| parallel pathways for nitrite reduction during anaerobic growth in thermus thermophilus. | respiratory reduction of nitrate and nitrite is encoded in thermus thermophilus by the respective transferable gene clusters. nitrate is reduced by a heterotetrameric nitrate reductase (nar) encoded along transporters and regulatory signal transduction systems within the nitrate respiration conjugative element (nce). the nitrite respiration cluster (nic) encodes homologues of nitrite reductase (nir) and nitric oxide reductase (nor). the expression and role of the nirsjm genes in nitrite respirat ... | 2014 | 24443532 |
| a sco protein among the hypothetical proteins of bacillus lehensis g1: its 3d macromolecular structure and association with cytochrome c oxidase. | at least a quarter of any complete genome encodes for hypothetical proteins (hps) which are largely non-similar to other known, well-characterized proteins. predicting and solving their structures and functions is imperative to aid understanding of any given organism as a complete biological system. the present study highlights the primary effort to classify and cluster 1202 hps of bacillus lehensis g1 alkaliphile to serve as a platform to mine and select specific hp(s) to be studied further in ... | 2014 | 24641837 |
| safety in numbers: multiple occurrences of highly similar homologs among azotobacter vinelandii carbohydrate metabolism proteins probably confer adaptive benefits. | gene duplication and horizontal gene transfer are common processes in bacterial and archaeal genomes, and are generally assumed to result in either diversification or loss of the redundant gene copies. however, a recent analysis of the genome of the soil bacterium azotobacter vinelandii dj revealed an abundance of highly similar homologs among carbohydrate metabolism genes. in many cases these multiple genes did not appear to be the result of recent duplications, or to function only as a means o ... | 2014 | 24625193 |
| identification and characterization of the 'missing' terminal enzyme for siroheme biosynthesis in α-proteobacteria. | it has recently been shown that the biosynthetic route for both the d1 -haem cofactor of dissimilatory cd1 nitrite reductases and haem, via the novel alternative-haem-synthesis pathway, involves siroheme as an intermediate, which was previously thought to occur only as a cofactor in assimilatory sulphite/nitrite reductases. in many denitrifiers (which require d1 -haem), the pathway to make siroheme remained to be identified. here we identify and characterize a sirohydrochlorin-ferrochelatase fro ... | 2014 | 24673795 |
| a soil actinobacterium scavenges atmospheric h2 using two membrane-associated, oxygen-dependent [nife] hydrogenases. | in the earth's lower atmosphere, h2 is maintained at trace concentrations (0.53 ppmv/0.40 nm) and rapidly turned over (lifetime ≤ 2.1 y(-1)). it is thought that soil microbes, likely actinomycetes, serve as the main global sink for tropospheric h2. however, no study has ever unambiguously proven that a hydrogenase can oxidize this trace gas. in this work, we demonstrate, by using genetic dissection and sensitive gc measurements, that the soil actinomycete mycobacterium smegmatis mc(2)155 constit ... | 2014 | 24591586 |
| achromobacter denitrificans strain yd35 pyruvate dehydrogenase controls nadh production to allow tolerance to extremely high nitrite levels. | we identified the extremely nitrite-tolerant bacterium achromobacter denitrificans yd35 that can grow in complex medium containing 100 mm nitrite (no2(-)) under aerobic conditions. nitrite induced global proteomic changes and upregulated tricarboxylate (tca) cycle enzymes as well as antioxidant proteins in yd35. transposon mutagenesis generated no2(-)-hypersensitive mutants of yd35 that had mutations at genes for aconitate hydratase and α-ketoglutarate dehydrogenase in the tca cycle and a pyruva ... | 2014 | 24413603 |
| siderophores in environmental research: roles and applications. | siderophores are organic compounds with low molecular masses that are produced by microorganisms and plants growing under low iron conditions. the primary function of these compounds is to chelate the ferric iron [fe(iii)] from different terrestrial and aquatic habitats and thereby make it available for microbial and plant cells. siderophores have received much attention in recent years because of their potential roles and applications in various areas of environmental research. their significan ... | 2014 | 24576157 |
| site-directed mutagenesis of gln103 reveals the influence of this residue on the redox properties and stability of maug. | the diheme enzyme maug catalyzes a six-electron oxidation that is required for the posttranslational modification of a precursor of methylamine dehydrogenase (premadh) to complete the biosynthesis of its protein-derived cofactor, tryptophan tryptophylquinone (ttq). crystallographic and computational studies have implicated gln103 in stabilizing the fe(iv)═o moiety of the bis-fe(iv) state by hydrogen bonding. the role of gln103 was probed by site-directed mutagenesis. q103l and q103e mutations re ... | 2014 | 24517455 |
| prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine. | through the use of genetic, enzymatic, metabolomic, and structural analyses, we have discovered the catabolic pathway for proline betaine, an osmoprotectant, in paracoccus denitrificans and rhodobacter sphaeroides. genetic and enzymatic analyses showed that several of the key enzymes of the hydroxyproline betaine degradation pathway also function in proline betaine degradation. metabolomic analyses detected each of the metabolic intermediates of the pathway. the proline betaine catabolic pathway ... | 2014 | 24520058 |
| 3-hydroxybutyrate oligomer hydrolase and 3-hydroxybutyrate dehydrogenase participate in intracellular polyhydroxybutyrate and polyhydroxyvalerate degradation in paracoccus denitrificans. | genes encoding 3-hydroxybutyrate oligomer hydrolase (phazc) and 3-hydroxybutyrate dehydrogenase (hbd) were isolated from paracoccus denitrificans. phazc and hbd were overproduced as his-tagged proteins in escherichia coli and purified by affinity and gel filtration chromatography. purified his-tagged proteins had molecular masses of 31 kda and 120 kda (a tetramer of 29-kda subunits). the his-tagged phazc hydrolyzed not only 3-hydroxybutyrate oligomers but also 3-hydroxyvalerate oligomers. the hi ... | 2014 | 24271169 |
| an improved medium for the anaerobic growth of paracoccus denitrificans pd1222. | paracoccus denitrificans is a well studied model organism with respect to its aerobic and anaerobic respiratory enzymes. however, until now, the growth medium for this organism has not been optimized for anaerobic growth. in particular, the requirements of p. denitrificans for trace elements (tes) are not well known. in the present study we aimed to improve growth rates of p. denitrificans pd1222 on a defined medium under anoxic conditions. we designed media containing different combinations of ... | 2014 | 24550891 |
| crystal structure of an (r)-selective ω-transaminase from aspergillus terreus. | chiral amines are important building blocks for the synthesis of pharmaceutical products, fine chemicals, and agrochemicals. ω-transaminases are able to directly synthesize enantiopure chiral amines by catalysing the transfer of an amino group from a primary amino donor to a carbonyl acceptor with pyridoxal 5'-phosphate (plp) as cofactor. in nature, (s)-selective amine transaminases are more abundant than the (r)-selective enzymes, and therefore more information concerning their structures is av ... | 2014 | 24498081 |
| the mononuclear molybdenum enzymes. | | 2014 | 24467397 |
