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fatty acid composition, oxidative stability and sensory quality of meat from broiler chicken fed autolysate from bacteria grown on natural gas.bacterial autolysate, a down stream product of bacterial biomass grown on natural gas by mainly the methanotrophic bacteria methylococcus capsulatus, was fed at 8% as is to broiler chickens from 1 to 35ôçâdays of age for studies of fatty acid composition, lipid oxidation and sensory quality of thigh meat stored frozen for 6ôçâmonth at -18ôçâ-¦c or -80ôçâ-¦c. lipid oxidation was measured by thiobarbituric acid reactive substances (tbars) and volatile profile by dynamic headspace gas chromatograph ...201121831229
autotrophic methanotrophy in verrucomicrobia: methylacidiphilum fumariolicumsolv uses the calvin-benson-bassham cycle for carbon dioxide fixation.genome data of the extreme acidophilic verrucomicrobial methanotroph methylacidiphilum fumariolicumstrain solv indicated the ability of autotrophic growth. this was further validated by transcriptome analysis, which showed that all genes required for a functional calvin-benson-bassham (cbb) cycle were transcribed. experiments with (13)ch(4)or (13)co(2)in batch and chemostat cultures demonstrated that co(2)is the sole carbon source for growth of strain solv. in the presence of ch(4), co(2)concent ...201121725016
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
shotgun isotope array for rapid, substrate-specific detection of microorganisms in a microbial community.the shotgun isotope array method has been proposed to be an effective new tool for use in substrate-specific microbe exploration without any prior knowledge of the community composition. proof of concept was demonstrated by detection of acetate-degrading microorganisms in activated sludge and further verified by independent stable isotope probing (sip).201121873478
Chemistry and Biology of the Copper Chelator Methanobactin.Methanotrophic bacteria, organisms that oxidize methane, produce a small copper chelating molecule called methanobactin (Mb). Mb binds Cu(I) with high affinity and is hypothesized to mediate copper acquisition from the environment. Recent advances in Mb characterization include revision of the chemical structure of Mb from Methylosinus trichosporium OB3b and further investigation of its biophysical properties. In addition, Mb production by several other methanotroph strains has been investigated ...201122126187
Chemistry and Biology of the Copper Chelator Methanobactin.Methanotrophic bacteria, organisms that oxidize methane, produce a small copper chelating molecule called methanobactin (Mb). Mb binds Cu(I) with high affinity and is hypothesized to mediate copper acquisition from the environment. Recent advances in Mb characterization include revision of the chemical structure of Mb from Methylosinus trichosporium OB3b and further investigation of its biophysical properties. In addition, Mb production by several other methanotroph strains has been investigated ...201122126187
Crystal structure and characterization of particulate methane monooxygenase from Methylocystis species strain M.Particulate methane monooxygenase (pMMO) is an integral membrane metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria. Previous biochemical and structural studies of pMMO have focused on preparations from Methylococcus capsulatus (Bath) and Methylosinus trichosporium OB3b. A pMMO from a third organism, Methylocystis species strain M, has been isolated and characterized. Both membrane-bound and solubilized Methylocystis sp. strain M pMMO contain ~2 copper ions per 100 kDa pr ...201122013879
the copper responding surfaceome of methylococccus capsulatus bath.proteins on the cellular surface of a bacterium, its surfaceome, are part of the interface between the bacterium and its environment, and are essential for the cells response to its habitat. methylococcus capsulatus bath is one of the most extensively studied methane-oxidizers and is considered as a model-methanotroph. the composition of proteins of the surfaceome of m. capsulatus bath varies with the availability of copper and changes significantly upon only minor changes of copper concentratio ...201122092708
Apoprotein isolation and activation, and vibrational structure of the Helicobacter mustelae iron urease.The micro aerophilic pathogen Helicobacter mustelae synthesizes an oxygen-labile, iron-containing urease (UreA2B2) in addition to its standard nickel-containing enzyme (UreAB). An apoprotein form of the iron urease was prepared from ureA2B2-expressing recombinant Escherichia coli cells that were grown in minimal medium. Temperature-dependent circular dichroism measurements of holoprotein and apoprotein demonstrate an enhancement of thermal stability associated with the UreA2B2 metallocenter. In ...201122196017
Apoprotein isolation and activation, and vibrational structure of the Helicobacter mustelae iron urease.The micro aerophilic pathogen Helicobacter mustelae synthesizes an oxygen-labile, iron-containing urease (UreA2B2) in addition to its standard nickel-containing enzyme (UreAB). An apoprotein form of the iron urease was prepared from ureA2B2-expressing recombinant Escherichia coli cells that were grown in minimal medium. Temperature-dependent circular dichroism measurements of holoprotein and apoprotein demonstrate an enhancement of thermal stability associated with the UreA2B2 metallocenter. In ...201122196017
dual pathways for copper uptake by methanotrophic bacteria.methanobactin (mb), a 1217-da copper chelator produced by the methanotroph methylosinus trichosporium ob3b, is hypothesized to mediate copper acquisition from the environment, particularly from insoluble copper mineral sources. although indirect evidence suggests that mb provides copper for the regulation and activity of methane monooxygenase enzymes, experimental data for direct uptake of copper loaded mb (cu-mb) are lacking. uptake of intact cu-mb by m. trichosporium ob3b was demonstrated by i ...201121900235
response to mercury (ii) ions in methylococcus capsulatus (bath).the mercury (ii) ion is toxic and is usually detoxified in bacteria by reduction to elemental mercury, which is less toxic. this is catalysed by an nad(p)h-dependent mercuric reductase (ec 1.16.1.1). here, we present strong evidence that methylococcus capsulatus (bath) - a methanotrophic member of the gammaproteobacteria - uses this enzyme to detoxify mercury. in radiorespirometry studies, it was found that cells exposed to mercury dissimilated 100% of [(14) c]-methane provided to generate reduc ...201122092810
Cholesterol catabolism as a therapeutic target in Mycobacterium tuberculosis.Mycobacterium tuberculosis (Mtb) is an intracellular pathogen that infects 10 million people worldwide and kills 2 million people every year. The uptake and utilization of nutrients by Mtb within the host cell is still poorly understood, although lipids play an important role in Mtb persistence. The recent identification of a large regulon of cholesterol catabolic genes suggests that Mtb can use host sterol for infection and persistence. In this review, we report on recent progress in elucidatio ...201121924910
