated high-lignin grasses and hardwood at an optimum temperature of ∼ 80 °c. it is a promising anaerobic bacterium for studying high-temperature biomass conversion. its genome contains 2666 protein-coding sequences organized into 1209 operons. expression of 2196 genes (83%) was confirmed experimentally. at least 322 genes appear to have been obtained by lateral gene transfer (lgt). putative functio ...	2011	21227922
comparative analyses imply that the enigmatic sigma factor 54 is a central controller of the bacterial exterior.	sigma-54 is a central regulator in many pathogenic bacteria and has been linked to a multitude of cellular processes like nitrogen assimilation and important functional traits such as motility, virulence, and biofilm formation. until now it has remained obscure whether these phenomena and the control by sigma-54 share an underlying theme.	2011	21806785
crystal structure of hyperthermophilic endo-β-1,4-glucanase: implications for catalytic mechanism and thermostability.	endo-β-1,4-glucanase from thermophilic fervidobacterium nodosum rt17-b1 (fncel5a), a new member of glycosyl hydrolase family 5, is highly thermostable and exhibits the highest activity on carboxymethylcellulose among the reported homologues. to understand the structural basis for the thermostability and catalytic mechanism, we report here the crystal structures of fncel5a and the complex with glucose at atomic resolution. fncel5a exhibited a (β/α)8-barrel structure typical of clan gh-a of glycos ...	2011	22128157
crystal structure of hyperthermophilic endo-β-1,4-glucanase: implications for catalytic mechanism and thermostability.	endo-β-1,4-glucanase from thermophilic fervidobacterium nodosum rt17-b1 (fncel5a), a new member of glycosyl hydrolase family 5, is highly thermostable and exhibits the highest activity on carboxymethylcellulose among the reported homologues. to understand the structural basis for the thermostability and catalytic mechanism, we report here the crystal structures of fncel5a and the complex with glucose at atomic resolution. fncel5a exhibited a (β/α)8-barrel structure typical of clan gh-a of glycos ...	2011	22128157
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
effects of elevated atmospheric co(2) on rhizosphere soil microbial communities in a mojave desert ecosystem.	the effects of elevated atmospheric carbon dioxide [co(2)] on microbial communities in arid rhizosphere soils beneath larrea tridentata were examined. roots of larrea were harvested from plots fumigated with elevated or ambient levels of [co(2)] using free-air co(2) enrichment (face) technology. twelve bacterial and fungal rrna gene libraries were constructed, sequenced and categorized into operational taxonomical units (otus). there was a significant decrease in otus within the firmicutes (bact ...	2011	21779135
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
novel metagenome-derived, cold-adapted alkaline phospholipase with superior lipase activity as an intermediate between phospholipase and lipase.	a novel lipolytic enzyme was isolated from a metagenomic library obtained from tidal flat sediments on the korean west coast. its putative functional domain, designated mplag, showed the highest similarity to phospholipase a from grimontia hollisae cip 101886, though it was screened from an emulsified tricaprylin plate. phylogenetic analysis showed that mplag is far from family i.6 lipases, including staphylococcus hyicus lipase, a unique lipase which can hydrolyze phospholipids, and is more evo ...	2012	22544255
genome signature difference between deinococcus radiodurans and thermus thermophilus.	the extremely radioresistant bacteria of the genus deinococcus and the extremely thermophilic bacteria of the genus thermus belong to a common taxonomic group. considering the distinct living environments of deinococcus and thermus, different genes would have been acquired through horizontal gene transfer after their divergence from a common ancestor. their guanine-cytosine (gc) contents are similar; however, we hypothesized that their genomic signatures would be different. our findings indicate ...	2012	22500246
methods of combinatorial optimization to reveal factors affecting gene length.	in this paper we present a novel method for genome ranking according to gene lengths. the main outcomes described in this paper are the following: the formulation of the genome ranking problem, presentation of relevant approaches to solve it, and the demonstration of preliminary results from prokaryotic genomes ordering. using a subset of prokaryotic genomes, we attempted to uncover factors affecting gene length. we have demonstrated that hyperthermophilic species have shorter genes as compared ...	2012	23300345
