Publications

gipsy: genomic island prediction software.	bacteria are highly diverse organisms that are able to adapt to a broad range of environments and hosts due to their high genomic plasticity. horizontal gene transfer plays a pivotal role in this genome plasticity and in evolution by leaps through the incorporation of large blocks of genome sequences, ordinarily known as genomic islands (geis). geis may harbor genes encoding virulence, metabolism, antibiotic resistance and symbiosis-related functions, namely pathogenicity islands (pais), metabol ...	2016	26376473
high-quality draft genome sequence of the lotus spp. microsymbiont mesorhizobium loti strain cj3sym.	mesorhizobium loti strain cj3sym was isolated in 1998 following transfer of the integrative and conjugative element icemlsym(r7a), also known as the r7a symbiosis island, in a laboratory mating from the donor m. loti strain r7a to a nonsymbiotic recipient mesorhizobium strain cj3. strain cj3 was originally isolated from a field site in the rocklands range in new zealand in 1994. cj3sym is an aerobic, gram-negative, non-spore-forming rod. this report reveals the genome of m. loti strain cj3sym cu ...	2015	26380641
genome-wide prediction of prokaryotic two-component system networks using a sequence-based meta-predictor.	two component systems (tcs) are signalling complexes manifested by a histidine kinase (receptor) and a response regulator (effector). they are the most abundant signalling pathways in prokaryotes and control a wide range of biological processes. the pairing of these two components is highly specific, often requiring costly and time-consuming experimental characterisation. therefore, there is considerable interest in developing accurate prediction tools to lessen the burden of experimental work a ...	2015	26384938
development of a multi-enzymatic cascade reaction for the synthesis of trans-3-hydroxy-l-proline from l-arginine.	naturally occurring l-hydroxyproline in its four regio- and stereoisomeric forms has been explored as a possible precursor for pharmaceutical agents, yet the selective synthesis of trans-3-hydroxy-l-proline has not been achieved. our aim was to develop a novel biocatalytic asymmetric method for the synthesis of trans-3-hydroxy-l-proline. so far, we focused on the rhizobial arginine catabolic pathway: arginase and ornithine cyclodeaminase are involved in l-arginine degradation to l-proline via l- ...	2016	26411456
two-dimensional crystallization procedure, from protein expression to sample preparation.	membrane proteins play important roles for living cells. structural studies of membrane proteins provide deeper understanding of their mechanisms and further aid in drug design. as compared to other methods, electron microscopy is uniquely suitable for analysis of a broad range of specimens, from small proteins to large complexes. of various electron microscopic methods, electron crystallography is particularly well-suited to study membrane proteins which are reconstituted into two-dimensional c ...	2015	26413539
biochemistry and genetics of acc deaminase: a weapon to "stress ethylene" produced in plants.	1-aminocyclopropane-1-carboxylate deaminase (accd), a pyridoxal phosphate-dependent enzyme, is widespread in diverse bacterial and fungal species. owing to accd activity, certain plant associated bacteria help plant to grow under biotic and abiotic stresses by decreasing the level of "stress ethylene" which is inhibitory to plant growth. accd breaks down acc, an immediate precursor of ethylene, to ammonia and α-ketobutyrate, which can be further metabolized by bacteria for their growth. acc deam ...	2015	26441873
legume-rhizobia signal exchange: promiscuity and environmental effects.	although signal exchange between legumes and their rhizobia is among the best-known examples of this biological process, most of the more characterized data comes from just a few legume species and environmental stresses. although a relative wealth of information is available for some model legumes and some of the major pulses such as soybean, little is known about tropical legumes. this relative disparity in current knowledge is also apparent in the research on the effects of environmental stre ...	2015	26441880
colonization of root cells and plant growth promotion by piriformospora indica occurs independently of plant common symbiosis genes.	arbuscular mycorrhiza (am) fungi (glomeromycota) form symbiosis with and deliver nutrients via the roots of most angiosperms. am fungal hyphae are taken up by living root epidermal cells, a program which relies on a set of plant common symbiosis genes (csgs). plant root epidermal cells are also infected by the plant growth-promoting fungus piriformospora indica (basidiomycota), raising the question whether this interaction relies on the am-related csgs. here we show that intracellular colonizati ...	2015	26441999
integrative and conjugative elements (ices): what they do and how they work.	horizontal gene transfer plays a major role in microbial evolution, allowing microbes to acquire new genes and phenotypes. integrative and conjugative elements (ices, a.k.a. conjugative transposons) are modular mobile genetic elements integrated into a host genome and are passively propagated during chromosomal replication and cell division. induction of ice gene expression leads to excision, production of the conserved conjugation machinery (a type iv secretion system), and the potential to tra ...	2015	26473380
