a natural view of microbial biodiversity within hot spring cyanobacterial mat communities.this review summarizes a decade of research in which we have used molecular methods, in conjunction with more traditional approaches, to study hot spring cyanobacterial mats as models for understanding principles of microbial community ecology. molecular methods reveal that the composition of these communities is grossly oversimplified by microscopic and cultivation methods. for example, none of 31 unique 16s rrna sequences detected in the octopus spring mat, yellowstone national park, matches t ...19989841675
the unique chaperone operon of thermotoga maritima: cloning and initial characterization of a functional hsp70 and small heat shock protein.the hyperthermophilic eubacterium thermotoga maritima possesses an operon encoding an hsp70 molecular chaperone protein and a protein with meaningful homology to the small heat shock protein family of chaperones. this represents the first demonstrated co-operon organization for these two important classes of molecular chaperones. we have cloned and initially characterized these proteins as functional chaperones in vitro: the hsp70 is capable of atp hydrolysis and substrate binding, and the small ...199910400580
bacterial primary colonization and early succession on surfaces in marine waters as determined by amplified rrna gene restriction analysis and sequence analysis of 16s rrna genes.the nearly universal colonization of surfaces in marine waters by bacteria and the formation of biofilms and biofouling communities have important implications for ecological function and industrial processes. however, the dynamics of surface attachment and colonization in situ, particularly during the early stages of biofilm establishment, are not well understood. experimental surfaces that differed in their degrees of hydrophilicity or hydrophobicity were incubated in a salt marsh estuary tida ...200010653705
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 ...200818359782
unexpected diversity and complexity of the guerrero negro hypersaline microbial mat.we applied nucleic acid-based molecular methods, combined with estimates of biomass (atp), pigments, and microelectrode measurements of chemical gradients, to map microbial diversity vertically on a millimeter scale in a hypersaline microbial mat from guerrero negro, baja california sur, mexico. to identify the constituents of the mat, small-subunit rrna genes were amplified by pcr from community genomic dna extracted from layers, cloned, and sequenced. bacteria dominated the mat and displayed u ...200616672518
cloning of cvipii nicking and modification system from chlorella virus nys-1 and application of nt.cvipii in random dna amplification.the cloning and expression of the cvipii dna nicking and modification system encoded by chlorella virus nys-1 is described. the system consists of a co-linear mtase encoding gene (cvipiim) and a nicking endonuclease encoding gene (cvipiint) separated by 12 nt. m.cvipii possesses eight conserved amino acid motifs (i to viii) typical of c5 mtases, but, like another chlorella virus mtase m.cviji, lacks conserved motifs ix and x. in addition to modification of the first cytosine in ccd (d = a, g or ...200415570069
molecular characterization of novel red green nonsulfur bacteria from five distinct hot spring communities in yellowstone national park.we characterized and compared five geographically isolated hot springs with distinct red-layer communities in yellowstone national park. individual red-layer communities were observed to thrive in temperatures ranging from 35 to 60 degrees c and at ph 7 to 9. all communities were dominated by red filamentous bacteria and contained bacteriochlorophyll a (bchl a), suggesting that they represented novel green nonsulfur (gns) bacteria. the in vivo absorption spectra of individual sites were differen ...200211772644
signature lipids and stable carbon isotope analyses of octopus spring hyperthermophilic communities compared with those of aquificales representatives.the molecular and isotopic compositions of lipid biomarkers of cultured aquificales genera have been used to study the community and trophic structure of the hyperthermophilic pink streamers and vent biofilm from octopus spring. thermocrinis ruber, thermocrinis sp. strain hi 11/12, hydrogenobacter thermophilus tk-6, aquifex pyrophilus, and aquifex aeolicus all contained glycerol-ether phospholipids as well as acyl glycerides. the n-c(20:1) and cy-c(21) fatty acids dominated all of the aquificale ...200111679343
phylogenetic relationships of cryptosporidium parasites based on the 70-kilodalton heat shock protein (hsp70) gene.we have characterized the nucleotide sequences of the 70-kda heat shock protein (hsp70) genes of cryptosporidium baileyi, c. felis, c. meleagridis, c. muris, c. serpentis, c. wrairi, and c. parvum from various animals. results of the phylogenetic analysis revealed the presence of several genetically distinct species in the genus cryptosporidium and eight distinct genotypes within the species c. parvum. some of the latter may represent cryptic species. the phylogenetic tree constructed from these ...200010831415
stress genes and proteins in the archaea.the field covered in this review is new; the first sequence of a gene encoding the molecular chaperone hsp70 and the first description of a chaperonin in the archaea were reported in 1991. these findings boosted research in other areas beyond the archaea that were directly relevant to bacteria and eukaryotes, for example, stress gene regulation, the structure-function relationship of the chaperonin complex, protein-based molecular phylogeny of organisms and eukaryotic-cell organelles, molecular ...199910585970
the 17-gene ethanolamine (eut) operon of salmonella typhimurium encodes five homologues of carboxysome shell proteins.the eut operon of salmonella typhimurium encodes proteins involved in the cobalamin-dependent degradation of ethanolamine. previous genetic analysis revealed six eut genes that are needed for aerobic use of ethanolamine; one (eutr), encodes a positive regulator which mediates induction of the operon by vitamin b12 plus ethanolamine. the dna sequence of the eut operon included 17 genes, suggesting a more complex pathway than that revealed genetically. we have correlated an open reading frame in t ...199910464203
