| oxidation of methyl halides by the facultative methylotroph strain imb-1. | washed cell suspensions of the facultative methylotroph strain imb-1 grown on methyl bromide (mebr) were able to consume methyl chloride (mecl) and methyl iodide (mei) as well as mebr. consumption of >100 microm mebr by cells grown on glucose, acetate, or monomethylamine required induction. induction was inhibited by chloramphenicol. however, cells had a constitutive ability to consume low concentrations (<20 nm) of mebr. glucose-grown cells were able to readily oxidize [(14)c]formaldehyde to (1 ... | 1999 | 10543820 |
| inhibition of nitrifiers and methanotrophs from an agricultural humisol by allylsulfide and its implications for environmental studies. | allylsulfide, an inhibitor of ammonia monooxygenase, was tested to determine its ability to inhibit nitrification and methane oxidation in pure cultures, in agricultural humisol enrichment cultures, and in humisol slurries. we confirmed that allylsulfide is a differential inhibitor of cultures of nitrifiers and methanotrophs at concentrations of 1 and 200 microm, respectively, which result in 50% inhibition. however, although a nitrifying enrichment culture added to sterilized humisol was inhibi ... | 1999 | 10347027 |
| contribution of methanotrophic and nitrifying bacteria to ch4 and nh4+ oxidation in the rhizosphere of rice plants as determined by new methods of discrimination | methanotrophic and nitrifying bacteria are both able to oxidize ch4 as well as nh4+. to date it is not possible to estimate the relative contribution of methanotrophs to nitrification and that of nitrifiers to ch4 oxidation and thus to assess their roles in n and c cycling in soils and sediments. this study presents new options for discrimination between the activities of methanotrophs and nitrifiers, based on the competitive inhibitor ch3f and on recovery after inhibition with c2h2. by using ri ... | 1999 | 10223965 |
| detection of methanotrophs in groundwater by pcr. | methanotrophic bacteria have significant potential for bioremediation, which would require methods for monitoring the presence and activity of these organisms in environmental samples. in this study, pcr was used to detect methanotrophic bacteria. primers were designed on the basis of a partial sequence of pmoa, which encodes one of the proteins of the particulate methane monooxygenase. specific amplification of a portion of pmoa was obtained with template dna isolated from lab strains of methan ... | 1999 | 9925595 |
| possible interactions within a methanotrophic-heterotrophic groundwater community able to transform linear alkylbenzenesulfonates. | the relationships and interactions within a methanotrophic-heterotrophic groundwater community were studied in a closed system (shake culture) in the presence of methane as the primary carbon and energy source and with the addition of the pure linear alkylbenzenesulfonate (las) congener 2-[4-(sulfophenyl)]decan as a cometabolic substrate. when cultured under different conditions, this community was shown to be a stable association, consisting of one obligate type ii methanotroph and four or five ... | 2000 | 11010895 |
| biomarker evidence for widespread anaerobic methane oxidation in mediterranean sediments by a consortium of methanogenic archaea and bacteria. the medinaut shipboard scientific party. | although abundant geochemical data indicate that anaerobic methane oxidation occurs in marine sediments, the linkage to specific microorganisms remains unclear. in order to examine processes of methane consumption and oxidation, sediment samples from mud volcanoes at two distinct sites on the mediterranean ridge were collected via the submersible nautile. geochemical data strongly indicate that methane is oxidized under anaerobic conditions, and compound-specific carbon isotope analyses indicate ... | 2000 | 10698781 |
| cholesterol in health and disease. | | 2002 | 12208856 |
| biological inorganic chemistry at the beginning of the 21st century. | advances in bioinorganic chemistry since the 1970s have been driven by three factors: rapid determination of high-resolution structures of proteins and other biomolecules, utilization of powerful spectroscopic tools for studies of both structures and dynamics, and the widespread use of macromolecular engineering to create new biologically relevant structures. today, very large molecules can be manipulated at will, with the result that certain proteins and nucleic acids themselves have become ver ... | 2003 | 12657732 |
| a new example of viral intein in mimivirus. | inteins are "protein introns" that remove themselves from their host proteins through an autocatalytic protein-splicing. after their discovery, inteins have been quickly identified in all domains of life, but only once to date in the genome of a eukaryote-infecting virus. | 2005 | 15707490 |
| facile o-atom insertion into c-c and c-h bonds by a trinuclear copper complex designed to harness a singlet oxene. | two trinuclear copper [cu(i)cu(i)cu(i)(l)](1+) complexes have been prepared with the multidentate ligands (l) 3,3'-(1,4-diazepane-1,4-diyl)bis(1-((2-(dimethylamino)ethyl)(methyl)amino)propan-2-ol) (7-me) and (3,3'-(1,4-diazepane-1,4-diyl)bis(1-((2-(diethylamino) ethyl)(ethyl) amino)propan-2-ol) (7-et) as models for the active site of the particulate methane monooxygenase (pmmo). the ligands were designed to form the proper spatial and electronic geometry to harness a "singlet oxene," according t ... | 2007 | 17804786 |
