| aerobic vanillate degradation and c1 compound metabolism in bradyrhizobium japonicum. | bradyrhizobium japonicum, a symbiotic nitrogen-fixing soil bacterium, has multiple gene copies for aromatic degradation on the genome and is able to use low concentrations of vanillate, a methoxylated lignin monomer, as an energy source. a transcriptome analysis indicated that one set of vana1b, pcag1h1, and genes for c(1) compound catabolism was upregulated in b. japonicum usda110 cells grown in vanillate (n. ito, m. itakura, s. eda, k. saeki, h. oomori, t. yokoyama, t. kaneko, s. tabata, t. oh ... | 2009 | 19502448 |
| asymmetric, bimodal trade-offs during adaptation of methylobacterium to distinct growth substrates. | trade-offs between selected and nonselected environments are often assumed to exist during adaptation. this phenomenon is prevalent in microbial metabolism, where many organisms have come to specialize on a narrow breadth of substrates. one well-studied example is methylotrophic bacteria that can use single-carbon (c(1)) compounds as their sole source of carbon and energy, but generally use few, if any, multi-c compounds. here, we use adaptation of experimental populations of the model methylotr ... | 2009 | 19545267 |
| the phyr-sigma(ecfg) signalling cascade is involved in stress response and symbiotic efficiency in bradyrhizobium japonicum. | phyr is an unusual type of response regulator consisting of a receiver domain and an extracytoplasmic function (ecf) sigma factor-like domain. it was recently described as a master regulator of general stress response in methylobacterium extorquens. orthologues of this regulator are present in essentially all free-living alphaproteobacteria. in most of them, phyr is genetically closely linked to a gene encoding an ecf sigma factor. here, we investigate the role of these two regulators in the soy ... | 2009 | 19555458 |
| (2s)-methylsuccinyl-coa dehydrogenase closes the ethylmalonyl-coa pathway for acetyl-coa assimilation. | many organic substrates are metabolized via acetyl-coenzyme a (coa) and enter central carbon metabolism at the level of this compound. we recently described the outlines of the ethylmalonyl-coa pathway, a new acetyl-coa assimilation strategy that operates in a number of bacteria such as rhodobacter sphaeroides, methylobacterium extorquens and streptomycetes and replaces the glyoxylate cycle. this new pathway involves a unique central reaction sequence catalysed by characteristic enzymes. here, w ... | 2009 | 19703103 |
| mutations that disrupt either the pqq or the gdh gene of rahnella aquatilis abolish the production of an antibacterial substance and result in reduced biological control of grapevine crown gall. | rahnella aquatilis hx2, a biocontrol agent for grapevine crown gall caused by agrobacterium vitis, produces an antibacterial substance that inhibits the growth of a. vitis in vitro. in this study, we show that mh15 and mh16, two tn5-induced mutants of hx2, have lost their abilities to inhibit a. vitis and have reduced biocontrol activities; they grow in logarithmic phase at a rate similar to that of the wild type and have single tn5 insertions. they are also impaired in producing pyrroloquinolin ... | 2009 | 19734331 |
| identification and characterization of new luxr/luxi-type quorum sensing systems from metagenomic libraries. | quorum sensing (qs) cell-cell communication systems are utilized by bacteria to coordinate their behaviour according to cell density. several different types of qs signal molecules have been identified, among which acyl-homoserine lactones (ahls) produced by proteobacteria have been studied to the greatest extent. although qs has been studied extensively in cultured microorganisms, little is known about the qs systems of uncultured microorganisms and the roles of these systems in microbial commu ... | 2010 | 19735279 |
| identification and characterization of new luxr/luxi-type quorum sensing systems from metagenomic libraries. | quorum sensing (qs) cell-cell communication systems are utilized by bacteria to coordinate their behaviour according to cell density. several different types of qs signal molecules have been identified, among which acyl-homoserine lactones (ahls) produced by proteobacteria have been studied to the greatest extent. although qs has been studied extensively in cultured microorganisms, little is known about the qs systems of uncultured microorganisms and the roles of these systems in microbial commu ... | 2010 | 19735279 |
| pyrroloquinoline quinone biogenesis: demonstration that pqqe from klebsiella pneumoniae is a radical s-adenosyl-l-methionine enzyme. | biogenesis of pyrroloquinoline quinone (pqq) in klebsiella pneumoniae requires the expression of six genes (pqqa-f). one of these genes (pqqe) encodes a 43 kda protein (pqqe) that plays a role in the initial steps in pqq formation [veletrop, j. s., et al. (1995) j. bacteriol. 177, 5088-5098]. pqqe contains two highly conserved cysteine motifs at the n- and c-termini, with the n-terminal motif comprised of a cx(3)cx(2)c consensus sequence that is unique to a family of proteins known as radical s- ... | 2009 | 19746930 |
| fast growth increases the selective advantage of a mutation arising recurrently during evolution under metal limitation. | understanding the evolution of biological systems requires untangling the molecular mechanisms that connect genetic and environmental variations to their physiological consequences. metal limitation across many environments, ranging from pathogens in the human body to phytoplankton in the oceans, imposes strong selection for improved metal acquisition systems. in this study, we uncovered the genetic and physiological basis of adaptation to metal limitation using experimental populations of methy ... | 2009 | 19763169 |
| small rna-dependent expression of secondary metabolism is controlled by krebs cycle function in pseudomonas fluorescens. | pseudomonas fluorescens cha0, an antagonist of phytopathogenic fungi in the rhizosphere of crop plants, elaborates and excretes several secondary metabolites with antibiotic properties. their synthesis depends on three small rnas (rsmx, rsmy, and rsmz), whose expression is positively controlled by the gacs-gaca two-component system at high cell population densities. to find regulatory links between primary and secondary metabolism in p. fluorescens and in the related species pseudomonas aerugino ... | 2009 | 19840935 |
| pantothenate kinase from the thermoacidophilic archaeon picrophilus torridus. | pantothenate kinase (coaa) catalyzes the first step of the coenzyme a (coa) biosynthetic pathway and controls the intracellular concentrations of coa through feedback inhibition in bacteria. an alternative enzyme found in archaea, pantoate kinase, is missing in the order thermoplasmatales. the pto0232 gene from picrophilus torridus, a thermoacidophilic euryarchaeon, is shown to be a distant homologue of the prokaryotic type i coaa. the cloned gene clearly complements the poor growth of the tempe ... | 2010 | 19854913 |
| pantothenate kinase from the thermoacidophilic archaeon picrophilus torridus. | pantothenate kinase (coaa) catalyzes the first step of the coenzyme a (coa) biosynthetic pathway and controls the intracellular concentrations of coa through feedback inhibition in bacteria. an alternative enzyme found in archaea, pantoate kinase, is missing in the order thermoplasmatales. the pto0232 gene from picrophilus torridus, a thermoacidophilic euryarchaeon, is shown to be a distant homologue of the prokaryotic type i coaa. the cloned gene clearly complements the poor growth of the tempe ... | 2010 | 19854913 |