discontinuous occurrence of the hsp70 (dnak) gene among archaea and sequence features of hsp70 suggest a novel outlook on phylogenies inferred from this protein.occurrence of the hsp70 (dnak) gene was investigated in various members of the domain archaea comprising both euryarchaeotes and crenarchaeotes and in the hyperthermophilic bacteria aquifex pyrophilus and thermotoga maritima representing the deepest offshoots in phylogenetic trees of bacterial 16s rrna sequences. the gene was not detected in 8 of 10 archaea examined but was found in a. pyrophilus and t. maritima, from which it was cloned and sequenced. comparative analyses of the hsp70 amino aci ...19999882656
protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes.the presence of shared conserved insertion or deletions (indels) in protein sequences is a special type of signature sequence that shows considerable promise for phylogenetic inference. an alternative model of microbial evolution based on the use of indels of conserved proteins and the morphological features of prokaryotic organisms is proposed. in this model, extant archaebacteria and gram-positive bacteria, which have a simple, single-layered cell wall structure, are termed monoderm prokaryote ...19989841678
comparative genomics of thermus thermophilus and deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance.thermus thermophilus and deinococcus radiodurans belong to a distinct bacterial clade but have remarkably different phenotypes. t. thermophilus is a thermophile, which is relatively sensitive to ionizing radiation and desiccation, whereas d. radiodurans is a mesophile, which is highly radiation- and desiccation-resistant. here we present an in-depth comparison of the genomes of these two related but differently adapted bacteria.200516242020
sequencing of heat shock protein 70 (dnak) homologs from deinococcus proteolyticus and thermomicrobium roseum and their integration in a protein-based phylogeny of prokaryotes.the 70-kda heat shock protein (hsp70) sequences define one of the most conserved proteins known to date. the hsp70 genes from deinococcus proteolyticus and thermomicrobium roseum, which were chosen as representatives of two of the most deeply branching divisions in the 16s rrna trees, were cloned and sequenced. hsp70 from both these species as well as thermus aquaticus contained a large insert in the n-terminal quadrant, which has been observed before as a unique characteristic of gram-negative ...19978990285
the phylogenetic relationships of chlorobium tepidum and chloroflexus aurantiacus based upon their reca sequences.using reca as the phylogenetic marker, the relationships of the green sulfur bacterium chlorobium tepidum and the green non-sulfur bacterium chloroflexus aurantiacus to other eubacteria were investigated. the reca genes of the two organisms were cloned, and the resulting protein sequences aligned with 86 other eubacterial reca sequences. cb. tepidum was placed as the nearest relative to the cytophaga/flexibacter/bacteriodes group, a relationship supported by results obtained with several phyloge ...19989595663
the biosynthetic pathway for myxol-2' fucoside (myxoxanthophyll) in the cyanobacterium synechococcus sp. strain pcc 7002.synechococcus sp. strain pcc 7002 produces a variety of carotenoids, which comprise predominantly dicylic beta-carotene and two dicyclic xanthophylls, zeaxanthin and synechoxanthin. however, this cyanobacterium also produces a monocyclic myxoxanthophyll, which was identified as myxol-2' fucoside. compared to the carotenoid glycosides produced by diverse microorganisms, cyanobacterial myxoxanthophyll and closely related compounds are unusual because they are glycosylated on the 2'-oh rather than ...200919304845
formation of multilayered photosynthetic biofilms in an alkaline thermal spring in yellowstone national park, this study, glass rods suspended at the air-water interface in the runoff channel of fairy geyser, yellowstone national park, wy, were used as a substratum to promote the development of biofilms that resembled multilayered mat communities in the splash zone at the geyser's source. this approach enabled the establishment of the temporal relationship between the appearance of cyanobacteria, which ultimately formed the outer green layer, and the development of a red underlayer containing roseifl ...200919218404
distribution analysis of hydrogenases in surface waters of marine and freshwater environments.surface waters of aquatic environments have been shown to both evolve and consume hydrogen and the ocean is estimated to be the principal natural source. in some marine habitats, h(2) evolution and uptake are clearly due to biological activity, while contributions of abiotic sources must be considered in others. until now the only known biological process involved in h(2) metabolism in marine environments is nitrogen fixation.201021079771
crystallization and preliminary x-ray crystallographic analysis of a bacterial tyrosinase from bacillus megaterium.tyrosinases are type 3 copper enzymes that are involved in the production of melanin and have two copper ions in the active site. here, the crystallization and primary analysis of a tyrosinase from bacillus megaterium is reported. the purified protein was crystallized in the absence or presence of zinc ions and the crystals diffracted to a resolution of 2.0 a. crystals obtained in the presence of zinc belonged to space group p2(1)2(1)2(1), while crystals grown in the absence of zinc belonged to ...201020823537
bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners.enzymes in the radical sam (rsam) domain family serve in a wide variety of biological processes, including rna modification, enzyme activation, bacteriocin core peptide maturation, and cofactor biosynthesis. evolutionary pressures and relationships to other cellular constituents impose recognizable grammars on each class of rsam-containing system, shaping patterns in results obtained through various comparative genomics analyses.201121223593
purification, characterization, and cloning of a bifunctional molybdoenzyme with hydratase and alcohol dehydrogenase activity.a bifunctional hydratase/alcohol dehydrogenase was isolated from the cyclohexanol degrading bacterium alicycliphilus denitrificans dsmz 14773. the enzyme catalyzes the addition of water to α,β-unsaturated carbonyl compounds and the subsequent alcohol oxidation. the purified enzyme showed three subunits in sds gel, and the gene sequence revealed that this enzyme belongs to the molybdopterin binding oxidoreductase family containing molybdopterins, fad, and iron-sulfur clusters.201021120472
