| type i pyridoxal 5'-phosphate dependent enzymatic domains embedded within multimodular nonribosomal peptide synthetase and polyketide synthase assembly lines. | pyridoxal 5'-phosphate (plp)-dependent enzymes of fold type i, the most studied structural class of the plp-dependent enzyme superfamily, are known to exist as stand-alone homodimers or homotetramers. these enzymes have been found also embedded in multimodular and multidomain assembly lines involved in the biosynthesis of polyketides (pks) and nonribosomal peptides (nrps). the aim of this work is to provide a proteome-wide view of the distribution and characteristics of type i domains covalently ... | 2013 | 24148833 |
| beating the acetyl coenzyme a-pathway to the origin of life. | attempts to draft plausible scenarios for the origin of life have in the past mainly built upon palaeogeochemical boundary conditions while, as detailed in a companion article in this issue, frequently neglecting to comply with fundamental thermodynamic laws. even if demands from both palaeogeochemistry and thermodynamics are respected, then a plethora of strongly differing models are still conceivable. although we have no guarantee that life at its origin necessarily resembled biology in extant ... | 2013 | 23754811 |
| the methanol dehydrogenase gene, mxaf, as a functional and phylogenetic marker for proteobacterial methanotrophs in natural environments. | the mxaf gene, coding for the large (α) subunit of methanol dehydrogenase, is highly conserved among distantly related methylotrophic species in the alpha-, beta- and gammaproteobacteria. it is ubiquitous in methanotrophs, in contrast to other methanotroph-specific genes such as the pmoa and mmox genes, which are absent in some methanotrophic proteobacterial genera. this study examined the potential for using the mxaf gene as a functional and phylogenetic marker for methanotrophs. mxaf and 16s r ... | 2013 | 23451130 |
| evolution of mitochondria reconstructed from the energy metabolism of living bacteria. | the ancestors of mitochondria, or proto-mitochondria, played a crucial role in the evolution of eukaryotic cells and derived from symbiotic α-proteobacteria which merged with other microorganisms - the basis of the widely accepted endosymbiotic theory. however, the identity and relatives of proto-mitochondria remain elusive. here we show that methylotrophic α-proteobacteria could be the closest living models for mitochondrial ancestors. we reached this conclusion after reconstructing the possibl ... | 2014 | 24804722 |
| the opportunity for high-performance biomaterials from methane. | polyhydroxyalkanoate (pha) biopolymers are widely recognised as outstanding candidates to replace conventional petroleum-derived polymers. their mechanical properties are good and can be tailored through copolymer composition, they are biodegradable, and unlike many alternatives, they do not rely on oil-based feedstocks. further, they are the only commodity polymer that can be synthesised intracellularly, ensuring stereoregularity and high molecular weight. however, despite offering enormous pot ... | 2016 | 27681905 |
| diversity of structure and function of response regulator output domains. | response regulators (rrs) within two-component signal transduction systems control a variety of cellular processes. most rrs contain dna-binding output domains and serve as transcriptional regulators. other rr types contain rna-binding, ligand-binding, protein-binding or transporter output domains and exert regulation at the transcriptional, post-transcriptional or post-translational levels. in a significant fraction of rrs, output domains are enzymes that themselves participate in signal transd ... | 2010 | 20226724 |
| 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 |
| evolutionary switches between two serine codon sets are driven by selection. | serine is the only amino acid that is encoded by two disjoint codon sets so that a tandem substitution of two nucleotides is required to switch between the two sets. previously published evidence suggests that, for the most evolutionarily conserved serines, the codon set switch occurs by simultaneous substitution of two nucleotides. here we report a genome-wide reconstruction of the evolution of serine codons in triplets of closely related species from diverse prokaryotes and eukaryotes. the res ... | 2016 | 27799560 |
| 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 |
| determination of enzyme mechanisms by molecular dynamics: studies on quinoproteins, methanol dehydrogenase, and soluble glucose dehydrogenase. | molecular dynamics (md) simulations have been carried out to study the enzymatic mechanisms of quinoproteins, methanol dehydrogenase (mdh), and soluble glucose dehydrogenase (sgdh). the mechanisms of reduction of the orthoquinone cofactor (pqq) of mdh and sgdh involve concerted base-catalyzed proton abstraction from the hydroxyl moiety of methanol or from the 1-hydroxyl of glucose, and hydride equivalent transfer from the substrate to the quinone carbonyl carbon c5 of pqq. the products of methan ... | 2004 | 15273299 |
