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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
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
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
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
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
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
coordinated expression of fdxd and molybdenum nitrogenase genes promotes nitrogen fixation by rhodobacter capsulatus in the presence of oxygen.rhodobacter capsulatus is able to grow with n2 as the sole nitrogen source using either a molybdenum-dependent or a molybdenum-free iron-only nitrogenase whose expression is strictly inhibited by ammonium. disruption of the fdxd gene, which is located directly upstream of the mo-nitrogenase genes, nifhdk, abolished diazotrophic growth via mo-nitrogenase at oxygen concentrations still tolerated by the wild type, thus demonstrating the importance of fdxd under semiaerobic conditions. in contrast, ...201424272776
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
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
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
a rice gene for microbial symbiosis, oryza sativa ccamk, reduces ch4 flux in a paddy field with low nitrogen input.plants have mutualistic symbiotic relationships with rhizobia and fungi by the common symbiosis pathway, of which ca(2+)/calmodulin-dependent protein kinase (encoded by ccamk) is a central component. although oryza sativa ccamk (osccamk) is required for fungal accommodation in rice roots, little is known about the role of osccamk in rice symbiosis with bacteria. here, we report the effect of a tos17-induced osccamk mutant (ne1115) on ch4 flux in low-nitrogen (ln) and standard-nitrogen (sn) paddy ...201424441161
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
diiron oxidation state control of substrate access to the active site of soluble methane monooxygenase mediated by the regulatory component.the regulatory component (mmob) of soluble methane monooxygenase (smmo) has a unique n-terminal tail not found in regulatory proteins of other bacterial multicomponent monooxygenases. this n-terminal tail is indispensable for proper function, yet its solution structure and role in catalysis remain elusive. here, by using double electron-electron resonance (deer) spectroscopy, we show that the oxidation state of the hydroxylase component, mmoh, modulates the conformation of the n-terminal tail in ...201424476336
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
cora is a copper repressible surface-associated copper(i)-binding protein produced in methylomicrobium album bg8.cora is a copper repressible protein previously identified in the methanotrophic bacterium methylomicrobium album bg8. in this work, we demonstrate that cora is located on the cell surface and binds one copper ion per protein molecule, which, based on x-ray absorption near edge structure analysis, is in the reduced state (cu(i)). the structure of endogenously expressed cora was solved using x-ray crystallography. the 1.6 å three-dimensional structure confirmed the binding of copper and revealed ...201424498370
identification of nitrogen-fixing genes and gene clusters from metagenomic library of acid mine drainage.biological nitrogen fixation is an essential function of acid mine drainage (amd) microbial communities. however, most acidophiles in amd environments are uncultured microorganisms and little is known about the diversity of nitrogen-fixing genes and structure of nif gene cluster in amd microbial communities. in this study, we used metagenomic sequencing to isolate nif genes in the amd microbial community from dexing copper mine, china. meanwhile, a metagenome microarray containing 7,776 large-in ...201424498417
a mass spectrometry-based hybrid method for structural modeling of protein complexes.we describe a method that integrates data derived from different mass spectrometry (ms)-based techniques with a modeling strategy for structural characterization of protein assemblies. we encoded structural data derived from native ms, bottom-up proteomics, ion mobility-ms and chemical cross-linking ms into modeling restraints to compute the most likely structure of a protein assembly. we used the method to generate near-native models for three known structures and characterized an assembly inte ...201424509631
autotrophic carbon dioxide fixation via the calvin-benson-bassham cycle by the denitrifying methanotroph "candidatus methylomirabilis oxyfera".methane is an important greenhouse gas and the most abundant hydrocarbon in the earth's atmosphere. methanotrophic microorganisms can use methane as their sole energy source and play a crucial role in the mitigation of methane emissions in the environment. "candidatus methylomirabilis oxyfera" is a recently described intra-aerobic methanotroph that is assumed to use nitric oxide to generate internal oxygen to oxidize methane via the conventional aerobic pathway, including the monooxygenase react ...201424509918
evolutionary insights about bacterial glxrs from whole genome analyses: is glurs2 a chimera?evolutionary histories of glutamyl-trna synthetase (glurs) and glutaminyl-trna synthetase (glnrs) in bacteria are convoluted. after the divergence of eubacteria and eukarya, bacterial glurs glutamylated both trnagln and trnaglu until glnrs appeared by horizontal gene transfer (hgt) from eukaryotes or a duplicate copy of glurs (glurs2) that only glutamylates trnagln appeared. the current understanding is based on limited sequence data and not always compatible with available experimental results. ...201424521160
structural conservation of the b subunit in the ammonia monooxygenase/particulate methane monooxygenase superfamily.the ammonia monooxygenase (amo)/particulate methane monooxygenase (pmmo) superfamily is a diverse group of membrane-bound enzymes of which only pmmo has been characterized on the molecular level. the pmmo active site is believed to reside in the soluble n-terminal region of the pmob subunit. to understand the degree of structural conservation within this superfamily, the crystal structure of the corresponding domain of an archaeal amob subunit from nitrosocaldus yellowstonii has been determined ...201424523098