phylogeny of symbiotic genes and the symbiotic properties of rhizobia specific to astragalus glycyphyllos l.	the phylogeny of symbiotic genes of astragalus glycyphyllos l. (liquorice milkvetch) nodule isolates was studied by comparative sequence analysis of noda, nodc, nodh and nifh loci. in all these genes phylograms, liquorice milkvetch rhizobia (closely related to bacteria of three species, i.e. mesorhizobium amorphae, mesorhizobium septentrionale and mesorhizobium ciceri) formed one clearly separate cluster suggesting the horizontal transfer of symbiotic genes from a single ancestor to the bacteria ...	2015	26496493
ethylene resistance in flowering ornamental plants - improvements and future perspectives.	various strategies of plant breeding have been attempted in order to improve the ethylene resistance of flowering ornamental plants. these approaches span from conventional techniques such as simple cross-pollination to new breeding techniques which modify the plants genetically such as precise genome-editing. the main strategies target the ethylene pathway directly; others focus on changing the ethylene pathway indirectly via pathways that are known to be antagonistic to the ethylene pathway, e ...	2015	26504580
the yhs-domain of an adenylyl cyclase from mycobacterium phlei is a probable copper-sensor module.	yhs-domains are small protein modules which have been proposed to bind transition-metal ions like the related trash-domains. they are found in a variety of enzymes including copper-transporting atpases and adenylyl cyclases. here we investigate a class iiic adenylyl cyclase from mycobacterium phlei which contains a c-terminal yhs-domain linked to the catalytic domain by a peptide of 8 amino acids. we expressed the isolated catalytic domain and the full-length enzyme in e. coli. the catalytic dom ...	2015	26512893
scarn a novel class of scar protein that is required for root-hair infection during legume nodulation.	rhizobial infection of legume root hairs requires a rearrangement of the actin cytoskeleton to enable the establishment of plant-made infection structures called infection threads. in the scar/wave (suppressor of camp receptor defect/wasp family verpolin homologous protein) actin regulatory complex, the conserved n-terminal domains of scar proteins interact with other components of the scar/wave complex. the conserved c-terminal domains of scar proteins bind to and activate the actin-related pro ...	2015	26517270
ensifer-mediated transformation: an efficient non-agrobacterium protocol for the genetic modification of rice.	while agrobacterium-mediated transformation (amt) remains the most widely used technique for gene transfer in plants, interest exists for the use of non-agrobacterium gene delivery systems due to freedom-to-operate issues that remain with amt across several jurisdictions. in addition, the plant pathogenic mode of action of agrobacterium tumefaciens significantly increases the costs to passage engineered cultivars through the regulatory process. ensifer adhaerens (ov14) is a soil-related bacteriu ...	2015	26543735
the type iii secretion system (t3ss) is a determinant for rice-endophyte colonization by non-photosynthetic bradyrhizobium.	plant associations by bradyrhizobia have been detected not only in leguminous plants, but also in non-leguminous species including rice. bradyrhizobium sp. sutn9-2 was isolated from aeschynomene americana l., which is a leguminous weed found in the rice fields of thailand. this strain promoted the highest total rice (oryza sativa l. cultivar pathum thani 1) dry weight among the endophytic bradyrhizobial strains tested, and was, thus, employed for the further characterization of rice-bradyrhizobi ...	2015	26582551
discovery of novel plant interaction determinants from the genomes of 163 root nodule bacteria.	root nodule bacteria (rnb) or "rhizobia" are a type of plant growth promoting bacteria, typified by their ability to fix nitrogen for their plant host, fixing nearly 65% of the nitrogen currently utilized in sustainable agricultural production of legume crops and pastures. in this study, we sequenced the genomes of 110 rnb from diverse hosts and biogeographical regions, and undertook a global exploration of all available rnb genera with the aim of identifying novel genetic determinants of symbio ...	2015	26584898
draft genome sequences of facultative methylotrophs, gemmobacter sp. strain lw1 and mesorhizobium sp. strain 1m-11, isolated from movile cave, romania.	facultative methylotrophs belonging to the genera gemmobacter and mesorhizobium were isolated from microbial mat and cave water samples obtained from the movile cave ecosystem. both bacteria can utilize methylated amines as their sole carbon and nitrogen source. here, we report the draft genome sequences of gemmobacter sp. strain lw1 and mesorhizobium sp. strain im1.	2015	26586870
possible role of 1-aminocyclopropane-1-carboxylate (acc) deaminase activity of sinorhizobium sp. bl3 on symbiosis with mung bean and determinate nodule senescence.	sinorhizobium sp. bl3 forms symbiotic interactions with mung bean (vigna radiata) and contains lrpl-acds genes, which encode the 1-aminocyclopropane-1-carboxylate (acc) deaminase enzyme that cleaves acc, a precursor of plant ethylene synthesis. since ethylene interferes with nodule formation in some legumes and plays a role in senescence in plant cells, bl3-enhancing acc deaminase activity (bl3(+)) and defective mutant (bl3(-)) strains were constructed in order to investigate the effects of this ...	2015	26657304