| key labeling technologies to tackle sizeable problems in rna structural biology. | the ability to adopt complex three-dimensional (3d) structures that can rapidly interconvert between multiple functional states (folding and dynamics) is vital for the proper functioning of rnas. consequently, rna structure and dynamics necessarily determine their biological function. in the post-genomic era, it is clear that rnas comprise a larger proportion (>50%) of the transcribed genome compared to proteins (< or =2%). yet the determination of the 3d structures of rnas lags considerably beh ... | 2008 | 19325801 |
| bacteria in crude oil survived autoclaving and stimulated differentially by exogenous bacteria. | autoclaving of crude oil is often used to evaluate the hydrocarbon-degrading abilities of bacteria. this may be potentially useful for bioaugmentation and microbial enhanced oil recovery (meor). however, it is not entirely clear if "endogenous" bacteria (e.g., spores) in/on crude oil survive the autoclaving process, or influence subsequent evaluation of the hydrocarbon-degradation abilities of the "exogenous" bacterial strains. to test this, we inoculated autoclaved crude oil medium with six exo ... | 2012 | 23028421 |
| the effect of nitrogen enrichment on c(1)-cycling microorganisms and methane flux in salt marsh sediments. | methane (ch(4)) flux from ecosystems is driven by c(1)-cycling microorganisms - the methanogens and the methylotrophs. little is understood about what regulates these communities, complicating predictions about how global change drivers such as nitrogen enrichment will affect methane cycling. using a nitrogen addition gradient experiment in three southern california salt marshes, we show that sediment ch(4) flux increased linearly with increasing nitrogen addition (1.23 μg ch(4) m(-2) day(-1) fo ... | 2012 | 22470369 |
| c1 metabolism in corynebacterium glutamicum: an endogenous pathway for oxidation of methanol to carbon dioxide. | methanol is considered an interesting carbon source in "bio-based" microbial production processes. since corynebacterium glutamicum is an important host in industrial biotechnology, in particular for amino acid production, we performed studies of the response of this organism to methanol. the c. glutamicum wild type was able to convert (13)c-labeled methanol to (13)co2. analysis of global gene expression in the presence of methanol revealed several genes of ethanol catabolism to be upregulated, ... | 2013 | 24014532 |
| crystallization and preliminary x-ray crystallographic analysis of mxaj, a component of the methanol-oxidizing system operon from the marine bacterium methylophaga aminisulfidivorans mpt. | the methanol-oxidizing system (mox) is essential for methylotrophic bacteria to extract energy during the oxidoreduction reaction and consists of a series of electron-transfer proteins encoded by the mox operon. one of the key enzymes is the α₂β₂ methanol dehydrogenase complex (type i mdh), which converts methanol to formaldehyde during the 2e⁻ transfer through the prosthetic group pyrroloquinoline quinone. mxaj, a product of mxaj of the mox operon, is a component of the mdh complex and enhances ... | 2013 | 23908039 |
| c₁-pathways in methyloversatilis universalis fam5: genome wide gene expression and mutagenesis studies. | methyloversatilis universalis fam5 utilizes single carbon compounds such as methanol or methylamine as a sole source of carbon and energy. expression profiling reveals distinct sets of genes altered during growth on methylamine vs methanol. as expected, all genes for the n-methylglutamate pathway were induced during growth on methylamine. among other functions responding to the aminated source of c₁-carbon, are a heme-containing amine dehydrogenase (qhp), a distant homologue of formaldehyde acti ... | 2015 | 27682085 |
| genomes of model organisms: know thy tools. | | 2008 | 18474084 |
| 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 |
| distribution of genes encoding nucleoid-associated protein homologs in plasmids. | bacterial nucleoid-associated proteins (naps) form nucleoprotein complexes and influence the expression of genes. recent studies have shown that some plasmids carry genes encoding nap homologs, which play important roles in transcriptional regulation networks between plasmids and host chromosomes. in this study, we determined the distributions of the well-known naps fis, h-ns, hu, ihf, and lrp and the newly found naps mvat and ndpa among the whole-sequenced 1382 plasmids found in gram-negative b ... | 2011 | 21350637 |
| 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 |
| 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 |
| 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 |
| genomes of the symbiotic nitrogen-fixing bacteria of legumes. | | 2007 | 17556525 |