| an extended active-site motif controls the reactivity of the thioredoxin fold. | proteins belonging to the thioredoxin (trx) superfamily are abundant in all organisms. they share the same structural features, arranged in a seemingly simple fold, but they perform a multitude of functions in oxidative protein folding and electron transfer pathways. we use the c-terminal domain of the unique transmembrane reductant conductor dsbd as a model for an in-depth analysis of the factors controlling the reactivity of the trx fold. we employ nmr spectroscopy, x-ray crystallography, muta ... | 2014 | 24469455 |
| a staphylococcus aureus tir domain protein virulence factor blocks tlr2-mediated nf-κb signaling. | signaling through toll-like receptors (tlrs), crucial molecules in the induction of host defense responses, requires adaptor proteins that contain a toll/interleukin-1 receptor (tir) domain. the pathogen staphylococcus aureus produces several innate immune-evasion molecules that interfere with the host's innate immune response. a database search analysis suggested the presence of a gene encoding a homologue of the human tir domain in s. aureus mssa476 which was named staphylococcal tir domain pr ... | 2014 | 24481289 |
| steady-state kinetic mechanism of loda, a novel cysteine tryptophylquinone-dependent oxidase. | loda is a novel lysine-ε-oxidase which possesses a cysteine tryptophylquinone cofactor. it is the first tryptophylquinone enzyme known to function as an oxidase. a steady-state kinetic analysis shows that loda obeys a ping-pong kinetic mechanism with values of kcat of 0.22±0.04 s(-1), klysine of 3.2±0.5 μm and ko2 of 37.2±6.1 μm. the kcat exhibited a ph optimum at 7.5 while kcat/klysine peaked at 7.0 and remained constant to ph 8.5. alternative electron acceptors could not effectively substitute ... | 2014 | 24462691 |
| a biochemical approach to study the role of the terminal oxidases in aerobic respiration in shewanella oneidensis mr-1. | the genome of the facultative anaerobic γ-proteobacterium shewanella oneidensis mr-1 encodes for three terminal oxidases: a bd-type quinol oxidase and two heme-copper oxidases, a a-type cytochrome c oxidase and a cbb 3-type oxidase. in this study, we used a biochemical approach and directly measured oxidase activities coupled to mass-spectrometry analysis to investigate the physiological role of the three terminal oxidases under aerobic and microaerobic conditions. our data revealed that the cbb ... | 2014 | 24466040 |
| biochemical and biophysical characterization of the two isoforms of cbb3-type cytochrome c oxidase from pseudomonas stutzeri. | the cbb3-type cytochrome c oxidases (cbb3-ccos) are members of the heme-copper oxidase superfamily that couple the reduction of oxygen to translocation of protons across the membrane. the cbb3-ccos are present only in bacteria and play a primary role in microaerobic respiration, being essential for nitrogen-fixing endosymbionts and for some human pathogens. as frequently observed in pseudomonads, pseudomonas stutzeri contains two independent ccono(q)p operons encoding the two cbb3 isoforms, cbb3 ... | 2014 | 24214947 |
| role of the twin arginine protein transport pathway in the assembly of the streptomyces coelicolor cytochrome bc1 complex. | the cytochrome bc1-cytochrome aa3 complexes together comprise one of the major branches of the bacterial aerobic respiratory chain. in actinobacteria, the cytochrome bc1 complex shows a number of unusual features in comparison to other cytochrome bc1 complexes. in particular, the rieske iron-sulfur protein component of this complex, qcra, is a polytopic rather than a monotopic membrane protein. bacterial rieske proteins are usually integrated into the membrane in a folded conformation by the twi ... | 2014 | 24142258 |
| transferable denitrification capability of thermus thermophilus. | laboratory-adapted strains of thermus spp. have been shown to require oxygen for growth, including the model strains t. thermophilus hb27 and hb8. in contrast, many isolates of this species that have not been intensively grown under laboratory conditions keep the capability to grow anaerobically with one or more electron acceptors. the use of nitrogen oxides, especially nitrate, as electron acceptors is one of the most widespread capabilities among these facultative strains. in this process, nit ... | 2014 | 24141123 |
| selective pressure of temperature on competition and cross-feeding within denitrifying and fermentative microbial communities. | in coastal marine sediments, denitrification and fermentation are important processes in the anaerobic decomposition of organic matter. microbial communities performing these two processes were enriched from tidal marine sediments in replicated, long term chemostat incubations at 10 and 25°c. whereas denitrification rates at 25°c were more or less stable over time, at 10°c denitrification activity was unstable and could only be sustained either by repeatedly increasing the amount of carbon subst ... | 2015 | 26779132 |
| selective pressure of temperature on competition and cross-feeding within denitrifying and fermentative microbial communities. | in coastal marine sediments, denitrification and fermentation are important processes in the anaerobic decomposition of organic matter. microbial communities performing these two processes were enriched from tidal marine sediments in replicated, long term chemostat incubations at 10 and 25°c. whereas denitrification rates at 25°c were more or less stable over time, at 10°c denitrification activity was unstable and could only be sustained either by repeatedly increasing the amount of carbon subst ... | 2015 | 26779132 |
| sarcosine catabolism in pseudomonas aeruginosa is transcriptionally regulated by sour. | sarcosine (n-methylglycine) is present in many environments inhabited by pseudomonads and is likely most often encountered as an intermediate in the metabolism of choline, carnitine, creatine, and glyphosate. while the enzymology of sarcosine metabolism has been relatively well studied in bacteria, the regulatory mechanisms governing catabolism have remained largely unknown. we previously determined that the sarcosine-catabolic (sox) operon of pseudomonas aeruginosa is induced by the arac family ... | 2015 | 26503852 |
| sarcosine catabolism in pseudomonas aeruginosa is transcriptionally regulated by sour. | sarcosine (n-methylglycine) is present in many environments inhabited by pseudomonads and is likely most often encountered as an intermediate in the metabolism of choline, carnitine, creatine, and glyphosate. while the enzymology of sarcosine metabolism has been relatively well studied in bacteria, the regulatory mechanisms governing catabolism have remained largely unknown. we previously determined that the sarcosine-catabolic (sox) operon of pseudomonas aeruginosa is induced by the arac family ... | 2015 | 26503852 |
| determining roles of accessory genes in denitrification by mutant fitness analyses. | enzymes of the denitrification pathway play an important role in the global nitrogen cycle, including release of nitrous oxide, an ozone-depleting greenhouse gas. in addition, nitric oxide reductase, maturation factors, and proteins associated with nitric oxide detoxification are used by pathogens to combat nitric oxide release by host immune systems. while the core reductases that catalyze the conversion of nitrate to dinitrogen are well understood at a mechanistic level, there are many periphe ... | 2015 | 26452555 |
| determining roles of accessory genes in denitrification by mutant fitness analyses. | enzymes of the denitrification pathway play an important role in the global nitrogen cycle, including release of nitrous oxide, an ozone-depleting greenhouse gas. in addition, nitric oxide reductase, maturation factors, and proteins associated with nitric oxide detoxification are used by pathogens to combat nitric oxide release by host immune systems. while the core reductases that catalyze the conversion of nitrate to dinitrogen are well understood at a mechanistic level, there are many periphe ... | 2015 | 26452555 |
