Publications
| Title | Abstract | Year Filter | PMID(sorted ascending) Filter |
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| metabolic engineering of methylobacterium extorquens am1 for 1-butanol production. | butanol is a promising next generation fuel and a bulk chemical precursor. although clostridia are the primary industrial microbes for the fermentative production of 1-butanol, alternative engineered hosts have the potential to generate 1-butanol from alternative carbon feedstocks via synthetic metabolic pathways. methylobacterium extorquens am1, a facultative methylotrophic α-proteobacterium, is a model system for assessing the possibility of generating products such as 1-butanol from one-carbo ... | 2014 | 25349627 |
| probing the diversity of chloromethane-degrading bacteria by comparative genomics and isotopic fractionation. | chloromethane (ch3cl) is produced on earth by a variety of abiotic and biological processes. it is the most important halogenated trace gas in the atmosphere, where it contributes to ozone destruction. current estimates of the global ch3cl budget are uncertain and suggest that microorganisms might play a more important role in degrading atmospheric ch3cl than previously thought. its degradation by bacteria has been demonstrated in marine, terrestrial, and phyllospheric environments. improving ou ... | 2014 | 25360131 |
| structure of the methanofuran/methanopterin-biosynthetic enzyme mj1099 from methanocaldococcus jannaschii. | prior studies have indicated that mj1099 from methanocaldococcus jannaschii has roles in the biosynthesis of tetrahydromethanopterin and methanofuran, two key cofactors of one-carbon (c1) metabolism in diverse organisms including the methanogenic archaea. here, the structure of mj1099 has been solved to 1.7 å resolution using anomalous scattering methods. the results indicate that mj1099 is a member of the tim-barrel superfamily and that it is a homohexamer. bioinformatic analyses identified a p ... | 2014 | 25372812 |
| cecafdb: a curated database for the documentation, visualization and comparative analysis of central carbon metabolic flux distributions explored by 13c-fluxomics. | the central carbon metabolic flux database (cecafdb, available at http://www.cecafdb.org) is a manually curated, multipurpose and open-access database for the documentation, visualization and comparative analysis of the quantitative flux results of central carbon metabolism among microbes and animal cells. it encompasses records for more than 500 flux distributions among 36 organisms and includes information regarding the genotype, culture medium, growth conditions and other specific information ... | 2014 | 25392417 |
| cecafdb: a curated database for the documentation, visualization and comparative analysis of central carbon metabolic flux distributions explored by 13c-fluxomics. | the central carbon metabolic flux database (cecafdb, available at http://www.cecafdb.org) is a manually curated, multipurpose and open-access database for the documentation, visualization and comparative analysis of the quantitative flux results of central carbon metabolism among microbes and animal cells. it encompasses records for more than 500 flux distributions among 36 organisms and includes information regarding the genotype, culture medium, growth conditions and other specific information ... | 2014 | 25392417 |
| complex two-component signaling regulates the general stress response in alphaproteobacteria. | the general stress response (gsr) in alphaproteobacteria was recently shown to be controlled by a partner-switching mechanism that is triggered by phosphorylation of the response regulator phyr. activation of phyr ultimately results in release of the alternative extracytoplasmic function sigma factor σ(ecfg), which redirects transcription toward the gsr. little is known about the signal transduction pathway(s) controlling phyr phosphorylation. here, we identified the single-domain response regul ... | 2014 | 25404331 |
| effective use of a horizontally-transferred pathway for dichloromethane catabolism requires post-transfer refinement. | when microbes acquire new abilities through horizontal gene transfer, the genes and pathways must function under conditions with which they did not coevolve. if newly-acquired genes burden the host, their utility will depend on further evolutionary refinement of the recombinant strain. we used laboratory evolution to recapitulate this process of transfer and refinement, demonstrating that effective use of an introduced dichloromethane degradation pathway required one of several mutations to the ... | 2014 | 25418043 |
| methylobacterium extorquens: methylotrophy and biotechnological applications. | methylotrophy is the ability to use reduced one-carbon compounds, such as methanol, as a single source of carbon and energy. methanol is, due to its availability and potential for production from renewable resources, a valuable feedstock for biotechnology. nature offers a variety of methylotrophic microorganisms that differ in their metabolism and represent resources for engineering of value-added products from methanol. the most extensively studied methylotroph is the alphaproteobacterium methy ... | 2015 | 25432674 |
| whole-proteome analysis of twelve species of alphaproteobacteria links four pathogens. | thousands of whole-genome and whole-proteome sequences have been made available through advances in sequencing technology, and sequences of millions more organisms will become available in the coming years. this wealth of genetic information will provide numerous opportunities to enhance our understanding of these organisms including a greater understanding of relationships among species. researchers have used 16s rrna and other gene sequences to study the evolutionary origins of bacteria, but t ... | 2013 | 25437336 |
| ethylmalonyl coenzyme a mutase operates as a metabolic control point in methylobacterium extorquens am1. | the metabolism of one- and two-carbon compounds by the methylotrophic bacterium methylobacterium extorquens am1 involves high carbon flux through the ethylmalonyl coenzyme a (ethylmalonyl-coa) pathway (emc pathway). during growth on ethylamine, the emc pathway operates as a linear pathway carrying the full assimilatory flux to produce glyoxylate, malate, and succinate. assimilatory carbon enters the ethylmalonyl-coa pathway directly as acetyl-coa, bypassing pathways for formaldehyde oxidation/as ... | 2014 | 25448820 |
| ethylmalonyl coenzyme a mutase operates as a metabolic control point in methylobacterium extorquens am1. | the metabolism of one- and two-carbon compounds by the methylotrophic bacterium methylobacterium extorquens am1 involves high carbon flux through the ethylmalonyl coenzyme a (ethylmalonyl-coa) pathway (emc pathway). during growth on ethylamine, the emc pathway operates as a linear pathway carrying the full assimilatory flux to produce glyoxylate, malate, and succinate. assimilatory carbon enters the ethylmalonyl-coa pathway directly as acetyl-coa, bypassing pathways for formaldehyde oxidation/as ... | 2014 | 25448820 |
| draft genome sequence of methylobacterium sp. strain l2-4, a leaf-associated endophytic n-fixing bacterium isolated from jatropha curcas l. | methylobacterium sp. strain l2-4 is an efficient nitrogen-fixing leaf colonizer of biofuel crop jatropha curcas. this strain is able to greatly improve the growth and seed yield of jatropha curcas and is the second reported genome sequence of plant growth-promoting bacteria isolated from jatropha curcas. | 2014 | 25502683 |