purification, characterization, and cloning of a bifunctional molybdoenzyme with hydratase and alcohol dehydrogenase activity.a bifunctional hydratase/alcohol dehydrogenase was isolated from the cyclohexanol degrading bacterium alicycliphilus denitrificans dsmz 14773. the enzyme catalyzes the addition of water to α,β-unsaturated carbonyl compounds and the subsequent alcohol oxidation. the purified enzyme showed three subunits in sds gel, and the gene sequence revealed that this enzyme belongs to the molybdopterin binding oxidoreductase family containing molybdopterins, fad, and iron-sulfur clusters.201021120472
cultivation and genomic, nutritional, and lipid biomarker characterization of roseiflexus strains closely related to predominant in situ populations inhabiting yellowstone hot spring microbial mats.roseiflexus sp. strains were cultivated from a microbial mat of an alkaline siliceous hot spring in yellowstone national park. these strains are closely related to predominant filamentous anoxygenic phototrophs found in the mat, as judged by the similarity of small-subunit rrna, lipid distributions, and genomic and metagenomic sequences. like a japanese isolate, r. castenholzii, the yellowstone isolates contain bacteriochlorophyll a, but not bacteriochlorophyll c or chlorosomes, and grow photohe ...201020363941
Identification of a novel gene for biosynthesis of a bacteroid-specific electron carrier menaquinone.Ubiquinone (UQ) has been considered as an electron mediator in electron transfer that generates ATP in Rhizobium under both free-living and symbiosis conditions. When mutated, the dmtH gene has a symbiotic phenotype of forming ineffective nodules on Astragalus sinicus. The gene was isolated from a Mesorhizobium huakuii 7653R transposon-inserted mutant library. The DNA sequence and conserved protein domain analyses revealed that dmtH encodes demethylmenaquinone (DMK) methyltransferase, which cata ...201122194970
complete genome sequence of the aerobic co-oxidizing thermophile thermomicrobium order to enrich the phylogenetic diversity represented in the available sequenced bacterial genomes and as part of an "assembling the tree of life" project, we determined the genome sequence of thermomicrobium roseum dsm 5159. t. roseum dsm 5159 is a red-pigmented, rod-shaped, gram-negative extreme thermophile isolated from a hot spring that possesses both an atypical cell wall composition and an unusual cell membrane that is composed entirely of long-chain 1,2-diols. its genome is composed o ...200919148287
genome data mining and soil survey for the novel group 5 [nife]-hydrogenase to explore the diversity and ecological importance of presumptive high-affinity h2-oxidizing bacteria.streptomyces soil isolates exhibiting the unique ability to oxidize atmospheric h(2) possess genes specifying a putative high-affinity [nife]-hydrogenase. this study was undertaken to explore the taxonomic diversity and the ecological importance of this novel functional group. we propose to designate the genes encoding the small and large subunits of the putative high-affinity hydrogenase hhys and hhyl, respectively. genome data mining revealed that the hhyl gene is unevenly distributed in the p ...201121742924
Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21).Ktedonobacter racemifer corrig. Cavaletti et al. 2007 is the type species of the genus Ktedonobacter, which in turn is the type genus of the family Ktedonobacteraceae, the type family of the order Ktedonobacterales within the class Ktedonobacteria in the phylum 'Chloroflexi'. Although K. racemifer shares some morphological features with the actinobacteria, it is of special interest because it was the first cultivated representative of a deep branching unclassified lineage of otherwise uncultivat ...201122180814
evolutionary variation in bacterial rnase p rnas.sequences encoding rnase p rnas from representatives of the last remaining classical phyla of bacteria have been determined, completing a general phylogenetic survey of rnase p rna sequence and structure. this broad sampling of rnase p rnas allows some refinement of the secondary structure, and reveals patterns in the evolutionary variation of sequences and secondary structures. although the sequences range from 100 to <25% identical to one another, and although only 40 of the nucleotides are in ...19989722626
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 ...200818851752
effect of growth temperature on the long-chain diols and fatty acids of thermomicrobium roseum.long-chain 1,2-diols constitute the hydrophobic backbone of membrane lipids (replacing glycerolipids) in the thermophilic eubacterium thermomicrobium roseum. the effects of incubation temperature on chain length and chain branching of diols and fatty acids were investigated. the percentage of branched chains decreased, and chain length increased slightly, with increased growth temperatures.19873818547
sorting out the mix in microbial genomics. 200819025554
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 ...201124710297
design and evaluation of useful bacterium-specific pcr primers that amplify genes coding for bacterial 16s rrna.we report the design and evaluation of pcr primers 63f and 1387r for amplification of 16s rrna genes from bacteria. their specificity and efficacy were tested systematically with a bacterial species and environmental samples. they were found to be more useful for 16s rrna gene amplification in ecological and systematic studies than pcr amplimers that are currently more generally used.19989464425
sequence, structure and functional diversity of pd-(d/e)xk phosphodiesterase superfamily.proteins belonging to pd-(d/e)xk phosphodiesterases constitute a functionally diverse superfamily with representatives involved in replication, restriction, dna repair and trna-intron splicing. their malfunction in humans triggers severe diseases, such as fanconi anemia and xeroderma pigmentosum. to date there have been several attempts to identify and classify new pd-(d/e)kk phosphodiesterases using remote homology detection methods. such efforts are complicated, because the superfamily exhibit ...201222638584