| icmf is a fusion between the radical b12 enzyme isobutyryl-coa mutase and its g-protein chaperone. | coenzyme b(12) is used by two highly similar radical enzymes, which catalyze carbon skeleton rearrangements, methylmalonyl-coa mutase and isobutyryl-coa mutase (icm). icm catalyzes the reversible interconversion of isobutyryl-coa and n-butyryl-coa and exists as a heterotetramer. in this study, we have identified >70 bacterial proteins, which represent fusions between the subunits of icm and a p-loop gtpase and are currently misannotated as methylmalonyl-coa mutases. we designate this fusion prot ... | 2010 | 19864421 |
| metabolite profiling uncovers plasmid-induced cobalt limitation under methylotrophic growth conditions. | the introduction and maintenance of plasmids in cells is often associated with a reduction of growth rate. the reason for this growth reduction is unclear in many cases. | 2009 | 19915676 |
| molecular and biochemical characterization of urease and survival of yersinia enterocolitica biovar 1a in acidic ph in vitro. | yersinia enterocolitica, an important food- and water-borne enteric pathogen is represented by six biovars viz. 1a, 1b, 2, 3, 4 and 5. despite the lack of recognized virulence determinants, some biovar 1a strains have been reported to produce disease symptoms resembling that produced by known pathogenic biovars (1b, 2-5). it is therefore imperative to identify determinants that might contribute to the pathogenicity of y. enterocolitica biovar 1a strains. y. enterocolitica invariably produces ure ... | 2009 | 20017936 |
| the apparent malate synthase activity of rhodobacter sphaeroides is due to two paralogous enzymes, (3s)-malyl-coenzyme a (coa)/{beta}-methylmalyl-coa lyase and (3s)- malyl-coa thioesterase. | assimilation of acetyl coenzyme a (acetyl-coa) is an essential process in many bacteria that proceeds via the glyoxylate cycle or the ethylmalonyl-coa pathway. in both assimilation strategies, one of the final products is malate that is formed by the condensation of acetyl-coa with glyoxylate. in the glyoxylate cycle this reaction is catalyzed by malate synthase, whereas in the ethylmalonyl-coa pathway the reaction is separated into two proteins: malyl-coa lyase, a well-known enzyme catalyzing t ... | 2010 | 20047909 |
| modified 3-oxoadipate pathway for the biodegradation of methylaromatics in pseudomonas reinekei mt1. | catechols are central intermediates in the metabolism of aromatic compounds. degradation of 4-methylcatechol via intradiol cleavage usually leads to the formation of 4-methylmuconolactone (4-ml) as a dead-end metabolite. only a few microorganisms are known to mineralize 4-ml. the mml gene cluster of pseudomonas reinekei mt1, which encodes enzymes involved in the metabolism of 4-ml, is shown here to encode 10 genes found in a 9.4-kb chromosomal region. reverse transcription assays revealed that t ... | 2010 | 20061479 |
| an automated system for rapid non-destructive enumeration of growing microbes. | the power and simplicity of visual colony counting have made it the mainstay of microbiological analysis for more than 130 years. a disadvantage of the method is the long time required to generate visible colonies from cells in a sample. new rapid testing technologies generally have failed to maintain one or more of the major advantages of culture-based methods. | 2010 | 20062794 |
| effects of aeration on the synthesis of poly(3-hydroxybutyrate) from glycerol and glucose in recombinant escherichia coli. | bioreactor cultures of escherichia coli recombinants carrying phabac and phap of azotobacter sp. fa8 grown on glycerol under low-agitation conditions accumulated more poly(3-hydroxybutyrate) (phb) and ethanol than at high agitation, while in glucose cultures, low agitation led to a decrease in phb formation. cells produced smaller amounts of acids from glycerol than from glucose. glycerol batch cultures stirred at 125 rpm accumulated, in 24 h, 30.1% (wt/wt) phb with a relative molecular mass of ... | 2010 | 20080998 |
| alternative route for glyoxylate consumption during growth on two-carbon compounds by methylobacterium extorquens am1. | methylobacterium extorquens am1 is a facultative methylotroph capable of growth on both single-carbon and multicarbon compounds. mutants defective in a pathway involved in converting acetyl-coenzyme a (coa) to glyoxylate (the ethylmalonyl-coa pathway) are unable to grow on both c(1) and c(2) compounds, showing that both modes of growth have this pathway in common. however, growth on c(2) compounds via the ethylmalonyl-coa pathway should require glyoxylate consumption via malate synthase, but a m ... | 2010 | 20118267 |
| dual control of sinorhizobium meliloti rpoe2 sigma factor activity by two phyr-type two-component response regulators. | rpoe2 is an extracytoplasmic function (ecf) sigma factor involved in the general stress response of sinorhizobium meliloti, the nitrogen-fixing symbiont of the legume plant alfalfa. rpoe2 orthologues are widely found among alphaproteobacteria, where they play various roles in stress resistance and/or host colonization. in this paper, we report a genetic and biochemical investigation of the mechanisms of signal transduction leading to s. meliloti rpoe2 activation in response to stress. we showed ... | 2010 | 20154128 |
| evolution and multifarious horizontal transfer of an alternative biosynthetic pathway for the alternative polyamine sym-homospermidine. | polyamines are small flexible organic polycations found in almost all cells. they likely existed in the last universal common ancestor of all extant life, and yet relatively little is understood about their biological function, especially in bacteria and archaea. unlike eukaryotes, where the predominant polyamine is spermidine, bacteria may contain instead an alternative polyamine, sym-homospermidine. we demonstrate that homospermidine synthase (hss) has evolved vertically, primarily in the alph ... | 2010 | 20194510 |
| a metaproteomic analysis of the human salivary microbiota by three-dimensional peptide fractionation and tandem mass spectrometry. | metagenomics uses gene expression patterns to understand the taxonomy and metabolic activities of microbial communities. metaproteomics applies the same approach to community proteomes. previously, we used a novel three-dimensional peptide separation method to identify over 2000 salivary proteins. this study used those data to carry out the first metaproteomic analysis of the human salivary microbiota. the metagenomic software megan generated a phylogenetic tree, which was checked against the hu ... | 2010 | 20331792 |
| organising metabolic networks: cycles in flux distributions. | metabolic networks are among the most widely studied biological systems. the topology and interconnections of metabolic reactions have been well described for many species. this is, however, not sufficient to understand how their activity is regulated in living organisms. these descriptions depict a static set of possible chains of reactions, with no information about the dynamic activity of reaction fluxes. cyclic structures are thought to play a central role in the homeostasis of biological sy ... | 2010 | 20435049 |
| functional investigation of methanol dehydrogenase-like protein xoxf in methylobacterium extorquens am1. | methanol dehydrogenase-like protein xoxf of methylobacterium extorquens am1 exhibits a sequence identity of 50 % to the catalytic subunit mxaf of periplasmic methanol dehydrogenase in the same organism. the latter has been characterized in detail, identified as a pyrroloquinoline quinone (pqq)-dependent protein, and shown to be essential for growth in the presence of methanol in this methylotrophic model bacterium. in contrast, the function of xoxf in m. extorquens am1 has not yet been elucidate ... | 2010 | 20447995 |