| community acquired roseomonas infection in a pre-existing tubercular lung lesion. | roseomonas are nonfermenting opportunistic gram-negative bacilli belonging to the newly established genus of roseomonas. the clinical experience with the species is limited and is difficult to diagnose because of limited expertise and lack of commercially available identification kits with any of the automated systems. this is a first ever reported case of secondary bacterial infection due to roseomonas genomospecies 6 in a patient of pulmonary tuberculosis from the indian subcontinent. | 2014 | 25125823 |
| 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 |
| molecular adaptation mechanisms employed by ethanologenic bacteria in response to lignocellulose-derived inhibitory compounds. | current international interest in finding alternative sources of energy to the diminishing supplies of fossil fuels has encouraged research efforts in improving biofuel production technologies. in countries which lack sufficient food, the use of sustainable lignocellulosic feedstocks, for the production of bioethanol, is an attractive option. in the pre-treatment of lignocellulosic feedstocks for ethanol production, various chemicals and/or enzymatic processes are employed. these methods general ... | 2013 | 23847442 |
| 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 |
| sinorhizobium meliloti sigma factors rpoe1 and rpoe4 are activated in stationary phase in response to sulfite. | rhizobia are soil bacteria able to establish a nitrogen-fixing symbiosis with legume plants. both in soil and in planta, rhizobia spend non-growing periods resembling the stationary phase of in vitro-cultured bacteria. the primary objective of this work was to better characterize gene regulation in this biologically relevant growth stage in sinorhizobium meliloti. by a tap-tag/mass spectrometry approach, we identified five sigma factors co-purifying with the rna polymerase in stationary phase: t ... | 2012 | 23226379 |
| metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. | | 2014 | 24758379 |
| unpublished but public microbial genomes with biotechnological relevance. | | 2008 | 21261839 |
| working together for the common good: cell-cell communication in bacteria. | the 4th asm conference on cell-cell communication in bacteria was held in miami, fl, from 6 to 9 november 2011. this review highlights three key themes that emerged from the many exciting talks and poster presentations in the area of quorum sensing: sociomicrobiology, signal transduction mechanisms, and interspecies communication. | 2012 | 22389476 |
| bacterial endosymbiosis in a chordate host: long-term co-evolution and conservation of secondary metabolism. | intracellular symbiosis is known to be widespread in insects, but there are few described examples in other types of host. these symbionts carry out useful activities such as synthesizing nutrients and conferring resistance against adverse events such as parasitism. such symbionts persist through host speciation events, being passed down through vertical transmission. due to various evolutionary forces, symbionts go through a process of genome reduction, eventually resulting in tiny genomes wher ... | 2013 | 24324632 |
| 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 |
| rhizosphere microbiome assemblage is affected by plant development. | there is a concerted understanding of the ability of root exudates to influence the structure of rhizosphere microbial communities. however, our knowledge of the connection between plant development, root exudation and microbiome assemblage is limited. here, we analyzed the structure of the rhizospheric bacterial community associated with arabidopsis at four time points corresponding to distinct stages of plant development: seedling, vegetative, bolting and flowering. overall, there were no sign ... | 2013 | 24196324 |
| rhizosphere microbiome assemblage is affected by plant development. | there is a concerted understanding of the ability of root exudates to influence the structure of rhizosphere microbial communities. however, our knowledge of the connection between plant development, root exudation and microbiome assemblage is limited. here, we analyzed the structure of the rhizospheric bacterial community associated with arabidopsis at four time points corresponding to distinct stages of plant development: seedling, vegetative, bolting and flowering. overall, there were no sign ... | 2013 | 24196324 |
| the dawn of synthetic genomics. | | 2008 | 18353151 |
| promoter propagation in prokaryotes. | transcriptional activation or 'rewiring' of silent genes is an important, yet poorly understood, phenomenon in prokaryotic genomes. anecdotal evidence coming from experimental evolution studies in bacterial systems has shown the promptness of adaptation upon appropriate selective pressure. in many cases, a partial or complete promoter is mobilized to silent genes from elsewhere in the genome. we term hereafter such recruited regulatory sequences as putative mobile promoters (pmps) and we hypothe ... | 2012 | 22933716 |