supplementing with non-glycoside hydrolase proteins enhances enzymatic deconstruction of plant biomass.	the glycoside hydrolases (gh) of caldicellulosiruptor bescii are thermophilic enzymes, and therefore they can hydrolyze plant cell wall polysaccharides at high temperatures. analyses of two c. bescii glycoside hydrolases, cbcela-tm1 and cbxyn10a with cellulase and endoxylanase activity, respectively, demonstrated that each enzyme is highly thermostable under static incubation at 70°c. both enzymes, however, rapidly lost their enzymatic activities when incubated at 70°c with end-over-end shaking. ...	2012	22952777
phylogenetic diversity and environment-specific distributions of glycosyl hydrolase family 10 xylanases in geographically distant soils.	xylan is one of the most abundant biopolymers on earth. its degradation is mediated primarily by microbial xylanase in nature. to explore the diversity and distribution patterns of xylanase genes in soils, samples of five soil types with different physicochemical characters were analyzed.	2012	22912883
a predictive model of intein insertion site for use in the engineering of molecular switches.	inteins are intervening protein domains with self-splicing ability that can be used as molecular switches to control activity of their host protein. successfully engineering an intein into a host protein requires identifying an insertion site that permits intein insertion and splicing while allowing for proper folding of the mature protein post-splicing. by analyzing sequence and structure based properties of native intein insertion sites we have identified four features that showed significant ...	2012	22649521
identification and characterization of novel cellulolytic and hemicellulolytic genes and enzymes derived from german grassland soil metagenomes.	soil metagenomes represent an unlimited resource for the discovery of novel biocatalysts from soil microorganisms. three large-inserts metagenomic dna libraries were constructed from different grassland soil samples and screened for genes conferring cellulase or xylanase activity. function-driven screening identified a novel cellulase-encoding gene (cel01) and two xylanase-encoding genes (xyn01 and xyn02). from sequence and protein domain analyses, cel01 (831 amino acids) belongs to glycoside hy ...	2012	22187078
identification and characterization of novel cellulolytic and hemicellulolytic genes and enzymes derived from german grassland soil metagenomes.	soil metagenomes represent an unlimited resource for the discovery of novel biocatalysts from soil microorganisms. three large-inserts metagenomic dna libraries were constructed from different grassland soil samples and screened for genes conferring cellulase or xylanase activity. function-driven screening identified a novel cellulase-encoding gene (cel01) and two xylanase-encoding genes (xyn01 and xyn02). from sequence and protein domain analyses, cel01 (831 amino acids) belongs to glycoside hy ...	2012	22187078
A novel cyanophage with a cyanobacterial nonbleaching protein a gene in the genome.	A cyanophage, PaV-LD, has been isolated from harmful filamentous cyanobacterium Planktothrix agardhii in Lake Donghu, a shallow freshwater lake in China. Here, we present the cyanophage's genomic organization and major structural proteins. The genome is a 95,299-bp-long, linear double-stranded DNA and contains 142 potential genes. BLAST searches revealed 29 proteins of known function in cyanophages, cyanobacteria, or bacteria. Thirteen major structural proteins ranging in size from 27 kDa to 172 ...	2012	22031930
multiple inter-kingdom horizontal gene transfers in the evolution of the phosphoenolpyruvate carboxylase gene family.	pepcase is a gene encoding phosphoenolpyruvate carboxylase that exists in bacteria, archaea and plants,playing an important role in plant metabolism and development. most plants have two or more pepcase genes belonging to two gene sub-families, while only one gene exists in other organisms. previous research categorized one plant pepcase gene as plant-type pepcase (ptpc) while the other as bacteria-type pepcase (btpc) because of its similarity with the pepcase gene found in bacteria. phylogeneti ...	2012	23251445
in situ production of branched glycerol dialkyl glycerol tetraethers in a great basin hot spring (usa).	branched glycerol dialkyl glycerol tetraethers (bgdgts) are predominantly found in soils and peat bogs. in this study, we analyzed core (c)-bgdgts after hydrolysis of polar fractions using liquid chromatography-atmospheric pressure chemical ionization-mass spectrometry and analyzed intact p-bgdgts using total lipid extract (tle) without hydrolysis by liquid chromatography-electrospray ionization-multiple stage mass spectrometry. our results show multiple lines of evidence for the production of b ...	2013	23847605