| [distribution of bacteria of methylobacterium genus in the terrestrial biotopes of the antarctic region]. | methylotrophs distribution has been studied in the terrestrial biotopes (moss, lichen, grass, soil, sludge of lakes) on the islands of galindez, barkhans, irizar, uruguay, jalour, petermann, berthelot, cruls, king george, corner, skua located in the pacific sector of the antarctic region, as well as in analogous biotopes on the western shore of the antarctic peninsula basing on a complex of diagnosis features the isolated pink-pigmented strains, which facultatively use methanol and realize the s ... | 2009 | 20455426 |
| {gamma}-glutamylmethylamide is an essential intermediate in the metabolism of methylamine by methylocella silvestris. | methylocella silvestris bl2, a facultative methane utilizer, can grow on monomethylamine (mma) as a sole carbon and nitrogen source. no activity of mma dehydrogenase was detectable. instead, this bacterium utilizes a methylated amino acid pathway (gamma-glutamylmethylamide [gma] and n-methylglutamate [nmg]) for mma metabolism. the activities of the two key enzymes in this pathway, gma synthetase and nmg dehydrogenase, were found when the bacterium was grown on mma. gma was detected by high-perfo ... | 2010 | 20472738 |
| the 1.4 a resolution structure of paracoccus pantotrophus pseudoazurin. | pseudoazurins are small type 1 copper proteins that are involved in the flow of electrons between various electron donors and acceptors in the bacterial periplasm, mostly under denitrifying conditions. the previously determined structure of paracoccus pantotrophus pseudoazurin in the oxidized form was improved to a nominal resolution of 1.4 a, with r and r(free) values of 0.188 and 0.206, respectively. this high-resolution structure makes it possible to analyze the interactions between the monom ... | 2010 | 20516588 |
| identification of the citrate-binding site of human atp-citrate lyase using x-ray crystallography. | atp-citrate lyase (acly) catalyzes the conversion of citrate and coa into acetyl-coa and oxaloacetate, coupled with the hydrolysis of atp. in humans, acly is the cytoplasmic enzyme linking energy metabolism from carbohydrates to the production of fatty acids. in situ proteolysis of full-length human acly gave crystals of a truncated form, revealing the conformations of residues 2-425, 487-750, and 767-820 of the 1101-amino acid protein. residues 2-425 form three domains homologous to the beta-su ... | 2010 | 20558738 |
| osmotically induced synthesis of the dipeptide n-acetylglutaminylglutamine amide is mediated by a new pathway conserved among bacteria. | the dipeptide n-acetylglutaminylglutamine amide (naggn) was discovered in the bacterium sinorhizobium meliloti grown at high osmolarity, and subsequently shown to be synthesized and accumulated by a few osmotically challenged bacteria. however, its biosynthetic pathway remained unknown. recently, two genes, which putatively encode a glutamine amidotransferase and an acetyltransferase and are up-regulated by osmotic stress, were identified in pseudomonas aeruginosa. in this work, a locus carrying ... | 2010 | 20571117 |
| production of the chiral compound (r)-3-hydroxybutyrate by a genetically engineered methylotrophic bacterium. | in this study, a methylotrophic bacterium, methylobacterium rhodesianum mb 126, was used for the production of the chiral compound (r)-3-hydroxybutyrate (r-3hb) from methanol. r-3hb is formed during intracellular degradation of the storage polymer (r)-3-polyhydroxybutyrate (phb). since the monomer r-3hb does not accumulate under natural conditions, m. rhodesianum was genetically modified. the gene (hbd) encoding the r-3hb-degrading enzyme, r-3hb dehydrogenase, was inactivated in m. rhodesianum. ... | 2010 | 20581197 |
| expressed genome of methylobacillus flagellatus as defined through comprehensive proteomics and new insights into methylotrophy. | in recent years, techniques have been developed and perfected for high-throughput identification of proteins and their accurate partial sequencing by shotgun nano-liquid chromatography-tandem mass spectrometry (nano-lc-ms/ms), making it feasible to assess global protein expression profiles in organisms with sequenced genomes. we implemented comprehensive proteomics to assess the expressed portion of the genome of methylobacillus flagellatus during methylotrophic growth. we detected a total of 1, ... | 2010 | 20639322 |
| monitoring the plant epiphyte methylobacterium extorquens dsm 21961 by real-time pcr and its influence on the strawberry flavor. | besides its influence on plant growth and health, plant-associated bacteria exert an impact on fruit quality. methylotrophic bacteria can enhance the biosynthesis of strawberry flavor compounds, especially the two furanoid compounds 2,5-dimethyl-4-hydroxy-2h-furanone (dmhf) and 2,5-dimethyl-4-methoxy-2h-furanone in vitro. here, we report the selection and characterization of methylobacterium extorquens dsm 21961, a strain that was able to enhance the furanone content ad planta under greenhouse c ... | 2010 | 20662926 |
| bathy phytochromes in rhizobial soil bacteria. | phytochromes are biliprotein photoreceptors that are found in plants, bacteria, and fungi. prototypical phytochromes have a pr ground state that absorbs in the red spectral range and is converted by light into the pfr form, which absorbs longer-wavelength, far-red light. recently, some bacterial phytochromes have been described that undergo dark conversion of pr to pfr and thus have a pfr ground state. we show here that such so-called bathy phytochromes are widely distributed among bacteria that ... | 2010 | 20675484 |
| antioxidant pathways are up-regulated during biological nitrogen fixation to prevent ros-induced nitrogenase inhibition in gluconacetobacter diazotrophicus. | gluconacetobacter diazotrophicus, an endophyte isolated from sugarcane, is a strict aerobe that fixates n(2). this process is catalyzed by nitrogenase and requires copious amounts of atp. nitrogenase activity is extremely sensitive to inhibition by oxygen and reactive oxygen species (ros). however, the elevated oxidative metabolic rates required to sustain biological nitrogen fixation (bnf) may favor an increased production of ros. here, we explored this paradox and observed that ros levels are, ... | 2010 | 20697694 |
| competitiveness of diverse methylobacterium strains in the phyllosphere of arabidopsis thaliana and identification of representative models, including m. extorquens pa1. | facultative methylotrophic bacteria of the genus methylobacterium are consistently found in association with plants, particularly in the phyllosphere. to gain a better understanding of the mechanisms underlying the dispersal and occurrence of methylobacterium on plants, diverse strains were isolated, identified, and studied with regard to their competitiveness on the model plant arabidopsis thaliana. as a basis for this study a comprehensive collection of methylobacterium isolates was establishe ... | 2010 | 20700590 |
| growth of wildtype and mutant e. coli strains in minimal media for optimal production of nucleic acids for preparing labeled nucleotides. | since rnas lie at the center of most cellular processes, there is a need for synthesizing large amounts of rnas made from stable isotope-labeled nucleotides to advance the study of their structure and dynamics by nuclear magnetic resonance (nmr) spectroscopy. a particularly effective means of obtaining labeled nucleotides is to harvest these nucleotides from bacteria grown in defined minimal media supplemented with 15nh4cl and various carbon sources. given the high cost of carbon precursors requ ... | 2010 | 20730533 |