| sequence variability of rhizobiales orthologs and relationship with physico-chemical characteristics of proteins. | chromosomal orthologs can reveal the shared ancestral gene set and their evolutionary trends. additionally, physico-chemical properties of encoded proteins could provide information about functional adaptation and ecological niche requirements. | 2011 | 21970442 |
| regen: ancestral genome reconstruction for bacteria. | ancestral genome reconstruction can be understood as a phylogenetic study with more details than a traditional phylogenetic tree reconstruction. we present a new computational system called regen for ancestral bacterial genome reconstruction at both the gene and replicon levels. regen reconstructs gene content, contiguous gene runs, and replicon structure for each ancestral genome. along each branch of the phylogenetic tree, regen infers evolutionary events, including gene creation and deletion ... | 2012 | 24704978 |
| riboregulation in plant-associated α-proteobacteria. | the symbiotic α-rhizobia sinorhizobium meliloti, bradyrhizobium japonicum, rhizobium etli and the related plant pathogen agrobacterium tumefaciens are important model organisms for studying plant-microbe interactions. these metabolically versatile soil bacteria are characterized by complex lifestyles and large genomes. here we summarize the recent knowledge on their small non-coding rnas (srnas) including conservation, function, and interaction of the srnas with the rna chaperone hfq. in each of ... | 2014 | 25003187 |
| 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 |
| repeated, selection-driven genome reduction of accessory genes in experimental populations. | genome reduction has been observed in many bacterial lineages that have adapted to specialized environments. the extreme genome degradation seen for obligate pathogens and symbionts appears to be dominated by genetic drift. in contrast, for free-living organisms with reduced genomes, the dominant force is proposed to be direct selection for smaller, streamlined genomes. most variation in gene content for these free-living species is of "accessory" genes, which are commonly gained as large chromo ... | 2012 | 22589730 |
| carbonic anhydrase is an ancient enzyme widespread in prokaryotes. | carbonic anhydrases catalyze the reversible hydration of co(2) and are ubiquitous in highly evolved eukaryotes. the recent identification of a third class of carbonic anhydrase (gamma class) in a methanoarchaeon and our present finding that the beta class also extends into thermophilic species from the archaea domain led us to initiate a systematic search for these enzymes in metabolically and phylogenetically diverse prokaryotes. here we show that carbonic anhydrase is widespread in the archaea ... | 1999 | 10611359 |
| spectroscopic characterization of a green copper site in a single-domain cupredoxin. | cupredoxins are widespread copper-binding proteins, mainly involved in electron transfer pathways. they display a typical rigid greek key motif consisting of an eight stranded β-sandwich. a fascinating feature of cupredoxins is the natural diversity of their copper center geometry. these geometry variations give rise to drastic changes in their color, such as blue, green, red or purple. based on several spectroscopic and structural analyses, a connection between the geometry of their copper-bind ... | 2014 | 24932914 |
| the lovk-lovr two-component system is a regulator of the general stress pathway in caulobacter crescentus. | a conserved set of regulators control the general stress response in caulobacter crescentus, including σ(t), its anti-σ factor nepr, the anti-anti-σ factor phyr, and the transmembrane sensor kinase phyk. we report that the soluble histidine kinase lovk and the single-domain response regulator lovr also function within the c. crescentus general stress pathway. our genetic data support a model in which lovk-lovr functions upstream of σ(t) by controlling the phosphorylation state and thus anti-anti ... | 2012 | 22408156 |
| structural basis of a protein partner switch that regulates the general stress response of α-proteobacteria. | α-proteobacteria uniquely integrate features of two-component signal transduction (tcs) and alternative sigma factor (σ) regulation to control transcription in response to general stress. the core of this regulatory system is the phyr protein, which contains a σ-like (sl) domain and a tcs receiver domain. aspartyl phosphorylation of the phyr receiver in response to stress signals promotes binding of the anti-σ factor, nepr, to phyr-sl. this mechanism, whereby nepr switches binding between its co ... | 2012 | 22550172 |
| 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 |