aquatic plant surface as a niche for methanotrophs.this study investigated the potential local ch4 sink in various plant parts as a boundary environment of ch4 emission and consumption. by comparing ch4 consumption activities in cultures inoculated with parts from 39 plant species, we observed significantly higher consumption of ch4 associated with aquatic plants than other emergent plant parts such as woody plant leaves, macrophytic marine algae, and sea grass. in situ activity of ch4 consumption by methanotrophs associated with different speci ...201424550901
multitarget drug discovery for tuberculosis and other infectious diseases.we report the discovery of a series of new drug leads that have potent activity against mycobacterium tuberculosis as well as against other bacteria, fungi, and a malaria parasite. the compounds are analogues of the new tuberculosis (tb) drug sq109 (1), which has been reported to act by inhibiting a transporter called mmpl3, involved in cell wall biosynthesis. we show that 1 and the new compounds also target enzymes involved in menaquinone biosynthesis and electron transport, inhibiting respirat ...201424568559
copper active sites in biology. 201424588098
controlled oxidation of aliphatic ch bonds in metallo-monooxygenases: mechanistic insights derived from studies on deuterated and fluorinated hydrocarbons.the control over the regio- and/or stereo-selective aliphatic ch oxidation by metalloenzymes is of great interest to scientists. typically, these enzymes invoke host-guest chemistry to sequester the substrates within the protein pockets, exploiting sizes, shapes and specific interactions such as hydrogen-bonding, electrostatic forces and/or van der waals interactions to control the substrate specificity, regio-specificity and stereo-selectivity. over the years, we have developed a series of deut ...201424629413
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
perspective: what is known, and not known, about the connections between alkane oxidation and metal uptake in alkanotrophs in the marine environment.should iron and copper be added to the environment to stimulate the natural bioremediation of marine oil spills? the key enzymes that catalyze the oxidation of alkanes require either iron or copper, and the concentration of these ions in seawater is vanishingly low. nevertheless, the dependence of alkane oxidation activity on external metal concentrations remains unclear. this perspective will summarize what is known about the co-regulation of alkane oxidation and metal acquisition and pose a se ...201424710692
membrane lipids in agrobacterium tumefaciens: biosynthetic pathways and importance for pathogenesis.many cellular processes critically depend on the membrane composition. in this review, we focus on the biosynthesis and physiological roles of membrane lipids in the plant pathogen agrobacterium tumefaciens. the major components of a. tumefaciens membranes are the phospholipids (pls), phosphatidylethanolamine (pe), phosphatidylglycerol, phosphatidylcholine (pc) and cardiolipin, and ornithine lipids (ols). under phosphate-limited conditions, the membrane composition shifts to phosphate-free lipid ...201424723930
life in a sea of oxygen. 201424737314
assembly of nonheme mn/fe active sites in heterodinuclear metalloproteins.the ferritin superfamily contains several protein groups that share a common fold and metal coordinating ligands. the different groups utilize different dinuclear cofactors to perform a diverse set of reactions. several groups use an oxygen-activating di-iron cluster, while others use di-manganese or heterodinuclear mn/fe cofactors. given the similar primary ligand preferences of mn and fe as well as the similarities between the binding sites, the basis for metal specificity in these systems rem ...201424771036
go2msig, an automated go based multi-species gene set generator for gene set enrichment analysis.despite the widespread use of high throughput expression platforms and the availability of a desktop implementation of gene set enrichment analysis (gsea) that enables non-experts to perform gene set based analyses, the availability of the necessary precompiled gene sets is rare for species other than human.201424884810
revision of n2o-producing pathways in the ammonia-oxidizing bacterium nitrosomonas europaea atcc 19718.nitrite reductase (nirk) and nitric oxide reductase (norb) have long been thought to play an essential role in nitrous oxide (n2o) production by ammonia-oxidizing bacteria. however, essential gaps remain in our understanding of how and when nirk and norb are active and functional, putting into question their precise roles in n2o production by ammonia oxidizers. the growth phenotypes of the nitrosomonas europaea atcc 19718 wild-type and mutant strains deficient in expression of nirk, norb, and bo ...201424907318
characterization of the xiamenmycin biosynthesis gene cluster in streptomyces xiamenensis 318.xiamenmycin (1) is a prenylated benzopyran derivative with anti-fibrotic activity. to investigate the genetic basis of xiamenmycin biosynthesis, we performed genome mining in the xiamenmycin-producing streptomyces xiamenensis wild-type strain 318 to identify a candidate gene cluster. the complete gene cluster, consisting of five genes, was confirmed by a series of gene inactivations and heterologous expression. based on bioinformatics analyses of each gene and feeding experiments, we found that ...201424919072
metaproteomic identification of diazotrophic methanotrophs and their localization in root tissues of field-grown rice plants.in a previous study by our group, ch4 oxidation and n2 fixation were simultaneously activated in the roots of wild-type rice plants in a paddy field with no n input; both processes are likely controlled by a rice gene for microbial symbiosis. the present study examined which microorganisms in rice roots were responsible for ch4 oxidation and n2 fixation under the field conditions. metaproteomic analysis of root-associated bacteria from field-grown rice (oryza sativa nipponbare) revealed that nit ...201424928870
electron transfer control in soluble methane monooxygenase.the hydroxylation or epoxidation of hydrocarbons by bacterial multicomponent monooxygenases (bmms) requires the interplay of three or four protein components. how component protein interactions control catalysis, however, is not well understood. in particular, the binding sites of the reductase components on the surface of their cognate hydroxylases and the role(s) that the regulatory proteins play during intermolecular electron transfer leading to the hydroxylase reduction have been enigmatic. ...201424937475