| a structural model of anti-anti-σ inhibition by a two-component receiver domain: the phyr stress response regulator. | phyr is a hybrid stress regulator conserved in α-proteobacteria that contains an n-terminal σ-like (sl) domain and a c-terminal receiver domain. phosphorylation of the receiver domain is known to promote binding of the sl domain to an anti-σ factor. phyr thus functions as an anti-anti-σ factor in its phosphorylated state. we present genetic evidence that caulobacter crescentus phyr is a phosphorylation-dependent stress regulator that functions in the same pathway as σ(t) and its anti-σ factor, n ... | 2010 | 20735776 |
| production of functionalized polyhydroxyalkanoates by genetically modified methylobacterium extorquens strains. | methylotrophic (methanol-utilizing) bacteria offer great potential as cell factories in the production of numerous products from biomass-derived methanol. bio-methanol is essentially a non-food substrate, an advantage over sugar-utilizing cell factories. low-value products as well as fine chemicals and advanced materials are envisageable from methanol. for example, several methylotrophic bacteria, including methylobacterium extorquens, can produce large quantities of the biodegradable polyester ... | 2010 | 20846434 |
| structures of the human gtpase mmaa and vitamin b12-dependent methylmalonyl-coa mutase and insight into their complex formation. | vitamin b(12) (cobalamin, cbl) is essential to the function of two human enzymes, methionine synthase (ms) and methylmalonyl-coa mutase (mut). the conversion of dietary cbl to its cofactor forms, methyl-cbl (mecbl) for ms and adenosyl-cbl (adocbl) for mut, located in the cytosol and mitochondria, respectively, requires a complex pathway of intracellular processing and trafficking. one of the processing proteins, mmaa (methylmalonic aciduria type a), is implicated in the mitochondrial assembly of ... | 2010 | 20876572 |
| biotechnological potential of the ethylmalonyl-coa pathway. | the ethylmalonyl-coa pathway is central to the carbon metabolism of many α-proteobacteria, like rhodobacter sphaeroides and methylobacterium extorquens as well as actinomycetes, like streptomyces spp. its function is to convert acetyl-coa, a central carbon intermediate, to other precursor metabolites for cell carbon biosynthesis. in contrast to the glyoxylate cycle--another widely distributed acetyl-coa assimilation strategy--the ethylmalonyl-coa pathway contains many unique coa-ester intermedia ... | 2010 | 20882276 |
| streamlined pentafluorophenylpropyl column liquid chromatography-tandem quadrupole mass spectrometry and global (13)c-labeled internal standards improve performance for quantitative metabolomics in bacteria. | streamlined quantitative metabolomics in central metabolism of bacteria would be greatly facilitated by a high-efficiency liquid chromatography (lc) method in conjunction with accurate quantitation. to achieve this goal, a methodology for lc-tandem quadrupole mass spectrometry (lc-ms/ms) involving a pentafluorophenylpropyl (pfpp) column and culture-derived global (13)c-labeled internal standards (i.ss.) has been developed and compared to hydrophilic interaction liquid chromatography (hilic)-ms/m ... | 2010 | 20950815 |
| methanol assimilation in methylobacterium extorquens am1: demonstration of all enzymes and their regulation. | methylobacterium extorquens am1 is an aerobic facultative methylotrophic α-proteobacterium that can use reduced one-carbon compounds such as methanol, but also multi-carbon substrates like acetate (c₂) or succinate (c₄) as sole carbon and energy source. the organism has gained interest as future biotechnological production platform based on methanol as feedstock. | 2010 | 20957036 |
| genetic disorders of vitamin b₁₂ metabolism: eight complementation groups--eight genes. | vitamin b12 (cobalamin, cbl) is an essential nutrient in human metabolism. genetic diseases of vitamin b12 utilisation constitute an important fraction of inherited newborn disease. functionally, b12 is the cofactor for methionine synthase and methylmalonyl coa mutase. to function as a cofactor, b12 must be metabolised through a complex pathway that modifies its structure and takes it through subcellular compartments of the cell. through the study of inherited disorders of vitamin b12 utilisatio ... | 2010 | 21114891 |
| a systems biology approach uncovers cellular strategies used by methylobacterium extorquens am1 during the switch from multi- to single-carbon growth. | when organisms experience environmental change, how does their metabolic network reset and adapt to the new condition? methylobacterium extorquens is a bacterium capable of growth on both multi- and single-carbon compounds. these different modes of growth utilize dramatically different central metabolic pathways with limited pathway overlap. | 2010 | 21124828 |
| environments that induce synthetic microbial ecosystems. | interactions between microbial species are sometimes mediated by the exchange of small molecules, secreted by one species and metabolized by another. both one-way (commensal) and two-way (mutualistic) interactions may contribute to complex networks of interdependencies. understanding these interactions constitutes an open challenge in microbial ecology, with applications ranging from the human microbiome to environmental sustainability. in parallel to natural communities, it is possible to explo ... | 2010 | 21124952 |
| characterization of a protein-generated o₂ binding pocket in pqqc, a cofactorless oxidase catalyzing the final step in pqq production. | pqq is an exogenous, tricyclic, quino-cofactor for a number of bacterial dehydrogenases. the final step of pqq formation is catalyzed by pqqc, a cofactorless oxidase. this study focuses on the activation of molecular oxygen in an enzyme active site without metal or cofactor and has identified a specific oxygen binding and activating pocket in pqqc. the active site variants h154n, y175f,s, and r179s were studied with the goal of defining the site of o(2) binding and activation. using apo-glucose ... | 2011 | 21155540 |
| nanoscale ion-pair reversed-phase hplc-ms for sensitive metabolome analysis. | in this article, we introduce a method using nanoscale ion-pair reversed-phase high-performance liquid chromatography (nano-ip-rp-hplc) hyphenated to nanoelectrospray ionization high-resolution mass spectrometry (nano-esi-hrms) to separate and identify metabolites in cell extracts. separation of metabolites was performed on a 100 μm i.d. c18 column with tributylamine (tba) as the ion-pairing reagent and methanol as the eluent. basic ph (9.4) of the mobile phase was critical to achieve sufficient ... | 2010 | 21166460 |
| dioxygenases in burkholderia ambifaria and yersinia pestis that hydroxylate the outer kdo unit of lipopolysaccharide. | several gram-negative pathogens, including yersinia pestis, burkholderia cepacia, and acinetobacter haemolyticus, synthesize an isosteric analog of 3-deoxy-d-manno-oct-2-ulosonic acid (kdo), known as d-glycero-d-talo-oct-2-ulosonic acid (ko), in which the axial hydrogen atom at the kdo 3-position is replaced with oh. here we report a unique kdo 3-hydroxylase (kdoo) from burkholderia ambifaria and yersinia pestis, encoded by the bamb_0774 (bakdoo) and the y1812 (ypkdoo) genes, respectively. when ... | 2010 | 21178073 |