Stimulation of methanotrophic growth in cocultures by cobalamin excreted by rhizobia.Methanotrophs play a key role in the global carbon cycle, in which they affect methane emissions and help to sustain diverse microbial communities through the conversion of methane to organic compounds. To investigate the microbial interactions that cause positive effects on methanotrophs, cocultures were constructed using Methylovulum miyakonense HT12 and each of nine nonmethanotrophic bacteria, which were isolated from a methane-utilizing microbial consortium culture established from forest so ...201121984248
distribution and functions of sterols and sphingolipids.sterols and sphingolipids are considered mainly eukaryotic lipids even though both are present in some prokaryotes, with sphingolipids being more widespread than sterols. both sterols and sphingolipids differ in their structural features in vertebrates, plants, and fungi. interestingly, some invertebrates cannot synthesize sterols de novo and seem to have a reduced dependence on sterols. sphingolipids and sterols are found in the plasma membrane, but we do not have a clear picture of their preci ...201121454248
a novel sterol desaturase-like protein promoting dealkylation of phytosterols in tetrahymena thermophila.the gene ttherm_00438800 (des24) from the ciliate tetrahymena thermophila encodes a protein with three conserved histidine clusters, typical of the fatty acid hydroxylase superfamily. despite its high similarity to sterol desaturase-like enzymes, the phylogenetic analysis groups des24p in a separate cluster more related to bacterial than to eukaryotic proteins, suggesting a possible horizontal gene transfer event. a somatic knockout of des24 revealed that the gene encodes a protein, des24p, whic ...201121257793
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
distribution of roseobacter rca and sar11 lineages in the north sea and characteristics of an abundant rca isolate.the roseobacter group and sar11 clade constitute high proportions of the marine bacterioplankton, but only scarce information exists on the abundance of distinct populations of either lineage. therefore, we quantified the abundance of the largest cluster of the roseobacter group, the rca (roseobacter clade affiliated) cluster together with the sar11 clade by quantitative pcr in the southern and eastern north sea. the rca cluster constituted up to 15 and 21% of total bacterial 16s ribosomal rna ( ...201120596072
distribution of roseobacter rca and sar11 lineages in the north sea and characteristics of an abundant rca isolate.the roseobacter group and sar11 clade constitute high proportions of the marine bacterioplankton, but only scarce information exists on the abundance of distinct populations of either lineage. therefore, we quantified the abundance of the largest cluster of the roseobacter group, the rca (roseobacter clade affiliated) cluster together with the sar11 clade by quantitative pcr in the southern and eastern north sea. the rca cluster constituted up to 15 and 21% of total bacterial 16s ribosomal rna ( ...201120596072
cultivating uncultured bacteria from northern wetlands: knowledge gained and remaining gaps.northern wetlands play a key role in the global carbon budget, particularly in the budgets of the greenhouse gas methane. these ecosystems also determine the hydrology of northern rivers and represent one of the largest reservoirs of fresh water in the northern hemisphere. sphagnum-dominated peat bogs and fens are the most extensive types of northern wetlands. in comparison to many other terrestrial ecosystems, the bacterial diversity in sphagnum-dominated wetlands remains largely unexplored. as ...201121954394
diversity and enrichment of nitrite-dependent anaerobic methane oxidizing bacteria from wastewater sludge.recently discovered microorganisms affiliated to the bacterial phylum nc10, named "candidatus methylomirabilis oxyfera", perform nitrite-dependent anaerobic methane oxidation. these microorganisms could be important players in a novel way of anaerobic wastewater treatment where ammonium and residual dissolved methane might be removed at the expense of nitrate or nitrite. to find suitable inocula for reactor startup, ten selected wastewater treatment plants (wwtps) located in the netherlands were ...201121667086
response of methanotrophic communities to afforestation and reforestation in new zealand.methanotrophs use methane (ch(4)) as a carbon source. they are particularly active in temperate forest soils. however, the rate of change of ch(4) oxidation in soil with afforestation or reforestation is poorly understood. here, soil ch(4) oxidation was examined in new zealand volcanic soils under regenerating native forests following burning, and in a mature native forest. results were compared with data for pasture to pine land-use change at nearby sites. we show that following soil disturbanc ...201121593799
dioxygen activation in soluble methane monooxygenase.the controlled oxidation of methane to methanol is a chemical transformation of great value, particularly in the pursuit of alternative fuels, but the reaction remains underutilized industrially because of inefficient and costly synthetic procedures. in contrast, methane monooxygenase enzymes (mmos) from methanotrophic bacteria achieve this chemistry efficiently under ambient conditions. in this account, we discuss the first observable step in the oxidation of methane at the carboxylate-bridged ...201121391602
flavin redox switching of protein functions.flavin cofactors impart remarkable catalytic diversity to enzymes, enabling them to participate in a broad array of biological processes. the properties of flavins also provide proteins with a versatile redox sensor that can be utilized for converting physiological signals such as cellular metabolism, light, and redox status into a unique functional output. the control of protein functions by the flavin redox state is important for transcriptional regulation, cell signaling pathways, and environ ...201121028987
an approach for searching insertions in bacterial genes leading to the phase shift of triplet periodicity.the concept of the phase shift of triplet periodicity (tp) was used for searching potential dna insertions in genes from 17 bacterial genomes. a mathematical algorithm for detection of these insertions has been developed. this approach can detect potential insertions and deletions with lengths that are not multiples of three bases, especially insertions of relatively large dna fragments (>100 bases). new similarity measure between triplet matrixes was employed to improve the sensitivity for dete ...201122196359
structural snapshots of yeast alkyl hydroperoxide reductase ahp1 peroxiredoxin reveal a novel two-cysteine mechanism of electron transfer to eliminate reactive oxygen species.peroxiredoxins (prxs) are thiol-specific antioxidant proteins that protect cells against reactive oxygen species and are involved in cellular signaling pathways. alkyl hydroperoxide reductase ahp1 belongs to the prx5 subfamily and is a two-cysteine (2-cys) prx that forms an intermolecular disulfide bond. enzymatic assays and bioinformatics enabled us to re-assign the peroxidatic cysteine (c(p)) to cys-62 and the resolving cysteine (c(r)) to cys-31 but not the previously reported cys-120. thus ah ...201222474296