effects of zinc on particulate methane monooxygenase activity and structure.particulate methane monooxygenase (pmmo) is a membrane-bound metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria. zinc is a known inhibitor of pmmo, but the details of zinc binding and the mechanism of inhibition are not understood. metal binding and activity assays on membrane-bound pmmo from methylococcus capsulatus (bath) reveal that zinc inhibits pmmo at two sites that are distinct from the copper active site. the 2.6 å resolution crystal structure of methylocystis spe ...201424942740
methane oxidation linked to chlorite dismutation.we examined the potential for ch4 oxidation to be coupled with oxygen derived from the dissimilatory reduction of perchlorate, chlorate, or via chlorite (clo(-) 2) dismutation. although dissimilatory reduction of clo(-) 4 and clo(-) 3 could be inferred from the accumulation of chloride ions either in spent media or in soil slurries prepared from exposed freshwater lake sediment, neither of these oxyanions evoked methane oxidation when added to either anaerobic mixed cultures or soil enriched in ...201424987389
inteins as indicators of gene flow in the halobacteria.this research uses inteins, a type of mobile genetic element, to infer patterns of gene transfer within the halobacteria. we surveyed 118 genomes representing 26 genera of halobacteria for intein sequences. we then used the presence-absence profile, sequence similarity and phylogenies from the inteins recovered to explore how intein distribution can provide insight on the dynamics of gene flow between closely related and divergent organisms. we identified 24 proteins in the halobacteria that hav ...201425018750
identification of the valence and coordination environment of the particulate methane monooxygenase copper centers by advanced epr characterization.particulate methane monooxygenase (pmmo) catalyzes the oxidation of methane to methanol in methanotrophic bacteria. as a copper-containing enzyme, pmmo has been investigated extensively by electron paramagnetic resonance (epr) spectroscopy, but the presence of multiple copper centers has precluded correlation of epr signals with the crystallographically identified monocopper and dicopper centers. a soluble recombinant fragment of the pmob subunit of pmmo, spmob, like pmmo itself, contains two di ...201425059917
a combined approach to assess the microbial contamination of the archimedes palimpsest.a combined approach, using molecular and microscopic techniques, was used to identify the microbiota associated with the archimedes palimpsest, an unusual parchment manuscript. sem analyses revealed the microbial damage to the collagen fibers and the presence of characteristic cell chains typical of filamentous bacteria and fungal spores. molecular analysis confirmed a homogeneous bacterial community colonizing the manuscript. the phyla proteobacteria and actinobacteria were associated with this ...201425135817
a combined approach to assess the microbial contamination of the archimedes palimpsest.a combined approach, using molecular and microscopic techniques, was used to identify the microbiota associated with the archimedes palimpsest, an unusual parchment manuscript. sem analyses revealed the microbial damage to the collagen fibers and the presence of characteristic cell chains typical of filamentous bacteria and fungal spores. molecular analysis confirmed a homogeneous bacterial community colonizing the manuscript. the phyla proteobacteria and actinobacteria were associated with this ...201425135817
ribosylhopane, a novel bacterial hopanoid, as precursor of c35 bacteriohopanepolyols in streptomyces coelicolor a3(2).wild-type streptomyces coelicolor a3(2) produces aminobacteriohopanetriol as the only elongated c35 hopanoid. the hopanoid phenotype of two mutants bearing a deletion of genes from a previously identified hopanoid biosynthesis gene cluster provides clues to the formation of c35 bacteriohopanepolyols. orf14 encodes a putative nucleosidase; its deletion induces the accumulation of adenosylhopane as it cannot be converted into ribosylhopane. orf18 encodes a putative transaminase; its deletion resul ...201425155017
multiplex degenerate primer design for targeted whole genome amplification of many viral genomes.background. targeted enrichment improves coverage of highly mutable viruses at low concentration in complex samples. degenerate primers that anneal to conserved regions can facilitate amplification of divergent, low concentration variants, even when the strain present is unknown. results. a tool for designing multiplex sets of degenerate sequencing primers to tile overlapping amplicons across multiple whole genomes is described. the new script, run_tiled_primers, is part of the primux software. ...201425157264
expanding the verrucomicrobial methanotrophic world: description of three novel species of methylacidimicrobium gen. nov.methanotrophic verrucomicrobia have been found in geothermal environments characterized by high temperatures and low ph values. however, it has recently been hypothesized that methanotrophic verrucomicrobia could be present under a broader range of environmental conditions. here we describe the isolation and characterization of three new species of mesophilic acidophilic verrucomicrobial methanotrophs from a volcanic soil in italy. the three new species showed 97% to 98% 16s rrna gene identity t ...201425172849
structure and protein-protein interactions of methanol dehydrogenase from methylococcus capsulatus (bath).in the initial steps of their metabolic pathway, methanotrophic bacteria oxidize methane to methanol with methane monooxygenases (mmos) and methanol to formaldehyde with methanol dehydrogenases (mdhs). several lines of evidence suggest that the membrane-bound or particulate mmo (pmmo) and mdh interact to form a metabolic supercomplex. to further investigate the possible existence of such a supercomplex, native mdh from methylococcus capsulatus (bath) has been purified and characterized by size e ...201425185034