| evaluation of 3 dental unit waterline contamination testing methods. | previous studies have found inconsistent results from testing methods used to measure heterotrophic plate count (hpc) bacteria in dental unit waterline (duwl) samples. this study used 63 samples to compare the results obtained from an in-office chairside method and 2 currently used commercial laboratory hpc methods (standard methods 9215c and 9215e). the results suggest that the standard method 9215e is not suitable for application to duwl quality monitoring, due to the detection of limited numb ... | 2015 | 25574718 |
| metabolic engineering of corynebacterium glutamicum for methanol metabolism. | methanol is already an important carbon feedstock in the chemical industry, but it has found only limited application in biotechnological production processes. this can be mostly attributed to the inability of most microbial platform organisms to utilize methanol as a carbon and energy source. with the aim to turn methanol into a suitable feedstock for microbial production processes, we engineered the industrially important but nonmethylotrophic bacterium corynebacterium glutamicum toward the ut ... | 2015 | 25595770 |
| role of extracytoplasmic function sigma factors in biofilm formation of porphyromonas gingivalis. | porphyromonas gingivalis has been implicated as a major pathogen in the development and progression of chronic periodontitis. p. gingivalis biofilm formation in the subgingival crevice plays an important role in the ability of the bacteria to tolerate stress signals outside the cytoplasmic membrane. some bacteria use a distinct subfamily of sigma factors to regulate their extracytoplasmic functions (the ecf subfamily). the objective of this study was to determine if p. gingivalis ecf sigma facto ... | 2015 | 25596817 |
| high-level production of ethylmalonyl-coa pathway-derived dicarboxylic acids by methylobacterium extorquens under cobalt-deficient conditions and by polyhydroxybutyrate negative strains. | bio-based production of dicarboxylic acids is an emerging research field with remarkable progress during the last decades. the recently established synthesis of the ethylmalonyl-coa pathway (emcp)-derived dicarboxylic acids, mesaconic acid and (2s)-methylsuccinic acid, from the alternative carbon source methanol (sonntag et al., appl microbiol biotechnol 98:4533-4544, 2014) gave a proof of concept for the sustainable production of hitherto biotechnologically inaccessible monomers. in this study, ... | 2015 | 25661812 |
| sulfur isotope fractionation during the evolutionary adaptation of a sulfate-reducing bacterium. | dissimilatory sulfate reduction is a microbial catabolic pathway that preferentially processes less massive sulfur isotopes relative to their heavier counterparts. this sulfur isotope fractionation is recorded in ancient sedimentary rocks and generally is considered to reflect a phenotypic response to environmental variations rather than to evolutionary adaptation. modern sulfate-reducing microorganisms isolated from similar environments can exhibit a wide range of sulfur isotope fractionations, ... | 2015 | 25662968 |
| the bacterial rhizobiome of hyperaccumulators: future perspectives based on omics analysis and advanced microscopy. | hyperaccumulators are plants that can extract heavy metal ions from the soil and translocate those ions to the shoots, where they are sequestered and detoxified. hyperaccumulation depends not only on the availability of mobilized metal ions in the soil, but also on the enhanced activity of metal transporters and metal chelators which may be provided by the plant or its associated microbes. the rhizobiome is captured by plant root exudates from the complex microbial community in the soil, and may ... | 2014 | 25709609 |
| the bacterial rhizobiome of hyperaccumulators: future perspectives based on omics analysis and advanced microscopy. | hyperaccumulators are plants that can extract heavy metal ions from the soil and translocate those ions to the shoots, where they are sequestered and detoxified. hyperaccumulation depends not only on the availability of mobilized metal ions in the soil, but also on the enhanced activity of metal transporters and metal chelators which may be provided by the plant or its associated microbes. the rhizobiome is captured by plant root exudates from the complex microbial community in the soil, and may ... | 2014 | 25709609 |
| transhydrogenase promotes the robustness and evolvability of e. coli deficient in nadph production. | metabolic networks revolve around few metabolites recognized by diverse enzymes and involved in myriad reactions. though hub metabolites are considered as stepping stones to facilitate the evolutionary expansion of biochemical pathways, changes in their production or consumption often impair cellular physiology through their system-wide connections. how does metabolism endure perturbations brought immediately by pathway modification and restore hub homeostasis in the long run? to address this qu ... | 2015 | 25715029 |
| an integrated approach to reconstructing genome-scale transcriptional regulatory networks. | transcriptional regulatory networks (trns) program cells to dynamically alter their gene expression in response to changing internal or environmental conditions. in this study, we develop a novel workflow for generating large-scale trn models that integrates comparative genomics data, global gene expression analyses, and intrinsic properties of transcription factors (tfs). an assessment of this workflow using benchmark datasets for the well-studied γ-proteobacterium escherichia coli showed that ... | 2015 | 25723545 |
| metagenomic analysis of the bacterial community associated with the taproot of sugar beet. | we analyzed a metagenome of the bacterial community associated with the taproot of sugar beet (beta vulgaris l.) in order to investigate the genes involved in plant growth-promoting traits (pgpts), namely 1-aminocyclopropane-1-carboxylic acid (acc) deaminase, indole acetic acid (iaa), n2 fixation, phosphate solubilization, pyrroloquinoline quinone, siderophores, and plant disease suppression as well as methanol, sucrose, and betaine utilization. the most frequently detected gene among the pgpt c ... | 2015 | 25740621 |
| electro-biocatalytic production of formate from carbon dioxide using an oxygen-stable whole cell biocatalyst. | the use of biocatalysts to convert co2 into useful chemicals is a promising alternative to chemical conversion. in this study, the electro-biocatalytic conversion of co2 to formate was attempted with a whole cell biocatalyst. eight species of methylobacteria were tested for co2 reduction, and one of them, methylobacterium extorquens am1, exhibited an exceptionally higher capability to synthesize formate from co2 by supplying electrons with electrodes, which produced formate concentrations of up ... | 2015 | 25746476 |
| [genetic modification of methylobacterium extorquens g10 producer strain of polyhydroxybutyrate]. | the effect of the increased copy number of polyhydroxybutyrate (phb) biosynthesis genes in pink-pigmented methylobacterium methylobacterium extorquens g10 on properties of the biopolymer was studied. the activity of poly-3-hydroxybutyril-synthase (phb-synthase) was shown to increase and the molecular weight of synthesized phb decreases twofold (150 --> 79 kda) after insertion of extra copies of phac and phacab genes into cells of the producer strain, whereas the physicochemical properties of the ... | 2015 | 25757337 |