mesopelagic n2 fixation related to organic matter composition in the solomon and bismarck seas (southwest pacific).	dinitrogen (n2) fixation was investigated together with organic matter composition in the mesopelagic zone of the bismarck (transect 1) and solomon (transect 2) seas (southwest pacific). transparent exopolymer particles (tep) and the presence of compounds sharing molecular formulae with saturated fatty acids and sugars, as well as dissolved organic matter (dom) compounds containing nitrogen (n) and phosphorus (p) were higher on transect 1 than on transect 2, while oxygen concentrations showed an ...	2015	26659074
a functional 4-hydroxybenzoate degradation pathway in the phytopathogen xanthomonas campestris is required for full pathogenicity.	plants contain significant levels of natural phenolic compounds essential for reproduction and growth, as well as defense mechanisms against pathogens. xanthomonas campestris pv. campestris (xcc) is the causal agent of crucifers black rot. here we showed that genes required for the synthesis, utilization, transportation, and degradation of 4-hydroxybenzoate (4-hba) are present in xcc. xcc rapidly degrades 4-hba, but has no effect on 2-hydroxybenzoate and 3-hydroxybenzoate when grown in xoln medi ...	2015	26672484
genetic analysis reveals the essential role of nitrogen phosphotransferase system components in sinorhizobium fredii ccbau 45436 symbioses with soybean and pigeonpea plants.	the nitrogen phosphotransferase system (pts(ntr)) consists of ei(ntr), npr, and eiia(ntr). the active phosphate moiety derived from phosphoenolpyruvate is transferred through ei(ntr) and npr to eiia(ntr). sinorhizobium fredii can establish a nitrogen-fixing symbiosis with the legume crops soybean (as determinate nodules) and pigeonpea (as indeterminate nodules). in this study, s. fredii strains with mutations in ptsp and ptso (encoding ei(ntr) and npr, respectively) formed ineffective nodules on ...	2016	26682851
regulation of the rhaewrbma operon involved in l-rhamnose catabolism through two transcriptional factors, rhar and ccpa, in bacillus subtilis.	the bacillus subtilis rhaewrbma (formerly yuxg-yulbcde) operon consists of four genes encoding enzymes for l-rhamnose catabolism and the rhar gene encoding a deor-type transcriptional regulator. dnase i footprinting analysis showed that the rhar protein specifically binds to the regulatory region upstream of the rhaew gene, in which two imperfect direct repeats are included. gel retardation analysis revealed that the direct repeat farther upstream is essential for the high-affinity binding of rh ...	2016	26712933
discrete responses to limitation for iron and manganese in agrobacterium tumefaciens: influence on attachment and biofilm formation.	transition metals such as iron and manganese are crucial trace nutrients for the growth of most bacteria, functioning as catalytic cofactors for many essential enzymes. dedicated uptake and regulatory systems have evolved to ensure their acquisition for growth, while preventing toxicity. transcriptomic analysis of the iron- and manganese-responsive regulons of agrobacterium tumefaciens revealed that there are discrete regulatory networks that respond to changes in iron and manganese levels. comp ...	2016	26712936
discovery of novel haloalkane dehalogenase inhibitors.	haloalkane dehalogenases (hlds) have recently been discovered in a number of bacteria, including symbionts and pathogens of both plants and humans. however, the biological roles of hlds in these organisms are unclear. the development of efficient hld inhibitors serving as molecular probes to explore their function would represent an important step toward a better understanding of these interesting enzymes. here we report the identification of inhibitors for this enzyme family using two different ...	2016	26773086
epigenetic mechanisms and microbiota as a toolbox for plant phenotypic adjustment to environment.	the classic understanding of organisms focuses on genes as the main source of species evolution and diversification. the recent concept of genetic accommodation questions this gene centric view by emphasizing the importance of phenotypic plasticity on evolutionary trajectories. recent discoveries on epigenetics and symbiotic microbiota demonstrated their deep impact on plant survival, adaptation and evolution thus suggesting a novel comprehension of the plant phenotype. in addition, interplays b ...	2015	26779191
vasohibins: new transglutaminase-like cysteine proteases possessing a non-canonical cys-his-ser catalytic triad.	vasohibin-1 and vasohibin-2 regulate angiogenesis, tumour growth and metastasis. their molecular functions, however, were previously unknown, in large part owing to their perceived lack of homology to proteins of known structure and function. to identify their functional amino acids and domains, their molecular activity and their evolutionary history, we undertook an in-depth analysis of vasohibin sequences. we find that vasohibin proteins are previously undetected members of the transglutaminas ...	2016	26794318
inoculation insensitive promoters for cell type enriched gene expression in legume roots and nodules.	establishment and maintenance of mutualistic plant-microbial interactions in the rhizosphere and within plant roots involve several root cell types. the processes of host-microbe recognition and infection require complex signal exchange and activation of downstream responses. these molecular events coordinate host responses across root cell layers during microbe invasion, ultimately triggering changes of root cell fates. the progression of legume root interactions with rhizobial bacteria has bee ...	2016	26807140