| nitrate storage and dissimilatory nitrate reduction by eukaryotic microbes. | the microbial nitrogen cycle is one of the most complex and environmentally important element cycles on earth and has long been thought to be mediated exclusively by prokaryotic microbes. rather recently, it was discovered that certain eukaryotic microbes are able to store nitrate intracellularly and use it for dissimilatory nitrate reduction in the absence of oxygen. the paradigm shift that this entailed is ecologically significant because the eukaryotes in question comprise global players like ... | 2015 | 26734001 |
| studies on the glutathione-dependent formaldehyde-activating enzyme from paracoccus denitrificans. | formaldehyde is a toxin and carcinogen that is both an environmental pollutant and an endogenous metabolite. formaldehyde metabolism, which is probably essential for all aerobic cells, likely proceeds via multiple mechanisms, including via a glutathione-dependent pathway that is widely conserved in bacteria, plants and animals. however, it is unclear whether the first step in the glutathione-dependent pathway (i.e. formation of s-hydroxymethylglutathione (hmg)) is enzyme-catalysed. we report stu ... | 2015 | 26675168 |
| flavin binding to the deca-heme cytochrome mtrc: insights from computational molecular simulation. | certain dissimilatory bacteria have the remarkable ability to use extracellular metal oxide minerals instead of oxygen as terminal electron sinks, using a process known as "extracellular respiration". specialized multiheme cytochromes located on the outer membrane of the microbe were shown to be crucial for electron transfer from the cell surface to the mineral. this process is facilitated by soluble, biogenic flavins secreted by the organism for the purpose of acting as an electron shuttle. how ... | 2015 | 26682818 |
| visualization of no3⁻/no2⁻ dynamics in living cells by fluorescence resonance energy transfer (fret) imaging employing a rhizobial two-component regulatory system. | nitrate (no3(-)) and nitrite (no2(-)) are the physiological sources of nitric oxide (no), a key biological messenger molecule. no3(-)/no2(-) exerts a beneficial impact on no homeostasis and its related cardiovascular functions. to visualize the physiological dynamics of no3(-)/no2(-) for assessing the precise roles of these anions, we developed a genetically encoded intermolecular fluorescence resonance energy transfer (fret)-based indicator, named snooopy (sensor for no3(-)/no2(-) in physiology ... | 2015 | 26631727 |
| visualization of no3⁻/no2⁻ dynamics in living cells by fluorescence resonance energy transfer (fret) imaging employing a rhizobial two-component regulatory system. | nitrate (no3(-)) and nitrite (no2(-)) are the physiological sources of nitric oxide (no), a key biological messenger molecule. no3(-)/no2(-) exerts a beneficial impact on no homeostasis and its related cardiovascular functions. to visualize the physiological dynamics of no3(-)/no2(-) for assessing the precise roles of these anions, we developed a genetically encoded intermolecular fluorescence resonance energy transfer (fret)-based indicator, named snooopy (sensor for no3(-)/no2(-) in physiology ... | 2015 | 26631727 |
| the inhibitory mechanism of the ζ subunit of the f1fo-atpase nanomotor of paracoccus denitrificans and related α-proteobacteria. | the ζ subunit is a novel inhibitor of the f1fo-atpase of paracoccus denitrificans and related α-proteobacteria. it is different from the bacterial (ϵ) and mitochondrial (if1) inhibitors. the n terminus of ζ blocks rotation of the γ subunit of the f1-atpase of p. denitrificans (zarco-zavala, m., morales-ríos, e., mendoza-hernández, g., ramírez-silva, l., pérez-hernández, g., and garcía-trejo, j. j. (2014) faseb j. 24, 599-608) by a hitherto unknown quaternary structure that was first modeled here ... | 2015 | 26546676 |
| the inhibitory mechanism of the ζ subunit of the f1fo-atpase nanomotor of paracoccus denitrificans and related α-proteobacteria. | the ζ subunit is a novel inhibitor of the f1fo-atpase of paracoccus denitrificans and related α-proteobacteria. it is different from the bacterial (ϵ) and mitochondrial (if1) inhibitors. the n terminus of ζ blocks rotation of the γ subunit of the f1-atpase of p. denitrificans (zarco-zavala, m., morales-ríos, e., mendoza-hernández, g., ramírez-silva, l., pérez-hernández, g., and garcía-trejo, j. j. (2014) faseb j. 24, 599-608) by a hitherto unknown quaternary structure that was first modeled here ... | 2015 | 26546676 |
| fold and flexibility: what can proteins' mechanical properties tell us about their folding nucleus? | the determination of a protein's folding nucleus, i.e. a set of native contacts playing an important role during its folding process, remains an elusive yet essential problem in biochemistry. in this work, we investigate the mechanical properties of 70 protein structures belonging to 14 protein families presenting various folds using coarse-grain brownian dynamics simulations. the resulting rigidity profiles combined with multiple sequence alignments show that a limited set of rigid residues, wh ... | 2015 | 26577596 |
| the characterization of novel tissue microbiota using an optimized 16s metagenomic sequencing pipeline. | substantial progress in high-throughput metagenomic sequencing methodologies has enabled the characterisation of bacteria from various origins (for example gut and skin). however, the recently-discovered bacterial microbiota present within animal internal tissues has remained unexplored due to technical difficulties associated with these challenging samples. | 2015 | 26544955 |
| metagenomic sequencing of marine periphyton: taxonomic and functional insights into biofilm communities. | periphyton communities are complex phototrophic, multispecies biofilms that develop on surfaces in aquatic environments. these communities harbor a large diversity of organisms comprising viruses, bacteria, algae, fungi, protozoans, and metazoans. however, thus far the total biodiversity of periphyton has not been described. in this study, we use metagenomics to characterize periphyton communities from the marine environment of the swedish west coast. although we found approximately ten times mo ... | 2015 | 26579098 |
| alteration of intracellular protein expressions as a key mechanism of the deterioration of bacterial denitrification caused by copper oxide nanoparticles. | the increasing production and utilization of copper oxide nanoparticles (cuo nps) result in the releases into the environment. however, the influence of cuo nps on bacterial denitrification, one of the most important pathways to transform nitrate to dinitrogen in environment, has seldom been studied. here we reported that cuo nps caused a significant alteration of key protein expressions of a model denitrifier, paracoccus denitrificans, leading to severe inhibition to denitrification. total nitr ... | 2015 | 26508362 |
| production of ergothioneine by methylobacterium species. | metabolomic analysis revealed that methylobacterium cells accumulate a large amount of ergothioneine (egt), which is a sulfur-containing, non-proteinogenic, antioxidative amino acid derived from histidine. egt biosynthesis and its role in methylotrophy and physiology for plant surface-symbiotic methylobacterium species were investigated in this study. almost all methylobacterium type strains can synthesize egt. we selected one of the most productive strains (m. aquaticum strain 22a isolated from ... | 2015 | 26579093 |