characterization of novel long-chain 1,2-diols in thermus species and demonstration that thermus strains contain both glycerol-linked and diol-linked this study, we purified and characterized tetra- and triglycosyl glycolipids (gl-1 and gl-2, respectively) from two different colonial forms of thermus scotoductus x-1, from t. filiformis tok4 a2, and from t. oshimai sps-11. acid hydrolysis of the purified glycolipids liberated, in addition to the expected long-chain fatty acids, two components which were identified by gas chromatography-mass spectrometry as 16-methylheptadecane-1,2-diol and 15-methylheptadecane-1,2-diol. fast atom bombardmen ...19979324266
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 ...201222500246
identification of differentially expressed proteins of arthrospira (spirulina) plantensis-yz under salt-stress conditions by proteomics and qrt-pcr analysis.arthrospira (spirulina) platensis as a representative species of cyanobacteria has been recognized and used worldwide as a source of protein in the food, which possesses some unusual and valuable physiological characteristics, such as alkali and salt tolerance. based on complete genome sequencing of arthrospira (spirulina) plantensis-yz, we compared the protein expression profiles of this organism under different salt-stress conditions (i.e. 0.02 m, 0.5 m and 1.0 m nacl, respectively), using 2-d ...201323363438
complete genome sequence of sphaerobacter thermophilus type strain (s 6022).sphaerobacter thermophilus demharter et al. 1989 is the sole and type species of the genus sphaerobacter, which is the type genus of the family sphaerobacteraceae, the order sphaerobacterales and the subclass sphaerobacteridae. phylogenetically, it belongs to the genomically little studied class of the thermomicrobia in the bacterial phylum chloroflexi. here, the genome of strain s 6022(t) is described which is an obligate aerobe that was originally isolated from an aerated laboratory-scale ferm ...201021304677
assessment of microbial richness in pelagic sediment of andaman sea by bacterial tag encoded flx titanium amplicon pyrosequencing (btefap).microbial diversity of 1,000 m deep pelagic sediment from off coast of andaman sea was analyzed by a culture independent technique, bacterial tag encoded flx titanium amplicon pyrosequencing. the hypervariable region of small subunit ribosomal rrna gene covering v6-v9, was amplified from the metagenomic dna and sequenced. we obtained 19,271 reads, of which 18,206 high quality sequences were subjected to diversity analysis. a total of 305 operational taxonomic units (otus) were obtained correspon ...201224293708
the quest for a unified view of bacterial land colonization.exploring molecular mechanisms underlying bacterial water-to-land transition represents a critical start toward a better understanding of the functioning and stability of the terrestrial ecosystems. here, we perform comprehensive analyses based on a large variety of bacteria by integrating taxonomic, phylogenetic and metagenomic data, in the quest for a unified view that elucidates genomic, evolutionary and ecological dynamics of the marine progenitors in adapting to nonaquatic environments. we ...201424451209
distribution of genes encoding nucleoid-associated protein homologs in plasmids.bacterial nucleoid-associated proteins (naps) form nucleoprotein complexes and influence the expression of genes. recent studies have shown that some plasmids carry genes encoding nap homologs, which play important roles in transcriptional regulation networks between plasmids and host chromosomes. in this study, we determined the distributions of the well-known naps fis, h-ns, hu, ihf, and lrp and the newly found naps mvat and ndpa among the whole-sequenced 1382 plasmids found in gram-negative b ...201121350637
dcia is an ancestral replicative helicase operator essential for bacterial replication 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 ...201627830752
relevance of gc content to the conservation of dna polymerase iii/mismatch repair system in gram-positive bacteria.the mechanism of dna replication is one of the driving forces of genome evolution. bacterial dna polymerase iii, the primary complex of dna replication, consists of polc and dnae. polc is conserved in gram-positive bacteria, especially in the firmicutes with low gc content, whereas dnae is widely conserved in most gram-negative and gram-positive bacteria. polc contains two domains, the 3'-5'exonuclease domain and the polymerase domain, while dnae only possesses the polymerase domain. accordingly ...201324062730
molecular detection of bacteria in plant tissues, using universal 16s ribosomal dna degenerated primers.highly specific, sensitive and rapid tests are required for the detection and identification of covert bacterial contaminations in plant tissue cultures. current methods available for this purpose are tedious, time consuming, highly error prone, expensive, require advanced technical expertise and are sometimes ineffective. we report here the development of a sensitive polymerase chain reaction (pcr) based method for the rapid detection and identification of bacteria occurring in plant tissue cul ...201426019546
glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass.industrial-scale biofuel production requires robust enzymatic cocktails to produce fermentable sugars from lignocellulosic biomass. thermophilic bacterial consortia are a potential source of cellulases and hemicellulases adapted to harsher reaction conditions than commercial fungal enzymes. compost-derived microbial consortia were adapted to switchgrass at 60-¦c to develop thermophilic biomass-degrading consortia for detailed studies. microbial community analysis using small-subunit rrna gene am ...201121724886
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 ...201121779135
community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential.phototrophic microbial mat communities from 60-¦c and 65-¦c regions in the effluent channels of mushroom and octopus springs (yellowstone national park, wy, usa) were investigated by shotgun metagenomic sequencing. analyses of assembled metagenomic sequences resolved six dominant chlorophototrophic populations and permitted the discovery and characterization of undescribed but predominant community members and their physiological potential. linkage of phylogenetic marker genes and functional gen ...201121697961