genomes of the class erysipelotrichia clarify the firmicute origin of the class mollicutes.	the tree of life is paramount for achieving an integrated understanding of microbial evolution and the relationships between physiology, genealogy and genomics. it provides the framework for interpreting environmental sequence data, whether applied to microbial ecology or to human health. however, there remain many instances where there is ambiguity in our understanding of the phylogeny of major lineages, and/or confounding nomenclature. here we apply recent genomic sequence data to examine the ...	2013	23606477
metagenome reveals potential microbial degradation of hydrocarbon coupled with sulfate reduction in an oil-immersed chimney from guaymas basin.	deep-sea hydrothermal vent chimneys contain a high diversity of microorganisms, yet the metabolic activity and the ecological functions of the microbial communities remain largely unexplored. in this study, a metagenomic approach was applied to characterize the metabolic potential in a guaymas hydrothermal vent chimney and to conduct comparative genomic analysis among a variety of environments with sequenced metagenomes. complete clustering of functional gene categories with a comparative metage ...	2013	23785357
microbial diversity and biochemical potential encoded by thermal spring metagenomes derived from the kamchatka peninsula.	volcanic regions contain a variety of environments suitable for extremophiles. this study was focused on assessing and exploiting the prokaryotic diversity of two microbial communities derived from different kamchatkian thermal springs by metagenomic approaches. samples were taken from a thermoacidophilic spring near the mutnovsky volcano and from a thermophilic spring in the uzon caldera. environmental dna for metagenomic analysis was isolated from collected sediment samples by direct cell lysi ...	2013	23533327
luxr solos in photorhabdus species.	bacteria communicate via small diffusible molecules to mediate group-coordinated behavior, a process designated as quorum sensing. the basic molecular quorum sensing system of gram-negative bacteria consists of a luxi-type autoinducer synthase producing acyl-homoserine lactones (ahls) as signaling molecules, and a luxr-type receptor detecting the ahls to control expression of specific genes. however, many proteobacteria possess one or more unpaired luxr-type receptors that lack a cognate luxi-li ...	2014	25478328
purification and characterization of [formula: see text]-mannanase from bacillus pumilus (m27) and its applications in some fruit juices.	thermo alkaline mannanase was purified from the bacteria of bacillus pumilus (m27) using the techniques of ammonium sulphate precipitation, deae-sephadex ion exchange chromatography and sephacryl s200 gel filtration chromatography with 111-fold and 36 % yield. it was determined that the enzyme had 2 sub-units including 35 kda and 55 kda in gel filtration chromatography and sds-page electrophoresis systems. the optimum ph and temperature was determined as 8 and 60 °c, respectively. it was also no ...	2014	26243955
purification and characterization of [formula: see text]-mannanase from bacillus pumilus (m27) and its applications in some fruit juices.	thermo alkaline mannanase was purified from the bacteria of bacillus pumilus (m27) using the techniques of ammonium sulphate precipitation, deae-sephadex ion exchange chromatography and sephacryl s200 gel filtration chromatography with 111-fold and 36 % yield. it was determined that the enzyme had 2 sub-units including 35 kda and 55 kda in gel filtration chromatography and sds-page electrophoresis systems. the optimum ph and temperature was determined as 8 and 60 °c, respectively. it was also no ...	2014	26243955
temperature-dependent variations in sulfate-reducing communities associated with a terrestrial hydrocarbon seep.	terrestrial hydrocarbon seeps are an important source of naturally emitted methane over geological time. the exact community compositions responsible for carbon cycling beneath these surface features remain obscure. as sulfate reduction represents an essential process for anoxic organic mineralization, this study collected muddy fluids from a high-temperature hydrocarbon seep in taiwan and analyzed community structures of sulfate-supplemented sediment slurries incubated anoxically at elevated te ...	2014	25273230
expression and characterization of a gh43 endo-arabinanase from thermotoga thermarum.	arabinan is an important plant polysaccharide degraded mainly by two hydrolytic enzymes, endo-arabinanase and α-l-arabinofuranosidase. in this study, the characterization and application in arabinan degradation of an endo-arabinanase from thermotoga thermarum were investigated.	2014	24886412