mixed group of rhizobiales microbes in lung and blood of a patient with fatal pulmonary illness.	we examined the microbial composition in the diseased lung and early-phase microbial cultures from the blood of a patient with a rapidly progressing fatal pulmonary illness. although no microbes could be isolated from such cultures during the initial study, the hts-microbiome study revealed the presence of a unique mixture of alphaproteobacteria, composed mainly of different families of rhizobiales microbes. microbial 16s rdna sequences matching closely to afipia cberi were identified mainly in ...	2015	26823697
atkc1 and cipk23 synergistically modulate akt1-mediated low-potassium stress responses in arabidopsis.	in arabidopsis (arabidopsis thaliana), the shaker k(+) channel akt1 conducts k(+) uptake in root cells, and its activity is regulated by cbl1/9-cipk23 complexes as well as by the atkc1 channel subunit. cipk23 and atkc1 are both involved in the akt1-mediated low-k(+) (lk) response; however, the relationship between them remains unclear. in this study, we screened suppressors of low-k(+) sensitive [lks1 (cipk23)] and isolated the suppressor of lks1 (sls1) mutant, which suppressed the leaf chlorosi ...	2016	26829980
whole genome sequencing revealed host adaptation-focused genomic plasticity of pathogenic leptospira.	leptospirosis, caused by pathogenic leptospira spp., has recently been recognized as an emerging infectious disease worldwide. despite its severity and global importance, knowledge about the molecular pathogenesis and virulence evolution of leptospira spp. remains limited. here we sequenced and analyzed 102 isolates representing global sources. a high genomic variability were observed among different leptospira species, which was attributed to massive gene gain and loss events allowing for adapt ...	2016	26833181
plant pathogens affecting the establishment of plant-symbiont interaction.		2016	26834779
medicago truncatula gaertn. as a model for understanding the mechanism of growth promotion by bacteria from rhizosphere and nodules of alfalfa.	the present study showed all the 16 strains isolated and identified from the alfalfa rhizosphere and nodules, and registered in genbank, to be good candidates for targeted use in studies addressing the rather weak known mechanism of plant growth promotion, including that of medicago truncatula, a molecular crop model. based on physiological, biochemical and molecular analysis, the 16 isolates obtained were ascribed to the following five families: bacillaceae, rhizobiaceae, xantomonadaceae, enter ...	2016	26861677
plant er geometry and dynamics: biophysical and cytoskeletal control during growth and biotic response.	the endoplasmic reticulum (er) is an intricate and dynamic network of membrane tubules and cisternae. in plant cells, the er 'web' pervades the cortex and endoplasm and is continuous with adjacent cells as it passes through plasmodesmata. it is therefore the largest membranous organelle in plant cells. it performs essential functions including protein and lipid synthesis, and its morphology and movement are linked to cellular function. an emerging trend is that organelles can no longer be seen a ...	2016	26862751
plant er geometry and dynamics: biophysical and cytoskeletal control during growth and biotic response.	the endoplasmic reticulum (er) is an intricate and dynamic network of membrane tubules and cisternae. in plant cells, the er 'web' pervades the cortex and endoplasm and is continuous with adjacent cells as it passes through plasmodesmata. it is therefore the largest membranous organelle in plant cells. it performs essential functions including protein and lipid synthesis, and its morphology and movement are linked to cellular function. an emerging trend is that organelles can no longer be seen a ...	2016	26862751
contributions of sinorhizobium meliloti transcriptional regulator dksa to bacterial growth and efficient symbiosis with medicago sativa.	the stringent response, mediated by the (p)ppgpp synthetase rela and the rna polymerase-binding protein dksa, is triggered by limiting nutrient conditions. for some bacteria, it is involved in regulation of virulence. we investigated the role of two dksa-like proteins from the gram-negative nitrogen-fixing symbiont sinorhizobium meliloti in free-living culture and in interaction with its host plant medicago sativa the two paralogs, encoded by the genes smc00469 and smc00049, differ in the consti ...	2016	26883825
evolutionary and functional relationships of the dha regulon by genomic context analysis.	3-hydroxypropionaldehyde (3-hpa) and 1,3-propanediol (1,3-pd) are subproducts of glycerol degradation and of economical interest as they are used for polymers synthesis, such as polyesters and polyurethanes. some few characterized bacterial species (mostly from firmicutes and gamma-proteobacteria groups) are able to catabolize these monomers from glycerol using the gene products from the dha regulon. to expand our knowledge and direct further experimental studies on the regulon and related genes ...	2016	26938861
the dualistic nature of integrative and conjugative elements.	integrative and conjugative elements (ices) are mobile genetic elements that play a key role in bacterial adaptation. such elements are found in almost every bacterial genera and species, and often code for adaptive traits conferring selective advantages to their host. ices maintain by integrating into and replicating along with a replicon of the host genome. ices can propagate by conjugative transfer toward a recipient cell following excision from the replicon as a circular covalently-closed mo ...	2015	26942046