complete sequence analysis of two methanotroph-specific repabc-containing plasmids from methylocystis sp. strain sc2.the complete nucleotide sequences of two large, low-copy-number plasmids of 229.6 kb (pbsc2-1) and 143.5 kb (pbsc2-2) were determined during assembly of the whole-genome shotgun sequences of the methane-oxidizing bacterium methylocystis sp. strain sc2. the physical existence of the two plasmids in strain sc2 was confirmed by pulsed-field gel electrophoresis followed by southern hybridization. both plasmids have a conserved replication module of the repabc system and carry genes involved in their ...201222504811
pandaseq: paired-end assembler for illumina sequences.illumina paired-end reads are used to analyse microbial communities by targeting amplicons of the 16s rrna gene. publicly available tools are needed to assemble overlapping paired-end reads while correcting mismatches and uncalled bases; many errors could be corrected to obtain higher sequence yields using quality information.201222333067
analyses of the large subunit histidine-rich motif expose an alternative proton transfer pathway in [nife] hydrogenases.a highly conserved histidine-rich region with unknown function was recognized in the large subunit of [nife] hydrogenases. the hxhxxhxxhxh sequence occurs in most membrane-bound hydrogenases, but only two of these histidines are present in the cytoplasmic ones. site-directed mutagenesis of the his-rich region of the t. roseopersicina membrane-attached hyn hydrogenase disclosed that the enzyme activity was significantly affected only by the replacement of the his104 residue. computational analysi ...201222511957
characterization and two-dimensional crystallization of membrane component alkb of the medium-chain alkane hydroxylase system from pseudomonas putida gpo1.the alkane hydroxylase system of pseudomonas putida gpo1 allows it to use alkanes as the sole source of carbon and energy. bacterial alkane hydroxylases have tremendous potential as biocatalysts for the stereo- and regioselective transformation of a wide range of chemically inert unreactive alkanes into valuable reactive chemical precursors. we have produced and characterized the first 2-dimensional crystals of the integral membrane component of the p. putida alkane hydroxylase system, the nonhe ...201222941083
unusual spectroscopic and ligand binding properties of the cytochrome p450-flavodoxin fusion enzyme xpla.the rhodococcus rhodochrous strain 11y xpla enzyme is an unusual cytochrome p450-flavodoxin fusion enzyme that catalyzes reductive denitration of the explosive hexahydro-1,3,5-trinitro-1,3,5-triazene (rdx). we show by light scattering that xpla is a monomeric enzyme. xpla has high affinity for imidazole (k(d) = 1.6 μm), explaining previous reports of a red-shifted xpla soret band in pure enzyme. the true soret maximum of xpla is at 417 nm. similarly, unusually weak xpla flavodoxin fmn binding (k ...201222500029
bacteriohemerythrin bolsters the activity of the particulate methane monooxygenase (pmmo) in methylococcus capsulatus (bath).recently, a native bacteriohemerythrin (mchr) has been identified in methylococcus capsulatus (bath). both the particulate methane monooxygenase (pmmo) and mchr are over-expressed in cells of this bacterium when this strain of methanotroph is cultured and grown under high copper to biomass conditions. it has been suggested that the role of the mchr is to provide a shuttle to transport dioxygen from the cytoplasm of the cell to the intra-cytoplasmic membranes for consumption by the pmmo. indeed, ...201222484247
methanotrophic bacteria in oilsands tailings ponds of northern alberta.we investigated methanotrophic bacteria in slightly alkaline surface water (ph 7.4-8.7) of oilsands tailings ponds in fort mcmurray, canada. these large lakes (up to 10 km(2)) contain water, silt, clay and residual hydrocarbons that are not recovered in oilsands mining. they are primarily anoxic and produce methane but have an aerobic surface layer. aerobic methane oxidation was measured in the surface water at rates up to 152 nmol ch4 ml(-1) water d(-1). microbial diversity was investigated via ...201223254511
methanotrophic bacteria in oilsands tailings ponds of northern alberta.we investigated methanotrophic bacteria in slightly alkaline surface water (ph 7.4-8.7) of oilsands tailings ponds in fort mcmurray, canada. these large lakes (up to 10 km(2)) contain water, silt, clay and residual hydrocarbons that are not recovered in oilsands mining. they are primarily anoxic and produce methane but have an aerobic surface layer. aerobic methane oxidation was measured in the surface water at rates up to 152 nmol ch4 ml(-1) water d(-1). microbial diversity was investigated via ...201223254511
draft genome sequence of the methane-oxidizing bacterium methylococcus capsulatus (texas).methanotrophic bacteria perform major roles in global carbon cycles via their unique enzymatic activities that enable the oxidation of one-carbon compounds, most notably methane. here we describe the annotated draft genome sequence of the aerobic methanotroph methylococcus capsulatus (texas), a type strain originally isolated from sewer sludge.201223144383
transcriptome profile of a bovine respiratory disease pathogen: mannheimia haemolytica phl213.computational methods for structural gene annotation have propelled gene discovery but face certain drawbacks with regards to prokaryotic genome annotation. identification of transcriptional start sites, demarcating overlapping gene boundaries, and identifying regulatory elements such as small rna are not accurate using these approaches. in this study, we re-visit the structural annotation of mannheimia haemolytica phl213, a bovine respiratory disease pathogen. m. haemolytica is one of the causa ...201223046475
the methylococcus capsulatus (bath) secreted protein, mope*, binds both reduced and oxidized copper.under copper limiting growth conditions the methanotrophic bacterium methylococcus capsulatus (bath) secrets essentially only one protein, mope*, to the medium. mope* is a copper-binding protein whose structure has been determined by x-ray crystallography. the structure of mope* revealed a unique high affinity copper binding site consisting of two histidine imidazoles and one kynurenine, the latter an oxidation product of trp130. in this study, we demonstrate that the copper ion coordinated by t ...201222916218
light-induced oxidative stress, n-formylkynurenine, and oxygenic photosynthesis.light stress in plants results in damage to the water oxidizing reaction center, photosystem ii (psii). redox signaling, through oxidative modification of amino acid side chains, has been proposed to participate in this process, but the oxidative signals have not yet been identified. previously, we described an oxidative modification, n-formylkynurenine (nfk), of w365 in the cp43 subunit. the yield of this modification increases under light stress conditions, in parallel with the decrease in oxy ...201222860088