| crispr recognition tool (crt): a tool for automatic detection of clustered regularly interspaced palindromic repeats. | clustered regularly interspaced palindromic repeats (crisprs) are a novel type of direct repeat found in a wide range of bacteria and archaea. crisprs are beginning to attract attention because of their proposed mechanism; that is, defending their hosts against invading extrachromosomal elements such as viruses. existing repeat detection tools do a poor job of identifying crisprs due to the presence of unique spacer sequences separating the repeats. in this study, a new tool, crt, is introduced ... | 2007 | 17577412 |
| cryoradiolytic reduction of heme proteins: maximizing dose dependent yield. | radiolytic reduction in frozen solutions and crystals is a useful method for generation of trapped intermediates in protein based radical reactions. in this communication we define the conditions which provide the maximum yield of one electron reduced myoglobin at 77 k using (60)co γ-irradiation in aqueous glycerol glass. the yield reached 50% after 20 kgy, was almost complete at ∼160 kgy total dose, and does not depend on the protein concentration in the range 0.01 - 5 mm. | 2007 | 18379640 |
| intermediates in dioxygen activation by methane monooxygenase: a qm/mm study. | protein effects in the activation of dioxygen by methane monooxygenase (mmo) were investigated by using combined qm/mm and broken-symmetry density functional theory (dft) methods. the effects of a novel empirical scheme recently developed by our group on the relative dft energies of the various intermediates in the catalytic cycle are investigated. inclusion of the protein leads to much better agreement between the experimental and computed geometric structures for the reduced form (mmoh(red)). ... | 2007 | 17326634 |
| pdbsum new things. | pdbsum (http://www.ebi.ac.uk/pdbsum) provides summary information about each experimentally determined structural model in the protein data bank (pdb). here we describe some of its most recent features, including figures from the structure's key reference, citation data, pfam domain diagrams, topology diagrams and protein-protein interactions. furthermore, it now accepts users' own pdb format files and generates a private set of analyses for each uploaded structure. | 2008 | 18996896 |
| pdbsum new things. | pdbsum (http://www.ebi.ac.uk/pdbsum) provides summary information about each experimentally determined structural model in the protein data bank (pdb). here we describe some of its most recent features, including figures from the structure's key reference, citation data, pfam domain diagrams, topology diagrams and protein-protein interactions. furthermore, it now accepts users' own pdb format files and generates a private set of analyses for each uploaded structure. | 2008 | 18996896 |
| resilience of the iron environment in heme proteins. | conformational flexibility is essential to the functional behavior of proteins. we use an effective force constant introduced by zaccai, the resilience, to quantify this flexibility. site-selective experimental and computational methods allow us to determine the resilience of heme protein active sites. the vibrational density of states of the heme fe determined using nuclear resonance vibrational spectroscopy provides a direct experimental measure of the resilience of the fe environment, which w ... | 2008 | 18835904 |
| cd and mcd studies of the effects of component b variant binding on the biferrous active site of methane monooxygenase. | the multicomponent soluble form of methane monooxygenase (smmo) catalyzes the oxidation of methane through the activation of o 2 at a nonheme biferrous center in the hydroxylase component, mmoh. reactivity is limited without binding of the smmo effector protein, mmob. past studies show that mutations of specific mmob surface residues cause large changes in the rates of individual steps in the mmoh reaction cycle. to define the structural and mechanistic bases for these observations, cd, mcd, and ... | 2008 | 18627173 |
| structural model studies for the high-valent intermediate q of methane monooxygenase from broken-symmetry density functional calculations. | mössbauer isomer shift parameters have been obtained for both density functional theory (dft) opbe and olyp functionals by linear regressions between the measured isomer shifts and calculated electron densities at fe nuclei for a number of fe(2+,2.5+) and fe(2.5+,3+,3.5+,4+) complexes grouped separately. the calculated isomer shifts and quadrupole splittings on the sample fe complexes from opbe and olyp functionals are similar to those of pw91 calculations (j. comput. chem. 27 (2006) 1292), howe ... | 2008 | 19262682 |