| a bioinformatic survey of distribution, conservation, and probable functions of luxr solo regulators in bacteria. | luxr solo transcriptional regulators contain both an autoinducer binding domain (abd; n-terminal) and a dna binding helix-turn-helix domain (hth; c-terminal), but are not associated with a cognate n-acyl homoserine lactone (ahl) synthase coding gene in the same genome. although a few luxr solos have been characterized, their distributions as well as their role in bacterial signal perception and other processes are poorly understood. in this study we have carried out a systematic survey of distri ... | 2015 | 25759807 |
| the intracellular scots pine shoot symbiont methylobacterium extorquens dsm13060 aggregates around the host nucleus and encodes eukaryote-like proteins. | endophytes are microbes that inhabit plant tissues without any apparent signs of infection, often fundamentally altering plant phenotypes. while endophytes are typically studied in plant roots, where they colonize the apoplast or dead cells, methylobacterium extorquens strain dsm13060 is a facultatively intracellular symbiont of the meristematic cells of scots pine (pinus sylvestris l.) shoot tips. the bacterium promotes host growth and development without the production of known plant growth-st ... | 2015 | 25805725 |
| molecular, physiological and phenotypic characterization of paracoccus denitrificans atcc 19367 mutant strain p-87 producing improved coenzyme q10. | coenzyme q10 (coq10) is a blockbuster nutraceutical molecule which is often used as an oral supplement in the supportive therapy for cardiovascular diseases, cancer and neurodegenerative diseases. it is commercially produced by fermentation process, hence constructing the high yielding coq10 producing strains is a pre-requisite for cost effective production. paracoccus denitrificans atcc 19367, a biochemically versatile organism was selected to carry out the studies on coq10 yield improvement. t ... | 2014 | 25805905 |
| molecular, physiological and phenotypic characterization of paracoccus denitrificans atcc 19367 mutant strain p-87 producing improved coenzyme q10. | coenzyme q10 (coq10) is a blockbuster nutraceutical molecule which is often used as an oral supplement in the supportive therapy for cardiovascular diseases, cancer and neurodegenerative diseases. it is commercially produced by fermentation process, hence constructing the high yielding coq10 producing strains is a pre-requisite for cost effective production. paracoccus denitrificans atcc 19367, a biochemically versatile organism was selected to carry out the studies on coq10 yield improvement. t ... | 2014 | 25805905 |
| pqqd is a novel peptide chaperone that forms a ternary complex with the radical s-adenosylmethionine protein pqqe in the pyrroloquinoline quinone biosynthetic pathway. | pyrroloquinoline quinone (pqq) is a product of a ribosomally synthesized and post-translationally modified pathway consisting of five conserved genes, pqqa-e. pqqe is a radical s-adenosylmethionine (rs) protein with a c-terminal spasm domain, and is proposed to catalyze the formation of a carbon-carbon bond between the glutamate and tyrosine side chains of the peptide substrate pqqa. pqqd is a 10-kda protein with an unknown function, but is essential for pqq production. recently, in klebsiella p ... | 2015 | 25817994 |
| crystal structures of mycobacterial meab and mmaa-like gtpases. | the methylmalonyl co-a mutase-associated gtpase meab from methylobacterium extorquens is involved in glyoxylate regulation and required for growth. in humans, mutations in the homolog methylmalonic aciduria associated protein (mmaa) cause methylmalonic aciduria, which is often fatal. the central role of meab from bacteria to humans suggests that meab is also important in other, pathogenic bacteria such as mycobacterium tuberculosis. however, the identity of the mycobacterial meab homolog is pres ... | 2015 | 25832174 |
| [functional activity of the moda, gene in methylobacterium dichloromethanicum dm4]. | the putative metdi2644 (moda2) gene of methylobacterium dichloromethanicum dm4, present in the 126-kbp chromosomal fragment associated with dichloromethane (dcm) degradation was investigated. while this gene is presumed to encode the periplasmic substrate-binding subunit of the molybdate abc transporter, its conceptual translation also exhibits similarity to the proteins containing the osta conservative domain and responsible for resistance of gram-negative bacteria to organic solvents. reverse ... | 2015 | 25844439 |
| methenyl-dephosphotetrahydromethanopterin is a regulatory signal for acclimation to changes in substrate availability in methylobacterium extorquens am1. | during an environmental perturbation, the survival of a cell and its response to the perturbation depend on both the robustness and functionality of the metabolic network. the regulatory mechanisms that allow the facultative methylotrophic bacterium methylobacterium extorquens am1 to effect the metabolic transition from succinate to methanol growth are not well understood. methenyl-dephosphotetrahydromethanopterin (methenyl-dh4mpt), an early intermediate during methanol metabolism, transiently a ... | 2015 | 25845846 |
| highly active and specific tyrosine ammonia-lyases from diverse origins enable enhanced production of aromatic compounds in bacteria and saccharomyces cerevisiae. | phenylalanine and tyrosine ammonia-lyases form cinnamic acid and p-coumaric acid, which are precursors of a wide range of aromatic compounds of biotechnological interest. lack of highly active and specific tyrosine ammonia-lyases has previously been a limitation in metabolic engineering approaches. we therefore identified 22 sequences in silico using synteny information and aiming for sequence divergence. we performed a comparative in vivo study, expressing the genes intracellularly in bacteria ... | 2015 | 25911487 |
| 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 |
| lov histidine kinase modulates the general stress response system and affects the virb operon expression in brucella abortus. | brucella is the causative agent of the zoonotic disease brucellosis, and its success as an intracellular pathogen relies on its ability to adapt to the harsh environmental conditions that it encounters inside the host. the brucella genome encodes a sensor histidine kinase containing a lov domain upstream from the kinase, lovhk, which plays an important role in light-regulated brucella virulence. in this report we study the intracellular signaling pathway initiated by the light sensor lovhk using ... | 2015 | 25993430 |
| proteins related to the type i secretion system are associated with secondary seca_dead domain proteins in some species of planctomycetes, verrucomicrobia, proteobacteria, nitrospirae and chlorobi. | a number of bacteria belonging to the pvc (planctomycetes-verrucomicrobia-chlamydiae) super-phylum contain unusual ribosome-bearing intracellular membranes. the evolutionary origins and functions of these membranes are unknown. some proteins putatively associated with the presence of intracellular membranes in pvc bacteria contain signal peptides. signal peptides mark proteins for translocation across the cytoplasmic membrane in prokaryotes, and the membrane of the endoplasmic reticulum in eukar ... | 2015 | 26030905 |
| 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 |