biochemical characterization of the water-soluble squalene synthase from methylococcus capsulatus and the functional analyses of its two dxxd(e)d motifs and the highly conserved aromatic amino acid residues.information regarding squalene synthases (sqss) from prokaryotes is scarce. we aimed to characterize the sqs from methylococcus capsulatus. we studied its reaction mechanism by kinetic analysis and evaluated the structure of the substrate/inhibitor-binding sites via homology modeling. the cloned m. capsulatus sqs was expressed in escherichia coli and purified by nickel-nitrilotriacetic acid column chromatography. interestingly, m. capsulatus sqs was water-soluble and did not require any detergen ...201425283713
aerobic methanotrophic communities at the red sea brine-seawater interface.the central rift of the red sea contains 25 brine pools with different physicochemical conditions, dictating the diversity and abundance of the microbial community. three of these pools, the atlantis ii, kebrit and discovery deeps, are uniquely characterized by a high concentration of hydrocarbons. the brine-seawater interface, described as an anoxic-oxic (brine-seawater) boundary, is characterized by a high methane concentration, thus favoring aerobic methane oxidation. the current study analyz ...201425295031
drug strategies targeting cyp51 in neglected tropical diseases. 201425337991
the genome of the intracellular bacterium of the coastal bivalve, solemya velum: a blueprint for thriving in and out of symbiosis.symbioses between chemoautotrophic bacteria and marine invertebrates are rare examples of living systems that are virtually independent of photosynthetic primary production. these associations have evolved multiple times in marine habitats, such as deep-sea hydrothermal vents and reducing sediments, characterized by steep gradients of oxygen and reduced chemicals. due to difficulties associated with maintaining these symbioses in the laboratory and culturing the symbiotic bacteria, studies of ch ...201425342549
structure of a diguanylate cyclase from thermotoga maritima: insights into activation, feedback inhibition and thermostability.large-scale production of bis-3'-5'-cyclic-di-gmp (c-di-gmp) would facilitate biological studies of numerous bacterial signaling pathways and phenotypes controlled by this second messenger molecule, such as virulence and biofilm formation. c-di-gmp constitutes also a potentially interesting molecule as a vaccine adjuvant. even though chemical synthesis of c-di-gmp can be done, the yields are incompatible with mass-production. tdgc, a stand-alone diguanylate cyclase (dgc or ggdef domain) from the ...201425360685
occurrence of an unusual hopanoid-containing lipid a among lipopolysaccharides from bradyrhizobium species.the chemical structures of the unusual hopanoid-containing lipid a samples of the lipopolysaccharides (lps) from three strains of bradyrhizobium (slow-growing rhizobia) have been established. they differed considerably from other gram-negative bacteria in regards to the backbone structure, the number of ester-linked long chain hydroxylated fatty acids, as well as the presence of a tertiary residue that consisted of at least one molecule of carboxyl-bacteriohopanediol or its 2-methyl derivative. ...201425371196
methanobactin-mediated synthesis of gold nanoparticles supported over al2o3 toward an efficient catalyst for glucose oxidation.methanobactin (mb) is a copper-binding peptide that appears to function as an agent for copper sequestration and uptake in methanotrophs. mb can also bind and reduce au(iii) to au(0). in this paper, au/al2o3 catalysts prepared by a novel incipient wetness-mb-mediated bioreduction method were used for glucose oxidation. the catalysts were characterized, and the analysis revealed that very small gold nanoparticles with a particle size <4 nm were prepared by the incipient wetness-mb-mediated biored ...201425429424
structure-to-function relationships of bacterial translocator protein (tspo): a focus on pseudomonas.the translocator protein (tspo), which was previously designated as the peripheral-type benzodiazepine receptor, is a 3.5 billion year-old evolutionarily conserved protein expressed by most eukarya, archae and bacteria, but its organization and functions differ remarkably. by taking advantage of the genomic data available on tspo, we focused on bacterial tspo and attempted to define functions of tspo in pseudomonas via in silico approaches. a tspo ortholog has been identified in several fluoresc ...201425477872
computational and experimental analysis of the secretome of methylococcus capsulatus (bath).the gram-negative methanotroph methylococcus capsulatus (bath) was recently demonstrated to abrogate inflammation in a murine model of inflammatory bowel disease, suggesting interactions with cells involved in maintaining mucosal homeostasis and emphasizing the importance of understanding the many properties of m. capsulatus. secreted proteins determine how bacteria may interact with their environment, and a comprehensive knowledge of such proteins is therefore vital to understand bacterial phys ...201425479164
[surface layers of methanotrophic bacteria].structural and functional characteristics of the regular glycoprotein layers in prokaryotes are analyzed with a special emphasis on aerobic methanotrophic bacteria. s-layers are present at the surfaces of methylococcus, methylothermus, and methylomicrobium cells. different methylomicrobium species either synthesize s-layers with planar (p2, p4) symmetry or form cup-shaped or conicalstructures with hexagonal (p6) symmetry. a unique, copper-binding polypeptide 'cora'/mope (27/45 kda), which is coe ...201425509389
genetic tools for the industrially promising methanotroph methylomicrobium buryatense.aerobic methanotrophs oxidize methane at ambient temperatures and pressures and are therefore attractive systems for methane-based bioconversions. in this work, we developed and validated genetic tools for methylomicrobium buryatense, a haloalkaliphilic gammaproteobacterial (type i) methanotroph. m. buryatense was isolated directly on natural gas and grows robustly in pure culture with a 3-h doubling time, enabling rapid genetic manipulation compared to many other methanotrophic species. as a pr ...201525548049
inhibitory effects of c2 to c10 1-alkynes on ammonia oxidation in two nitrososphaera species.a previous study showed that ammonia oxidation by the thaumarchaeota nitrosopumilus maritimus (group 1.1a) was resistant to concentrations of the c8 1-alkyne, octyne, which completely inhibits activity by ammonia-oxidizing bacteria. in this study, the inhibitory effects of octyne and other c2 to c10 1-alkynes were evaluated on the nitrite production activity of two pure culture isolates from thaumarchaeota group 1.1b, nitrososphaera viennensis strain en76 and nitrososphaera gargensis. both n. vi ...201525576608