| methane oxidation at 55 degrees c and ph 2 by a thermoacidophilic bacterium belonging to the verrucomicrobia phylum. | methanotrophic bacteria constitute a ubiquitous group of microorganisms playing an important role in the biogeochemical carbon cycle and in control of global warming through natural reduction of methane emission. these bacteria share the unique ability of using methane as a sole carbon and energy source and have been found in a great variety of habitats. phylogenetically, known methanotrophs constitute a rather limited group and have so far only been affiliated with the proteobacteria. here, we ... | 2008 | 18172218 |
| structure and dynamics of metalloproteins in live cells. | x-ray absorption spectroscopy (xas) has emerged as one of the premier tools for investigating the structure and dynamic properties of metals in cells and in metal containing biomolecules. utilizing the high flux and broad energy range of x-rays supplied by synchrotron light sources, one can selectively excite core electronic transitions in each metal. spectroscopic signals from these electronic transitions can be used to dissect the chemical architecture of metals in cells, in cellular component ... | 2008 | 19195552 |
| review: studies of ferric heme proteins with highly anisotropic/highly axial low spin (s = 1/2) electron paramagnetic resonance signals with bis-histidine and histidine-methionine axial iron coordination. | six-coordinated heme groups are involved in a large variety of electron transfer reactions because of their ability to exist in both the ferrous (fe(2+)) and ferric (fe(3+)) state without any large differences in structure. our studies on hemes coordinated by two histidines (bis-his) and hemes coordinated by histidine and methionine (his-met) will be reviewed. in both of these coordination environments, the heme core can exhibit ferric low spin (electron paramagnetic resonance epr) signals with ... | 2009 | 19536822 |
| large d/h variations in bacterial lipids reflect central metabolic pathways. | large hydrogen-isotopic (d/h) fractionations between lipids and growth water have been observed in most organisms studied to date. these fractionations are generally attributed to isotope effects in the biosynthesis of lipids, and are frequently assumed to be approximately constant for the purpose of reconstructing climatic variables. here, we report d/h fractionations between lipids and water in 4 cultured members of the phylum proteobacteria, and show that they can vary by up to 500 per thousa ... | 2009 | 19617564 |
| a diiron(iv) complex that cleaves strong c-h and o-h bonds. | the controlled cleavage of strong c-h bonds like those of methane poses a significant challenge for chemists. in nature methane is oxidized to methanol by soluble methane monooxygenase via a diiron(iv) intermediate called q. to model the chemistry of mmo-q, an oxo-bridged diiron(iv) complex has been generated by electrochemical oxidation and characterized by several spectroscopic methods. this novel species has an fe(iv/iii) redox potential of +1.50 v vs. ferrocene (>2 v vs. nhe), the highest va ... | 2009 | 19885382 |
| copper-dioxygen complex mediated c-h bond oxygenation: relevance for particulate methane monooxygenase (pmmo). | particulate methane monooxygenase (pmmo), an integral membrane protein found in methanotrophic bacteria, catalyzes the oxidation of methane to methanol. expression and greater activity of the enzyme in the presence of copper ion suggest that pmmo is a cuprous metalloenzyme. recent advances - especially the first crystal structures of pmmo - have energized the field, but the nature of the active site(s) and the mechanism of methane oxidation remain poorly understood-yet hotly contested. herein th ... | 2009 | 19286415 |
| spectroscopic definition of the biferrous and biferric sites in de novo designed four-helix bundle dfsc peptides: implications for o2 reactivity of binuclear non-heme iron enzymes. | dfsc is a single chain de novo designed four-helix bundle peptide that mimics the core protein fold and primary ligand set of various binuclear non-heme iron enzymes. dfsc and the e11d, y51l, and y18f single amino acid variants have been studied using a combination of near-ir circular dichroism (cd), magnetic circular dichroism (mcd), variable temperature variable field mcd (vtvh mcd), and x-ray absorption (xas) spectroscopies. the biferrous sites are all weakly antiferromagnetically coupled wit ... | 2009 | 19090676 |
| determining macromolecular assembly structures by molecular docking and fitting into an electron density map. | structural models of macromolecular assemblies are instrumental for gaining a mechanistic understanding of cellular processes. determining these structures is a major challenge for experimental techniques, such as x-ray crystallography, nmr spectroscopy and electron microscopy (em). thus, computational modeling techniques, including molecular docking, are required. the development of most molecular docking methods has so far been focused on modeling of binary complexes. we have recently introduc ... | 2010 | 20827723 |
| evolutionary origin of a secondary structure: π-helices as cryptic but widespread insertional variations of α-helices that enhance protein functionality. | formally annotated π-helices are rare in protein structures but have been correlated with functional sites. here, we analyze protein structures to show that π-helices are the same as structures known as α-bulges, α-aneurisms, π-bulges, and looping outs, and are evolutionarily derived by the insertion of a single residue into an α-helix. this newly discovered evolutionary origin explains both why π-helices are cryptic, being rarely annotated despite occurring in 15% of known proteins, and why the ... | 2010 | 20888342 |