intein applications: from protein purification and labeling to metabolic control methods.	the discovery of inteins in the early 1990s opened the door to a wide variety of new technologies. early engineered inteins from various sources allowed the development of self-cleaving affinity tags and new methods for joining protein segments through expressed protein ligation. some applications were developed around native and engineered split inteins, which allow protein segments expressed separately to be spliced together in vitro. more recently, these early applications have been expanded ...	2014	24700459
structural analysis of a glycoside hydrolase family 11 xylanase from neocallimastix patriciarum: insights into the molecular basis of a thermophilic enzyme.	the catalytic domain of xyncdbfv, a glycoside hydrolase family 11 (gh11) xylanase from ruminal fungus neocallimastix patriciarum previously engineered to exhibit higher specific activity and broader ph adaptability, holds great potential in commercial applications. here, the crystal structures of xyncdbfv and its complex with substrate were determined to 1.27-1.43 å resolution. these structures revealed a typical gh11 β-jelly-roll fold and detailed interaction networks between the enzyme and lig ...	2014	24619408
developing a xylanase xynzg from plectosphaerella cucumerina for baking by heterologously expressed in kluyveromyces lactis.	xylanase can replace chemical additives to improve the volume and sensory properties of bread in the baking. suitable baking xylanase with improved yield will promote the application of xylanase in baking industry. the xylanase xynzg from the plectosphaerella cucumerina has been previously characterized by heterologous expression in pichia pastoris. however, p. pastoris is not a suitable host for xylanase to be used in the baking process since p. pastoris does not have gras (generally regarded a ...	2014	25511290
carbohydrate metabolism in archaea: current insights into unusual enzymes and pathways and their regulation.	the metabolism of archaea, the third domain of life, resembles in its complexity those of bacteria and lower eukarya. however, this metabolic complexity in archaea is accompanied by the absence of many "classical" pathways, particularly in central carbohydrate metabolism. instead, archaea are characterized by the presence of unique, modified variants of classical pathways such as the embden-meyerhof-parnas (emp) pathway and the entner-doudoroff (ed) pathway. the pentose phosphate pathway is only ...	2014	24600042
complete genome sequence of the extreme thermophile dictyoglomus thermophilum h-6-12.	here, we present the complete genome of the extreme thermophile, dictyoglomus thermophilum h-6-12 (phylum dictyoglomi), which consists of 1,959,987 bp.	2014	24558247
recent advances in in vivo applications of intein-mediated protein splicing.	intein-mediated protein splicing has become an essential tool in modern biotechnology. fundamental progress in the structure and catalytic strategies of cis- and trans-splicing inteins has led to the development of modified inteins that promote efficient protein purification, ligation, modification and cyclization. recent work has extended these in vitro applications to the cell or to whole organisms. we review recent advances in intein-mediated protein expression and modification, post-translat ...	2014	24490831
evolution of the f0f1 atp synthase complex in light of the patchy distribution of different bioenergetic pathways across prokaryotes.	bacteria and archaea are characterized by an amazing metabolic diversity, which allows them to persist in diverse and often extreme habitats. apart from oxygenic photosynthesis and oxidative phosphorylation, well-studied processes from chloroplasts and mitochondria of plants and animals, prokaryotes utilize various chemo- or lithotrophic modes, such as anoxygenic photosynthesis, iron oxidation and reduction, sulfate reduction, and methanogenesis. most bioenergetic pathways have a similar general ...	2014	25188293
mesaconase/fumarase fumd in escherichia coli o157:h7 and promiscuity of escherichia coli class i fumarases fuma and fumb.	mesaconase catalyzes the hydration of mesaconate (methylfumarate) to (s)-citramalate. the enzyme participates in the methylaspartate pathway of glutamate fermentation as well as in the metabolism of various c5-dicarboxylic acids such as mesaconate or l-threo-β-methylmalate. we have recently shown that burkholderia xenovorans uses a promiscuous class i fumarase to catalyze this reaction in the course of mesaconate utilization. here we show that classical escherichia coli class i fumarases a and b ...	2015	26658641