silencing quorum sensing and ice mobility through antiactivation and ribosomal frameshifting.	mobile genetic elements run an evolutionary gauntlet to maintain their mobility in the face of selection against their selfish dissemination but, paradoxically, they can accelerate the adaptability of bacteria through the gene-transfer events that they facilitate. these temporally conflicting evolutionary forces have shaped exquisite regulation systems that silence mobility and maximize the competitive fitness of the host bacterium, but maintain the ability of the element to deliver itself to a ...	2015	26942047
gene expression and localization of a β-1,3-glucanase of lotus japonicus.	phytohormone abscisic acid (aba) inhibits root nodule formation of leguminous plants. ljglu1, a β-1,3-glucanase gene of lotus japonicus, has been identified as an aba responsive gene. rna interference of ljglu1 increased nodule number. this suggests that ljglu1 is involved in the regulation of nodule formation. host legumes control nodule number by autoregulation of nodulation (aon), in which the presence of existing root nodules inhibits further nodulation. for further characterization of ljglu ...	2016	26951113
development of a microemulsion formulation for antimicrobial seca inhibitors.	in our previous study, we have identified five antimicrobial small molecules via structure based design, which inhibit seca of candidatus liberibacter asiaticus (las). seca is a critical protein translocase atpase subunit and is involved in pre-protein translocation across and integration into the cellular membrane in bacteria. in this study, eleven compounds were identified using similarity search method based on the five lead seca inhibitors identified previously. the identified seca inhibitor ...	2016	26963811
preservation of ancestral cretaceous microflora recovered from a hypersaline oil reservoir.	microbiology of a hypersaline oil reservoir located in central africa was investigated with molecular and culture methods applied to preserved core samples. here we show that the community structure was partially acquired during sedimentation, as many prokaryotic 16s rrna gene sequences retrieved from the extracted dna are phylogenetically related to actual archaea inhabiting surface evaporitic environments, similar to the cretaceous sediment paleoenvironment. results are discussed in term of mi ...	2016	26965360
draft genome sequence of mesorhizobium sp. ufla 01-765, a multitolerant, efficient symbiont and plant growth-promoting strain isolated from zn-mining soil using leucaena leucocephala as a trap plant.	we report the 7.4-mb draft genome sequence of mesorhizobium sp. strain ufla 01-765, a gram-negative bacterium of the phyllobacteriaceae isolated from zn-mining soil in minas gerais, brazil. this strain promotes plant growth, efficiently fixes n2 in symbiosis with leucaena leucocephala on multicontaminated soil, and has potential for application in bioremediation of marginal lands.	2016	26966214
a functional bacterium-to-plant dna transfer machinery of rhizobium etli.	different strains and species of the soil phytopathogen agrobacterium possess the ability to transfer and integrate a segment of dna (t-dna) into the genome of their eukaryotic hosts, which is mainly mediated by a set of virulence (vir) genes located on the bacterial ti-plasmid that also contains the t-dna. to date, agrobacterium is considered to be unique in its capacity to mediate genetic transformation of eukaryotes. however, close homologs of the vir genes are encoded by the p42a plasmid of ...	2016	26968003
identification and functional analysis of secreted effectors from phytoparasitic nematodes.	plant parasitic nematodes develop an intimate and long-term feeding relationship with their host plants. they induce a multi-nucleate feeding site close to the vascular bundle in the roots of their host plant and remain sessile for the rest of their life. nematode secretions, produced in the oesophageal glands and secreted through a hollow stylet into the host plant cytoplasm, are believed to play key role in pathogenesis. to combat these persistent pathogens, the identity and functional analysi ...	2016	27001199
a novel biosensor to study camp dynamics in cilia and flagella.	the cellular messenger camp regulates multiple cellular functions, including signaling in cilia and flagella. the camp dynamics in these subcellular compartments are ill-defined. we introduce a novel fret-based camp biosensor with nanomolar sensitivity that is out of reach for other sensors. to measure camp dynamics in the sperm flagellum, we generated transgenic mice and reveal that the hitherto methods determining total camp levels do not reflect changes in free camp levels. moreover, camp dyn ...	2016	27003291
molecular mechanisms and clinical impact of acquired and intrinsic fosfomycin resistance.	bacterial infections caused by antibiotic-resistant isolates have become a major health problem in recent years, since they are very difficult to treat, leading to an increase in morbidity and mortality. fosfomycin is a broad-spectrum bactericidal antibiotic that inhibits cell wall biosynthesis in both gram-negative and gram-positive bacteria. this antibiotic has a unique mechanism of action and inhibits the initial step in peptidoglycan biosynthesis by blocking the enzyme, mura. fosfomycin has ...	2013	27029300