| heme binding by corynebacterium diphtheriae hmut: function and heme environment. | the heme uptake pathway (hmu) of corynebacterium diphtheriae utilizes multiple proteins to bind and transport heme into the cell. one of these proteins, hmut, delivers heme to the abc transporter hmuuv. in this study, the axial ligation of the heme in ferric hmut is probed by examination of wild-type (wt) hmut and a series of conserved heme pocket residue mutants, h136a, y235a, and m292a. characterization by uv-visible, resonance raman, and magnetic circular dichroism spectroscopies indicates th ... | 2015 | 26478504 |
| converting the bis-feiv state of the diheme enzyme maug to compound i decreases the reorganization energy for electron transfer. | the electron transfer (et) properties of two types of high-valent hemes were studied within the same protein matrix; the bis-fe(iv) state of maug and the compound i state of y294h maug. the latter is formed as a consequence of mutation of the tyrosine which forms the distal axial ligand of the six-coordinate heme that allows it to stabilize fe(iv) in the absence of an external ligand. the rates of the et reaction of each high-valent species with the type i copper protein, amicyanin, were determi ... | 2015 | 26494530 |
| converting the bis-feiv state of the diheme enzyme maug to compound i decreases the reorganization energy for electron transfer. | the electron transfer (et) properties of two types of high-valent hemes were studied within the same protein matrix; the bis-fe(iv) state of maug and the compound i state of y294h maug. the latter is formed as a consequence of mutation of the tyrosine which forms the distal axial ligand of the six-coordinate heme that allows it to stabilize fe(iv) in the absence of an external ligand. the rates of the et reaction of each high-valent species with the type i copper protein, amicyanin, were determi ... | 2015 | 26494530 |
| aztd, a periplasmic zinc metallochaperone to an atp-binding cassette (abc) transporter system in paracoccus denitrificans. | bacterial atp-binding cassette (abc) transporters of transition metals are essential for acquisition of necessary elements from the environment. a large number of gram-negative bacteria, including human pathogens, have a fourth conserved gene of unknown function adjacent to the canonical permease, atpase, and solute-binding protein (sbp) genes of the aztabc zinc transporter system. to assess the function of this putative accessory factor (aztd) from paracoccus denitrificans, we have analyzed its ... | 2015 | 26468286 |
| type iv secretion system of brucella spp. and its effectors. | brucella spp. are intracellular bacterial pathogens that cause infection in domestic and wild animals. they are often used as model organisms to study intracellular bacterial infections. brucella virb t4ss is a key virulence factor that plays important roles in mediating intracellular survival and manipulating host immune response to infection. in this review, we discuss the roles of brucella virb t4ss and 15 effectors that are proposed to be crucial for brucella pathogenesis. virb t4ss regulate ... | 2015 | 26528442 |
| structure of atp synthase from paracoccus denitrificans determined by x-ray crystallography at 4.0 å resolution. | the structure of the intact atp synthase from the α-proteobacterium paracoccus denitrificans, inhibited by its natural regulatory ζ-protein, has been solved by x-ray crystallography at 4.0 å resolution. the ζ-protein is bound via its n-terminal α-helix in a catalytic interface in the f1 domain. the bacterial f1 domain is attached to the membrane domain by peripheral and central stalks. the δ-subunit component of the peripheral stalk binds to the n-terminal regions of two α-subunits. the stalk ex ... | 2015 | 26460036 |
| binuclear cu(a) formation in biosynthetic models of cu(a) in azurin proceeds via a novel cu(cys)2his mononuclear copper intermediate. | cu(a) is a binuclear electron transfer (et) center found in cytochrome c oxidases (ccos), nitrous oxide reductases (n₂ors), and nitric oxide reductase (nor). in these proteins, the cu(a) centers facilitate efficient et (ket > 10⁴s⁻¹) under low thermodynamic driving forces (10-90 mv). while the structure and functional properties of cu(a) are well understood, a detailed mechanism of the incorporation of copper into the protein and the identity of the intermediates formed during the cu(a) maturati ... | 2015 | 26352296 |
| 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 ... | 2015 | 26500622 |
| purification, characterization and crystallization of the f-atpase from paracoccus denitrificans. | the structures of f-atpases have been determined predominantly with mitochondrial enzymes, but hitherto no f-atpase has been crystallized intact. a high-resolution model of the bovine enzyme built up from separate sub-structures determined by x-ray crystallography contains about 85% of the entire complex, but it lacks a crucial region that provides a transmembrane proton pathway involved in the generation of the rotary mechanism that drives the synthesis of atp. here the isolation, characterizat ... | 2015 | 26423580 |
| ph-driven shifts in overall and transcriptionally active denitrifiers control gaseous product stoichiometry in growth experiments with extracted bacteria from soil. | soil ph is a strong regulator for activity as well as for size and composition of denitrifier communities. low ph not only lowers overall denitrification rates but also influences denitrification kinetics and gaseous product stoichiometry. n2o reductase is particularly sensitive to low ph which seems to impair its activity post-transcriptionally, leading to higher net n2o production. little is known about how complex soil denitrifier communities respond to ph change and whether their ability to ... | 2015 | 26441895 |
| structure of a catalytic dimer of the α- and β-subunits of the f-atpase from paracoccus denitrificans at 2.3 å resolution. | the structures of f-atpases have predominantly been determined from mitochondrial enzymes, and those of the enzymes in eubacteria have been less studied. paracoccus denitrificans is a member of the α-proteobacteria and is related to the extinct protomitochondrion that became engulfed by the ancestor of eukaryotic cells. the p. denitrificans f-atpase is an example of a eubacterial f-atpase that can carry out atp synthesis only, whereas many others can catalyse both the synthesis and the hydrolysi ... | 2015 | 26457523 |
| active-site engineering of ω-transaminase for production of unnatural amino acids carrying a side chain bulkier than an ethyl substituent. | ω-transaminase (ω-ta) is a promising enzyme for use in the production of unnatural amino acids from keto acids using cheap amino donors such as isopropylamine. the small substrate-binding pocket of most ω-tas permits entry of substituents no larger than an ethyl group, which presents a significant challenge to the preparation of structurally diverse unnatural amino acids. here we report on the engineering of an (s)-selective ω-ta from ochrobactrum anthropi (oata) to reduce the steric constraint ... | 2015 | 26231640 |
| the identification of an integral membrane, cytochrome c urate oxidase completes the catalytic repertoire of a therapeutic enzyme. | in living organisms, the conversion of urate into allantoin requires three consecutive enzymes. the pathway was lost in hominid, predisposing humans to hyperuricemia and gout. among other species, the genomic distribution of the two last enzymes of the pathway is wider than that of urate oxidase (uox), suggesting the presence of unknown genes encoding uox. here we combine gene network analysis with association rule learning to identify the missing urate oxidase. in contrast with the known solubl ... | 2015 | 26349049 |