strategies for the production of cell wall-deconstructing enzymes in lignocellulosic biomass and their utilization for biofuel production.	microbial cell wall-deconstructing enzymes are widely used in the food, wine, pulp and paper, textile, and detergent industries and will be heavily utilized by cellulosic biorefineries in the production of fuels and chemicals. due to their ability to use freely available solar energy, genetically engineered bioenergy crops provide an attractive alternative to microbial bioreactors for the production of cell wall-deconstructing enzymes. this review article summarizes the efforts made within the l ...	2015	26627868
strategies for the production of cell wall-deconstructing enzymes in lignocellulosic biomass and their utilization for biofuel production.	microbial cell wall-deconstructing enzymes are widely used in the food, wine, pulp and paper, textile, and detergent industries and will be heavily utilized by cellulosic biorefineries in the production of fuels and chemicals. due to their ability to use freely available solar energy, genetically engineered bioenergy crops provide an attractive alternative to microbial bioreactors for the production of cell wall-deconstructing enzymes. this review article summarizes the efforts made within the l ...	2015	26627868
complete genome sequence of the thermophilic acidobacteria, pyrinomonas methylaliphatogenes type strain k22(t).	strain k22(t) is the type species of the recently- described genus pyrinomonas, in subdivision 4 of the phylum acidobacteria (int j syst evol micr. 2014; 64(1):220-7). it was isolated from geothermally-heated soil from mt. ngauruhoe, new zealand, using low-nutrient medium. p. methylaliphatogenes k22(t) has a chemoheterotrophic metabolism; it can hydrolyze a limited range of simple carbohydrates and polypeptides. its cell membrane is dominated by iso-branching fatty acids, and up to 40 % of its l ...	2015	26568784
single cells within the puerto rico trench suggest hadal adaptation of microbial lineages.	hadal ecosystems are found at a depth of 6,000 m below sea level and below, occupying less than 1% of the total area of the ocean. the microbial communities and metabolic potential in these ecosystems are largely uncharacterized. here, we present four single amplified genomes (sags) obtained from 8,219 m below the sea surface within the hadal ecosystem of the puerto rico trench (prt). these sags are derived from members of deep-sea clades, including the thaumarchaeota and sar11 clade, and two ar ...	2015	26386059
crystal structures of crispr-associated csx3 reveal a manganese-dependent deadenylation exoribonuclease.	in prokaryotes, the crispr/cas system is known to target and degrade invading phages and foreign genetic elements upon subsequent infection. however, the structure and function of many cas proteins remain largely unknown, due to the high diversity of cas proteins. here we report 3 crystal structures of archaeoglobus fulgidus csx3 (afcsx3) in free form, in complex with manganese ions and in complex with a single-stranded rna (ssrna) fragment, respectively. afcsx3 harbors a ferredoxin-like fold an ...	2015	26106927
lengths of orthologous prokaryotic proteins are affected by evolutionary factors.	proteins of the same functional family (for example, kinases) may have significantly different lengths. it is an open question whether such variation in length is random or it appears as a response to some unknown evolutionary driving factors. the main purpose of this paper is to demonstrate existence of factors affecting prokaryotic gene lengths. we believe that the ranking of genomes according to lengths of their genes, followed by the calculation of coefficients of association between genome ...	2015	26114113
distinct roles for carbohydrate-binding modules of glycoside hydrolase 10 (gh10) and gh11 xylanases from caldicellulosiruptor sp. strain f32 in thermostability and catalytic efficiency.	xylanases are crucial for lignocellulosic biomass deconstruction and generally contain noncatalytic carbohydrate-binding modules (cbms) accessing recalcitrant polymers. understanding how multimodular enzymes assemble can benefit protein engineering by aiming at accommodating various environmental conditions. two multimodular xylanases, xyna and xynb, which belong to glycoside hydrolase families 11 (gh11) and gh10, respectively, have been identified from caldicellulosiruptor sp. strain f32. in th ...	2015	25576604
cell wall modification in tobacco by differential targeting of recombinant endoglucanase from trichoderma reesei.	the development of transgenic plants as a production platform for biomass-degrading enzymes is a promising tool for an economically feasible allocation of enzymes processing lignocellulose. previous research has already identified a major limitation of in planta production such as interference with the structure and integrity of the plant cell wall resulting in a negative influence on plant growth and development.	2015	25849300