cyanobacteria and eukaryotic algae use different chemical variants of vitamin b12.	eukaryotic microalgae and prokaryotic cyanobacteria are the major components of the phytoplankton. determining factors that govern growth of these primary producers, and how they interact, is therefore essential to understanding aquatic ecosystem productivity. over half of microalgal species representing marine and freshwater habitats require for growth the corrinoid cofactor b12, which is synthesized de novo only by certain prokaryotes, including the majority of cyanobacteria. there are several ...	2016	27040778
swimming performance of bradyrhizobium diazoefficiens is an emergent property of its two flagellar systems.	many bacterial species use flagella for self-propulsion in aqueous media. in the soil, which is a complex and structured environment, water is found in microscopic channels where viscosity and water potential depend on the composition of the soil solution and the degree of soil water saturation. therefore, the motility of soil bacteria might have special requirements. an important soil bacterial genus is bradyrhizobium, with species that possess one flagellar system and others with two different ...	2016	27053439
symbiotic nitrogen fixation and the challenges to its extension to nonlegumes.	access to fixed or available forms of nitrogen limits the productivity of crop plants and thus food production. nitrogenous fertilizer production currently represents a significant expense for the efficient growth of various crops in the developed world. there are significant potential gains to be had from reducing dependence on nitrogenous fertilizers in agriculture in the developed world and in developing countries, and there is significant interest in research on biological nitrogen fixation ...	2016	27084023
reactive oxygen species and nitric oxide control early steps of the legume - rhizobium symbiotic interaction.	the symbiotic interaction between legumes and nitrogen-fixing rhizobium bacteria leads to the formation of a new organ, the nodule. early steps of the interaction are characterized by the production of bacterial nod factors, the reorientation of root-hair tip growth, the formation of an infection thread (it) in the root hair, and the induction of cell division in inner cortical cells of the root, leading to a nodule primordium formation. reactive oxygen species (ros) and nitric oxide (no) have b ...	2016	27092165
the entner-doudoroff pathway is an overlooked glycolytic route in cyanobacteria and plants.	glucose degradation pathways are central for energy and carbon metabolism throughout all domains of life. they provide atp, nad(p)h, and biosynthetic precursors for amino acids, nucleotides, and fatty acids. it is general knowledge that cyanobacteria and plants oxidize carbohydrates via glycolysis [the embden-meyerhof-parnas (emp) pathway] and the oxidative pentose phosphate (opp) pathway. however, we found that both possess a third, previously overlooked pathway of glucose breakdown: the entner ...	2016	27114545
use of transcriptomics and co-expression networks to analyze the interconnections between nitrogen assimilation and photorespiratory metabolism.	nitrogen is one of the most important nutrients for plants and, in natural soils, its availability is often a major limiting factor for plant growth. here we examine the effect of different forms of nitrogen nutrition and of photorespiration on gene expression in the model legume lotus japonicus with the aim of identifying regulatory candidate genes co-ordinating primary nitrogen assimilation and photorespiration. the transcriptomic changes produced by the use of different nitrogen sources in le ...	2016	27117340
hormonal control of lateral root and nodule development in legumes.	many plants can establish symbioses with nitrogen-fixing bacteria, some of which lead to nodulation, including legumes. indeed, in the rhizobium/legume symbiosis, new root organs, called nodules, are formed by the plant in order to host the rhizobia in protective conditions, optimized for nitrogen fixation. in this way, these plants can benefit from the reduction of atmospheric dinitrogen into ammonia by the hosted bacteria, and in exchange the plant provides the rhizobia with a carbon source. s ...	2015	27135340
the control of auxin transport in parasitic and symbiotic root-microbe interactions.	most field-grown plants are surrounded by microbes, especially from the soil. some of these, including bacteria, fungi and nematodes, specifically manipulate the growth and development of their plant hosts, primarily for the formation of structures housing the microbes in roots. these developmental processes require the correct localization of the phytohormone auxin, which is involved in the control of cell division, cell enlargement, organ development and defense, and is thus a likely target fo ...	2015	27135343
integrating dna methylation and gene expression data in the development of the soybean-bradyrhizobium n2-fixing symbiosis.	very little is known about the role of epigenetics in the differentiation of a bacterium from the free-living to the symbiotic state. here genome-wide analysis of dna methylation changes between these states is described using the model of symbiosis between soybean and its root nodule-forming, nitrogen-fixing symbiont, bradyrhizobium diazoefficiens. pacbio resequencing of the b. diazoefficiens genome from both states revealed 43,061 sites recognized by five motifs with the potential to be methyl ...	2016	27148207