| molecular characterization of a novel temperate sinorhizobium bacteriophage, фlm21, encoding dna methyltransferase with ccrm-like specificity. | φlm21 is a temperate phage isolated from sinorhizobium sp. strain lm21 (alphaproteobacteria). genomic analysis and electron microscopy suggested that φlm21 is a member of the family siphoviridae. the phage has an isometric head and a long noncontractile tail. the genome of φlm21 has 50,827 bp of linear double-stranded dna encoding 72 putative proteins, including proteins responsible for the assembly of the phage particles, dna packaging, transcription, replication, and lysis. virion proteins wer ... | 2014 | 25187538 |
| a putative bifunctional histidine kinase/phosphatase of the hwe family exerts positive and negative control on the sinorhizobium meliloti general stress response. | the ecfg-type sigma factor rpoe2 is the regulator of the general stress response in sinorhizobium meliloti. rpoe2 activity is negatively regulated by two nepr-type anti-sigma factors (rsia1/a2), themselves under the control of two anti-anti-sigma factors (rsib1/b2) belonging to the phyr family of response regulators. the current model of rpoe2 activation suggests that in response to stress, rsib1/b2 are activated by phosphorylation of an aspartate residue in their receiver domain. once activated ... | 2014 | 24794560 |
| 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 |
| 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 |
| 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 |
| metacyc: a multiorganism database of metabolic pathways and enzymes. | metacyc is a database of metabolic pathways and enzymes located at http://metacyc.org/. its goal is to serve as a metabolic encyclopedia, containing a collection of non-redundant pathways central to small molecule metabolism, which have been reported in the experimental literature. most of the pathways in metacyc occur in microorganisms and plants, although animal pathways are also represented. metacyc contains metabolic pathways, enzymatic reactions, enzymes, chemical compounds, genes and revie ... | 2005 | 16381923 |
| metacyc: a multiorganism database of metabolic pathways and enzymes. | metacyc is a database of metabolic pathways and enzymes located at http://metacyc.org/. its goal is to serve as a metabolic encyclopedia, containing a collection of non-redundant pathways central to small molecule metabolism, which have been reported in the experimental literature. most of the pathways in metacyc occur in microorganisms and plants, although animal pathways are also represented. metacyc contains metabolic pathways, enzymatic reactions, enzymes, chemical compounds, genes and revie ... | 2005 | 16381923 |
| the moxr atpase rava and its cofactor viaa interact with the nadh:ubiquinone oxidoreductase i in escherichia coli. | moxr atpases are widespread throughout bacteria and archaea. the experimental evidence to date suggests that these proteins have chaperone-like roles in facilitating the maturation of dedicated protein complexes that are functionally diverse. in escherichia coli, the moxr atpase rava and its putative cofactor viaa are found to exist in early stationary-phase cells at 37 °c at low levels of about 350 and 90 molecules per cell, respectively. both proteins are predominantly localized to the cytopla ... | 2014 | 24454883 |
| molecular ecology techniques for the study of aerobic methanotrophs. | | 2007 | 18165358 |
| molecular ecology techniques for the study of aerobic methanotrophs. | | 2007 | 18165358 |
| the expanding world of methylotrophic metabolism. | in the past few years, the field of methylotrophy has undergone a significant transformation in terms of discovery of novel types of methylotrophs, novel modes of methylotrophy, and novel metabolic pathways. this time has also been marked by the resolution of long-standing questions regarding methylotrophy and the challenge of long-standing dogmas. this chapter is not intended to provide a comprehensive review of metabolism of methylotrophic bacteria. instead we focus on significant recent disco ... | 2009 | 19514844 |
| carboxylases in natural and synthetic microbial pathways. | carboxylases are among the most important enzymes in the biosphere, because they catalyze a key reaction in the global carbon cycle: the fixation of inorganic carbon (co₂). this minireview discusses the physiological roles of carboxylases in different microbial pathways that range from autotrophy, carbon assimilation, and anaplerosis to biosynthetic and redox-balancing functions. in addition, the current and possible future uses of carboxylation reactions in synthetic biology are discussed. such ... | 2011 | 22003013 |
| copper starvation-inducible protein for cytochrome oxidase biogenesis in bradyrhizobium japonicum. | microarray analysis of bradyrhizobium japonicum grown under copper limitation uncovered five genes named pcuabcde, which are co-transcribed and co-regulated as an operon. the predicted gene products are periplasmic proteins (pcua, pcuc, and pcud), a tonb-dependent outer membrane receptor (pcub), and a cytoplasmic membrane-integral protein (pcue). homologs of pcuc and pcue had been discovered in other bacteria, namely pcu(a)c and ycnj, where they play a role in cytochrome oxidase biogenesis and c ... | 2012 | 23012364 |