| oxidation reactions performed by soluble methane monooxygenase hydroxylase intermediates h(peroxo) and q proceed by distinct mechanisms. | soluble methane monooxygenase is a bacterial enzyme that converts methane to methanol at a carboxylate-bridged diiron center with exquisite control. because the oxidizing power required for this transformation is demanding, it is not surprising that the enzyme is also capable of hydroxylating and epoxidizing a broad range of hydrocarbon substrates in addition to methane. in this work we took advantage of this promiscuity of the enzyme to gain insight into the mechanisms of action of h(peroxo) an ... | 2010 | 20681546 |
| current challenges of modeling diiron enzyme active sites for dioxygen activation by biomimetic synthetic complexes. | this tutorial review describes recent progress in modeling the active sites of carboxylate-rich non-heme diiron enzymes that activate dioxygen to carry out several key reactions in nature. the chemistry of soluble methane monooxygenase, which catalyzes the selective oxidation of methane to methanol, is of particular interest for (bio)technological applications. novel synthetic diiron complexes that mimic structural, and, to a lesser extent, functional features of these diiron enzymes are discuss ... | 2010 | 20485834 |
| abundance and diversity of ammonia-oxidizing bacteria in relation to ammonium in a chinese shallow eutrophic urban lake. | the measures of most-probable-number and restriction fragment length polymorphism analysis were used to analyze the abundance and diversity of ammonia-oxidizing bacteria in sediment of a chinese shallow eutrophic urban lake (lake yuehu). among the 5 sampling sites, ammonia concentration in interstitial water was positively proportional not only to the content of organic matter, but also to ammonia-oxidizing bacteria numbers (at a magnitude of 10(5) cells g(-1) dry weight) in sediment significant ... | 2010 | 24031484 |
| 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 ... | 2011 | 21954394 |
| 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 ... | 2011 | 21667086 |
| 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 ... | 2011 | 21593799 |
| 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 ... | 2011 | 21391602 |
| 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 ... | 2012 | 23254511 |
| 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 ... | 2012 | 23254511 |
| 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. | 2012 | 23144383 |
| 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 ... | 2012 | 23046475 |
| 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 ... | 2012 | 22916218 |
| 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 ... | 2012 | 22860088 |
| 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 ... | 2012 | 22826256 |
| 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 ... | 2012 | 22826704 |
| 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 ... | 2012 | 22544266 |
| 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 ... | 2012 | 22725967 |
| 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- ... | 2012 | 22607542 |
| 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 ... | 2012 | 22540911 |
| 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 ... | 2012 | 22517752 |
| 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 ... | 2012 | 22483118 |
| 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 ... | 2013 | 24386162 |
| 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 ... | 2013 | 24077702 |
| 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 ... | 2013 | 24189217 |
| 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 ... | 2013 | 24013630 |
| 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 ... | 2013 | 24142950 |
| 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 ... | 2013 | 24142950 |
| 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 ... | 2013 | 24134722 |
| 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% ... | 2013 | 23902988 |
| 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. | 2013 | 23898868 |
| 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 ... | 2013 | 23842654 |
| 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 ... | 2013 | 23718184 |
| 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 ... | 2013 | 23671678 |
| 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 ... | 2013 | 23574645 |
| metalloenzymes: put a ring on it. | | 2013 | 23508187 |
| 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 ... | 2013 | 23475542 |
| 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 ... | 2013 | 23484056 |
| 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 ... | 2013 | 24496464 |
| 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 ... | 2013 | 24019993 |