The elusive third subunit IIa of the bacterial B-type oxidases: the enzyme from the hyperthermophile Aquifex aeolicus.The reduction of molecular oxygen to water is catalyzed by complicated membrane-bound metallo-enzymes containing variable numbers of subunits, called cytochrome c oxidases or quinol oxidases. We previously described the cytochrome c oxidase II from the hyperthermophilic bacterium Aquifex aeolicus as a ba(3)-type two-subunit (subunits I and II) enzyme and showed that it is included in a supercomplex involved in the sulfide-oxygen respiration pathway. It belongs to the B-family of the heme-copper ...201121738733
metatranscriptomic analyses of chlorophototrophs of a hot-spring microbial mat.the phototrophic microbial mat community of mushroom spring, an alkaline siliceous hot spring in yellowstone national park, was studied by metatranscriptomic methods. rna was extracted from mat specimens collected at four timepoints during light-to-dark and dark-to-light transitions in one diel cycle, and these rna samples were analyzed by both pyrosequencing and solid technologies. pyrosequencing was used to assess the community composition, which showed that ~84% of the rrna was derived from m ...201121697962
dispersal and regulation of an adaptive mutagenesis cassette in the bacteria domain.recently, a multiple gene cassette with mutagenic translation synthesis activity was identified and shown to be under lexa regulation in several proteobacteria species. in this work, we have traced down instances of this multiple gene cassette across the bacteria domain. phylogenetic analyses show that this cassette has undergone several reorganizations since its inception in the actinobacteria, and that it has dispersed across the bacterial domain through a combination of vertical inheritance, ...200616407325
complete genome sequence of the filamentous anoxygenic phototrophic bacterium chloroflexus aurantiacus.chloroflexus aurantiacus is a thermophilic filamentous anoxygenic phototrophic (fap) bacterium, and can grow phototrophically under anaerobic conditions or chemotrophically under aerobic and dark conditions. according to 16s rrna analysis, chloroflexi species are the earliest branching bacteria capable of photosynthesis, and cfl. aurantiacus has been long regarded as a key organism to resolve the obscurity of the origin and early evolution of photosynthesis. cfl. aurantiacus contains a chimeric ...201121714912
metagenomics of an alkaline hot spring in galicia (spain): microbial diversity analysis and screening for novel lipolytic enzymes.a fosmid library was constructed with the metagenomic dna from the water of the lobios hot spring (76°c, ph = 8.2) located in ourense (spain). metagenomic sequencing of the fosmid library allowed the assembly of 9722 contigs ranging in size from 500 to 56,677 bp and spanning ~18 mbp. 23,207 orfs (open reading frames) were predicted from the assembly. biodiversity was explored by taxonomic classification and it revealed that bacteria were predominant, while the archaea were less abundant. the six ...201526635759
molecular phylogeny and intricate evolutionary history of the three isofunctional enzymes involved in the oxidation of protoporphyrinogen ix.tetrapyrroles such as heme and chlorophyll are essential for biological processes, including oxygenation, respiration, and photosynthesis. in the tetrapyrrole biosynthesis pathway, protoporphyrinogen ix oxidase (protox) catalyzes the formation of protoporphyrin ix, the last common intermediate for the biosynthesis of heme and chlorophyll. three nonhomologous isofunctional enzymes, hemg, hemj, and hemy, for protox have been identified. to reveal the distribution and evolution of the three protox ...201425108393
a potential source for cellulolytic enzyme discovery and environmental aspects revealed through metagenomics of brazilian mangroves.the mangroves are among the most productive and biologically important environments. the possible presence of cellulolytic enzymes and microorganisms useful for biomass degradation as well as taxonomic and functional aspects of two brazilian mangroves were evaluated using cultivation and metagenomic approaches. from a total of 296 microorganisms with visual differences in colony morphology and growth (including bacteria, yeast and filamentous fungus), 179 (60.5%) and 117 (39.5%) were isolated fr ...201324160319
co dehydrogenase genes found in metagenomic fosmid clones from the deep mediterranean sea.the use of carbon monoxide (co) as a biological energy source is widespread in microbes. in recent years, the role of co oxidation in superficial ocean waters has been shown to be an important energy supplement for heterotrophs (carboxydovores). the key enzyme co dehydrogenase was found in both isolates and metagenomes from the ocean's photic zone, where co is continuously generated by organic matter photolysis. we have also found genes that code for both forms i (low affinity) and ii (high affi ...200919801465
draft genome sequence of calcium-dependent paenibacillus sp. strain tca20, isolated from a hot spring containing a high concentration of calcium ions.calcium-dependent paenibacillus sp. strain tca20 was isolated from a water sample of a hot spring containing a high concentration of calcium ions. here, we report the draft genome sequence of this bacterium, which may be the basis for the research of calcium ion homeostasis.201425189580
systematic analysis of compositional order of proteins reveals new characteristics of biological functions and a universal correlate of macroevolution.we present a novel analysis of compositional order (co) based on the occurrence of frequent amino-acid triplets (fts) that appear much more than random in protein sequences. the method captures all types of proteomic compositional order including single amino-acid runs, tandem repeats, periodic structure of motifs and otherwise low complexity amino-acid regions. we introduce new order measures, distinguishing between 'regularity', 'periodicity' and 'vocabulary', to quantify these phenomena and t ...201324278003
nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum chloroflexi.nitrite-oxidizing bacteria (nob) catalyze the second step of nitrification, a major process of the biogeochemical nitrogen cycle, but the recognized diversity of this guild is surprisingly low and only two bacterial phyla contain known nob. here, we report on the discovery of a chemolithoautotrophic nitrite oxidizer that belongs to the widespread phylum chloroflexi not previously known to contain any nitrifying organism. this organism, named nitrolancetus hollandicus, was isolated from a nitrify ...201222763649
dna polymerases engineered by directed evolution to incorporate non-standard nucleotides.dna polymerases have evolved for billions of years to accept natural nucleoside triphosphate substrates with high fidelity and to exclude closely related structures, such as the analogous ribonucleoside triphosphates. however, polymerases that can accept unnatural nucleoside triphosphates are desired for many applications in biotechnology. the focus of this review is on non-standard nucleotides that expand the genetic "alphabet." this review focuses on experiments that, by directed evolution, ha ...201425400626
the unaccounted yet abundant nitrous oxide-reducing microbial community: a potential nitrous oxide sink.nitrous oxide (n(2)o) is a major radiative forcing and stratospheric ozone-depleting gas emitted from terrestrial and aquatic ecosystems. it can be transformed to nitrogen gas (n(2)) by bacteria and archaea harboring the n(2)o reductase (n(2)or), which is the only known n(2)o sink in the biosphere. despite its crucial role in mitigating n(2)o emissions, knowledge of the n(2)or in the environment remains limited. here, we report a comprehensive phylogenetic analysis of the nosz gene coding the n( ...201223151640
discovery and characterization of ionic liquid-tolerant thermophilic cellulases from a switchgrass-adapted microbial community.the development of advanced biofuels from lignocellulosic biomass will require the use of both efficient pretreatment methods and new biomass-deconstructing enzyme cocktails to generate sugars from lignocellulosic substrates. certain ionic liquids (ils) have emerged as a promising class of compounds for biomass pretreatment and have been demonstrated to reduce the recalcitrance of biomass for enzymatic hydrolysis. however, current commercial cellulase cocktails are strongly inhibited by most of ...201424479406
the unaccounted yet abundant nitrous oxide-reducing microbial community: a potential nitrous oxide sink.nitrous oxide (n(2)o) is a major radiative forcing and stratospheric ozone-depleting gas emitted from terrestrial and aquatic ecosystems. it can be transformed to nitrogen gas (n(2)) by bacteria and archaea harboring the n(2)o reductase (n(2)or), which is the only known n(2)o sink in the biosphere. despite its crucial role in mitigating n(2)o emissions, knowledge of the n(2)or in the environment remains limited. here, we report a comprehensive phylogenetic analysis of the nosz gene coding the n( ...201223151640
coordinating environmental genomics and geochemistry reveals metabolic transitions in a hot spring ecosystem.we have constructed a conceptual model of biogeochemical cycles and metabolic and microbial community shifts within a hot spring ecosystem via coordinated analysis of the "bison pool" (bp) environmental genome and a complementary contextual geochemical dataset of ~75 geochemical parameters. 2,321 16s rrna clones and 470 megabases of environmental sequence data were produced from biofilms at five sites along the outflow of bp, an alkaline hot spring in sentinel meadow (lower geyser basin) of yell ...201222675512
complete genome of ignavibacterium album, a metabolically versatile, flagellated, facultative anaerobe from the phylum chlorobi.prior to the recent discovery of ignavibacterium album (i. album), anaerobic photoautotrophic green sulfur bacteria (gsb) were the only members of the bacterial phylum chlorobi that had been grown axenically. in contrast to gsb, sequence analysis of the 3.7-mbp genome of i. album shows that this recently described member of the phylum chlorobi is a chemoheterotroph with a versatile metabolism. i. album lacks genes for photosynthesis and sulfur oxidation but has a full set of genes for flagella a ...201222661972
a metastable equilibrium model for the relative abundances of microbial phyla in a hot spring.many studies link the compositions of microbial communities to their environments, but the energetics of organism-specific biomass synthesis as a function of geochemical variables have rarely been assessed. we describe a thermodynamic model that integrates geochemical and metagenomic data for biofilms sampled at five sites along a thermal and chemical gradient in the outflow channel of the hot spring known as "bison pool" in yellowstone national park. the relative abundances of major phyla in in ...201324023738
the dark side of the mushroom spring microbial mat: life in the shadow of chlorophototrophs. i. microbial diversity based on 16s rrna gene amplicons and metagenomic sequencing.microbial-mat communities in the effluent channels of octopus and mushroom springs within the lower geyser basin at yellowstone national park have been studied for nearly 50 years. the emphasis has mostly focused on the chlorophototrophic bacterial organisms of the phyla cyanobacteria and chloroflexi. in contrast, the diversity and metabolic functions of the heterotrophic community in the microoxic/anoxic region of the mat are not well understood. in this study we analyzed the orange-colored und ...201627379049
thermophilic bacteria are potential sources of novel rieske non-heme iron oxygenases.rieske non-heme iron oxygenases, which have a rieske-type [2fe-2s] cluster and a non-heme catalytic iron center, are an important family of oxidoreductases involved mainly in regio- and stereoselective transformation of a wide array of aromatic hydrocarbons. though present in all domains of life, the most widely studied rieske non-heme iron oxygenases are found in mesophilic bacteria. the present study explores the potential for isolating novel rieske non-heme iron oxygenases from thermophilic s ...201728050858
complex structure and biochemical characterization of the staphylococcus aureus cyclic diadenylate monophosphate (c-di-amp)-binding protein psta, the founding member of a new signal transduction protein family.signaling nucleotides are integral parts of signal transduction systems allowing bacteria to cope with and rapidly respond to changes in the environment. the staphylococcus aureus pii-like signal transduction protein psta was recently identified as a cyclic diadenylate monophosphate (c-di-amp)-binding protein. here, we present the crystal structures of the apo- and c-di-amp-bound psta protein, which is trimeric in solution as well as in the crystals. the structures combined with detailed bioinfo ...201425505271