methanobactin from methylocystis sp. strain sb2 affects gene expression and methane monooxygenase activity in methylosinus trichosporium ob3b.methanotrophs can express a cytoplasmic (soluble) methane monooxygenase (smmo) or membrane-bound (particulate) methane monooxygenase (pmmo). expression of these mmos is strongly regulated by the availability of copper. many methanotrophs have been found to synthesize a novel compound, methanobactin (mb), that is responsible for the uptake of copper, and methanobactin produced by methylosinus trichosporium ob3b plays a key role in controlling expression of mmo genes in this strain. as all known f ...201525616801
a coxiella-like endosymbiont is a potential vitamin source for the lone star tick.amblyomma americanum (lone star tick) is an important disease vector in the united states. it transmits several human pathogens, including the agents of human monocytic ehrlichiosis, tularemia, and southern tick-associated rash illness. blood-feeding insects (class insecta) depend on bacterial endosymbionts to provide vitamins and cofactors that are scarce in blood. it is unclear how this deficiency is compensated in ticks (class arachnida) that feed exclusively on mammalian blood. a bacterium r ...201525618142
natural hot spots for gain of multiple resistances: arsenic and antibiotic resistances in heterotrophic, aerobic bacteria from marine hydrothermal vent fields.microorganisms are responsible for multiple antibiotic resistances that have been associated with resistance/tolerance to heavy metals, with consequences to public health. many genes conferring these resistances are located on mobile genetic elements, easily exchanged among phylogenetically distant bacteria. the objective of the present work was to isolate arsenic-, antimonite-, and antibiotic-resistant strains and to determine the existence of plasmids harboring antibiotic/arsenic/antimonite re ...201525636836
a bacterial hemerythrin-like protein msmhr inhibits the sigf-dependent hydrogen peroxide response in mycobacteria.hydrogen peroxide (h2o2) is one of a variety of reactive oxygen species (ros) produced by aerobic organisms. host production of toxic h2o2 in response to pathogen infection is an important classical innate defense mechanism against invading microbes. understanding the mechanisms by which pathogens, in response to oxidative stress, mediate defense against toxic ros, can reveal anti-microbial targets and shed light on pathogenic mechanisms. in this study, we provide evidence that a mycobacterium s ...201425642228
a bacterial hemerythrin-like protein msmhr inhibits the sigf-dependent hydrogen peroxide response in mycobacteria.hydrogen peroxide (h2o2) is one of a variety of reactive oxygen species (ros) produced by aerobic organisms. host production of toxic h2o2 in response to pathogen infection is an important classical innate defense mechanism against invading microbes. understanding the mechanisms by which pathogens, in response to oxidative stress, mediate defense against toxic ros, can reveal anti-microbial targets and shed light on pathogenic mechanisms. in this study, we provide evidence that a mycobacterium s ...201425642228
genome-wide gene order distances support clustering the gram-positive bacteria.initially using 143 genomes, we developed a method for calculating the pair-wise distance between prokaryotic genomes using a monte carlo method to estimate the conservation of gene order. the method was based on repeatedly selecting five or six non-adjacent random orthologs from each of two genomes and determining if the chosen orthologs were in the same order. the raw distances were then corrected for gene order convergence using an adaptation of the jukes-cantor model, as well as using the co ...201525653643
genome-wide gene order distances support clustering the gram-positive bacteria.initially using 143 genomes, we developed a method for calculating the pair-wise distance between prokaryotic genomes using a monte carlo method to estimate the conservation of gene order. the method was based on repeatedly selecting five or six non-adjacent random orthologs from each of two genomes and determining if the chosen orthologs were in the same order. the raw distances were then corrected for gene order convergence using an adaptation of the jukes-cantor model, as well as using the co ...201525653643
methane oxidation coupled to oxygenic photosynthesis in anoxic waters.freshwater lakes represent large methane sources that, in contrast to the ocean, significantly contribute to non-anthropogenic methane emissions to the atmosphere. particularly mixed lakes are major methane emitters, while permanently and seasonally stratified lakes with anoxic bottom waters are often characterized by strongly reduced methane emissions. the causes for this reduced methane flux from anoxic lake waters are not fully understood. here we identified the microorganisms and processes r ...201525679533
effects of the non-commensal methylococcus capsulatus bath on mammalian immune cells.dietary inclusions of a bacterial meal consisting mainly of the non-commensal, methanotrophic bacteria methylococcus capsulatus bath have been shown to ameliorate symptoms of intestinal inflammation in different animal models. in order to investigate the molecular mechanisms causing these effects, we have studied the influence of this strain on different immune cells central for the regulation of inflammatory responses. effects were compared to those induced by the closely related strain m. caps ...201525771177
enzymatic oxidation of methane.methane monooxygenases (mmos) are enzymes that catalyze the oxidation of methane to methanol in methanotrophic bacteria. as potential targets for new gas-to-liquid methane bioconversion processes, mmos have attracted intense attention in recent years. there are two distinct types of mmo, a soluble, cytoplasmic mmo (smmo) and a membrane-bound, particulate mmo (pmmo). both oxidize methane at metal centers within a complex, multisubunit scaffold, but the structures, active sites, and chemical mecha ...201525806595