| synttax: a web server linking synteny to prokaryotic taxonomy. | the study of the conservation of gene order or synteny constitutes a powerful methodology to assess the orthology of genomic regions and to predict functional relationships between genes. the exponential growth of microbial genomic databases is expected to improve synteny predictions significantly. paradoxically, this genomic data plethora, without information on organisms relatedness, could impair the performance of synteny analysis programs. | 2013 | 23323735 |
| the noncommensal bacterium methylococcus capsulatus (bath) ameliorates dextran sulfate (sodium salt)-induced ulcerative colitis by influencing mechanisms essential for maintenance of the colonic barrier function. | dietary inclusion of a bacterial meal has recently been shown to efficiently abolish soybean meal-induced enteritis in atlantic salmon. the objective of this study was to investigate whether inclusion of this bacterial meal in the diet could abrogate disease development in a murine model of epithelial injury and colitis and thus possibly have therapeutic potential in human inflammatory bowel disease. c57bl/6n mice were fed ad libitum a control diet or an experimental diet containing 254 g/kg of ... | 2013 | 23064342 |
| 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 ... | 2014 | 25642228 |
| 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 ... | 2014 | 25642228 |
| 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 ... | 2014 | 25479164 |
| 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 ... | 2014 | 25429424 |
| 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 ... | 2014 | 25172849 |
| 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 ... | 2014 | 25295031 |
| 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 ... | 2014 | 25135817 |
| 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 ... | 2014 | 25135817 |
| 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. ... | 2014 | 25157264 |
| 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 ... | 2014 | 24907318 |
| 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 ... | 2014 | 25059917 |
| 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. ... | 2014 | 24937475 |
| 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 ... | 2014 | 24987389 |
| 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 ... | 2014 | 24710692 |
| 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 ... | 2014 | 24771036 |
| life in a sea of oxygen. | | 2014 | 24737314 |
| 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 ... | 2014 | 24523098 |
| 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 ... | 2014 | 24441161 |
| 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 ... | 2014 | 24568559 |
| potential benefits of the application of yeast starters in table olive processing. | yeasts play an important role in the food and beverage industry, especially in products such as bread, wine, and beer, among many others. however, their use as a starter in table olive processing has not yet been studied in detail. the candidate yeast strains should be able to dominate fermentation, together with lactic acid bacteria, but should also provide a number of beneficial advantages. technologically, yeasts should resist low ph and high salt concentrations, produce desirable aromas, imp ... | 2014 | 22558000 |
| 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 ... | 2014 | 24498370 |
| 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 ... | 2014 | 24550901 |
| 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 ... | 2014 | 24476336 |
| bacterial composition and survival on sahara dust particles transported to the european alps. | deposition of sahara dust (sd) particles is a frequent phenomenon in europe, but little is known about the viability and composition of the bacterial community transported with sd. the goal of this study was to characterize sd-associated bacteria transported to the european alps, deposited and entrapped in snow. during two distinct events in february and may 2014, sd particles were deposited and promptly covered by falling snow, thus preserving them in distinct ochre layers within the snowpack. ... | 2015 | 26733988 |
| 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 ... | 2015 | 26635785 |
| 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 ... | 2015 | 26597082 |
| 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 ... | 2015 | 26593439 |
| 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 ... | 2015 | 26572866 |
| 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 ... | 2015 | 26393422 |
| novel methanotrophs of the family methylococcaceae from different geographical regions and habitats. | terrestrial methane seeps and rice paddy fields are important ecosystems in the methane cycle. methanotrophic bacteria in these ecosystems play a key role in reducing methane emission into the atmosphere. here, we describe three novel methanotrophs, designated brs-k6, gfs-k6 and ak-k6, which were recovered from three different habitats in contrasting geographic regions and ecosystems: waterlogged rice-field soil and methane seep pond sediments from bangladesh; and warm spring sediments from arme ... | 2015 | 27682101 |
| 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 ... | 2015 | 26293615 |
| 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 ... | 2015 | 26092454 |