discovery, taxonomic distribution, and phenotypic characterization of a gene required for 3-methylhopanoid production.hopanoids methylated at the c-3 position are a subset of bacterial triterpenoids that are readily preserved in modern and ancient sediments and in petroleum. the production of 3-methylhopanoids by extant aerobic methanotrophs and their common occurrence in modern and fossil methane seep communities, in conjunction with carbon isotope analysis, has led to their use as biomarker proxies for aerobic methanotrophy. in addition, these lipids are also produced by aerobic acetic acid bacteria and, lack ...201222826256
global biodiversity of aquatic ammonia-oxidizing archaea is partitioned by habitat.archaea play an important role in nitrification and are, thus, inextricably linked to the global carbon and nitrogen cycles. since the initial discovery of an ammonia monooxygenase α-subunit (amoa) gene associated with an archaeal metagenomic fragment, archaeal amoa sequences have been detected in a wide variety of nitrifying environments. recent sequencing efforts have revealed extensive diversity of archaeal amoa sequences within different habitats. in this study, we have examined over 8000 am ...201222826704
the divergent amoc3 subunit of ammonia monooxygenase functions as part of a stress response system in nitrosomonas europaea.the ammonia monooxygenase of chemolithotrophic ammonia-oxidizing bacteria (aob) catalyzes the first step in ammonia oxidation by converting ammonia to hydroxylamine. the monooxygenase of nitrosomonas europaea is encoded by two nearly identical operon copies (amocab(1,2)). several aob, including n. europaea, also possess a divergent monocistronic copy of amoc (amoc(3)) of unknown function. previous work suggested a possible functional role for amoc(3) as part of the σ(e) stress response regulon d ...201222544266
architecture and active site of particulate methane monooxygenase.particulate methane monooxygenase (pmmo) is an integral membrane metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria, organisms that live on methane gas as their sole carbon source. understanding pmmo function has important implications for bioremediation applications and for the development of new, environmentally friendly catalysts for the direct conversion of methane to methanol. crystal structures of pmmos from three different methanotrophs reveal a trimeric architectu ...201222725967
9-mercaptodethiobiotin is generated as a ligand to the [2fe-2s]+ cluster during the reaction catalyzed by biotin synthase from escherichia coli.biotin synthase catalyzes formation of the thiophane ring through stepwise substitution of a sulfur atom for hydrogen atoms at the c9 and c6 positions of dethiobiotin. biotin synthase is a radical s-adenosylmethionine (sam) enzyme that reductively cleaves s-adenosylmethionine, generating 5'-deoxyadenosyl radicals that initially abstract a hydrogen atom from the c9 position of dethiobiotin. we have proposed that the resulting dethiobiotinyl radical is quenched by the μ-sulfide of the nearby [2fe- ...201222607542
evidence for oxygen binding at the active site of particulate methane monooxygenase.particulate methane monooxygenase (pmmo) is an integral membrane metalloenzyme that converts methane to methanol in methanotrophic bacteria. the enzyme consists of three subunits, pmob, pmoa, and pmoc, organized in an α(3)β(3)γ(3) trimer. studies of intact pmmo and a recombinant soluble fragment of the pmob subunit (denoted as spmob) indicate that the active site is located within the soluble region of pmob at the site of a crystallographically modeled dicopper center. in this work, we have inve ...201222540911
metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use.low nutrient and energy availability has led to the evolution of numerous strategies for overcoming these limitations, of which symbiotic associations represent a key mechanism. particularly striking are the associations between chemosynthetic bacteria and marine animals that thrive in nutrient-poor environments such as the deep sea because the symbionts allow their hosts to grow on inorganic energy and carbon sources such as sulfide and co(2). remarkably little is known about the physiological ...201222517752
detection of spatial correlations in protein structures and molecular complexes.protein structures are frequently related by spectacular and often surprising similarities. structural correlations among protein chains are routinely detected by various structure-matching techniques, but the comparison of oligomers and molecular complexes is largely uncharted territory. here we solve the structure-matching problem for oligomers and large molecular aggregates, including the largest molecular complexes known today. we provide several challenging examples that cannot be handled b ...201222483118
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
bioinformatic characterization of the 4-toluene sulfonate uptake permease (tsup) family of transmembrane proteins.the ubiquitous sequence diverse 4-toluene sulfonate uptake permease (tsup) family contains few characterized members and is believed to catalyze the transport of several sulfur-based compounds. prokaryotic members of the tsup family outnumber the eukaryotic members substantially, and in prokaryotes, but not eukaryotes, extensive lateral gene transfer occurred during family evolution. despite unequal representation, homologues from the three taxonomic domains of life share well-conserved motifs. ...201222192777
bioinformatic characterization of the 4-toluene sulfonate uptake permease (tsup) family of transmembrane proteins.the ubiquitous sequence diverse 4-toluene sulfonate uptake permease (tsup) family contains few characterized members and is believed to catalyze the transport of several sulfur-based compounds. prokaryotic members of the tsup family outnumber the eukaryotic members substantially, and in prokaryotes, but not eukaryotes, extensive lateral gene transfer occurred during family evolution. despite unequal representation, homologues from the three taxonomic domains of life share well-conserved motifs. ...201222192777
ubiquitous dissolved inorganic carbon assimilation by marine bacteria in the pacific northwest coastal ocean as determined by stable isotope probing.in order to identify bacteria that assimilate dissolved inorganic carbon (dic) in the northeast pacific ocean, stable isotope probing (sip) experiments were conducted on water collected from 3 different sites off the oregon and washington coasts in may 2010, and one site off the oregon coast in september 2008 and march 2009. samples were incubated in the dark with 2 mm (13)c-nahco(3), doubling the average concentration of dic typically found in the ocean. our results revealed a surprising divers ...201223056406
comparative molecular analysis of chemolithoautotrophic bacterial diversity and community structure from coastal saline soils, gujarat, india.soils harbour high diversity of obligate as well as facultative chemolithoautotrophic bacteria that contribute significantly to co2 dynamics in soil. in this study, we used culture dependent and independent methods to assess the community structure and diversity of chemolithoautotrophs in agricultural and coastal barren saline soils (low and high salinity). we studied the composition and distribution of chemolithoautotrophs by means of functional marker gene cbbl encoding large subunit of ribulo ...201222834535