estimating divergence times and substitution rates in rhizobia.	accurate estimation of divergence times of soil bacteria that form nitrogen-fixing associations with most leguminous plants is challenging because of a limited fossil record and complexities associated with molecular clocks and phylogenetic diversity of root nodule bacteria, collectively called rhizobia. to overcome the lack of fossil record in bacteria, divergence times of host legumes were used to calibrate molecular clocks and perform phylogenetic analyses in rhizobia. the 16s rrna gene and i ...	2016	27168719
legume nadph oxidases have crucial roles at different stages of nodulation.	plant nadph oxidases, formerly known as respiratory burst oxidase homologues (rbohs), are plasma membrane enzymes dedicated to reactive oxygen species (ros) production. these oxidases are implicated in a wide variety of processes, ranging from tissue and organ growth and development to signaling pathways in response to abiotic and biotic stimuli. research on the roles of rbohs in the plant's response to biotic stresses has mainly focused on plant-pathogen interactions; nonetheless, recent findin ...	2016	27213330
bacterial molecular signals in the sinorhizobium fredii-soybean symbiosis.	sinorhizobium (ensifer) fredii (s. fredii) is a rhizobial species exhibiting a remarkably broad nodulation host-range. thus, s. fredii is able to effectively nodulate dozens of different legumes, including plants forming determinate nodules, such as the important crops soybean and cowpea, and plants forming indeterminate nodules, such as glycyrrhiza uralensis and pigeon-pea. this capacity of adaptation to different symbioses makes the study of the molecular signals produced by s. fredii strains ...	2016	27213334
impact of microalgae-bacteria interactions on the production of algal biomass and associated compounds.	a greater insight on the control of the interactions between microalgae and other microorganisms, particularly bacteria, should be useful for enhancing the efficiency of microalgal biomass production and associated valuable compounds. little attention has been paid to the controlled utilization of microalgae-bacteria consortia. however, the studies of microalgal-bacterial interactions have revealed a significant impact of the mutualistic or parasitic relationships on algal growth. the algal grow ...	2016	27213407
metabolomic profiling of bradyrhizobium diazoefficiens-induced root nodules reveals both host plant-specific and developmental signatures.	bradyrhizobium diazoefficiens is a nitrogen-fixing endosymbiont, which can grow inside root-nodule cells of the agriculturally important soybean and other host plants. our previous studies described b. diazoefficiens host-specific global expression changes occurring during legume infection at the transcript and protein level. in order to further characterize nodule metabolism, we here determine by flow injection-time-of-flight mass spectrometry analysis the metabolome of (i) nodules and roots fr ...	2016	27240350
rhizobium leguminosarum symbiovar trifolii, ensifer numidicus and mesorhizobium amorphae symbiovar ciceri (or mesorhizobium loti) are new endosymbiotic bacteria of lens culinaris medik.	a total of 142 rhizobial bacteria were isolated from root nodules of lens culinaris medik endemic to tunisia and they belonged to the species rhizobium leguminosarum, and for the first time to ensifer and mesorhizobium, genera never previously described as microsymbionts of lentil. phenotypically, our results indicate that l. culinaris medik strains showed heterogenic responses to the different phenotypic features and they effectively nodulated their original host. based on the concatenation of ...	2016	27267929
how mutualisms arise in phytoplankton communities: building eco-evolutionary principles for aquatic microbes.	extensive sampling and metagenomics analyses of plankton communities across all aquatic environments are beginning to provide insights into the ecology of microbial communities. in particular, the importance of metabolic exchanges that provide a foundation for ecological interactions between microorganisms has emerged as a key factor in forging such communities. here we show how both studies of environmental samples and physiological experimentation in the laboratory with defined microbial co-cu ...	2016	27282316
complete genome sequence of mesorhizobium ciceri bv. biserrulae strain wsm1284, an efficient nitrogen-fixing microsymbiont of the pasture legume biserrula pelecinus.	we report the complete genome sequence of mesorhizobium ciceri bv. biserrulae strain wsm1284, a nitrogen-fixing microsymbiont of the pasture legume biserrula pelecinus the genome consists of 6.88 mb distributed between a single chromosome (6.33 mb) and a single plasmid (0.55 mb).	2016	27284134
rhizobial gibberellin negatively regulates host nodule number.	in legume-rhizobia symbiosis, the nodule number is controlled to ensure optimal growth of the host. in lotus japonicus, the nodule number has been considered to be tightly regulated by host-derived phytohormones and glycopeptides. however, we have discovered a symbiont-derived phytohormonal regulation of nodule number in mesorhizobium loti. in this study, we found that m. loti synthesized gibberellic acid (ga) under symbiosis. hosts inoculated with a ga-synthesis-deficient m. loti mutant formed ...	2016	27307029