| pivotal roles of phyllosphere microorganisms at the interface between plant functioning and atmospheric trace gas dynamics. | the phyllosphere, which lato sensu consists of the aerial parts of plants, and therefore primarily, of the set of photosynthetic leaves, is one of the most prevalent microbial habitats on earth. phyllosphere microbiota are related to original and specific processes at the interface between plants, microorganisms and the atmosphere. recent -omics studies have opened fascinating opportunities for characterizing the spatio-temporal structure of phyllosphere microbial communities in relation with st ... | 2015 | 26052316 |
| comparative genomics and mutagenesis analyses of choline metabolism in the marine roseobacter clade. | choline is ubiquitous in marine eukaryotes and appears to be widely distributed in surface marine waters; however, its metabolism by marine bacteria is poorly understood. here, using comparative genomics and molecular genetic approaches, we reveal that the capacity for choline catabolism is widespread in marine heterotrophs of the marine roseobacter clade (mrc). using the model bacterium ruegeria pomeroyi, we confirm that the beta, betb and betc genes, encoding choline dehydrogenase, betaine ald ... | 2015 | 26058574 |
| bacterial cellulose biosynthesis: diversity of operons, subunits, products, and functions. | recent studies of bacterial cellulose biosynthesis, including structural characterization of a functional cellulose synthase complex, provided the first mechanistic insight into this fascinating process. in most studied bacteria, just two subunits, bcsa and bcsb, are necessary and sufficient for the formation of the polysaccharide chain in vitro. other subunits - which differ among various taxa - affect the enzymatic activity and product yield in vivo by modulating (i) the expression of the bios ... | 2015 | 26077867 |
| nitrite-oxidizing bacterium nitrobacter winogradskyi produces n-acyl-homoserine lactone autoinducers. | nitrobacter winogradskyi is a chemolithotrophic bacterium that plays a role in the nitrogen cycle by oxidizing nitrite to nitrate. here, we demonstrate a functional n-acyl-homoserine lactone (acyl-hsl) synthase in this bacterium. the n. winogradskyi genome contains genes encoding a putative acyl-hsl autoinducer synthase (nwi0626, nwii) and a putative acyl-hsl autoinducer receptor (nwi0627, nwir) with amino acid sequences 38 to 78% identical to those in rhodopseudomonas palustris and other rhizob ... | 2015 | 26092466 |
| metabolic network modeling of microbial communities. | genome-scale metabolic network reconstructions and constraint-based analyses are powerful methods that have the potential to make functional predictions about microbial communities. genome-scale metabolic networks are used to characterize the metabolic functions of microbial communities via several techniques including species compartmentalization, separating species-level and community-level objectives, dynamic analysis, the 'enzyme-soup' approach, multiscale modeling, and others. there are man ... | 2015 | 26109480 |
| 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 |
| the hidden world within plants: ecological and evolutionary considerations for defining functioning of microbial endophytes. | all plants are inhabited internally by diverse microbial communities comprising bacterial, archaeal, fungal, and protistic taxa. these microorganisms showing endophytic lifestyles play crucial roles in plant development, growth, fitness, and diversification. the increasing awareness of and information on endophytes provide insight into the complexity of the plant microbiome. the nature of plant-endophyte interactions ranges from mutualism to pathogenicity. this depends on a set of abiotic and bi ... | 2015 | 26136581 |
| pqqe from methylobacterium extorquens am1: a radical s-adenosyl-l-methionine enzyme with an unusual tolerance to oxygen. | methylobacterium extorquens am1 is an aerobic facultative methylotroph known to secrete pyrroloquinoline quinone (pqq), a cofactor of a number of bacterial dehydrogenases, into the culture medium. to elucidate the molecular mechanism of pqq biosynthesis, we are focusing on pqqe which is believed to be the enzyme catalysing the first reaction of the pathway. pqqe belongs to the radical s-adenosyl-l-methionine (sam) superfamily, in which most, if not all, enzymes are very sensitive to dissolved ox ... | 2015 | 26188050 |
| pqqe from methylobacterium extorquens am1: a radical s-adenosyl-l-methionine enzyme with an unusual tolerance to oxygen. | methylobacterium extorquens am1 is an aerobic facultative methylotroph known to secrete pyrroloquinoline quinone (pqq), a cofactor of a number of bacterial dehydrogenases, into the culture medium. to elucidate the molecular mechanism of pqq biosynthesis, we are focusing on pqqe which is believed to be the enzyme catalysing the first reaction of the pathway. pqqe belongs to the radical s-adenosyl-l-methionine (sam) superfamily, in which most, if not all, enzymes are very sensitive to dissolved ox ... | 2015 | 26188050 |
| structured and dynamic disordered domains regulate the activity of a multifunctional anti-σ factor. | the anti-σ factor nepr plays a central role in regulation of the general stress response (gsr) in alphaproteobacteria. this small protein has two known interaction partners: its cognate extracytoplasmic function (ecf) σ factor and the anti-anti-σ factor, phyr. stress-dependent phosphorylation of phyr initiates a protein partner switch that promotes phospho-phyr binding to nepr, which frees ecf σ to activate transcription of genes required for cell survival under adverse or fluctuating conditions ... | 2015 | 26220965 |
| diversity, bacterial symbionts and antibacterial potential of gut-associated fungi isolated from the pantala flavescens larvae in china. | the diversity of fungi associated with the gut of pantala flavescens larvae was investigated using a culture-dependent method and molecular identification based on an analysis of the internally transcribed spacer sequence. in total, 48 fungal isolates were obtained from p. flavescens larvae. based on phylogenetic analyses, the fungal isolates were grouped in 5 classes and 12 different genera. fourteen bacterial 16s rdna sequences derived from total genomic dna extractions of fungal mycelia were ... | 2015 | 26221957 |
| assessing the genetic diversity of cu resistance in mine tailings through high-throughput recovery of full-length copa genes. | characterizing the genetic diversity of microbial copper (cu) resistance at the community level remains challenging, mainly due to the polymorphism of the core functional gene copa. in this study, a local blastn method using a copa database built in this study was developed to recover full-length putative copa sequences from an assembled tailings metagenome; these sequences were then screened for potentially functioning copa using conserved metal-binding motifs, inferred by evolutionary trace an ... | 2015 | 26286020 |
| cerium regulates expression of alternative methanol dehydrogenases in methylosinus trichosporium ob3b. | methanotrophs have multiple methane monooxygenases that are well known to be regulated by copper, i.e., a "copper switch." at low copper/biomass ratios the soluble methane monooxygenase (smmo) is expressed while expression and activity of the particulate methane monooxygenase (pmmo) increases with increasing availability of copper. in many methanotrophs there are also multiple methanol dehydrogenases (medhs), one based on mxa and another based on xox. mxa-medh is known to have calcium in its act ... | 2015 | 26296730 |