phylogenomic analysis and predicted physiological role of the proton-translocating nadh:quinone oxidoreductase (complex i) across bacteria.the proton-translocating nadh:quinone oxidoreductase (complex i) is a multisubunit integral membrane enzyme found in the respiratory chains of both bacteria and eukaryotic organelles. although much research has focused on the enzyme's central role in the mitochondrial respiratory chain, comparatively little is known about its role in the diverse energetic lifestyles of different bacteria. here, we used a phylogenomic approach to better understand the distribution of complex i across bacteria, th ...201525873378
the bacteriohemerythrin from methylococcus capsulatus (bath): crystal structures reveal that leu114 regulates a water tunnel.the bacteriohemerythrin (mchr) from methylococcus capsulatus (bath) is an oxygen carrier that serves as a transporter to deliver o2 from the cytosol of the bacterial cell body to the particulate methane monooxygenase residing in the intracytoplasmic membranes for methane oxidation. here we report x-ray protein crystal structures of the recombinant wild type (wt) mchr and its l114a, l114y and l114f mutants. the structure of the wt reveals a possible water tunnel in the mchr that might be linked t ...201525890483
a novel type ii nad+-specific isocitrate dehydrogenase from the marine bacterium congregibacter litoralis kt71.in most living organisms, isocitrate dehydrogenases (idhs) convert isocitrate into ɑ-ketoglutarate (ɑ-kg). phylogenetic analyses divide the idh protein family into two subgroups: types i and ii. based on cofactor usage, idhs are either nad+-specific (nad-idh) or nadp+-specific (nadp-idh); nadp-idh evolved from nad-idh. type i idhs include nad-idhs and nadp-idhs; however, no type ii nad-idhs have been reported to date. this study reports a novel type ii nad-idh from the marine bacterium congregib ...201525942017
evidence of kinetic cooperativity in dimeric ketopantoate reductase from staphylococcus aureus.ketopantoate reductase (kpr) catalyzes the nadph-dependent production of pantoate, an essential precursor in the biosynthesis of coenzyme a. previous structural studies have been limited to escherichia coli kpr, a monomeric enzyme that follows a sequential ordered mechanism. here we report the crystal structure of the staphylococcus aureus enzyme at 1.8 å resolution, the first description of a dimeric kpr. using sedimentation velocity analysis, we show that the s. aureus kpr dimer is stable in s ...201525946571
impact of metabolism and growth phase on the hydrogen isotopic composition of microbial fatty acids.microorganisms are involved in all elemental cycles and therefore it is important to study their metabolism in the natural environment. a recent technique to investigate this is the hydrogen isotopic composition of microbial fatty acids, i.e., heterotrophic microorganisms produce fatty acids enriched in deuterium (d) while photoautotrophic and chemoautotrophic microorganisms produce fatty acids depleted in d compared to the water in the culture medium (growth water). however, the impact of facto ...201526005437
growth of rhodococcus sp. strain bcp1 on gaseous n-alkanes: new metabolic insights and transcriptional analysis of two soluble di-iron monooxygenase genes.rhodococcus sp. strain bcp1 was initially isolated for its ability to grow on gaseous n-alkanes, which act as inducers for the co-metabolic degradation of low-chlorinated compounds. here, both molecular and metabolic features of bcp1 cells grown on gaseous and short-chain n-alkanes (up to n-heptane) were examined in detail. we show that propane metabolism generated terminal and sub-terminal oxidation products such as 1- and 2-propanol, whereas 1-butanol was the only terminal oxidation product de ...201526029173
structural organization of enzymes of the phenylacetate catabolic hybrid pathway.aromatic compounds are the second most abundant class of molecules on the earth and frequent environmental pollutants. they are difficult to metabolize due to an inert chemical structure, and of all living organisms, only microbes have evolved biochemical pathways that can open an aromatic ring and catabolize thus formed organic molecules. in bacterial genomes, the phenylacetate (pa) utilization pathway is abundant and represents the central route for degradation of a variety of organic compound ...201526075354
methanotrophic and methanogenic communities in swiss alpine fens dominated by carex rostrata and eriophorum angustifolium.vascular plants play a key role in controlling ch4 emissions from natural wetlands, because they influence ch4 production, oxidation, and transport to the atmosphere. here we investigated differences in the abundance and composition of methanotrophic and methanogenic communities in three swiss alpine fens dominated by different vascular plant species under natural conditions. the sampling locations either were situated at geographically distinct sites with different physicochemical properties bu ...201526092454
discrimination of the prochiral hydrogens at the c-2 position of n-alkanes by the methane/ammonia monooxygenase family proteins.the selectivity of ammonia monooxygenase from nitrosomonas europaea (amo-ne) for the oxidation of c4-c8n-alkanes to the corresponding alcohol isomers was examined to show the ability of amo-ne to recognize the n-alkane orientation within the catalytic site. amo-ne in whole cells produces 1- and 2-alcohols from c4-c8n-alkanes, and the regioselectivity is dependent on the length of the carbon chain. 2-alcohols produced from c4-c7n-alkanes were predominantly either the r- or s-enantiomers, while 2- ...201526138087
common cell shape evolution of two nasopharyngeal pathogens.respiratory infectious diseases are the third cause of worldwide death. the nasopharynx is the portal of entry and the ecological niche of many microorganisms, of which some are pathogenic to humans, such as neisseria meningitidis and moraxella catarrhalis. these microbes possess several surface structures that interact with the actors of the innate immune system. in our attempt to understand the past evolution of these bacteria and their adaption to the nasopharynx, we first studied differences ...201526162030