| dioxygenases in burkholderia ambifaria and yersinia pestis that hydroxylate the outer kdo unit of lipopolysaccharide. | several gram-negative pathogens, including yersinia pestis, burkholderia cepacia, and acinetobacter haemolyticus, synthesize an isosteric analog of 3-deoxy-d-manno-oct-2-ulosonic acid (kdo), known as d-glycero-d-talo-oct-2-ulosonic acid (ko), in which the axial hydrogen atom at the kdo 3-position is replaced with oh. here we report a unique kdo 3-hydroxylase (kdoo) from burkholderia ambifaria and yersinia pestis, encoded by the bamb_0774 (bakdoo) and the y1812 (ypkdoo) genes, respectively. when ... | 2010 | 21178073 |
| autoregulation of nodulation interferes with impacts of nitrogen fertilization levels on the leaf-associated bacterial community in soybeans. | the diversities leaf-associated bacteria on nonnodulated (nod(-)), wild-type nodulated (nod(+)), and hypernodulated (nod(++)) soybeans were evaluated by clone library analyses of the 16s rrna gene. to analyze the impact of nitrogen fertilization on the bacterial leaf community, soybeans were treated with standard nitrogen (sn) (15 kg n ha(-1)) or heavy nitrogen (hn) (615 kg n ha(-1)) fertilization. under sn fertilization, the relative abundance of alphaproteobacteria was significantly higher in ... | 2011 | 21239540 |
| physiological responses of pseudomonas putida to formaldehyde during detoxification. | pseudomonas putida kt2440 exhibits two formaldehyde dehydrogenases and two formate dehydrogenase complexes that allow the strain to stoichiometrically convert formaldehyde into co(2). the strain tolerated up to 1.5 mm formaldehyde and died in the presence of 10 mm. in the presence of 0.5 mm formaldehyde, a sublethal concentration of this chemical, the growth rate decreased by about 40% with respect to growth in the absence of the toxicant. transcriptomic analysis revealed that in response to low ... | 2008 | 21261833 |
| physiological responses of pseudomonas putida to formaldehyde during detoxification. | pseudomonas putida kt2440 exhibits two formaldehyde dehydrogenases and two formate dehydrogenase complexes that allow the strain to stoichiometrically convert formaldehyde into co(2). the strain tolerated up to 1.5 mm formaldehyde and died in the presence of 10 mm. in the presence of 0.5 mm formaldehyde, a sublethal concentration of this chemical, the growth rate decreased by about 40% with respect to growth in the absence of the toxicant. transcriptomic analysis revealed that in response to low ... | 2008 | 21261833 |
| chloride-associated adaptive response in aerobic methylotrophic dichloromethane-utilising bacteria. | aerobic methylotrophic bacteria able to grow with dichloromethane (dcm) as the sole carbon and energy source possess a specific glutathione s-transferase, dcm dehalogenase, which transforms dcm to formaldehyde, used for biomass and energy production, and hydrochloric acid, which is excreted. evidence is presented for chloride-specific responses for three dcm-degrading bacteria, methylobacterium extorquens dm4, methylopila helvetica dm6 and albibacter methylovorans dm10. chloride release into the ... | 2011 | 21298685 |
| a novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and dna viral systems. | the use of nucleases as toxins for defense, offense or addiction of selfish elements is widely encountered across all life forms. using sensitive sequence profile analysis methods, we characterize a novel superfamily (the sukh superfamily) that unites a diverse group of proteins including smi1/knr4, pgs2, fbxo3, skip16, syd, herpesviral us22, irs1 and trs1, and their bacterial homologs. using contextual analysis we present evidence that the bacterial members of this superfamily are potential imm ... | 2011 | 21306995 |
| cloning and characterization of indolepyruvate decarboxylase from methylobacterium extorquens am1. | for the first time for methylotrophic bacteria an enzyme of phytohormone indole-3-acetic acid (iaa) biosynthesis, indole-3-pyruvate decarboxylase (ec 4.1.1.74), has been found. an open reading frame (orf) was identified in the genome of facultative methylotroph methylobacterium extorquens am1 using blast. this orf encodes thiamine diphosphate-dependent 2-keto acid decarboxylase and has similarity with indole-3-pyruvate decarboxylases, which are key enzymes of iaa biosynthesis. the orf of the gen ... | 2010 | 21314613 |
| stress response regulators identified through genome-wide transcriptome analysis of the (p)ppgpp-dependent response in rhizobium etli. | abstract: background: the alarmone (p)ppgpp mediates a global reprogramming of gene expression upon nutrient limitation and other stresses to cope with these unfavorable conditions. synthesis of (p)ppgpp is, in most bacteria, controlled by rela/spot (rsh) proteins. the role of (p)ppgpp has been characterized primarily in escherichia coli and several gram-positive bacteria. here, we report the first in-depth analysis of the (p)ppgpp-regulon in an a-proteobacterium using a high-resolution tiling a ... | 2011 | 21324192 |
| protection of arabidopsis thaliana against leaf-pathogenic pseudomonas syringae by sphingomonas strains in a controlled model system. | diverse bacterial taxa live in association with plants without causing deleterious effects. previous analyses of phyllosphere communities revealed the predominance of few bacterial genera on healthy dicotyl plants, provoking the question of whether these commensals play a particular role in plant protection. here, we tested two of them, methylobacterium and sphingomonas, with respect to their ability to diminish disease symptom formation and the proliferation of the foliar plant pathogen pseudom ... | 2011 | 21421777 |
| evaluation of pink-pigmented facultative methylotrophic bacteria for phosphate solubilization. | thirteen pink-pigmented facultative methylotrophic (ppfm) strains isolated from adyar and cooum rivers in chennai and forest soil samples in tamil nadu, india, along with methylobacterium extorquens, m. organophilum, m. gregans, and m. komagatae were screened for phosphate solubilization in plates. p-solubilization index of the ppfms grown on nbrip-bpb plates for 7 days ranged from 1.1 to 2.7. the growth of ppfms in tricalcium phosphate amended media was found directly proportional to the glucos ... | 2011 | 21445558 |
| housekeeping genes essential for pantothenate biosynthesis are plasmid-encoded in rhizobium etli and rhizobium leguminosarum. | a traditional concept in bacterial genetics states that housekeeping genes, those involved in basic metabolic functions needed for maintenance of the cell, are encoded in the chromosome, whereas genes required for dealing with challenging environmental conditions are located in plasmids. exceptions to this rule have emerged from genomic sequence data of bacteria with multipartite genomes. the genome sequence of r. etli cfn42 predicts the presence of panc and panb genes clustered together on the ... | 2011 | 21463532 |
| regulatory response to carbon starvation in caulobacter crescentus. | bacteria adapt to shifts from rapid to slow growth, and have developed strategies for long-term survival during prolonged starvation and stress conditions. we report the regulatory response of c. crescentus to carbon starvation, based on combined high-throughput proteome and transcriptome analyses. our results identify cell cycle changes in gene expression in response to carbon starvation that involve the prominent role of the fixk fnr/cap family transcription factor and the ctra cell cycle regu ... | 2011 | 21494595 |