evaluation of various factors affecting bioconversion of l-tyrosine to l-dopa by yeast yarrowia lipolytica-ncim 3450 using response surface methodology.3,4-dihydroxy l-phenylalanine (l-dopa) is considered a potent drug for the treatment of parkinson disease. physical and nutritional parameters where optimized by using yarrowia lipolytica-ncim 3450 to accomplished the highest production of l-dopa. screenings of critical components were completed by using a plackett-burman design, while further optimization was carried out using the box-behnken design. the optimized factor levels predicted by the model were ph 6.1, 1.659 g l(-1) yeast extract, 1. ...201424955295
anaerobic thermophiles.the term "extremophile" was introduced to describe any organism capable of living and growing under extreme conditions. with the further development of studies on microbial ecology and taxonomy, a variety of "extreme" environments have been found and an increasing number of extremophiles are being described. extremophiles have also been investigated as far as regarding the search for life on other planets and even evaluating the hypothesis that life on earth originally came from space. the first ...201425370030
genomic analysis of chthonomonas calidirosea, the first sequenced isolate of the phylum armatimonadetes.most of the lineages of bacteria have remained unknown beyond environmental surveys using molecular markers. until the recent characterisation of several strains, the phylum armatimonadetes (formerly known as 'candidate division op10') was a dominant and globally-distributed lineage within this 'uncultured majority'. here we report the first armatimonadetes genome from the thermophile chthonomonas calidirosea t49(t) and its role as a saccharide scavenger in a geothermal steam-affected soil envir ...201424477196
the mprb extracytoplasmic domain negatively regulates activation of the mycobacterium tuberculosis mprab two-component system.mycobacterium tuberculosis is an acid-fast pathogen of humans and the etiological agent of tuberculosis (tb). it is estimated that one-third of the world's population is latently (persistently) infected with m. tuberculosis. m. tuberculosis persistence is regulated, in part, by the mprab two-component signal transduction system, which is activated by and mediates resistance to cell envelope stress. here we identify mprab as part of an evolutionarily conserved cell envelope stress response networ ...201424187094
cvtree3 web server for whole-genome-based and alignment-free prokaryotic phylogeny and taxonomy.a faithful phylogeny and an objective taxonomy for prokaryotes should agree with each other and ultimately follow the genome data. with the number of sequenced genomes reaching tens of thousands, both tree inference and detailed comparison with taxonomy are great challenges. we now provide one solution in the latest release 3.0 of the alignment-free and whole-genome-based web server cvtree3. the server resides in a cluster of 64 cores and is equipped with an interactive, collapsible, and expanda ...201526563468
a prevalent peptide-binding domain guides ribosomal natural product biosynthesis.ribosomally synthesized and post-translationally modified peptides (ripps) are a rapidly growing class of natural products. ripp precursor peptides can undergo extensive enzymatic tailoring to yield structurally and functionally diverse products, and their biosynthetic logic makes them attractive bioengineering targets. recent work suggests that unrelated ripp-modifying enzymes contain structurally similar precursor peptide-binding domains. using profile hidden markov model comparisons, we disco ...201526167873
the origin and evolution of the plant cell surface: algal integrin-associated proteins and a new family of integrin-like cytoskeleton-ecm linker proteins.the extracellular matrix of scaly green flagellates consists of small organic scales consisting of polysaccharides and scale-associated proteins (saps). molecular phylogenies have shown that these organisms represent the ancestral stock of flagellates from which all green plants (viridiplantae) evolved. the molecular characterization of four different saps is presented. three saps are type-2 membrane proteins with an arginine/alanine-rich short cytoplasmic tail and an extracellular domain that i ...201525977459
bacterial community structure in the hyperarid core of the atacama desert, chile.soils from the hyperarid atacama desert of northern chile were sampled along an east-west elevational transect (23.75 to 24.70 degrees s) through the driest sector to compare the relative structure of bacterial communities. analysis of denaturing gradient gel electrophoresis (dgge) profiles from each of the samples revealed that microbial communities from the extreme hyperarid core of the desert clustered separately from all of the remaining communities. bands sequenced from dgge profiles of two ...200617028238
biosynthesis of ether-type polar lipids in archaea and evolutionary considerations.this review deals with the in vitro biosynthesis of the characteristics of polar lipids in archaea along with preceding in vivo studies. isoprenoid chains are synthesized through the classical mevalonate pathway, as in eucarya, with minor modifications in some archaeal species. most enzymes involved in the pathway have been identified enzymatically and/or genomically. three of the relevant enzymes are found in enzyme families different from the known enzymes. the order of reactions in the phosph ...200717347520
the ancient history of the structure of ribonuclease p and the early origins of archaea.ribonuclease p is an ancient endonuclease that cleaves precursor trna and generally consists of a catalytic rna subunit (rpr) and one or more proteins (rpps). it represents an important macromolecular complex and model system that is universally distributed in life. its putative origins have inspired fundamental hypotheses, including the proposal of an ancient rna world.201020334683