evaluating the evolutionary origins of unexpected character distributions within the bacterial planctomycetes-verrucomicrobia-chlamydiae superphylum.recently, several characters that are absent from most bacteria, but which are found in many eukaryotes or archaea, have been identified within the bacterial planctomycetes-verrucomicrobia-chlamydiae (pvc) superphylum. hypotheses of the evolutionary history of such characters are commonly based on the inference of phylogenies of gene or protein families associated with the traits, estimated from multiple sequence alignments (msas). so far, studies of this kind have focused on the distribution of ...201223189077
acetate activation in methanosaeta thermophila: characterization of the key enzymes pyrophosphatase and acetyl-coa synthetase.the thermophilic methanogen methanosaeta thermophila uses acetate as sole substrate for methanogenesis. it was proposed that the acetate activation reaction that is needed to feed acetate into the methanogenic pathway requires the hydrolysis of two atp, whereas the acetate activation reaction in methanosarcina sp. is known to require only one atp. as these organisms live at the thermodynamic limit that sustains life, the acetate activation reaction in mt. thermophila seems too costly and was thu ...201222927778
elemental economy: microbial strategies for optimizing growth in the face of nutrient limitation.microorganisms play a dominant role in the biogeochemical cycling of nutrients. they are rightly praised for their facility for fixing both carbon and nitrogen into organic matter, and microbial driven processes have tangibly altered the chemical composition of the biosphere and its surrounding atmosphere. despite their prodigious capacity for molecular transformations, microorganisms are powerless in the face of the immutability of the elements. limitations for specific elements, either fleetin ...201222633059
the transcriptome of bathymodiolus azoricus gill reveals expression of genes from endosymbionts and free-living deep-sea bacteria.deep-sea environments are largely unexplored habitats where a surprising number of species may be found in large communities, thriving regardless of the darkness, extreme cold, and high pressure. their unique geochemical features result in reducing environments rich in methane and sulfides, sustaining complex chemosynthetic ecosystems that represent one of the most surprising findings in oceans in the last 40 years. the deep-sea lucky strike hydrothermal vent field, located in the mid atlantic r ...201223015773
survival or revival: long-term preservation induces a reversible viable but non-culturable state in methane-oxidizing bacteria.knowledge on long-term preservation of micro-organisms is limited and research in the field is scarce despite its importance for microbial biodiversity and biotechnological innovation. preservation of fastidious organisms such as methane-oxidizing bacteria (mob) has proven difficult. most mob do not survive lyophilization and only some can be cryopreserved successfully for short periods. a large-scale study was designed for a diverse set of mob applying fifteen cryopreservation or lyophilization ...201222539945
identification and characterization of rhodopseudomonas palustris tie-1 hopanoid biosynthesis mutants.hopanes preserved in both modern and ancient sediments are recognized as the molecular fossils of bacteriohopanepolyols, pentacyclic hopanoid lipids. based on the phylogenetic distribution of hopanoid production by extant bacteria, hopanes have been used as indicators of specific bacterial groups and/or their metabolisms. however, our ability to interpret them ultimately depends on understanding the physiological roles of hopanoids in modern bacteria. toward this end, we set out to identify gene ...201222221333
the histidine kinase pdhs controls cell cycle progression of the pathogenic alphaproteobacterium brucella abortus.bacterial differentiation is often associated with the asymmetric localization of regulatory proteins, such as histidine kinases. pdhs is an essential and polarly localized histidine kinase in the pathogenic alphaproteobacterium brucella abortus. after cell division, pdhs is asymmetrically segregated between the two sibling cells, highlighting a differentiation event. however, the function(s) of pdhs in the b. abortus cell cycle remains unknown. we used an original approach, the pentapeptide sca ...201222843843
microbial survey of a full-scale, biologically active filter for treatment of drinking water.the microbial community of a full-scale, biologically active drinking water filter was surveyed using molecular techniques. nitrosomonas, nitrospira, sphingomonadales, and rhizobiales dominated the clone libraries. the results elucidate the microbial ecology of biological filters and demonstrate that biological treatment of drinking water should be considered a viable alternative to physicochemical methods.201222752177
impact of quaternary structure upon bacterial cytochrome c peroxidases: does homodimerization matter?all known active forms of diheme bacterial cytochrome c peroxidase (bccp) enzymes are described by a homodimeric state. further, the majority of bccps reported display activity only when the high-potential electron transfer heme of the protein (fe(h)) is reduced to the ferrous oxidation state. reduction of fe(h) results in a set of conformational changes allowing for the low-potential peroxidatic heme (fe(l)) to adopt a high-spin, five-coordinate state that is capable of binding substrate. here ...201223189923
trace metal requirements for microbial enzymes involved in the production and consumption of methane and nitrous oxide.fluxes of greenhouse gases to the atmosphere are heavily influenced by microbiological activity. microbial enzymes involved in the production and consumption of greenhouse gases often contain metal cofactors. while extensive research has examined the influence of fe bioavailability on microbial co(2) cycling, fewer studies have explored metal requirements for microbial production and consumption of the second- and third-most abundant greenhouse gases, methane (ch(4)), and nitrous oxide (n(2)o). ...201222363333
mercury resistance and mercuric reductase activities and expression among chemotrophic thermophilic aquificae.mercury (hg) resistance (mer) by the reduction of mercuric to elemental hg is broadly distributed among the bacteria and archaea and plays an important role in hg detoxification and biogeochemical cycling. mera is the protein subunit of the homodimeric mercuric reductase (mr) enzyme, the central function of the mer system. mera sequences in the phylum aquificae form the deepest-branching lineage in bayesian phylogenetic reconstructions of all known mera homologs. we therefore hypothesized that t ...201222773655