| purification, crystallization and preliminary x-ray crystallographic analysis of a methanol dehydrogenase from the marine bacterium methylophaga aminisulfidivorans mp(t). | methylophaga aminisulfidivorans mp(t) is a marine methylotrophic bacterium that utilizes c(1) compounds such as methanol as a carbon and energy source. the released electron from oxidation flows through a methanol-oxidizing system (mox) consisting of a series of electron-transfer proteins encoded by the mox operon. one of the key enzymes in the pathway is methanol dehydrogenase (mdh), which contains the prosthetic group pyrroloquinoline quinone (pqq) and converts methanol to formaldehyde in the ... | 2011 | 21505255 |
| squalene-hopene cyclases. | hopanoids and sterols are members of a large group of cyclic triterpenoic compounds that have important functions in many prokaryotic and eukaryotic organisms. they are biochemically synthesized from linear precursors (squalene, 2,3-oxidosqualene) in only one enzymatic step that is catalyzed by squalene-hopene cyclase (shc) or oxidosqualene cyclase (osc). shcs and oscs are related in amino acid sequences and probably are derived from a common ancestor. the shc reaction requires the formation of ... | 2011 | 21531832 |
| detection and isolation of chloromethane-degrading bacteria from the arabidopsis thaliana phyllosphere, and characterization of chloromethane utilization genes. | chloromethane gas is produced naturally in the phyllosphere, the compartment defined as the aboveground parts of vegetation, which hosts a rich bacterial flora. chloromethane may serve as a growth substrate for specialized aerobic methylotrophic bacteria, which have been isolated from soil and water environments, and use cmu genes for chloromethane utilization. evidence for the presence of chloromethane-degrading bacteria on the leaf surfaces of arabidopsis thaliana was obtained by specific quan ... | 2011 | 21545604 |
| genomic insights into the physiology and ecology of the marine filamentous cyanobacterium lyngbya majuscula. | filamentous cyanobacteria of the genus lyngbya are important contributors to coral reef ecosystems, occasionally forming dominant cover and impacting the health of many other co-occurring organisms. moreover, they are extraordinarily rich sources of bioactive secondary metabolites, with 35% of all reported cyanobacterial natural products deriving from this single pantropical genus. however, the true natural product potential and life strategies of lyngbya strains are poorly understood because of ... | 2011 | 21555588 |
| loss of allostery and coenzyme b(12) delivery by a pathogenic mutation in adenosyltransferase. | atp-dependent cob(i)alamin adenosyltransferase (atr) is a bifunctional protein: an enzyme that catalyzes the adenosylation of cob(i)alamin and an escort that delivers the product, adenosylcobalamin (adocbl or coenzyme b(12)), to methylmalonyl-coa mutase (mcm), resulting in holoenzyme formation. failure to assemble holo-mcm leads to methylmalonic aciduria. we have previously demonstrated that only 2 equiv of adocbl bind per homotrimer of atr and that binding of atp to the vacant active site trigg ... | 2011 | 21604717 |
| genomes of three methylotrophs from a single niche uncover genetic and metabolic divergence of methylophilaceae. | the genomes of three representatives of the family methylophilaceae, methylotenera mobilis jlw8, methylotenera versatilis 301 and methylovorus glucosetrophus sip3-4, all isolated from a single study site, lake washington in seattle, were completely sequenced. these were compared to each other and to the previously published genomes of methylobacillus flagellatus kt and an unclassified methylophilales strain htcc2181. comparative analysis revealed that the core genome of methylophilaceae may be a ... | 2011 | 21622745 |
| diminishing returns epistasis among beneficial mutations decelerates adaptation. | epistasis has substantial impacts on evolution, in particular, the rate of adaptation. we generated combinations of beneficial mutations that arose in a lineage during rapid adaptation of a bacterium whose growth depended on a newly introduced metabolic pathway. the proportional selective benefit for three of the four loci consistently decreased when they were introduced onto more fit backgrounds. these three alleles all reduced morphological defects caused by expression of the foreign pathway. ... | 2011 | 21636771 |
| introducing a new bioengineered bug: methylobacterium extorquens tuned as a microbial bioplastic factory. | discussion on and use of methanol as chemical feedstock and as alternative fuel has gained momentum during the past years. consequently, microorganism and product design based on ''methylotrophism'' is in vogue as reflected by increasing research and development activities in methanol-related areas. a recent example of microorganism and product development is the use of recombinant methylobacterium extorquens atcc 55366 strains in the production of second generation biopolyesters. feeding n-alke ... | 2011 | 21636993 |
| genome and characterization of phages bcep22 and bcepil02, founders of a novel phage type in burkholderia cenocepacia. | within the burkholderia cepacia complex (bcc), b. cenocepacia is the most common species associated with aggressive infections in the lungs of cystic fibrosis patients, causing disease that is often refractive to treatment by antibiotics. phage therapy may be a potential alternative form of treatment for these infections. here we describe the genome of the previously described therapeutic b. cenocepacia podophage bcepil02 and its close relative, bcep22. phage bcep22 was found to contain a circul ... | 2011 | 21804006 |
| pole age affects cell size and the timing of cell division in methylobacterium extorquens am1. | a number of recent experiments at the single-cell level have shown that genetically identical bacteria that live in homogeneous environments often show a substantial degree of phenotypic variation between cells. often, this variation is attributed to stochastic aspects of biology - the fact that many biological processes involve small numbers of molecules, and are thus inherently variable. however, not all variation between cells needs to be stochastic in nature; one deterministic process that c ... | 2011 | 21784923 |
| effects of elevated atmospheric co(2) on rhizosphere soil microbial communities in a mojave desert ecosystem. | the effects of elevated atmospheric carbon dioxide [co(2)] on microbial communities in arid rhizosphere soils beneath larrea tridentata were examined. roots of larrea were harvested from plots fumigated with elevated or ambient levels of [co(2)] using free-air co(2) enrichment (face) technology. twelve bacterial and fungal rrna gene libraries were constructed, sequenced and categorized into operational taxonomical units (otus). there was a significant decrease in otus within the firmicutes (bact ... | 2011 | 21779135 |
| type ivb secretion systems of legionella and other gram-negative bacteria. | type iv secretion systems (t4sss) play a central role in the pathogenicity of many important pathogens, including agrobacterium tumefaciens, helicobacter pylori, and legionella pneumophila. the t4sss are related to bacterial conjugation systems, and are classified into two subgroups, type iva (t4ass) and type ivb (t4bss). the t4bss, which is closely related to conjugation systems of inci plasmids, was originally found in human pathogen l. pneumophila; pathogenesis by l. pneumophila infection req ... | 2011 | 21743810 |
| detection of dichloromethane with a bioluminescent (lux) bacterial bioreporter. | the focus of this research effort was to develop an autonomous, inducible, lux-based bioluminescent bioreporter for the real-time detection of dichloromethane. dichloromethane (dcm), also known as methylene chloride, is a volatile organic compound and one of the most commonly used halogenated solvents in the u.s., with applications ranging from grease and paint stripping to aerosol propellants and pharmaceutical tablet coatings. predictably, it is released into the environment where it contamina ... | 2011 | 21688172 |