| fe biomineralization mirrors individual metabolic activity in a nitrate-dependent fe(ii)-oxidizer. | microbial biomineralization sometimes leads to periplasmic encrustation, which is predicted to enhance microorganism preservation in the fossil record. mineral precipitation within the periplasm is, however, thought to induce death, as a result of permeability loss preventing nutrient and waste transit across the cell wall. this hypothesis had, however, never been investigated down to the single cell level. here, we cultured the nitrate reducing fe(ii) oxidizing bacteria acidovorax sp. strain bo ... | 2015 | 26441847 |
| characterization of clinically identified mutations in ndufv1, the flavin-binding subunit of respiratory complex i, using a yeast model system. | dysfunctions in mitochondrial complex i (nadh:ubiquinone oxidoreductase) are both genetically and clinically highly diverse and a major cause of human mitochondrial diseases. the genetic determinants of individual clinical cases are increasingly being described, but how these genetic defects affect complex i on the molecular and cellular level, and have different clinical consequences in different individuals, is little understood. furthermore, without molecular-level information innocent geneti ... | 2015 | 26345448 |
| structural changes and proton transfer in cytochrome c oxidase. | in cytochrome c oxidase electron transfer from cytochrome c to o2 is linked to transmembrane proton pumping, which contributes to maintaining a proton electrochemical gradient across the membrane. the mechanism by which cytochrome c oxidase couples the exergonic electron transfer to the endergonic proton translocation is not known, but it presumably involves local structural changes that control the alternating proton access to the two sides of the membrane. such redox-induced structural changes ... | 2015 | 26310633 |
| genome-guided insight into the methylotrophy of paracoccus aminophilus jcm 7686. | paracoccus aminophilus jcm 7686 (alphaproteobacteria) is a facultative, heterotrophic methylotroph capable of utilizing a wide range of c1 compounds as sole carbon and energy sources. analysis of the jcm 7686 genome revealed the presence of genes involved in the oxidation of methanol, methylamine, dimethylamine, trimethylamine, n,n-dimethylformamide, and formamide, as well as the serine cycle, which appears to be the only c1 assimilatory pathway in this strain. many of these genes are located in ... | 2015 | 26347732 |
| isolation of aerobic cultivable cellulolytic bacteria from different regions of the gastrointestinal tract of giant land snail achatina fulica. | the enzymatic hydrolysis of cellulose by cellulases is one of the major limiting steps in the conversion of lignocellulosic biomass to yield bioethanol. to overcome this hindrance, significant efforts are underway to identify novel cellulases. the snail achatina fulica is a gastropod with high cellulolytic activity, mainly due to the abundance of glycoside hydrolases produced by both the animal and its resident microbiota. in this study, we partially assessed the cellulolytic aerobic bacterial d ... | 2015 | 26347735 |
| roles of multiple-proton transfer pathways and proton-coupled electron transfer in the reactivity of the bis-feiv state of maug. | the high-valent state of the diheme enzyme maug exhibits charge-resonance (cr) stabilization in which the major species is a bis-fe(iv) state with one heme present as fe(iv)=o and the other as fe(iv) with axial heme ligands provided by his and tyr side chains. in the absence of its substrate, the high-valent state is relatively stable and returns to the diferric state over several minutes. it is shown that this process occurs in two phases. the first phase is redistribution of the resonance spec ... | 2015 | 26283395 |
| a structural view of negative regulation of the toll-like receptor-mediated inflammatory pathway. | even though the toll-like receptor (tlr) pathway is integral to inflammatory defense mechanisms, its excessive signaling may be devastating. cells have acquired a cascade of strategies to regulate tlr signaling by targeting protein-protein interactions, or ubiquitin chains, but the details of the inhibition mechanisms are still unclear. here, we provide the structural basis for the regulation of tlr signaling by constructing architectures of protein-protein interactions. structural data suggest ... | 2015 | 26276688 |
| the organization of domains in proteins obeys menzerath-altmann's law of language. | the combination of domains in multidomain proteins enhances their function and structure but lengthens the molecules and increases their cost at cellular level. | 2015 | 26260760 |
| physiological and transcriptional responses of different industrial microbes at near-zero specific growth rates. | the current knowledge of the physiology and gene expression of industrially relevant microorganisms is largely based on laboratory studies under conditions of rapid growth and high metabolic activity. however, in natural ecosystems and industrial processes, microbes frequently encounter severe calorie restriction. as a consequence, microbial growth rates in such settings can be extremely slow and even approach zero. furthermore, uncoupling microbial growth from product formation, while cellular ... | 2015 | 26048933 |
| broken symmetry dft calculations/analysis for oxidized and reduced dinuclear center in cytochrome c oxidase: relating structures, protonation states, energies, and mössbauer properties in ba3 thermus thermophilus. | the fea3(3+)···cub(2+) dinuclear center (dnc) structure of the as-isolated oxidized ba3 cytochrome c oxidase (cco) from thermus thermophilus (tt) is still not fully understood. when the proteins are initially crystallized in the oxidized state, they typically become radiolyticly reduced through x-ray irradiation. several x-ray crystal structures of reduced ba3 cco from tt are available. however, depending on whether the crystals were prepared in a lipidic cubic phase environment or in detergent ... | 2015 | 26192749 |
| draft genomic sequence of a selenite-reducing bacterium, paenirhodobacter enshiensis dw2-9(t). | paenirhodobacter enshiensis is a non-photosynthetic species that belongs to family rhodobacteraceae. here we report the draft genome sequence of paenirhodobacter enshiensis dw2-9(t) and comparison results to the available related genomes. the strain has a 3.4 mbp genome sequence with g + c content of 66.82 % and 2781 protein-coding genes. it lacks photosynthetic gene clusters and putative proteins necessary in embden-meyerhof-parnas (emp) pathway, but contains proteins in entner-doudoroff (ed) p ... | 2015 | 26221419 |
| h2o2 production rate in lactobacillus johnsonii is modulated via the interplay of a heterodimeric flavin oxidoreductase with a soluble 28 kd pas domain containing protein. | host and commensals crosstalk, mediated by reactive oxygen species (ros), has triggered a growing scientific interest to understand the mechanisms governing such interaction. however, the majority of the scientific studies published do not evaluate the ros production by commensals bacteria. in this context we recently showed that lactobacillus johnsonii n6.2, a strain of probiotic value, modulates the activity of the critical enzymes 2,3-indoleamine dioxygenase via h2o2 production. l. johnsonii ... | 2015 | 26236298 |