pqqe from methylobacterium extorquens am1: a radical s-adenosyl-l-methionine enzyme with an unusual tolerance to oxygen.methylobacterium extorquens am1 is an aerobic facultative methylotroph known to secrete pyrroloquinoline quinone (pqq), a cofactor of a number of bacterial dehydrogenases, into the culture medium. to elucidate the molecular mechanism of pqq biosynthesis, we are focusing on pqqe which is believed to be the enzyme catalysing the first reaction of the pathway. pqqe belongs to the radical s-adenosyl-l-methionine (sam) superfamily, in which most, if not all, enzymes are very sensitive to dissolved ox ...201526188050
pqqe from methylobacterium extorquens am1: a radical s-adenosyl-l-methionine enzyme with an unusual tolerance to oxygen.methylobacterium extorquens am1 is an aerobic facultative methylotroph known to secrete pyrroloquinoline quinone (pqq), a cofactor of a number of bacterial dehydrogenases, into the culture medium. to elucidate the molecular mechanism of pqq biosynthesis, we are focusing on pqqe which is believed to be the enzyme catalysing the first reaction of the pathway. pqqe belongs to the radical s-adenosyl-l-methionine (sam) superfamily, in which most, if not all, enzymes are very sensitive to dissolved ox ...201526188050
hole hopping through tyrosine/tryptophan chains protects proteins from oxidative damage.living organisms have adapted to atmospheric dioxygen by exploiting its oxidizing power while protecting themselves against toxic side effects. reactive oxygen and nitrogen species formed during oxidative stress, as well as high-potential reactive intermediates formed during enzymatic catalysis, could rapidly and irreversibly damage polypeptides were protective mechanisms not available. chains of redox-active tyrosine and tryptophan residues can transport potentially damaging oxidizing equivalen ...201526195784
biosynthesis of squalene from farnesyl diphosphate in bacteria: three steps catalyzed by three enzymes.squalene (sq) is an intermediate in the biosynthesis of sterols in eukaryotes and a few bacteria and of hopanoids in bacteria where they promote membrane stability and the formation of lipid rafts in their hosts. the genes for hopanoid biosynthesis are typically located on clusters that consist of four highly conserved genes-hpnc, hpnd, hpne, and hpnf-for conversion of farnesyl diphosphate (fpp) to hopene or related pentacyclic metabolites. while hpnf is known to encode a squalene cyclase, the f ...201526258173
inactivation of the particulate methane monooxygenase (pmmo) in methylococcus capsulatus (bath) by acetylene.acetylene (hcch) has a long history as a mechanism-based enzyme inhibitor and is considered an active-site probe of the particulate methane monooxygenase (pmmo). here, we report how hcch inactivates pmmo in methylococcus capsulatus (bath) by using high-resolution mass spectrometry and computational simulation. high-resolution maldi-tof ms of intact pmmo complexes has allowed us to confirm that the enzyme oxidizes hcch to the ketene (c2h2o) intermediate, which then forms an acetylation adduct wit ...201526275807
coupling oxygen consumption with hydrocarbon oxidation in bacterial multicomponent monooxygenases.a fundamental goal in catalysis is the coupling of multiple reactions to yield a desired product. enzymes have evolved elegant approaches to address this grand challenge. a salient example is the biological conversion of methane to methanol catalyzed by soluble methane monooxygenase (smmo), a member of the bacterial multicomponent monooxygenase (bmm) superfamily. smmo is a dynamic protein complex of three components: a hydroxylase, a reductase, and a regulatory protein. the active site, a carbox ...201526293615
cbbr, the master regulator for microbial carbon dioxide fixation.biological carbon dioxide fixation is an essential and crucial process catalyzed by both prokaryotic and eukaryotic organisms to allow ubiquitous atmospheric co2 to be reduced to usable forms of organic carbon. this process, especially the calvin-bassham-benson (cbb) pathway of co2 fixation, provides the bulk of organic carbon found on earth. the enzyme ribulose 1,5-bisphosphate (rubp) carboxylase/oxygenase (rubisco) performs the key and rate-limiting step whereby co2 is reduced and incorporated ...201526324454
tripping up trp: modification of protein tryptophan residues by reactive oxygen species, modes of detection, and biological consequences.proteins comprise a majority of the dry weight of a cell, rendering them a major target for oxidative modification. oxidation of proteins can result in significant alterations in protein molecular mass such as breakage of the polypeptide backbone and/or polymerization of monomers into dimers, multimers, and sometimes insoluble aggregates. protein oxidation can also result in structural changes to amino acid residue side chains, conversions that have only a modest effect on protein size but can h ...201526393422
a distinct pathway for tetrahymanol synthesis in bacteria.tetrahymanol is a polycyclic triterpenoid lipid first discovered in the ciliate tetrahymena pyriformis whose potential diagenetic product, gammacerane, is often used as a biomarker for water column stratification in ancient ecosystems. bacteria are also a potential source of tetrahymanol, but neither the distribution of this lipid in extant bacteria nor the significance of bacterial tetrahymanol synthesis for interpreting gammacerane biosignatures is known. here we couple comparative genomics wi ...201526483502
specific hopanoid classes differentially affect free-living and symbiotic states of bradyrhizobium diazoefficiens.a better understanding of how bacteria resist stresses encountered during the progression of plant-microbe symbioses will advance our ability to stimulate plant growth. here, we show that the symbiotic system comprising the nitrogen-fixing bacterium bradyrhizobium diazoefficiens and the legume aeschynomene afraspera requires hopanoid production for optimal fitness. while methylated (2me) hopanoids contribute to growth under plant-cell-like microaerobic and acidic conditions in the free-living st ...201526489859
diverse electron sources support denitrification under hypoxia in the obligate methanotroph methylomicrobium album strain bg8.aerobic methane-oxidizing bacteria (mob) are a diverse group of microorganisms that are ubiquitous in natural environments. along with anaerobic mob and archaea, aerobic methanotrophs are critical for attenuating emission of methane to the atmosphere. clearly, nitrogen availability in the form of ammonium and nitrite have strong effects on methanotrophic activity and their natural community structures. previous findings show that nitrite amendment inhibits the activity of some cultivated methano ...201526500622