| Biochemical and Mutational Studies of the Bacillus cereus CECT 5050T Formamidase Support the Existence of a C-E-E-K Tetrad in Several Members of the Nitrilase Superfamily. | Formamidases (EC 3.5.1.49) are poorly characterized proteins. In spite of this scarce knowledge, ammonia has been described as playing a central role in the pathogenesis of human pathogens such as Helicobacter pylori, for which formamidase has been shown to participate in the nitrogen metabolic pathway. Sequence analysis has revealed that at least two different groups of formamidases are classified as EC 3.5.1.49: on the one hand, the derivatives of the FmdA-AmdA superfamily, which are the best ... | 2011 | 21705545 |
| The Ethylmalonyl-CoA Pathway Is Used in Place of the Glyoxylate Cycle by Methylobacterium extorquens AM1 during Growth on Acetate. | Acetyl-CoA assimilation was extensively studied in organisms harboring the glyoxylate cycle. In this study, we analyzed the metabolism of the facultative methylotroph Methylobacterium extorquens AM1, which lacks isocitrate lyase, the key enzyme in the glyoxylate cycle, during growth on acetate. MS/MS-based proteomic analysis revealed that the protein repertoire of M. extorquens AM1 grown on acetate is similar to that of cells grown on methanol and includes enzymes of the ethylmalonyl-CoA (EMC) p ... | 2012 | 22105076 |
| XoxF is required for expression of methanol dehydrogenase in Methylobacterium extorquens AM1. | In Gram-negative methylotrophic bacteria, the first step in methylotrophic growth is the oxidation of methanol to formaldehyde in the periplasm by methanol dehydrogenase. In most organisms studied to date, this enzyme consists of the MxaF and MxaI proteins, which make up the large and small subunits of this heterotetrameric enzyme. The Methylobacterium extorquens AM1 genome contains two homologs of MxaF, XoxF1 and XoxF2, which are ~50% identical to MxaF and ~90% identical to each other. It was p ... | 2011 | 21873495 |
| Isovaleryl-homoserine lactone, an unusual branched-chain quorum-sensing signal from the soybean symbiont Bradyrhizobium japonicum. | Many species of Proteobacteria communicate by using LuxI-LuxR-type quorum-sensing systems that produce and detect acyl-homoserine lactone (acyl-HSL) signals. Most of the known signals are straight-chain fatty acyl-HSLs, and evidence indicates that LuxI homologs prefer fatty acid-acyl carrier protein (ACP) over fatty acyl-CoA as the acyl substrate for signal synthesis. Two related LuxI homologs, RpaI and BtaI from Rhodopseudomonas palustris and photosynthetic stem-nodulating bradyrhizobia, direct ... | 2011 | 21949379 |
| Genomes and Virulence Factors of Novel Bacterial Pathogens Causing Bleaching Disease in the Marine Red Alga Delisea pulchra. | Nautella sp. R11, a member of the marine Roseobacter clade, causes a bleaching disease in the temperate-marine red macroalga, Delisea pulchra. To begin to elucidate the molecular mechanisms underpinning the ability of Nautella sp. R11 to colonize, invade and induce bleaching of D. pulchra, we sequenced and analyzed its genome. The genome encodes several factors such as adhesion mechanisms, systems for the transport of algal metabolites, enzymes that confer resistance to oxidative stress, cytolys ... | 2011 | 22162749 |
| genome-scale reconstruction and system level investigation of the metabolic network of methylobacterium extorquens am1. | methylotrophic microorganisms are playing a key role in biogeochemical processes - especially the global carbon cycle - and have gained interest for biotechnological purposes. significant progress was made in the recent years in the biochemistry, genetics, genomics, and physiology of methylotrophic bacteria, showing that methylotrophy is much more widespread and versatile than initially assumed. despite such progress, system-level description of the methylotrophic metabolism is currently lacking ... | 2011 | 22074569 |
| transport genes and chemotaxis in laribacter hongkongensis: a genome-wide analysis. | abstract: | 2011 | 21849034 |
| widespread genetic switches and toxicity resistance proteins for fluoride. | most riboswitches are metabolite-binding rna structures located in bacterial messenger rnas where they control gene expression. we have discovered a riboswitch class in many bacterial and archaeal species whose members are selectively triggered by fluoride but reject other small anions, including chloride. these fluoride riboswitches activate expression of genes that encode putative fluoride transporters, enzymes that are known to be inhibited by fluoride, and additional proteins of unknown func ... | 2011 | 22194412 |
| widespread genetic switches and toxicity resistance proteins for fluoride. | most riboswitches are metabolite-binding rna structures located in bacterial messenger rnas where they control gene expression. we have discovered a riboswitch class in many bacterial and archaeal species whose members are selectively triggered by fluoride but reject other small anions, including chloride. these fluoride riboswitches activate expression of genes that encode putative fluoride transporters, enzymes that are known to be inhibited by fluoride, and additional proteins of unknown func ... | 2011 | 22194412 |
| functional genomics of dichloromethane utilization in methylobacterium extorquens dm4. | dichloromethane (ch(2)cl(2) , dcm) is a chlorinated solvent mainly produced by industry, and a common pollutant. some aerobic methylotrophic bacteria are able to grow with this chlorinated methane as their sole carbon and energy source, using a dcm dehalogenase/glutathione s-transferase encoded by dcma to transform dcm into two molecules of hcl and one molecule of formaldehyde, a toxic intermediate of methylotrophic metabolism. in methylobacterium extorquens dm4 of known genome sequence, dcma li ... | 2011 | 21854516 |
| mdor is a novel positive transcriptional regulator for the oxidation of methanol in mycobacterium sp. strain jc1. | mycobacterium sp. strain jc1 is able to grow on methanol as a sole source of carbon and energy using methanol:n,n'-dimethyl-4-nitrosoaniline oxidoreductase (mdo) as a key enzyme for methanol oxidation. the second open reading frame (mdor) upstream of, and running divergently from, the mdo gene was identified as a gene for a tetr family transcriptional regulator. the n-terminal region of mdor contained a helix-turn-helix dna-binding motif. an electrophoretic mobility shift assay (emsa) indicated ... | 2011 | 21908665 |
| one carbon metabolism in sar11 pelagic marine bacteria. | the sar11 alphaproteobacteria are the most abundant heterotrophs in the oceans and are believed to play a major role in mineralizing marine dissolved organic carbon. their genomes are among the smallest known for free-living heterotrophic cells, raising questions about how they successfully utilize complex organic matter with a limited metabolic repertoire. here we show that conserved genes in sar11 subgroup ia (candidatus pelagibacter ubique) genomes encode pathways for the oxidation of a varie ... | 2011 | 21886845 |
| complete genome sequence of the chloromethane-degrading hyphomicrobium sp. strain mc1. | hyphomicrobium sp. strain mc1 is an aerobic methylotroph originally isolated from industrial sewage. this prosthecate bacterium was the first strain reported to grow with chloromethane as the sole carbon and energy source. its genome, consisting of a single 4.76-mb chromosome, is the first for a chloromethane-degrading bacterium to be formally reported. | 2011 | 21868803 |