| revelation of the ability of burkholderia sp. usm (jcm 15050) pha synthase to polymerize 4-hydroxybutyrate monomer. | the nutrition-versatility of burkholderia sp. strain usm (jcm 15050) has initiated the studies on the use of this bacterium for polyhydroxyalkanoate (pha) production. to date, the burkholderia sp. has been reported to synthesize 3-hydroxybutyrate, 3-hydroxyvalerate and 3-hydroxy-4-methylvalerate monomers. in this study, the pha biosynthetic genes of this strain were successfully cloned and characterized. the pha biosynthetic cluster of this strain consisted of a pha synthase (phac), β-ketothiola ... | 2012 | 22877240 |
| recovering from a bad start: rapid adaptation and tradeoffs to growth below a threshold density. | bacterial growth in well-mixed culture is often assumed to be an autonomous process only depending upon the external conditions under control of the investigator. however, increasingly there is awareness that interactions between cells in culture can lead to surprising phenomena such as density-dependence in the initiation of growth. | 2012 | 22762241 |
| intrigues and intricacies of the biosynthetic pathways for the enzymatic quinocofactors: pqq, ttq, ctq, tpq, and ltq. | | 2013 | 24350630 |
| intrigues and intricacies of the biosynthetic pathways for the enzymatic quinocofactors: pqq, ttq, ctq, tpq, and ltq. | | 2013 | 24350630 |
| cumate-inducible gene expression system for sphingomonads and other alphaproteobacteria. | tunable promoters represent a pivotal genetic tool for a wide range of applications. here we present such a system for sphingomonads, a phylogenetically diverse group of bacteria that have gained much interest for their potential in bioremediation and their use in industry and for which no dedicated inducible gene expression system has been described so far. a strong, constitutive synthetic promoter was first identified through a genetic screen and subsequently combined with the repressor and th ... | 2013 | 23995928 |
| elucidation of the role of the methylene-tetrahydromethanopterin dehydrogenase mtda in the tetrahydromethanopterin-dependent oxidation pathway in methylobacterium extorquens am1. | the methylotroph methylobacterium extorquens am1 oxidizes methanol and methylamine to formaldehyde and subsequently to formate, an intermediate that serves as the branch point between assimilation (formation of biomass) and dissimilation (oxidation to co₂). the oxidation of formaldehyde to formate is dephosphotetrahydromethanopterin (dh₄mpt) dependent, while the assimilation of carbon into biomass is tetrahydrofolate (h₄f) dependent. this bacterium contains two different enzymes, mtda and mtdb, ... | 2013 | 23504017 |
| insights into denitrification in methylotenera mobilis from denitrification pathway and methanol metabolism mutants. | we investigated phenotypes of mutants of methylotenera mobilis jlw8 with lesions in genes predicted to encode functions of the denitrification pathway, as well as mutants with mutations in methanol dehydrogenase-like structural genes xoxf1 and xoxf2, in order to obtain insights into denitrification and methanol metabolism by this bacterium. by monitoring the accumulation of nitrous oxide, we demonstrate that a periplasmic nitrate reductase, nad(p)-linked and copper-containing nitrite reductases, ... | 2013 | 23475964 |
| evolution after introduction of a novel metabolic pathway consistently leads to restoration of wild-type physiology. | organisms cope with physiological stressors through acclimatizing mechanisms in the short-term and adaptive mechanisms over evolutionary timescales. during adaptation to an environmental or genetic perturbation, beneficial mutations can generate numerous physiological changes: some will be novel with respect to prior physiological states, while others might either restore acclimatizing responses to a wild-type state, reinforce them further, or leave them unchanged. we examined the interplay of a ... | 2013 | 23593025 |
| 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 |
| biotechnological strategies to improve production of microbial poly-(3-hydroxybutyrate): a review of recent research work. | poly-(3-hydroxybutyrate) [p(3hb)] is a polyester synthesized as a carbon and energy reserve material by a wide number of bacteria. this polymer is characterized by its thermo-plastic properties similar to plastics derived from petrochemical industry, such as polyethylene and polypropylene. furthermore, p(3hb) is an inert, biocompatible and biodegradable material which has been proposed for several uses in medical and biomedical areas. currently, only few bacterial species such as cupriavidus nec ... | 2014 | 24898500 |
| 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 |
| 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 |