| establishment of markerless gene deletion tools in thermophilic bacillus smithii and construction of multiple mutant strains. | microbial conversion of biomass to fuels or chemicals is an attractive alternative for fossil-based fuels and chemicals. thermophilic microorganisms have several operational advantages as a production host over mesophilic organisms, such as low cooling costs, reduced contamination risks and a process temperature matching that of commercial hydrolytic enzymes, enabling simultaneous saccharification and fermentation at higher efficiencies and with less enzymes. however, genetic tools for biotechno ... | 2015 | 26148486 |
| proteome-wide dataset generated by itraq-3dlcms/ms technique for studying the role of ferb protein in oxidative stress in paracoccus denitrificans. | 3dlc protein- and peptide-fractionation technique combined with itraq-peptide labeling and orbitrap mass spectrometry was employed to quantitate paracoccus dentirificans total proteome with maximal coverage. this resulted in identification of 24,948 peptides representing 2627 proteins (fdr<0.01) in p. dentirificans wild type and ferb mutant strains grown in the presence or absence of methyl viologen as an oxidative stressor. the data were generated for assessment of ferb protein role in oxidativ ... | 2015 | 26306309 |
| helicobacter pylori hp0377, a member of the dsb family, is an untypical multifunctional ccmg that cooperates with dimeric thioldisulfide oxidase hp0231. | in the genome of h. pylori 26695, 149 proteins containing the cxxc motif characteristic of thioldisulfide oxidoreductases have been identified to date. however, only two of these proteins have a thioredoxin-like fold (i.e., hp0377 and hp0231) and are periplasm-located. we have previously shown that hp0231 is a dimeric oxidoreductase that catalyzes disulfide bond formation in the periplasm. although hp0377 was originally described as dsbc homologue, its resolved structure and location of the hp03 ... | 2015 | 26141380 |
| protonation state of the cu4s2 cuz site in nitrous oxide reductase: redox dependence and insight into reactivity. | spectroscopic and computational methods have been used to determine the protonation state of the edge sulfur ligand in the cu4s2 cuz form of the active site of nitrous oxide reductase (n2or) in its 3cu(i)cu(ii) (1-hole) and 2cu(i)2cu(ii) (2-hole) redox states. the epr, absorption, and mcd spectra of 1-hole cuz indicate that the unpaired spin in this site is evenly delocalized over cui, cuii, and cuiv. 1-hole cuz is shown to have a μ2-thiolate edge ligand from the observation of s-h bending modes ... | 2015 | 26417423 |
| checkm: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. | large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. although this increasing breadth of draft genomes is providing key information regarding the evolutionary and functional diversity of microbial life, it has become impractical to finish all available reference genomes. making robust biological inferences from draft genomes requires accurate estimates of their ... | 2015 | 25977477 |
| characterization of the free energy dependence of an interprotein electron transfer reaction by variation of ph and site-directed mutagenesis. | the interprotein electron transfer (et) reactions of the cupredoxin amicyanin, which mediates et from the tryptophan tryptophylquinone (ttq) cofactor of methylamine dehydrogenase to cytochrome c-551i have been extensively studied. however, it was not possible to perform certain key experiments in that native system. this study examines the et reaction from reduced amicyanin to an alternative electron acceptor, the diheme protein maug. it was possible to vary the δg° for this et reaction by simpl ... | 2015 | 26087387 |
| cytochrome cbb3 of thioalkalivibrio is a na+-pumping cytochrome oxidase. | cytochrome c oxidases (coxs) are the basic energy transducers in the respiratory chain of the majority of aerobic organisms. coxs studied to date are redox-driven proton-pumping enzymes belonging to one of three subfamilies: a-, b-, and c-type oxidases. the c-type oxidases (cbb3 cytochromes), which are widespread among pathogenic bacteria, are the least understood. in particular, the proton-pumping machinery of these coxs has not yet been elucidated despite the availability of x-ray structure in ... | 2015 | 26056262 |
| metabolism at evolutionary optimal states. | metabolism is generally required for cellular maintenance and for the generation of offspring under conditions that support growth. the rates, yields (efficiencies), adaptation time and robustness of metabolism are therefore key determinants of cellular fitness. for biotechnological applications and our understanding of the evolution of metabolism, it is necessary to figure out how the functional system properties of metabolism can be optimized, via adjustments of the kinetics and expression of ... | 2015 | 26042723 |
| anoxic growth of ensifer meliloti 1021 by n2o-reduction, a potential mitigation strategy. | denitrification in agricultural soils is a major source of n2o. legume crops enhance n2o emission by providing n-rich residues, thereby stimulating denitrification, both by free-living denitrifying bacteria and by the symbiont (rhizobium) within the nodules. however, there are limited data concerning n2o production and consumption by endosymbiotic bacteria associated with legume crops. it has been reported that the alfalfa endosymbiont ensifer meliloti strain 1021, despite possessing and express ... | 2015 | 26074913 |
| the crystal structure of nitrosomonas europaea sucrose synthase reveals critical conformational changes and insights into sucrose metabolism in prokaryotes. | in this paper we report the first crystal structure of a prokaryotic sucrose synthase from the nonphotosynthetic bacterium nitrosomonas europaea. the obtained structure was in an open form, whereas the only other available structure, from the plant arabidopsis thaliana, was in a closed conformation. comparative structural analysis revealed a "hinge-latch" combination, which is critical to transition between the open and closed forms of the enzyme. the n. europaea sucrose synthase shares the same ... | 2015 | 26013491 |
| during cytochrome c maturation ccmi chaperones the class i apocytochromes until the formation of their b-type cytochrome intermediates. | the c-type cytochromes are electron transfer proteins involved in energy transduction. they have heme-binding (cxxch) sites that covalently ligate heme b via thioether bonds and are classified into different classes based on their protein folds and the locations and properties of their cofactors. rhodobacter capsulatus produces various c-type cytochromes using the cytochrome c maturation (ccm) system i, formed from the ccmabcdefghi proteins. ccmi, a component of the heme ligation complex ccmfhi, ... | 2015 | 25979338 |
| tcpc as a prospective new virulence marker in blood escherichia coli isolates from sepsis patients admitted to the intensive care unit. | the prevalence of the tcpc in the blood escherichia coli isolates collected from the sepsis patients admitted to the intensive care unit was investigated for the first time. the blood and faecal samples were collected from sepsis and nonsepsis patients, respectively. the prevalence of the tcpc and phylogroups was confirmed by gene-specific pcr. the occurrence of the tcpc in the blood e. coli isolates from sepsis patients was significantly higher than the faecal isolates. the higher prevalence of ... | 2015 | 26137310 |
| a t67a mutation in the proximal pocket of the high-spin heme of maug stabilizes formation of a mixed-valent feii/feiii state and enhances charge resonance stabilization of the bis-feiv state. | the diheme enzyme maug catalyzes a six-electron oxidation required for posttranslational modification of a precursor of methylamine dehydrogenase (premadh) to complete the biosynthesis of its protein-derived tryptophan tryptophylquinone (ttq) cofactor. one heme is low-spin with ligands provided by his205 and tyr294, and the other is high-spin with a ligand provided by his35. the side chain methyl groups of thr67 and leu70 are positioned at a distance of 3.4å on either side of his35, maintaining ... | 2015 | 25896561 |