| Diversity of Five Anaerobic Toluene Degrading Microbial Communities Investigated using Stable Isotope Probing (SIP). | Time-series DNA-stable isotope probing (SIP) was used to identify the microbes assimilating carbon from (13)C-toluene under nitrate or sulfate amended conditions in a range of inoculum sources, including uncontaminated and contaminated soil and wastewater treatment samples. In all, five different phylotypes were found to be responsible for toluene degradation and these included previously identified toluene degraders as well as novel toluene degrading microorganisms. In microcosms inoculated fro ... | 2011 | 22156434 |
| Microbial degradation of furanic compounds: biochemistry, genetics, and impact. | Microbial metabolism of furanic compounds, especially furfural and 5-hydroxymethylfurfural (HMF), is rapidly gaining interest in the scientific community. This interest can largely be attributed to the occurrence of toxic furanic aldehydes in lignocellulosic hydrolysates. However, these compounds are also widespread in nature and in human processed foods, and are produced in industry. Although several microorganisms are known to degrade furanic compounds, the variety of species is limited mostly ... | 2011 | 22031465 |
| Phylogenomics of Reichenowia parasitica, an Alphaproteobacterial Endosymbiont of the Freshwater Leech Placobdella parasitica. | Although several commensal alphaproteobacteria form close relationships with plant hosts where they aid in (e.g.,) nitrogen fixation and nodulation, only a few inhabit animal hosts. Among these, Reichenowia picta, R. ornata and R. parasitica, are currently the only known mutualistic, alphaproteobacterial endosymbionts to inhabit leeches. These bacteria are harbored in the epithelial cells of the mycetomal structures of their freshwater leech hosts, Placobdella spp., and these structures have no ... | 2011 | 22132238 |
| role of sphingomonas sp. strain fr1 phyr-nepr-σecfg cascade in general stress response and identification of a negative regulator of phyr. | the general stress response in alphaproteobacteria was recently described to depend on the alternative sigma factor σ(ecfg), whose activity is regulated by its anti-sigma factor nepr. the response regulator phyr, in turn, regulates nepr activity in a partner-switching mechanism according to which phosphorylation of phyr triggers sequestration of nepr by the sigma factor-like effector domain of phyr. although genes encoding predicted histidine kinases can often be found associated with phyr, litt ... | 2011 | 21949070 |
| identification and characterization of rhodopseudomonas palustris tie-1 hopanoid biosynthesis mutants. | hopanes preserved in both modern and ancient sediments are recognized as the molecular fossils of bacteriohopanepolyols, pentacyclic hopanoid lipids. based on the phylogenetic distribution of hopanoid production by extant bacteria, hopanes have been used as indicators of specific bacterial groups and/or their metabolisms. however, our ability to interpret them ultimately depends on understanding the physiological roles of hopanoids in modern bacteria. toward this end, we set out to identify gene ... | 2012 | 22221333 |
| endophytic methylobacterium extorquens expresses a heterologous β-1,4-endoglucanase a (egla) in catharanthus roseus seedlings, a model host plant for xylella fastidiosa. | based on the premise of symbiotic control, we genetically modified the citrus endophytic bacterium methylobacterium extorquens, strain ar1.6/2, and evaluated its capacity to colonize a model plant and its interaction with xylella fastidiosa, the causative agent of citrus variegated chlorosis (cvc). ar1.6/2 was genetically transformed to express heterologous gfp (green fluorescent protein) and an endoglucanase a (egla), generating the strains argfp and aregla, respectively. by fluorescence micros ... | 2011 | 22805929 |
| [3' flanking region analysis of the dichloromethane dehalogenase gene of dcma methylobacterium dichloromethanicum dm4]. | | 2011 | 22393764 |
| metagenomic profiles of free-living archaea, bacteria and small eukaryotes in coastal areas of sichang island, thailand. | tha wang and tham phang coasts, though situated at similar oceanographic positions on sichang island, chonburi province, thailand, are different in bay geography and amount of municipal disturbances. these affect the marine ecosystems. the study used metagenomics combined with 16s and 18s rdna pyrosequencing to identify types and distributions of archaea, bacteria, fungi and small eukaryotes of sizes ranges 0.45 and ~30 μm. | 2012 | 23282134 |
| annotation of protein domains reveals remarkable conservation in the functional make up of proteomes across superkingdoms. | the functional repertoire of a cell is largely embodied in its proteome, the collection of proteins encoded in the genome of an organism. the molecular functions of proteins are the direct consequence of their structure and structure can be inferred from sequence using hidden markov models of structural recognition. here we analyze the functional annotation of protein domain structures in almost a thousand sequenced genomes, exploring the functional and structural diversity of proteomes. we find ... | 2011 | 24710297 |
| practical application of methanol-mediated mutualistic symbiosis between methylobacterium species and a roof greening moss, racomitrium japonicum. | bryophytes, or mosses, are considered the most maintenance-free materials for roof greening. racomitrium species are most often used due to their high tolerance to desiccation. because they grow slowly, a technology for forcing their growth is desired. we succeeded in the efficient production of r. japonicum in liquid culture. the structure of the microbial community is crucial to stabilize the culture. a culture-independent technique revealed that the cultures contain methylotrophic bacteria. u ... | 2012 | 22479445 |
| the mysterious orphans of mycoplasmataceae. | the length of a protein sequence is largely determined by its function. in certain species, it may be also affected by additional factors, such as growth temperature or acidity. in 2002, it was shown that in the bacterium escherichia coli and in the archaeon archaeoglobus fulgidus, protein sequences with no homologs were, on average, shorter than those with homologs (bmc evol biol 2:20, 2002). it is now generally accepted that in bacterial and archaeal genomes the distributions of protein length ... | 2016 | 26747447 |
| bacterial sigma factors and anti-sigma factors: structure, function and distribution. | sigma factors are multi-domain subunits of bacterial rna polymerase (rnap) that play critical roles in transcription initiation, including the recognition and opening of promoters as well as the initial steps in rna synthesis. this review focuses on the structure and function of the major sigma-70 class that includes the housekeeping sigma factor (group 1) that directs the bulk of transcription during active growth, and structurally-related alternative sigma factors (groups 2-4) that control a w ... | 2015 | 26131973 |
| olsg (sinac_1600) is an ornithine lipid n-methyltransferase from the planctomycete singulisphaera acidiphila. | ornithine lipids (ols) are phosphorus-free membrane lipids widespread in bacteria but absent from archaea and eukaryotes. in addition to the unmodified ols, a variety of ol derivatives hydroxylated in different structural positions has been reported. recently, methylated derivatives of ols were described in several planctomycetes isolated from a peat bog in northern russia, although the gene/enzyme responsible for the n-methylation of ol remained obscure. here we identify and characterize the ol ... | 2015 | 25925947 |