| parallel and divergent evolutionary solutions for the optimization of an engineered central metabolism in methylobacterium extorquens am1. | bioengineering holds great promise to provide fast and efficient biocatalysts for methanol-based biotechnology, but necessitates proven methods to optimize physiology in engineered strains. here, we highlight experimental evolution as an effective means for optimizing an engineered methylobacterium extorquens am1. replacement of the native formaldehyde oxidation pathway with a functional analog substantially decreased growth in an engineered methylobacterium, but growth rapidly recovered after s ... | 2015 | 27682084 |
| mxay regulates the lanthanide-mediated methanol dehydrogenase switch in methylomicrobium buryatense. | many methylotrophs, microorganisms that consume carbon compounds lacking carbon-carbon bonds, use two different systems to oxidize methanol for energy production and biomass accumulation. the mxafi methanol dehydrogenase (mdh) contains calcium in its active site, while the xoxf enzyme contains a lanthanide in its active site. the genes encoding the mdh enzymes are differentially regulated by the presence of lanthanides. in this study, we found that the histidine kinase mxay controls the lanthani ... | 2016 | 27651996 |
| adaptation in bacillus cereus: from stress to disease. | bacillus cereus is a food-borne pathogen that causes diarrheal disease in humans. after ingestion, b. cereus experiences in the human gastro-intestinal tract abiotic physical variables encountered in food, such as acidic ph in the stomach and changing oxygen conditions in the human intestine. b. cereus responds to environmental changing conditions (stress) by reversibly adjusting its physiology to maximize resource utilization while maintaining structural and genetic integrity by repairing and m ... | 2016 | 27757102 |
| shear rate moderates community diversity in freshwater biofilms. | the development of freshwater multispecies biofilms at solid-liquid interfaces occurs both in quiescent waters and under conditions of high shear rates. however, the influence of hydrodynamic shear rates on bacterial biofilm diversity is poorly understood. we hypothesized that different shear rates would significantly influence biofilm diversity and alter the relative proportions of coaggregating and autoaggregating community isolates. in order to study this hypothesis, freshwater biofilms were ... | 2004 | 15574945 |
| 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 |
| the 380 kb pcmu01 plasmid encodes chloromethane utilization genes and redundant genes for vitamin b12- and tetrahydrofolate-dependent chloromethane metabolism in methylobacterium extorquens cm4: a proteomic and bioinformatics study. | chloromethane (ch3cl) is the most abundant volatile halocarbon in the atmosphere and contributes to the destruction of stratospheric ozone. the only known pathway for bacterial chloromethane utilization (cmu) was characterized in methylobacterium extorquens cm4, a methylotrophic bacterium able to utilize compounds without carbon-carbon bonds such as methanol and chloromethane as the sole carbon source for growth. previous work demonstrated that tetrahydrofolate and vitamin b12 are essential cofa ... | 2013 | 23593113 |
| 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 |
| distribution and properties of the genes encoding the biosynthesis of the bacterial cofactor, pyrroloquinoline quinone. | pyrroloquinoline quinone (pqq) is a small, redox active molecule that serves as a cofactor for several bacterial dehydrogenases, introducing pathways for carbon utilization that confer a growth advantage. early studies had implicated a ribosomally translated peptide as the substrate for pqq production. this study presents a sequence- and structure-based analysis of the components of the pqq operon. we find the necessary components for pqq production are present in 126 prokaryotes, most of which ... | 2012 | 22324760 |
| 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 |
| kdo hydroxylase is an inner core assembly enzyme in the ko-containing lipopolysaccharide biosynthesis. | the lipopolysaccharide (lps) isolated from certain important gram-negative pathogens including a human pathogen yersinia pestis and opportunistic pathogens burkholderia mallei and burkholderia pseudomallei contains d-glycero-d-talo-oct-2-ulosonic acid (ko), an isosteric analog of 3-deoxy-d-manno-oct-2-ulosonic acid (kdo). kdo 3-hydroxylase (kdoo), a fe(2+)/α-kg/o2 dependent dioxygenase from burkholderia ambifaria and yersinia pestis is responsible for ko formation with kdo2-lipid a as a substrat ... | 2014 | 25204504 |
| a closer look on the polyhydroxybutyrate- (phb-) negative phenotype of ralstonia eutropha phb-4. | the undefined poly(3-hydroxybutyrate)- (phb-) negative mutant r. eutropha phb-4 was generated in 1970 by 1-nitroso-3-nitro-1-methylguanidine (nmg) treatment. although being scientific relevant, its genotype remained unknown since its isolation except a recent first investigation. in this study, the mutation causing the pha-negative phenotype of r. eutropha phb-4 was confirmed independently: sequence analysis of the phacab operon identified a g320a mutation in phac yielding a stop codon, leading ... | 2014 | 24787649 |