automatic assignment of prokaryotic genes to functional categories using literature profiling.in the last years, there was an exponential increase in the number of publicly available genomes. once finished, most genome projects lack financial support to review annotations. a few of these gene annotations are based on a combination of bioinformatics evidence, however, in most cases, annotations are based solely on sequence similarity to a previously known gene, which was most probably annotated in the same way. as a result, a large number of predicted genes remain unassigned to any functi ...201223077617
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
simple absolute quantification method correcting for quantitative pcr efficiency variations for microbial community samples.real-time quantitative pcr (qpcr) is a widely used technique in microbial community analysis, allowing the quantification of the number of target genes in a community sample. currently, the standard-curve (sc) method of absolute quantification is widely employed for these kinds of analysis. however, the sc method assumes that the amplification efficiency (e) is the same for both the standard and the sample target template. we analyzed 19 bacterial strains and nine environmental samples in qpcr a ...201222492459
homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily.the rapid advance in genome sequencing presents substantial challenges for protein functional assignment, with half or more of new protein sequences inferred from these genomes having uncertain assignments. the assignment of enzyme function in functionally diverse superfamilies represents a particular challenge, which we address through a combination of computational predictions, enzymology, and structural biology. here we describe the results of a focused investigation of a group of enzymes in ...201222392983
lipids of prokaryotic origin at the base of marine food webs.in particular niches of the marine environment, such as abyssal trenches, icy waters and hot vents, the base of the food web is composed of bacteria and archaea that have developed strategies to survive and thrive under the most extreme conditions. some of these organisms are considered "extremophiles" and modulate the fatty acid composition of their phospholipids to maintain the adequate fluidity of the cellular membrane under cold/hot temperatures, elevated pressure, high/low salinity and ph. ...201223342392
why do bacteria use so many enzymes to scavenge hydrogen peroxide?hydrogen peroxide (h(2)o(2)) is continuously formed by the autoxidation of redox enzymes in aerobic cells, and it also enters from the environment, where it can be generated both by chemical processes and by the deliberate actions of competing organisms. because h(2)o(2) is acutely toxic, bacteria elaborate scavenging enzymes to keep its intracellular concentration at nanomolar levels. mutants that lack such enzymes grow poorly, suffer from high rates of mutagenesis, or even die. in order to und ...201222609271
identification of residues required for stalled-ribosome rescue in the codon-independent release factor yaej.the yaej protein is a codon-independent release factor with peptidyl-trna hydrolysis (pth) activity, and functions as a stalled-ribosome rescue factor in escherichia coli. to identify residues required for yaej function, we performed mutational analysis for in vitro pth activity towards rescue of ribosomes stalled on a non-stop mrna, and for ribosome-binding efficiency. we focused on residues conserved among bacterial yaej proteins. additionally, we determined the solution structure of the ggq d ...201324322300
identification of residues required for stalled-ribosome rescue in the codon-independent release factor yaej.the yaej protein is a codon-independent release factor with peptidyl-trna hydrolysis (pth) activity, and functions as a stalled-ribosome rescue factor in escherichia coli. to identify residues required for yaej function, we performed mutational analysis for in vitro pth activity towards rescue of ribosomes stalled on a non-stop mrna, and for ribosome-binding efficiency. we focused on residues conserved among bacterial yaej proteins. additionally, we determined the solution structure of the ggq d ...201324322300
mechanisms of copper homeostasis in bacteria.copper is an important micronutrient required as a redox co-factor in the catalytic centers of enzymes. however, free copper is a potential hazard because of its high chemical reactivity. consequently, organisms exert a tight control on cu(+) transport (entry-exit) and traffic through different compartments, ensuring the homeostasis required for cuproprotein synthesis and prevention of toxic effects. recent studies based on biochemical, bioinformatics, and metalloproteomics approaches, reveal a ...201324205499
unusual cytochrome p450 enzymes and reactions.cytochrome p450 enzymes primarily catalyze mixed-function oxidation reactions, plus some reductions and rearrangements of oxygenated species, e.g. prostaglandins. most of these reactions can be rationalized in a paradigm involving compound i, a high-valent iron-oxygen complex (feo(3+)), to explain seemingly unusual reactions, including ring couplings, ring expansion and contraction, and fusion of substrates. most p450s interact with flavoenzymes or iron-sulfur proteins to receive electrons from ...201323632016
structural insights into diversity and n-alkane biodegradation mechanisms of alkane hydroxylases.environmental microbes utilize four degradation pathways for the oxidation of n-alkanes. although the enzymes degrading n-alkanes in different microbes may vary, enzymes functioning in the first step in the aerobic degradation of alkanes all belong to the alkane hydroxylases. alkane hydroxylases are a class of enzymes that insert oxygen atoms derived from molecular oxygen into different sites of the alkane terminus (or termini) depending on the type of enzymes. in this review, we summarize the d ...201323519435
unusual properties of the cytochrome p450 superfamily.during the early years of cytochrome p450 research, a picture of conserved properties arose from studies of mammalian forms of these monooxygenases. they included the protohaem prosthetic group, the cysteine residue that coordinates to the haem iron and the reduced co difference spectrum. alternatively, the most variable feature of p450s was the enzymatic activities, which led to the conclusion that there are a large number of these enzymes, most of which have yet to be discovered. more recently ...201323297356
multi-heme proteins: nature's electronic multi-purpose tool.while iron is often a limiting nutrient to biology, when the element is found in the form of heme cofactors (iron protoporphyrin ix), living systems have excelled at modifying and tailoring the chemistry of the metal. in the context of proteins and enzymes, heme cofactors are increasingly found in stoichiometries greater than one, where a single protein macromolecule contains more than one heme unit. when paired or coupled together, these protein associated heme groups perform a wide variety of ...201323558243
genome analysis coupled with physiological studies reveals a diverse nitrogen metabolism in methylocystis sp. strain sc2.methylocystis sp. strain sc2 can adapt to a wide range of methane concentrations. this is due to the presence of two isozymes of particulate methane monooxygenase exhibiting different methane oxidation kinetics. to gain insight into the underlying genetic information, its genome was sequenced and found to comprise a 3.77 mb chromosome and two large plasmids.201324130670