a zinc-dependent protease amz-tk from a thermophilic archaeon is a new member of the archaemetzincin protein family.	a putative zinc-dependent protease (tk0512) in thermococcus kodakarensis kod1 shares a conserved motif with archaemetzincins, which are metalloproteases found in archaea, bacteria, and eukarya. phylogenetic and sequence analyses showed that tk0512 and its homologues in thermococcaceae represent new members in the archaemetzincins family, which we named amz-tk. we further confirmed its proteolytic activity biochemically by overexpression of the recombinant amz-tk in escherichia coli and character ...	2015	26733945
transgenic plant-produced hydrolytic enzymes and the potential of insect gut-derived hydrolases for biofuels.	various perennial c4 grass species have tremendous potential for use as lignocellulosic biofuel feedstocks. currently available grasses require costly pre-treatment and exogenous hydrolytic enzyme application to break down complex cell wall polymers into sugars that can then be fermented into ethanol. it has long been hypothesized that engineered feedstock production of cell wall degrading (cwd) enzymes would be an efficient production platform for of exogenous hydrolytic enzymes. most research ...	2016	27303411
hyperthermostable thermotoga maritima xylanase xyn10b shows high activity at high temperatures in the presence of biomass-dissolving hydrophilic ionic liquids.	the gene of thermotoga maritima gh10 xylanase (tmxyn10b) was synthesised to study the extreme limits of this hyperthermostable enzyme at high temperatures in the presence of biomass-dissolving hydrophilic ionic liquids (ils). tmxyn10b expressed from pichia pastoris showed maximal activity at 100 °c and retained 92 % of maximal activity at 105 °c in a 30-min assay. although the temperature optimum of activity was lowered by 1-ethyl-3-methylimidazolium acetate ([emim]oac), tmxyn10b retained partia ...	2016	27240671
global association between thermophilicity and vancomycin susceptibility in bacteria.	exploration of the aquatic microbiota of several circum-neutral (6.0-8.5 ph) mid-temperature (55-85°c) springs revealed rich diversities of phylogenetic relatives of mesophilic bacteria, which surpassed the diversity of the truly-thermophilic taxa. to gain insight into the potentially-thermophilic adaptations of the phylogenetic relatives of gram-negative mesophilic bacteria detected in culture-independent investigations we attempted pure-culture isolation by supplementing the enrichment media w ...	2016	27065976
the complete genome sequence of hyperthermophile dictyoglomus turgidum dsm 6724™ reveals a specialized carbohydrate fermentor.	here we report the complete genome sequence of the chemoorganotrophic, extremely thermophilic bacterium, dictyoglomus turgidum, which is a gram negative, strictly anaerobic bacterium. d. turgidum and d. thermophilum together form the dictyoglomi phylum. the two dictyoglomus genomes are highly syntenic, and both are distantly related to caldicellulosiruptor spp. d. turgidum is able to grow on a wide variety of polysaccharide substrates due to significant genomic commitment to glycosyl hydrolases, ...	2016	28066333
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
estdz3: a new esterolytic enzyme exhibiting remarkable thermostability.	lipolytic enzymes that retain high levels of catalytic activity when exposed to a variety of denaturing conditions are of high importance for a number of biotechnological applications. in this study, we aimed to identify new lipolytic enzymes, which are highly resistant to prolonged exposure to elevated temperatures. to achieve this, we searched for genes encoding for such proteins in the genomes of a microbial consortium residing in a hot spring located in china. after performing functional gen ...	2016	27899916
structural and functional characterization of a highly stable endo-β-1,4-xylanase from fusarium oxysporum and its development as an efficient immobilized biocatalyst.	replacing fossil fuel with renewable sources such as lignocellulosic biomass is currently a promising alternative for obtaining biofuel and for fighting against the consequences of climate change. however, the recalcitrant structure of lignocellulosic biomass residues constitutes a major limitation for its widespread use in industry. the efficient hydrolysis of lignocellulosic materials requires the complementary action of multiple enzymes including xylanases and β-xylosidases, which are respons ...	2016	27602054