| 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 |
| control of wilt and rot pathogens of tomato by antagonistic pink pigmented facultative methylotrophic delftia lacustris and bacillus spp. | the studies on the biocontrol potential of pink pigmented facultative methylotrophic (ppfm) bacteria other than the genus methylobacterium are scarce. in the present study, we report three facultative methylotrophic isolates; ppo-1, ppt-1, and ppb-1, respectively, identified as delftia lacustris, bacillus subtilis, and bacillus cereus by 16s rrna gene sequence analysis. hemolytic activity was tested to investigate the potential pathogenicity of isolates to plants and humans, the results indicate ... | 2016 | 27872630 |
| the diversity of citrus endophytic bacteria and their interactions with xylella fastidiosa and host plants. | the bacterium xylella fastidiosa is the causal agent of citrus variegated chlorosis (cvc) and has been associated with important losses in commercial orchards of all sweet orange [citrus sinensis (l.)] cultivars. the development of this disease depends on the environmental conditions, including the endophytic microbial community associated with the host plant. previous studies have shown that x. fastidiosa interacts with the endophytic community in xylem vessels as well as in the insect vector, ... | 2016 | 27727362 |
| identification of unanticipated and novel n-acyl l-homoserine lactones (ahls) using a sensitive non-targeted lc-ms/ms method. | n-acyl l-homoserine lactones (ahls) constitute a predominant class of quorum-sensing signaling molecules used by gram-negative bacteria. here, we report a sensitive and non-targeted hplc-ms/ms method based on parallel reaction monitoring (prm) to identify and quantitate known, unanticipated, and novel ahls in microbial samples. using a hybrid quadrupole-high resolution mass analyzer, this method integrates ms scans and all-ion fragmentation ms/ms scans to allow simultaneous detection of ahl pare ... | 2016 | 27706219 |
| 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 |
| methylobacterium-induced endophyte community changes correspond with protection of plants against pathogen attack. | plant inoculation with endophytic bacteria that normally live inside the plant without harming the host is a highly promising approach for biological disease control. the mechanism of resistance induction by beneficial bacteria is poorly understood, because pathways are only partly known and systemic responses are typically not seen. the innate endophytic community structures change in response to external factors such as inoculation, and bacterial endophytes can exhibit direct or indirect antag ... | 2012 | 23056459 |
| bacterial metabolism of methylated amines and identification of novel methylotrophs in movile cave. | movile cave, romania, is an unusual underground ecosystem that has been sealed off from the outside world for several million years and is sustained by non-phototrophic carbon fixation. methane and sulfur-oxidising bacteria are the main primary producers, supporting a complex food web that includes bacteria, fungi and cave-adapted invertebrates. a range of methylotrophic bacteria in movile cave grow on one-carbon compounds including methylated amines, which are produced via decomposition of orga ... | 2014 | 25050523 |
| bacterial metabolism of methylated amines and identification of novel methylotrophs in movile cave. | movile cave, romania, is an unusual underground ecosystem that has been sealed off from the outside world for several million years and is sustained by non-phototrophic carbon fixation. methane and sulfur-oxidising bacteria are the main primary producers, supporting a complex food web that includes bacteria, fungi and cave-adapted invertebrates. a range of methylotrophic bacteria in movile cave grow on one-carbon compounds including methylated amines, which are produced via decomposition of orga ... | 2014 | 25050523 |
| novel characteristics of succinate coenzyme a (succinate-coa) ligases: conversion of malate to malyl-coa and coa-thioester formation of succinate analogues in vitro. | three succinate coenzyme a (succinate-coa) ligases (succd) from escherichia coli, advenella mimigardefordensis dpn7(t), and alcanivorax borkumensis sk2 were characterized regarding their substrate specificity concerning succinate analogues. previous studies had suggested that succd enzymes might be promiscuous toward succinate analogues, such as itaconate and 3-sulfinopropionate (3sp). the latter is an intermediate of the degradation pathway of 3,3'-dithiodipropionate (dtdp), a precursor for the ... | 2014 | 24141127 |
| 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 |
| 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 |