functional gene analysis of freshwater iron-rich flocs at circumneutral ph and isolation of a stalk-forming microaerophilic iron-oxidizing bacterium.iron-rich flocs often occur where anoxic water containing ferrous iron encounters oxygenated environments. culture-independent molecular analyses have revealed the presence of 16s rrna gene sequences related to diverse bacteria, including autotrophic iron oxidizers and methanotrophs in iron-rich flocs; however, the metabolic functions of the microbial communities remain poorly characterized, particularly regarding carbon cycling. in the present study, we cultivated iron-oxidizing bacteria (feob) ...201323811518
microbial minorities modulate methane consumption through niche partitioning.microbes catalyze all major geochemical cycles on earth. however, the role of microbial traits and community composition in biogeochemical cycles is still poorly understood mainly due to the inability to assess the community members that are actually performing biogeochemical conversions in complex environmental samples. here we applied a polyphasic approach to assess the role of microbial community composition in modulating methane emission from a riparian floodplain. we show that the dynamics ...201323788331
genome mining for methanobactins.methanobactins (mbns) are a family of copper-binding natural products involved in copper uptake by methanotrophic bacteria. the few mbns that have been structurally characterized feature copper coordination by two nitrogen-containing heterocycles next to thioamide groups embedded in a peptidic backbone of varying composition. mbns are proposed to derive from post-translational modification of ribosomally synthesized peptides, but only a few genes encoding potential precursor peptides have been i ...201323442874
the methanol dehydrogenase gene, mxaf, as a functional and phylogenetic marker for proteobacterial methanotrophs in natural environments.the mxaf gene, coding for the large (α) subunit of methanol dehydrogenase, is highly conserved among distantly related methylotrophic species in the alpha-, beta- and gammaproteobacteria. it is ubiquitous in methanotrophs, in contrast to other methanotroph-specific genes such as the pmoa and mmox genes, which are absent in some methanotrophic proteobacterial genera. this study examined the potential for using the mxaf gene as a functional and phylogenetic marker for methanotrophs. mxaf and 16s r ...201323451130
two homologous ef-g proteins from pseudomonas aeruginosa exhibit distinct functions.genes encoding two proteins corresponding to elongation factor g (ef-g) were cloned from pseudomonas aeruginosa. the proteins encoded by these genes are both members of the efg i subfamily. the gene encoding one of the forms of ef-g is located in the str operon and the resulting protein is referred to as ef-g1a while the gene encoding the other form of ef-g is located in another part of the genome and the resulting protein is referred to as ef-g1b. these proteins were expressed and purified to 9 ...201324260360
beating the acetyl coenzyme a-pathway to the origin of life.attempts to draft plausible scenarios for the origin of life have in the past mainly built upon palaeogeochemical boundary conditions while, as detailed in a companion article in this issue, frequently neglecting to comply with fundamental thermodynamic laws. even if demands from both palaeogeochemistry and thermodynamics are respected, then a plethora of strongly differing models are still conceivable. although we have no guarantee that life at its origin necessarily resembled biology in extant ...201323754811
candida utilis and chlorella vulgaris counteract intestinal inflammation in atlantic salmon (salmo salar l.).intestinal inflammation, caused by impaired intestinal homeostasis, is a serious condition in both animals and humans. the use of conventional extracted soybean meal (sbm) in diets for atlantic salmon and several other fish species is known to induce enteropathy in the distal intestine, a condition often referred to as sbm induced enteropathy (sbmie). in the present study, we investigated the potential of different microbial ingredients to alleviate sbmie in atlantic salmon, as a model of feed-i ...201324386162
composite bacterial hopanoids and their microbial producers across oxygen gradients in the water column of the california current.hopanoids are pentacyclic triterpenoid lipids produced by many prokaryotes as cell membrane components. the structural variations of composite hopanoids, or bacteriohopanepolyols (bhps), produced by various bacterial genera make them potentially useful molecular biomarkers of bacterial communities and metabolic processes in both modern and ancient environments. building on previous work suggesting that organisms in low-oxygen environments are important contributors to bhp production in the marin ...201324077702
methanobactin-mediated one-step synthesis of gold nanoparticles.preparation of gold nanoparticles with a narrow size distribution has enormous importance in nanotechnology. methanobactin (mb) is a copper-binding small peptide that appears to function as an agent for copper sequestration and uptake in methanotrophs. mb can also bind and catalytically reduce au (iii) to au (0). in this study, we demonstrate a facile mb-mediated one-step synthetic route to prepare monodispersed gold nanoparticles. continuous reduction of au (iii) by mb can be achieved by using ...201324189217
characterization of fructose 1,6-bisphosphatase and sedoheptulose 1,7-bisphosphatase from the facultative ribulose monophosphate cycle methylotroph bacillus methanolicus.the genome of the facultative ribulose monophosphate (rump) cycle methylotroph bacillus methanolicus encodes two bisphosphatases (glpx), one on the chromosome (glpx(c)) and one on plasmid pbm19 (glpx(p)), which is required for methylotrophy. both enzymes were purified from recombinant escherichia coli and were shown to be active as fructose 1,6-bisphosphatases (fbpases). the fbpase-negative corynebacterium glutamicum δfbp mutant could be phenotypically complemented with glpx(c) and glpx(p) from ...201324013630
pear: a fast and accurate illumina paired-end read merger.the illumina paired-end sequencing technology can generate reads from both ends of target dna fragments, which can subsequently be merged to increase the overall read length. there already exist tools for merging these paired-end reads when the target fragments are equally long. however, when fragment lengths vary and, in particular, when either the fragment size is shorter than a single-end read, or longer than twice the size of a single-end read, most state-of-the-art mergers fail to generate ...201324142950