| a comparison of the microbial production and combustion characteristics of three alcohol biofuels: ethanol, 1-butanol, and 1-octanol. | over the last decade, microbes have been engineered for the manufacture of a variety of biofuels. saturated linear-chain alcohols have great potential as transport biofuels. their hydrocarbon backbones, as well as oxygenated content, confer combustive properties that make it suitable for use in internal combustion engines. herein, we compared the microbial production and combustion characteristics of ethanol, 1-butanol, and 1-octanol. in terms of productivity and efficiency, current microbial pl ... | 2015 | 26301219 |
| metabolic footprint of epiphytic bacteria on arabidopsis thaliana leaves. | the phyllosphere, which is defined as the parts of terrestrial plants above the ground, is a large habitat for different microorganisms that show a high extent of adaption to their environment. a number of hypotheses were generated by culture-independent functional genomics studies to explain the competitiveness of specialized bacteria in the phyllosphere. in contrast, in situ data at the metabolome level as a function of bacterial colonization are lacking. here, we aimed to obtain new insights ... | 2016 | 26305156 |
| cbbr, the master regulator for microbial carbon dioxide fixation. | biological carbon dioxide fixation is an essential and crucial process catalyzed by both prokaryotic and eukaryotic organisms to allow ubiquitous atmospheric co2 to be reduced to usable forms of organic carbon. this process, especially the calvin-bassham-benson (cbb) pathway of co2 fixation, provides the bulk of organic carbon found on earth. the enzyme ribulose 1,5-bisphosphate (rubp) carboxylase/oxygenase (rubisco) performs the key and rate-limiting step whereby co2 is reduced and incorporated ... | 2015 | 26324454 |
| 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 |
| hopanoids as functional analogues of cholesterol in bacterial membranes. | the functionality of cellular membranes relies on the molecular order imparted by lipids. in eukaryotes, sterols such as cholesterol modulate membrane order, yet they are not typically found in prokaryotes. the structurally similar bacterial hopanoids exhibit similar ordering properties as sterols in vitro, but their exact physiological role in living bacteria is relatively uncharted. we present evidence that hopanoids interact with glycolipids in bacterial outer membranes to form a highly order ... | 2015 | 26351677 |
| engineering methylobacterium extorquens for de novo synthesis of the sesquiterpenoid α-humulene from methanol. | over the last 10 to 15 years, metabolic engineering of microbes has become a versatile tool for high-level de novo synthesis of terpenoids, with the sesquiterpenoids armopha-1,4-diene, farnesene and artemisinic acid as prime examples. however, almost all cell factory approaches towards terpenoids to date have been based on sugar as the raw material, which is mainly used as a food resource and subject to high price volatilities. in this study we present de novo synthesis of the sesquiterpenoid α- ... | 2015 | 26369439 |
| general stress signaling in the alphaproteobacteria. | the alphaproteobacteria uniquely integrate features of two-component signal transduction and alternative σ factor regulation to control transcription of genes that ensure growth and survival across a range of stress conditions. research over the past decade has led to the discovery of the key molecular players of this general stress response (gsr) system, including the sigma factor σ(ecfg), its anti-σ factor nepr, and the anti-anti-σ factor phyr. the central molecular event of gsr activation ent ... | 2015 | 26442844 |
| roles of the crotonyl-coa carboxylase/reductase homologues in acetate assimilation and biosynthesis of immunosuppressant fk506 in streptomyces tsukubaensis. | in microorganisms lacking a functional glyoxylate cycle, acetate can be assimilated by alternative pathways of carbon metabolism such as the ethylmalonyl-coa (emc) pathway. among the enzymes converting coa-esters of the emc pathway, there is a unique carboxylase that reductively carboxylates crotonyl-coa, crotonyl-coa carboxylase/reductase (ccr). in addition to the emc pathway, gene homologues of ccr can be found in secondary metabolite gene clusters that are involved in the provision of structu ... | 2015 | 26466669 |
| identification of two mutations increasing the methanol tolerance of corynebacterium glutamicum. | methanol is present in most ecosystems and may also occur in industrial applications, e.g. as an impurity of carbon sources such as technical glycerol. methanol often inhibits growth of bacteria, thus, methanol tolerance may limit fermentative production processes. | 2015 | 26474849 |
| degradation of benzene by pseudomonas veronii 1ydbtex2 and 1yb2 is catalyzed by enzymes encoded in distinct catabolism gene clusters. | pseudomonas veronii 1ydbtex2, a benzene and toluene degrader, and pseudomonas veronii 1yb2, a benzene degrader, have previously been shown to be key players in a benzene-contaminated site. these strains harbor unique catabolic pathways for the degradation of benzene comprising a gene cluster encoding an isopropylbenzene dioxygenase where genes encoding downstream enzymes were interrupted by stop codons. extradiol dioxygenases were recruited from gene clusters comprising genes encoding a 2-hydrox ... | 2015 | 26475106 |
| degradation of benzene by pseudomonas veronii 1ydbtex2 and 1yb2 is catalyzed by enzymes encoded in distinct catabolism gene clusters. | pseudomonas veronii 1ydbtex2, a benzene and toluene degrader, and pseudomonas veronii 1yb2, a benzene degrader, have previously been shown to be key players in a benzene-contaminated site. these strains harbor unique catabolic pathways for the degradation of benzene comprising a gene cluster encoding an isopropylbenzene dioxygenase where genes encoding downstream enzymes were interrupted by stop codons. extradiol dioxygenases were recruited from gene clusters comprising genes encoding a 2-hydrox ... | 2015 | 26475106 |
| pentanol and benzyl alcohol attack bacterial surface structures differently. | the genus methylobacterium tolerates hygiene agents like benzalkonium chloride (bac), and infection with this organism is an important public health issue. here, we found that the combination of bac with particular alcohols at nonlethal concentrations in terms of their solitary uses significantly reduced bacterial viability after only 5 min of exposure. among the alcohols, raman spectroscopic analyses showed that pentanol (pentyl alcohol [pea]) and benzyl alcohol (bza) accelerated the cellular a ... | 2015 | 26519389 |
| pentanol and benzyl alcohol attack bacterial surface structures differently. | the genus methylobacterium tolerates hygiene agents like benzalkonium chloride (bac), and infection with this organism is an important public health issue. here, we found that the combination of bac with particular alcohols at nonlethal concentrations in terms of their solitary uses significantly reduced bacterial viability after only 5 min of exposure. among the alcohols, raman spectroscopic analyses showed that pentanol (pentyl alcohol [pea]) and benzyl alcohol (bza) accelerated the cellular a ... | 2015 | 26519389 |
| bioconversion of methanol to value-added mevalonate by engineered methylobacterium extorquens am1 containing an optimized mevalonate pathway. | methylotrophic biosynthesis using methanol as a feedstock is a promising and attractive method to solve the over-dependence of the bioindustry on sugar feedstocks derived from grains that are used for food. in this study, we introduced and engineered the mevalonate pathway into methylobacterium extorquens am1 to achieve high mevalonate production from methanol, which could be a platform for terpenoid synthesis. we first constructed a natural operon (mve) harboring the mvas and mvae genes from en ... | 2016 | 26521242 |