| production of polyhydroxybutyrate and alginate from glycerol by azotobacter vinelandii under nitrogen-free conditions. | glycerol is an interesting feedstock for biomaterials such as biofuels and bioplastics because of its abundance as a by-product during biodiesel production. here we demonstrate glycerol metabolism in the nitrogen-fixing species azotobacter vinelandii through metabolomics and nitrogen-free bacterial production of biopolymers, such as poly-d-3-hydroxybutyrate (phb) and alginate, from glycerol. glycerol-3-phosphate was accumulated in a. vinelandii cells grown on glycerol to the exponential phase, a ... | 2015 | 25880041 |
| parallel and divergent evolutionary solutions for the optimization of an engineered central metabolism in methylobacterium extorquens am1. | bioengineering holds great promise to provide fast and efficient biocatalysts for methanol-based biotechnology, but necessitates proven methods to optimize physiology in engineered strains. here, we highlight experimental evolution as an effective means for optimizing an engineered methylobacterium extorquens am1. replacement of the native formaldehyde oxidation pathway with a functional analog substantially decreased growth in an engineered methylobacterium, but growth rapidly recovered after s ... | 2015 | 27682084 |
| mosaic nature of the mitochondrial proteome: implications for the origin and evolution of mitochondria. | comparative studies of the mitochondrial proteome have identified a conserved core of proteins descended from the α-proteobacterial endosymbiont that gave rise to the mitochondrion and was the source of the mitochondrial genome in contemporary eukaryotes. a surprising result of phylogenetic analyses is the relatively small proportion (10-20%) of the mitochondrial proteome displaying a clear α-proteobacterial ancestry. a large fraction of mitochondrial proteins typically has detectable homologs o ... | 2015 | 25848019 |
| arsh is an organoarsenical oxidase that confers resistance to trivalent forms of the herbicide monosodium methylarsenate and the poultry growth promoter roxarsone. | environmental organoarsenicals are produced by microorganisms and are introduced anthropogenically as herbicides and antimicrobial growth promoters for poultry and swine. nearly every prokaryote has an ars (arsenic resistance) operon, and some have an arsh gene encoding an atypical flavodoxin. the role of arsh in arsenic resistance has been unclear. here we demonstrate that arsh is an organoarsenical oxidase that detoxifies trivalent methylated and aromatic arsenicals by oxidation to pentavalent ... | 2015 | 25732202 |
| non-pneumatic anti-shock garment for improving maternal survival following severe postpartum haemorrhage: a systematic review. | women with postpartum haemorrhage (pph) in developing countries often present in critical condition when treatment might be insufficient to save lives. few studies have shown that application of non-pneumatic anti-shock garment (nasg) could improve maternal survival. | 2015 | 25889868 |
| bending of protonema cells in a plastid glycolate/glycerate transporter knockout line of physcomitrella patens. | arabidopsis lrgb (synonym plgg1) is a plastid glycolate/glycerate transporter associated with recycling of 2-phosphoglycolate generated via the oxygenase activity of ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco). we isolated two homologous genes (pplrgb1 and b2) from the moss physcomitrella patens. phylogenetic tree analysis showed that pplrgb1 was monophyletic with lrgb proteins of land plants, whereas pplrgb2 was divergent from the green plant lineage. experiments with pplrgb-gfp f ... | 2015 | 25793376 |
| transcriptional regulation, metal binding properties and structure of pden1597, an unusual zinc transport protein from paracoccus denitrificans. | atp-binding cassette (abc) transporters of the cluster 9 family are ubiquitous among bacteria and essential for acquiring zn(2+) and mn(2+) from the environment or, in the case of pathogens, from the host. these rely on a substrate-binding protein (sbp) to coordinate the relevant metal with high affinity and specificity and subsequently release it to a membrane permease for translocation into the cytoplasm. although a number of cluster 9 sbp structures have been determined, the structural attrib ... | 2015 | 25787075 |
| ralstonia solanacearum uses inorganic nitrogen metabolism for virulence, atp production, and detoxification in the oxygen-limited host xylem environment. | genomic data predict that, in addition to oxygen, the bacterial plant pathogen ralstonia solanacearum can use nitrate (no3(-)), nitrite (no2(-)), nitric oxide (no), and nitrous oxide (n2o) as terminal electron acceptors (teas). genes encoding inorganic nitrogen reduction were highly expressed during tomato bacterial wilt disease, when the pathogen grows in xylem vessels. direct measurements found that tomato xylem fluid was low in oxygen, especially in plants infected by r. solanacearum. xylem f ... | 2015 | 25784703 |
| the radical s-adenosyl-l-methionine enzyme qhpd catalyzes sequential formation of intra-protein sulfur-to-methylene carbon thioether bonds. | the bacterial enzyme designated qhpd belongs to the radical s-adenosyl-l-methionine (sam) superfamily of enzymes and participates in the post-translational processing of quinohemoprotein amine dehydrogenase. qhpd is essential for the formation of intra-protein thioether bonds within the small subunit (maturated qhpc) of quinohemoprotein amine dehydrogenase. we overproduced qhpd from paracoccus denitrificans as a stable complex with its substrate qhpc, carrying the 28-residue leader peptide that ... | 2015 | 25778402 |
| a cluster of four homologous small rnas modulates c1 metabolism and the pyruvate dehydrogenase complex in rhodobacter sphaeroides under various stress conditions. | in bacteria, regulatory rnas play an important role in the regulation and balancing of many cellular processes and stress responses. among these regulatory rnas, trans-encoded small rnas (srnas) are of particular interest since one srna can lead to the regulation of multiple target mrnas. in the purple bacterium rhodobacter sphaeroides, several srnas are induced by oxidative stress. in this study, we focused on the functional characterization of four homologous srnas that are cotranscribed with ... | 2015 | 25777678 |
| node: a fast error-correction algorithm for pyrosequencing amplicon reads. | the popularity of new sequencing technologies has led to an explosion of possible applications, including new approaches in biodiversity studies. however each of these sequencing technologies suffers from sequencing errors originating from different factors. for 16s rrna metagenomics studies, the 454 pyrosequencing technology is one of the most frequently used platforms, but sequencing errors still lead to important data analysis issues (e.g. in clustering in taxonomic units and biodiversity est ... | 2015 | 25888405 |
| reassessment of the transhydrogenase/malate shunt pathway in clostridium thermocellum atcc 27405 through kinetic characterization of malic enzyme and malate dehydrogenase. | clostridium thermocellum produces ethanol as one of its major end products from direct fermentation of cellulosic biomass. therefore, it is viewed as an attractive model for the production of biofuels via consolidated bioprocessing. however, a better understanding of the metabolic pathways, along with their putative regulation, could lead to improved strategies for increasing the production of ethanol. in the absence of an annotated pyruvate kinase in the genome, alternate means of generating py ... | 2015 | 25616802 |