pear: a fast and accurate illumina paired-end read merger.the illumina paired-end sequencing technology can generate reads from both ends of target dna fragments, which can subsequently be merged to increase the overall read length. there already exist tools for merging these paired-end reads when the target fragments are equally long. however, when fragment lengths vary and, in particular, when either the fragment size is shorter than a single-end read, or longer than twice the size of a single-end read, most state-of-the-art mergers fail to generate ...201324142950
access to a cu(ii)-o-cu(ii) motif: spectroscopic properties, solution structure, and reactivity.we report a complex with a rare cu(ii)-o-cu(ii) structural motif that is stable at room temperature, which allows its in-depth characterization by a variety of spectroscopic methods. interest in such compounds is fueled by the recent discovery that a cu(ii)-o-cu(ii) species on the surface of cu-zsm-5 is capable of oxidizing methane to methanol, and this in turn ties into mechanistic discussions on the methane oxidation at the dicopper site within the particulate methane monooxygenase. for the sy ...201324134722
transcriptional response of bathypelagic marine bacterioplankton to the deepwater horizon oil spill.the deepwater horizon blowout released a massive amount of oil and gas into the deep ocean between april and july 2010, stimulating microbial blooms of petroleum-degrading bacteria. to understand the metabolic response of marine microorganisms, we sequenced ≈ 66 million community transcripts that revealed the identity of metabolically active microbes and their roles in petroleum consumption. reads were assigned to reference genes from ≈ 2700 bacterial and archaeal taxa, but most assignments (39% ...201323902988
stabilized homoserine o-succinyltransferases (meta) or l-methionine partially recovers the growth defect in escherichia coli lacking atp-dependent proteases or the dnak chaperone.the growth of escherichia coli at elevated temperatures is limited due to the inherent instability of homoserine o-succinyltransferase, meta, which is the first enzyme in the methionine biosynthesis pathway. meta is also unstable under other stressful conditions, such as weak organic acids and oxidative stress. the meta protein unfolds, even at 25°c, forms considerable aggregates at 37°c and completely aggregates at 44°c.201323898868
sulfur oxidizers dominate carbon fixation at a biogeochemical hot spot in the dark ocean.bacteria and archaea in the dark ocean (>200 m) comprise 0.3-1.3 billion tons of actively cycled marine carbon. many of these microorganisms have the genetic potential to fix inorganic carbon (autotrophs) or assimilate single-carbon compounds (methylotrophs). we identified the functions of autotrophic and methylotrophic microorganisms in a vent plume at axial seamount, where hydrothermal activity provides a biogeochemical hot spot for carbon fixation in the dark ocean. free-living members of the ...201323842654
intermediate p* from soluble methane monooxygenase contains a diferrous cluster.during a single turnover of the hydroxylase component (mmoh) of soluble methane monooxygenase from methylosinus trichosporium ob3b, several discrete intermediates are formed. the diiron cluster of mmoh is first reduced to the fe(ii)fe(ii) state (h(red)). o₂ binds rapidly at a site away from the cluster to form the fe(ii)fe(ii) intermediate o, which converts to an fe(iii)fe(iii)-peroxo intermediate p and finally to the fe(iv)fe(iv) intermediate q. q binds and reacts with methane to yield methanol ...201323718184
poles apart: arctic and antarctic octadecabacter strains share high genome plasticity and a new type of xanthorhodopsin.the genus octadecabacter is a member of the ubiquitous marine roseobacter clade. the two described species of this genus, octadecabacter arcticus and octadecabacter antarcticus, are psychrophilic and display a bipolar distribution. here we provide the manually annotated and finished genome sequences of the type strains o. arcticus 238 and o. antarcticus 307, isolated from sea ice of the arctic and antarctic, respectively. both genomes exhibit a high genome plasticity caused by an unusually high ...201323671678
assessing bacterial diversity in a seawater-processing wastewater treatment plant by 454-pyrosequencing of the 16s rrna and amoa genes.the bacterial community composition of activated sludge from a wastewater treatment plant (almería, spain) with the particularity of using seawater was investigated by applying 454-pyrosequencing. the results showed that deinococcus-thermus, proteobacteria, chloroflexi and bacteroidetes were the most abundant retrieved sequences, while other groups, such as actinobacteria, chlorobi, deferribacteres, firmicutes, planctomycetes, spirochaetes and verrumicrobia were reported at lower proportions. ra ...201323574645
metalloenzymes: put a ring on it. 201323508187
oxidative stress and the hiv-infected brain proteome.human immunodeficiency virus (hiv) is capable of infiltrating the brain and infecting brain cells. in the years following hiv infection, patients show signs of various levels of neurocognitive problems termed hiv-associated neurocognitive disorders (hand). although the introduction of highly active antiretroviral therapy (haart) has reduced the incidence of hiv-dementia, which is the most severe form of hand, the milder forms have become more prevalent today due to the increased life expectancy ...201323475542
isocitrate dehydrogenase from streptococcus mutans: biochemical properties and evaluation of a putative phosphorylation site at ser102.isocitrate deyhdrogenase (idh) is a reversible enzyme in the tricarboxylic acid cycle that catalyzes the nad(p)(+)-dependent oxidative decarboxylation of isocitrate to α-ketoglutarate (αkg) and the nad(p)h/co2-dependent reductive carboxylation of αkg to isocitrate. the idh gene from streptococcus mutans was fused with the icd gene promoter from escherichia coli to initiate its expression in the glutamate auxotrophic strain e. coli δicd::kan(r) of which the icd gene has been replaced by kanamycin ...201323484056
identification and quantification of polyfunctionalized hopanoids by high temperature gas chromatography-mass spectrometry.hopanoids are triterpenoids produced mainly by bacteria, are ubiquitous in the environment, and have many important applications as biological markers. a wide variety of related hopanoid structures exists, many of which are polyfunctionalized. these modifications render the hopanoids too involatile for conventional gas chromatography (gc) separation, so require either laborious oxidative cleavage of the functional groups or specialized high temperature (ht) columns. here we describe the systemat ...201324496464
complete genome sequence of nitrosomonas sp. is79, an ammonia oxidizing bacterium adapted to low ammonium concentrations.nitrosomonas sp. is79 is a chemolithoautotrophic ammonia-oxidizing bacterium that belongs to the family nitrosomonadaceae within the phylum proteobacteria. ammonia oxidation is the first step of nitrification, an important process in the global nitrogen cycle ultimately resulting in the production of nitrate. nitrosomonas sp. is79 is an ammonia oxidizer of high interest because it is adapted to low ammonium and can be found in freshwater environments around the world. the 3,783,444-bp chromosome ...201324019993
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