| dndei exhibits helicase activity essential for dna phosphorothioate modification and atpase activity strongly stimulated by dna substrate with a gaac/gttc motif. | phosphorothioate (pt) modification of dna, in which the non-bridging oxygen of the backbone phosphate group is replaced by sulfur, is governed by the dnda-e proteins in prokaryotes. to better understand the biochemical mechanism of pt modification, functional analysis of the recently found pt-modifying enzyme dndei, which has an additional domain compared with canonical dnde, from riemerella anatipestifer is performed in this study. the additional domain is identified as a dna helicase, and func ... | 2015 | 26631733 |
| dndei exhibits helicase activity essential for dna phosphorothioate modification and atpase activity strongly stimulated by dna substrate with a gaac/gttc motif. | phosphorothioate (pt) modification of dna, in which the non-bridging oxygen of the backbone phosphate group is replaced by sulfur, is governed by the dnda-e proteins in prokaryotes. to better understand the biochemical mechanism of pt modification, functional analysis of the recently found pt-modifying enzyme dndei, which has an additional domain compared with canonical dnde, from riemerella anatipestifer is performed in this study. the additional domain is identified as a dna helicase, and func ... | 2015 | 26631733 |
| comprehensive genomic analyses of the om43 clade, including a novel species from the red sea, indicate ecotype differentiation among marine methylotrophs. | the om43 clade within the family methylophilaceae of betaproteobacteria represents a group of methylotrophs that play important roles in the metabolism of c1 compounds in marine environments and other aquatic environments around the globe. using dilution-to-extinction cultivation techniques, we successfully isolated a novel species of this clade (here designated mbrs-h7) from the ultraoligotrophic open ocean waters of the central red sea. phylogenomic analyses indicate that mbrs-h7 is a novel sp ... | 2016 | 26655752 |
| isolation of radiation-resistant bacteria from mars analog antarctic dry valleys by preselection, and the correlation between radiation and desiccation resistance. | extreme radiation-resistant microorganisms can survive doses of ionizing radiation far greater than are present in the natural environment. radiation resistance is believed to be an incidental adaptation to desiccation resistance, as both hazards cause similar cellular damage. desert soils are, therefore, promising targets to prospect for new radiation-resistant strains. this is the first study to isolate radiation-resistant microbes by using gamma-ray exposure preselection from the extreme cold ... | 2015 | 26684506 |
| comparative genomics of pathogenic and nonpathogenic strains of xanthomonas arboricola unveil molecular and evolutionary events linked to pathoadaptation. | the bacterial species xanthomonas arboricola contains plant pathogenic and nonpathogenic strains. it includes the pathogen x. arboricola pv. juglandis, causing the bacterial blight of juglans regia. the emergence of a new bacterial disease of j. regia in france called vertical oozing canker (voc) was previously described and the causal agent was identified as a distinct genetic lineage within the pathovar juglandis. symptoms on walnut leaves and fruits are similar to those of a bacterial blight ... | 2015 | 26734033 |
| 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 |
| lignin engineering in field-grown poplar trees affects the endosphere bacterial microbiome. | cinnamoyl-coa reductase (ccr), an enzyme central to the lignin biosynthetic pathway, represents a promising biotechnological target to reduce lignin levels and to improve the commercial viability of lignocellulosic biomass. however, silencing of the ccr gene results in considerable flux changes of the general and monolignol-specific lignin pathways, ultimately leading to the accumulation of various extractable phenolic compounds in the xylem. here, we evaluated host genotype-dependent effects of ... | 2016 | 26755604 |
| non-targeted determination of (13)c-labeling in the methylobacterium extorquens am1 metabolome using the two-dimensional mass cluster method and principal component analysis. | a novel analytical workflow is presented for the analysis of time-dependent (13)c-labeling of the metabolites in the methylotrophic bacterium methylobacterium extorquens am1 using gas chromatography time-of-flight mass spectrometry (gc-tofms). using (13)c-methanol as the substrate in a time course experiment, the method provides an accurate determination of the number of carbons converted to the stable isotope. the method also extracts a quantitative isotopic dilution time course profile for (13 ... | 2016 | 26787164 |
| lanthanide-dependent regulation of methanol oxidation systems in methylobacterium extorquens am1 and their contribution to methanol growth. | methylobacterium extorquens am1 has two distinct types of methanol dehydrogenase (medh) enzymes that catalyze the oxidation of methanol to formaldehyde. mxafi-medh requires pyrroloquinoline quinone (pqq) and ca in its active site, while xoxf-medh requires pqq and lanthanides, such as ce and la. using medh mutant strains to conduct growth analysis and medh activity assays, we demonstrate that m. extorquens am1 has at least one additional lanthanide-dependent methanol oxidation system contributing ... | 2016 | 26833413 |
| xoxf acts as the predominant methanol dehydrogenase in the type i methanotroph methylomicrobium buryatense. | many methylotrophic taxa harbor two distinct methanol dehydrogenase (mdh) systems for oxidizing methanol to formaldehyde: the well-studied calcium-dependent mxafi type and the more recently discovered lanthanide-containing xoxf type. mxafi has traditionally been accepted as the major functional mdh in bacteria that contain both enzymes. however, in this study, we present evidence that, in a type i methanotroph, methylomicrobium buryatense, xoxf is likely the primary functional mdh in the environ ... | 2016 | 26858104 |
| the one-carbon carrier methylofuran from methylobacterium extorquens am1 contains a large number of α- and γ-linked glutamic acid residues. | methylobacterium extorquens am1 uses dedicated cofactors for one-carbon unit conversion. based on the sequence identities of enzymes and activity determinations, a methanofuran analog was proposed to be involved in formaldehyde oxidation in alphaproteobacteria. here, we report the structure of the cofactor, which we termed methylofuran. using an in vitro enzyme assay and lc-ms, methylofuran was identified in cell extracts and further purified. from the exact mass and ms-ms fragmentation pattern, ... | 2016 | 26895963 |
| large-effect beneficial synonymous mutations mediate rapid and parallel adaptation in a bacterium. | contrary to previous understanding, recent evidence indicates that synonymous codon changes may sometimes face strong selection. however, it remains difficult to generalize the nature, strength, and mechanism(s) of such selection. previously, we showed that synonymous variants of a key enzyme-coding gene (fae) of methylobacterium extorquens am1 decreased enzyme production and reduced fitness dramatically. we now show that during laboratory evolution, these variants rapidly regained fitness via p ... | 2016 | 26908584 |