bioreactor performance parameters for an industrially-promising methanotroph methylomicrobium buryatense 5gb1.methane is a feedstock of interest for the future, both from natural gas and from renewable biogas sources. methanotrophic bacteria have the potential to enable commercial methane bioconversion to value-added products such as fuels and chemicals. a strain of interest for such applications is methylomicrobium buryatense 5gb1, due to its robust growth characteristics. however, to take advantage of the potential of this methanotroph, it is important to generate comprehensive bioreactor-based datase ...201526572866
comparative metagenomics reveals impact of contaminants on groundwater microbiomes.to understand patterns of geochemical cycling in pristine versus contaminated groundwater ecosystems, pristine shallow groundwater (fw301) and contaminated groundwater (fw106) samples from the oak ridge integrated field research center (or-ifrc) were sequenced and compared to each other to determine phylogenetic and metabolic difference between the communities. proteobacteria (e.g., burkholderia, pseudomonas) are the most abundant lineages in the pristine community, though a significant proporti ...201526583008
high-throughput transcriptome sequencing of the cold seep mussel bathymodiolus platifrons.bathymodiolid mussels dominate hydrothermal vents, cold methane/sulfide-hydrocarbon seeps, and other sites of organic enrichment. here, we aimed to explore the innate immune system and detoxification mechanism of the deep sea mussel bathymodiolus platifrons collected from a methane seep in the south china sea. we sequenced the transcriptome of the mussels' gill, foot and mantle tissues and generated a transcriptomic database containing 96,683 transcript sequences. based on go and kegg annotation ...201526593439
eukaryotic opportunists dominate the deep-subsurface biosphere in south africa.following the discovery of the first eukarya in the deep subsurface, intense interest has developed to understand the diversity of eukaryotes living in these extreme environments. we identified that platyhelminthes, rotifera, annelida and arthropoda are thriving at 1.4 km depths in palaeometeoric fissure water up to 12,300 yr old in south african mines. protozoa and fungi have also been identified; however, they are present in low numbers. characterization of the different species reveals that m ...201526597082
differential roles of the hemerythrin-like proteins of mycobacterium smegmatis in hydrogen peroxide and erythromycin susceptibility.hemerythrin-like proteins are oxygen-carrying non-heme di-iron binding proteins and their functions have effect on oxidation-reduction regulation and antibiotic resistance. recent studies using bioinformatic analyses suggest that multiple hemerythrin-like protein coding sequences might have been acquired by lateral gene transfer and the number of hemerythrin-like proteins varies amongst different species. mycobacterium smegmatis contains three hemerythrin-like proteins, msmeg_3312, msmeg_2415 an ...201526607739
consistency analysis of genome-scale models of bacterial metabolism: a metamodel approach.genome-scale metabolic models usually contain inconsistencies that manifest as blocked reactions and gap metabolites. with the purpose to detect recurrent inconsistencies in metabolic models, a large-scale analysis was performed using a previously published dataset of 130 genome-scale models. the results showed that a large number of reactions (~22%) are blocked in all the models where they are present. to unravel the nature of such inconsistencies a metamodel was construed by joining the 130 mo ...201526629901
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
structures of microbial communities in alpine soils: seasonal and elevational effects.microbial communities in alpine environments are exposed to several environmental factors related to elevation and local site conditions and to extreme seasonal variations. however, little is known on the combined impact of such factors on microbial community structure. we assessed the effects of seasonal variations on soil fungal and bacterial communities along an elevational gradient (from alpine meadows to a glacier forefield, 1930-2519 m a.s.l.) over 14 months. samples were taken during all ...201526635785
transcriptomic profiling of methylococcus capsulatus (bath) during growth with two different methane monooxygenases.methylococcus capsulatus (bath) is a methanotroph that possesses both a membrane-embedded (pmmo) and a soluble methane monooxygenase (smmo). the expression of these two mmo's is tightly controlled by the availability of copper in the growth medium, but the underlying mechanisms and the number of genes involved in this switch in methane oxidation is not yet fully elucidated. microarray analyses were used to assess the transcriptome in cells producing either pmmo or smmo. a total of 137 genes were ...201526687591
transcriptomic profiling of methylococcus capsulatus (bath) during growth with two different methane monooxygenases.methylococcus capsulatus (bath) is a methanotroph that possesses both a membrane-embedded (pmmo) and a soluble methane monooxygenase (smmo). the expression of these two mmo's is tightly controlled by the availability of copper in the growth medium, but the underlying mechanisms and the number of genes involved in this switch in methane oxidation is not yet fully elucidated. microarray analyses were used to assess the transcriptome in cells producing either pmmo or smmo. a total of 137 genes were ...201526687591
diversity and habitat preferences of cultivated and uncultivated aerobic methanotrophic bacteria evaluated based on pmoa as molecular marker.methane-oxidizing bacteria are characterized by their capability to grow on methane as sole source of carbon and energy. cultivation-dependent and -independent methods have revealed that this functional guild of bacteria comprises a substantial diversity of organisms. in particular the use of cultivation-independent methods targeting a subunit of the particulate methane monooxygenase (pmoa) as functional marker for the detection of aerobic methanotrophs has resulted in thousands of sequences rep ...201526696968
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