community genomic analyses constrain the distribution of metabolic traits across the chloroflexi phylum and indicate roles in sediment carbon cycling.sediments are massive reservoirs of carbon compounds and host a large fraction of microbial life. microorganisms within terrestrial aquifer sediments control buried organic carbon turnover, degrade organic contaminants, and impact drinking water quality. recent 16s rrna gene profiling indicates that members of the bacterial phylum chloroflexi are common in sediment. only the role of the class dehalococcoidia, which degrade halogenated solvents, is well understood. genomic sampling is available f ...201324450983
complex structure and biochemical characterization of the staphylococcus aureus cyclic diadenylate monophosphate (c-di-amp)-binding protein psta, the founding member of a new signal transduction protein family.signaling nucleotides are integral parts of signal transduction systems allowing bacteria to cope with and rapidly respond to changes in the environment. the staphylococcus aureus pii-like signal transduction protein psta was recently identified as a cyclic diadenylate monophosphate (c-di-amp)-binding protein. here, we present the crystal structures of the apo- and c-di-amp-bound psta protein, which is trimeric in solution as well as in the crystals. the structures combined with detailed bioinfo ...201425505271
geoarchaeota: a new candidate phylum in the archaea from high-temperature acidic iron mats in yellowstone national park.geothermal systems in yellowstone national park (ynp) provide an outstanding opportunity to understand the origin and evolution of metabolic processes necessary for life in extreme environments including low ph, high temperature, low oxygen and elevated concentrations of reduced iron. previous phylogenetic studies of acidic ferric iron mats from ynp have revealed considerable diversity of uncultivated and undescribed archaea. the goal of this study was to obtain replicate de novo genome assembli ...201223151644
geoarchaeota: a new candidate phylum in the archaea from high-temperature acidic iron mats in yellowstone national park.geothermal systems in yellowstone national park (ynp) provide an outstanding opportunity to understand the origin and evolution of metabolic processes necessary for life in extreme environments including low ph, high temperature, low oxygen and elevated concentrations of reduced iron. previous phylogenetic studies of acidic ferric iron mats from ynp have revealed considerable diversity of uncultivated and undescribed archaea. the goal of this study was to obtain replicate de novo genome assembli ...201223151644
thermal adaptation of the archaeal and bacterial lipid membranes.the physiological characteristics that distinguish archaeal and bacterial lipids, as well as those that define thermophilic lipids, are discussed from three points of view that (1) the role of the chemical stability of lipids in the heat tolerance of thermophilic organisms: (2) the relevance of the increase in the proportion of certain lipids as the growth temperature increases: (3) the lipid bilayer membrane properties that enable membranes to function at high temperatures. it is concluded that ...201222927779
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 ...201627340512
complete genome sequence of dehalogenimonas lykanthroporepellens type strain (bl-dc-9(t)) and comparison to "dehalococcoides" strains.dehalogenimonas lykanthroporepellens is the type species of the genus dehalogenimonas, which belongs to a deeply branching lineage within the phylum chloroflexi. this strictly anaerobic, mesophilic, non spore-forming, gram-negative staining bacterium was first isolated from chlorinated solvent contaminated groundwater at a superfund site located near baton rouge, louisiana, usa. d. lykanthroporepellens was of interest for genome sequencing for two reasons: (a) an unusual ability to couple growth ...201222768368
identification of genes and pathways related to phenol degradation in metagenomic libraries from petroleum refinery wastewater.two fosmid libraries, totaling 13,200 clones, were obtained from bioreactor sludge of petroleum refinery wastewater treatment system. the library screening based on pcr and biological activity assays revealed more than 400 positive clones for phenol degradation. from these, 100 clones were randomly selected for pyrosequencing in order to evaluate the genetic potential of the microorganisms present in wastewater treatment plant for biodegradation, focusing mainly on novel genes and pathways of ph ...201323637911
microbial tyrosinases: promising enzymes for pharmaceutical, food bioprocessing, and environmental industry.tyrosinase is a natural enzyme and is often purified to only a low degree and it is involved in a variety of functions which mainly catalyse the o-hydroxylation of monophenols into their corresponding o-diphenols and the oxidation of o-diphenols to o-quinones using molecular oxygen, which then polymerizes to form brown or black pigments. the synthesis of o-diphenols is a potentially valuable catalytic ability and thus tyrosinase has attracted a lot of attention with respect to industrial applica ...201424895537
differences in lateral gene transfer in hypersaline versus thermal environments.the role of lateral gene transfer (lgt) in the evolution of microorganisms is only beginning to be understood. while most lgt events occur between closely related individuals, inter-phylum and inter-domain lgt events are not uncommon. these distant transfer events offer potentially greater fitness advantages and it is for this reason that these "long distance" lgt events may have significantly impacted the evolution of microbes. one mechanism driving distant lgt events is microbial transformatio ...201121740576
average oxidation state of carbon in proteins.the formal oxidation state of carbon atoms in organic molecules depends on the covalent structure. in proteins, the average oxidation state of carbon (z(c)) can be calculated as an elemental ratio from the chemical formula. to investigate oxidation-reduction (redox) patterns, groups of proteins from different subcellular locations and phylogenetic groups were selected for comparison. extracellular proteins of yeast have a relatively high oxidation state of carbon, corresponding with oxidizing co ...201425165594
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