| mutation of a single residue in the ba3 oxidase specifically impairs protonation of the pump site. | the ba3-type cytochrome c oxidase from thermus thermophilus is a membrane-bound protein complex that couples electron transfer to o2 to proton translocation across the membrane. to elucidate the mechanism of the redox-driven proton pumping, we investigated the kinetics of electron and proton transfer in a structural variant of the ba3 oxidase where a putative "pump site" was modified by replacement of asp372 by ile. in this structural variant, proton pumping was uncoupled from internal electron ... | 2015 | 25733886 |
| inhibition of the growth of bacillus subtilis dsm10 by a newly discovered antibacterial protein from the soil metagenome. | a functional metagenomics based approach exploiting the microbiota of suppressive soils from an organic field site has succeeded in the identification of a clone with the ability to inhibit the growth of bacillus subtilis dsm10. sequencing of the fosmid identified a putative β-lactamase-like gene abgt. transposon mutagenesis of the abgt gene resulted in a loss in ability to inhibit the growth of b. subtilis dsm10. further analysis of the deduced amino acid sequence of abgt revealed moderate homo ... | 2015 | 25692994 |
| evaluation of simultaneous nutrient and cod removal with polyhydroxybutyrate (phb) accumulation using mixed microbial consortia under anoxic condition and their bioinformatics analysis. | simultaneous nitrate-n, phosphate and cod removal was evaluated from synthetic waste water using mixed microbial consortia in an anoxic environment under various initial carbon load (icl) in a batch scale reactor system. within 6 hours of incubation, enriched dnpaos (denitrifying polyphosphate accumulating microorganisms) were able to remove maximum cod (87%) at 2 g/l of icl whereas maximum nitrate-n (97%) and phosphate (87%) removal along with phb accumulation (49 mg/l) was achieved at 8 g/l of ... | 2015 | 25689047 |
| syntrophic growth via quinone-mediated interspecies electron transfer. | the mechanisms by which microbial species exchange electrons are of interest because interspecies electron transfer can expand the metabolic capabilities of microbial communities. previous studies with the humic substance analog anthraquinone-2,6-disulfonate (aqds) suggested that quinone-mediated interspecies electron transfer (quiet) is feasible, but it was not determined if sufficient energy is available from quiet to support the growth of both species. furthermore, there have been no previous ... | 2015 | 25741332 |
| iron corrosion induced by nonhydrogenotrophic nitrate-reducing prolixibacter sp. strain mic1-1. | microbiologically influenced corrosion (mic) of metallic materials imposes a heavy economic burden. the mechanism of mic of metallic iron (fe(0)) under anaerobic conditions is usually explained as the consumption of cathodic hydrogen by hydrogenotrophic microorganisms that accelerates anodic fe(0) oxidation. in this study, we describe fe(0) corrosion induced by a nonhydrogenotrophic nitrate-reducing bacterium called mic1-1, which was isolated from a crude-oil sample collected at an oil well in a ... | 2015 | 25548048 |
| phospholipid fatty acids as physiological indicators of paracoccus denitrificans encapsulated in silica sol-gel hydrogels. | the phospholipid fatty acid (plfa) content was determined in samples of paracoccus denitrificans encapsulated in silica hydrogel films prepared from prepolymerized tetramethoxysilane (tmos). immediately after encapsulation the total plfa concentration was linearly proportional to the optical density (600 nm) of the input microbial suspension (r2 = 0.99). after 7 days this relationship remained linear, but with significantly decreased slope, indicating a higher extinction of bacteria in suspensio ... | 2015 | 25690547 |
| atmospheric hydrogen scavenging: from enzymes to ecosystems. | we have known for 40 years that soils can consume the trace amounts of molecular hydrogen (h2) found in the earth’s atmosphere.this process is predicted to be the most significant term in the global hydrogen cycle. however, the organisms and enzymes responsible for this process were only recently identified. pure culture experiments demonstrated that several species of actinobacteria, including streptomycetes and mycobacteria, can couple the oxidation of atmospheric h2 to the reduction of ambien ... | 2015 | 25501483 |
| association between chloroplast and mitochondrial dna sequences in chinese prunus genotypes (prunus persica, prunus domestica, and prunus avium). | the nuclear dna is conventionally used to assess the diversity and relatedness among different species, but variations at the dna genome level has also been used to study the relationship among different organisms. in most species, mitochondrial and chloroplast genomes are inherited maternally; therefore it is anticipated that organelle dna remains completely associated. many research studies were conducted simultaneously on organelle genome. the objectives of this study was to analyze the genet ... | 2015 | 25592231 |
| use of the amicyanin signal sequence for efficient periplasmic expression in e. coli of a human antibody light chain variable domain. | periplasmic localization of recombinant proteins offers advantages over cytoplasmic protein expression. in this study signal sequence of amicyanin, which is encoded by the mauc gene of paracoccus denitrificans, was used to express the light chain variable domain of the human κio8/o18 germline antibody in the periplasm of escherichiacoli. the expressed protein was purified in good yield (70mg/l of culture) in one step from the periplasmic fraction by affinity chromatography using an engineered he ... | 2015 | 25573388 |
| microscopic basis for kinetic gating in cytochrome c oxidase: insights from qm/mm analysis. | understanding the mechanism of vectorial proton pumping in biomolecules requires establishing the microscopic basis for the regulation of both thermodynamic and kinetic features of the relevant proton transfer steps. for the proton pump cytochrome c oxidase, while the regulation of thermodynamic driving force for key proton transfers has been discussed in great detail, the microscopic basis for the control of proton transfer kinetics has been poorly understood. here we carry out extensive qm/mm ... | 2015 | 25678950 |
| electronic connection between the quinone and cytochrome c redox pools and its role in regulation of mitochondrial electron transport and redox signaling. | mitochondrial respiration, an important bioenergetic process, relies on operation of four membranous enzymatic complexes linked functionally by mobile, freely diffusible elements: quinone molecules in the membrane and water-soluble cytochromes c in the intermembrane space. one of the mitochondrial complexes, complex iii (cytochrome bc1 or ubiquinol:cytochrome c oxidoreductase), provides an electronic connection between these two diffusible redox pools linking in a fully reversible manner two-ele ... | 2015 | 25540143 |
| cryo-em structures of the autoinhibited e. coli atp synthase in three rotational states. | a molecular model that provides a framework for interpreting the wealth of functional information obtained on the e. coli f-atp synthase has been generated using cryo-electron microscopy. three different states that relate to rotation of the enzyme were observed, with the central stalk's ε subunit in an extended autoinhibitory conformation in all three states. the fo motor comprises of seven transmembrane helices and a decameric c-ring and invaginations on either side of the membrane indicate th ... | 2016 | 28001127 |