| versatile vectors for efficient mutagenesis of bradyrhizobium diazoefficiens and other alphaproteobacteria. | analysis of bacterial gene function commonly relies on gene disruption or replacement followed by phenotypic characterization of the resulting mutant strains. deletion or replacement of targeted regions is commonly achieved via two homologous recombination (hr) events between the bacterial genome and a nonreplicating plasmid carrying dna fragments flanking the region to be deleted. the counterselection of clones that have integrated the entire plasmid in their genome via a single hr event is cru ... | 2016 | 26921431 |
| [functionality of the xoxf gene in methylobacterium dichloromethanicum dm4]. | activation of expression of the xoxfgene encoding pqq-dependent methanol/ethanol dehydrogenase (metdi2492) in dichloromethane- (dcm) -grown methylobacterium dichloromethanicum dm4 was first demonstrated. the sequence of the only xoxf homolog found in the genome of strain dm4 exhibited 50% identity to that of the protein (mxaf) of the large subunit of methanol dehydrogenase (mdh). a knockout mutant with the inactivate xoxf gene (δxoxf) was found to be unable to grow on methanol due to the absence ... | 2016 | 26964359 |
| multiple σecfg and nepr proteins are involved in the general stress response in methylobacterium extorquens. | in alphaproteobacteria, the general stress response (gsr) is controlled by a conserved partner switch composed of the sigma factor σ(ecfg), its anti-sigma factor nepr and the anti-sigma factor antagonist phyr. many species possess paralogues of one or several components of the system, but their roles remain largely elusive. among alphaproteobacteria that have been genome-sequenced so far, the genus methylobacterium possesses the largest number of σ(ecfg) proteins. here, we analyzed the six σ(ecf ... | 2016 | 27028226 |
| calorespirometric feeding control enhances bioproduction from toxic feedstocks-demonstration for biopolymer production out of methanol. | the sustainable production of fuels and industrial bulk chemicals by microorganisms in biotechnological processes is promising but still facing various challenges. in particular, toxic substrates require an efficient process control strategy. methanol, as an example, has the potential to become a major future feedstock due to its availability from fossil and renewable resources. however, besides being toxic, methanol is highly volatile. to optimize its dosage during microbial cultivations, an in ... | 2016 | 27043974 |
| shifts in plant foliar and floral metabolomes in response to the suppression of the associated microbiota. | the phyllospheric microbiota is assumed to play a key role in the metabolism of host plants. its role in determining the epiphytic and internal plant metabolome, however, remains to be investigated. we analyzed the liquid chromatography-mass spectrometry (lc-ms) profiles of the epiphytic and internal metabolomes of the leaves and flowers of sambucus nigra with and without external antibiotic treatment application. | 2016 | 27048394 |
| epistasis and the structure of fitness landscapes: are experimental fitness landscapes compatible with fisher's geometric model? | the fitness landscape defines the relationship between genotypes and fitness in a given environment and underlies fundamental quantities such as the distribution of selection coefficient and the magnitude and type of epistasis. a better understanding of variation in landscape structure across species and environments is thus necessary to understand and predict how populations will adapt. an increasing number of experiments investigate the properties of fitness landscapes by identifying mutations ... | 2016 | 27052568 |
| associations between ectomycorrhizal fungi and bacterial needle endophytes in pinus radiata: implications for biotic selection of microbial communities. | studies of the ecological and evolutionary relationships between plants and their associated microbes have long been focused on single microbes, or single microbial guilds, but in reality, plants associate with a diverse array of microbes from a varied set of guilds. as such, multitrophic interactions among plant-associated microbes from multiple guilds represent an area of developing research, and can reveal how complex microbial communities are structured around plants. interactions between co ... | 2016 | 27065966 |
| comprehensive molecular characterization of methylobacterium extorquens am1 adapted for 1-butanol tolerance. | the toxicity of alcohols is one of the major roadblocks of biological fermentation for biofuels production. methylobacterium extorquens am1, a facultative methylotrophic α-proteobacterium, has been engineered to generate 1-butanol from cheap carbon feedstocks through a synthetic metabolic pathway. however, m. extorquens am1 is vulnerable to solvent stress, which impedes further development for 1-butanol production. only a few studies have reported the general stress response of m. extorquens am1 ... | 2016 | 27069508 |
| metabolomics revealed an association of metabolite changes and defective growth in methylobacterium extorquens am1 overexpressing ecm during growth on methanol. | methylobacterium extorquens am1 is a facultative methylotroph capable of growth on both single-carbon and multi-carbon compounds. the ethylmalonyl-coa (emc) pathway is one of the central assimilatory pathways in m. extorquens during growth on c1 and c2 substrates. previous studies had shown that ethylmalonyl-coa mutase functioned as a control point during the transition from growth on succinate to growth on ethylamine. in this study we overexpressed ecm, phaa, mcmab and found that upregulating e ... | 2016 | 27116459 |
| perturbation of the two-component signal transduction system, bprrs, results in attenuated virulence and motility defects in burkholderia pseudomallei. | burkholderia pseudomallei is the causative agent of melioidosis, a severe invasive disease of humans and animals. initial screening of a b. pseudomallei signature-tagged mutagenesis library identified an attenuated mutant with a transposon insertion in a gene encoding the sensor component of an uncharacterised two-component signal transduction system (tcsts), which we designated bprrs. | 2016 | 27147217 |
| the frequency of internal shine-dalgarno-like motifs in prokaryotes. | in prokaryotes, translation initiation typically depends on complementary binding between a g-rich shine-dalgarno (sd) motif in the 5' untranslated region of mrnas, and the 3' tail of the 16s ribosomal rna (the anti-sd sequence). in some cases, internal sd-like motifs in the coding region generate "programmed" ribosomal pauses that are beneficial for protein folding or accurate targeting. on the other hand, such pauses can also reduce protein production, generating purifying selection against in ... | 2016 | 27189998 |
| isolation of oxamyl-degrading bacteria and identification of ceha as a novel oxamyl hydrolase gene. | microbial degradation is the main process controlling the environmental dissipation of the nematicide oxamyl. despite that, little is known regarding the microorganisms involved in its biotransformation. we report the isolation of four oxamyl-degrading bacterial strains from an agricultural soil exhibiting enhanced biodegradation of oxamyl. multilocus sequence analysis (mlsa) assigned the isolated bacteria to different subgroups of the genus pseudomonas. the isolated bacteria hydrolyzed oxamyl t ... | 2016 | 27199945 |
| selection maintains apparently degenerate metabolic pathways due to tradeoffs in using methylamine for carbon versus nitrogen. | microorganisms often encode multiple non-orthologous metabolic modules that catalyze the same reaction. however, little experimental evidence actually demonstrates a selective basis for metabolic degeneracy. many methylotrophs-microorganisms that grow on reduced single-carbon compounds-like methylobacterium extorquens am1 encode two routes for methylamine oxidation: the periplasmic methylamine dehydrogenase (madh) and the cytoplasmic n-methylglutamate (nmg) pathway. in methylobacterium extorquen ... | 2016 | 27212407 |
| metabolic network modeling of microbial interactions in natural and engineered environmental systems. | we review approaches to characterize metabolic interactions within microbial communities using stoichiometric metabolic network (smn) models for applications in environmental and industrial biotechnology. smn models are computational tools used to evaluate the metabolic engineering potential of various organisms. they have successfully been applied to design and optimize the microbial production of antibiotics, alcohols and amino acids by single strains. to date however, such models have been ra ... | 2016 | 27242701 |
| [enhanced resistance of pea plants to oxidative: stress caused by paraquat during colonization by aerobic methylobacteria]. | the influence of colonization of the pea (pisum sativum l.) by aerobic methylobacteria of five different species (methylophilus flavus ship, methylobacterium extorquens g10, methylobacillus arboreus iva, methylopila musalis musa, methylopila turkiensis sidel) on plant resistance to paraquat-induced stresses has been studied. the normal conditions of pea colonization by methylobacteria were characterized by a decrease in the activity of antioxidant enzymes (superoxide dismutase, catalase, and per ... | 2016 | 27266250 |
| adding biotic complexity alters the metabolic benefits of mutualism. | mutualism is ubiquitous in nature and plays an integral role in most communities. to predict the eco-evolutionary dynamics of mutualism it is critical to extend classic pair-wise analysis to include additional species. we investigated the effect of adding a third species to a pair-wise mutualism in a spatially structured environment. we tested the hypotheses that selection for costly excretions in a focal population (i) decreases when an exploiter is added (ii) increases when a third mutualist i ... | 2016 | 27272242 |
| regulation of pyrroloquinoline quinone-dependent glucose dehydrogenase activity in the model rhizosphere-dwelling bacterium pseudomonas putida kt2440. | soil-dwelling microbes solubilize mineral phosphates by secreting gluconic acid, which is produced from glucose by a periplasmic glucose dehydrogenase (gdh) that requires pyrroloquinoline quinone (pqq) as a redox coenzyme. while gdh-dependent phosphate solubilization has been observed in numerous bacteria, little is known concerning the mechanism by which this process is regulated. here we use the model rhizosphere-dwelling bacterium pseudomonas putida kt2440 to explore gdh activity and pqq synt ... | 2016 | 27287323 |
| the arabidopsis leaf transcriptome reveals distinct but also overlapping responses to colonization by phyllosphere commensals and pathogen infection with impact on plant health. | plants are colonized by a variety of bacteria, most of which are not pathogenic. currently, the plant responses to phyllosphere commensals or to pathogen infection in the presence of commensals are not well understood. here, we examined the transcriptional response of arabidopsis thaliana leaves to colonization by common commensal bacteria in a gnotobiotic system using rna sequencing and conducted plant mutant assays. arabidopsis responded differently to the model bacteria sphingomonas melonis f ... | 2016 | 27306148 |
| towards stable kinetics of large metabolic networks: nonequilibrium potential function approach. | while the biochemistry of metabolism in many organisms is well studied, details of the metabolic dynamics are not fully explored yet. acquiring adequate in vivo kinetic parameters experimentally has always been an obstacle. unless the parameters of a vast number of enzyme-catalyzed reactions happened to fall into very special ranges, a kinetic model for a large metabolic network would fail to reach a steady state. in this work we show that a stable metabolic network can be systematically establi ... | 2016 | 27415300 |
| metagenomic analysis revealed methylamine and ureide utilization of soybean-associated methylobacterium. | methylobacterium inhabits the phyllosphere of a large number of plants. we herein report the results of comparative metagenome analyses on methylobacterial communities of soybean plants grown in an experimental field in tohoku university (kashimadai, miyagi, japan). methylobacterium was identified as the most dominant genus (33%) among bacteria inhabiting soybean stems. we classified plant-derived methylobacterium species into groups i, ii, and iii based on 16s rrna gene sequences, and found tha ... | 2016 | 27431374 |
| difference in c3-c4 metabolism underlies tradeoff between growth rate and biomass yield in methylobacterium extorquens am1. | two variants of methylobacterium extorquens am1 demonstrated a trade-off between growth rate and biomass yield. in addition, growth rate and biomass yield were also affected by supplementation of growth medium with different amounts of cobalt. the metabolism changes relating to these growth phenomena as well as the trade-off were investigated in this study. (13)c metabolic flux analysis was used to generate a detailed central carbon metabolic flux map with both absolute and normalized flux value ... | 2016 | 27435978 |
| systems-level proteomics of two ubiquitous leaf commensals reveals complementary adaptive traits for phyllosphere colonization. | plants are colonized by a diverse community of microorganisms, the plant microbiota, exhibiting a defined and conserved taxonomic structure. niche separation based on spatial segregation and complementary adaptation strategies likely forms the basis for coexistence of the various microorganisms in the plant environment. to gain insights into organism-specific adaptations on a molecular level, we selected two exemplary community members of the core leaf microbiota and profiled their proteomes upo ... | 2016 | 27457762 |
| transfer of a catabolic pathway for chloromethane in methylobacterium strains highlights different limitations for growth with chloromethane or with dichloromethane. | chloromethane (cm) is an ozone-depleting gas, produced predominantly from natural sources, that provides an important carbon source for microbes capable of consuming it. cm catabolism has been difficult to study owing to the challenging genetics of its native microbial hosts. since the pathways for cm catabolism show evidence of horizontal gene transfer, we reproduced this transfer process in the laboratory to generate new cm-catabolizing strains in tractable hosts. we demonstrate that six putat ... | 2016 | 27486448 |
| love the one you're with: replicate viral adaptations converge on the same phenotypic change. | parallelism is important because it reveals how inherently stochastic adaptation is. even as we come to better understand evolutionary forces, stochasticity limits how well we can predict evolutionary outcomes. here we sought to quantify parallelism and some of its underlying causes by adapting a bacteriophage (id11) with nine different first-step mutations, each with eight-fold replication, for 100 passages. this was followed by whole-genome sequencing five isolates from each endpoint. a large ... | 2016 | 27547540 |