function of succinoglycan polysaccharide in sinorhizobium meliloti host plant invasion depends on succinylation, not molecular weight.	the acidic polysaccharide succinoglycan produced by the rhizobial symbiont sinorhizobium meliloti 1021 is required for this bacterium to invade the host plant medicago truncatula and establish a nitrogen-fixing symbiosis. s. meliloti mutants that cannot make succinoglycan cannot initiate invasion structures called infection threads in plant root hairs. s. meliloti exoh mutants that cannot succinylate succinoglycan are also unable to form infection threads, despite the fact that they make large q ...	2016	27329751
growth rate of and gene expression in bradyrhizobium diazoefficiens usda110 due to a mutation in blr7984, a tetr family transcriptional regulator gene.	previous transcriptome analyses have suggested that a gene cluster including a transcriptional regulator (blr7984) of the tetracycline repressor family was markedly down-regulated in symbiosis. since blr7984 is annotated to be the transcriptional repressor, we hypothesized that it is involved in the repression of genes in the genomic cluster including blr7984 in symbiotic bacteroids. in order to examine the function and involvement of the blr7984 gene in differentiation into bacteroids, we compa ...	2016	27383683
transfer of dna from bacteria to eukaryotes.	historically, the members of the agrobacterium genus have been considered the only bacterial species naturally able to transfer and integrate dna into the genomes of their eukaryotic hosts. yet, increasing evidence suggests that this ability to genetically transform eukaryotic host cells might be more widespread in the bacterial world. indeed, analyses of accumulating genomic data reveal cases of horizontal gene transfer from bacteria to eukaryotes and suggest that it represents a significant fo ...	2016	27406565
a comparative proteomics study of a synovial cell line stimulated with tnf-α.	to elucidate the pathogenesis of rheumatoid arthritis (ra), we used proteomic analysis to determine the protein profile in a synovial cell line, mh7a, established from patients with ra. proteins were extracted from mh7a cells that were or were not stimulated with tumor necrosis factor-α (tnf-α), and then analyzed on a liquid chromatography/mass spectrometry system equipped with a unique long monolithic silica capillary. on the basis of the results of this proteomic analysis, we identified 2650 p ...	2016	27419047
origin and evolution of nitrogen fixation genes on symbiosis islands and plasmid in bradyrhizobium.	the nitrogen fixation (nif) genes of nodule-forming bradyrhizobium strains are generally located on symbiosis islands or symbiosis plasmids, suggesting that these genes have been transferred laterally. the nif genes of rhizobial and non-rhizobial bradyrhizobium strains were compared in order to infer the evolutionary histories of nif genes. based on all codon positions, the phylogenetic tree of concatenated nifd and nifk sequences showed that nifdk on symbiosis islands formed a different clade f ...	2016	27431195
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
intraradical colonization by arbuscular mycorrhizal fungi triggers induction of a lipochitooligosaccharide receptor.	functional divergence of paralogs following gene duplication is one of the mechanisms leading to evolution of novel pathways and traits. here we show that divergence of lys11 and nfr5 lysm receptor kinase paralogs of lotus japonicus has affected their specificity for lipochitooligosaccharides (lcos) decorations, while the innate capacity to recognize and induce a downstream signalling after perception of rhizobial lcos (nod factors) was maintained. regardless of this conserved ability, lys11 was ...	2016	27435342
hemoglobin ljglb1-1 is involved in nodulation and regulates the level of nitric oxide in the lotus japonicus-mesorhizobium loti symbiosis.	leghemoglobins transport and deliver o2 to the symbiosomes inside legume nodules and are essential for nitrogen fixation. however, the roles of other hemoglobins (hbs) in the rhizobia-legume symbiosis are unclear. several lotus japonicus mutants affecting ljglb1-1, a non-symbiotic class 1 hb, have been used to study the function of this protein in symbiosis. two tilling alleles with single amino acid substitutions (a102v and e127k) and a lore1 null allele with a retrotransposon insertion in the ...	2016	27443280
region 4 of rhizobium etli primary sigma factor (siga) confers transcriptional laxity in escherichia coli.	sigma factors are rna polymerase subunits engaged in promoter recognition and dna strand separation during transcription initiation in bacteria. primary sigma factors are responsible for the expression of housekeeping genes and are essential for survival. rpod, the primary sigma factor of escherichia coli, a γ-proteobacteria, recognizes consensus promoter sequences highly similar to those of some α-proteobacteria species. despite this resemblance, rpod is unable to sustain transcription from mos ...	2016	27468278
global transcriptional response to salt shock of the plant microsymbiont mesorhizobium loti maff303099.	soil salinity affects rhizobia both as free-living bacteria and in symbiosis with the host. the aim of this study was to examine the transcriptional response of the lotus microsymbiont mesorhizobium loti maff303099 to salt shock. changes in the transcriptome of bacterial cells subjected to a salt shock of 10% nacl for 30 min were analyzed. from a total of 7231 protein-coding genes, 385 were found to be differentially expressed upon salt shock, among which 272 were overexpressed. although a large ...	2017	27481227
genome of rhizobium leucaenae strains cfn 299(t) and cpao 29.8: searching for genes related to a successful symbiotic performance under stressful conditions.	common bean (phaseolus vulgaris l.) is the most important legume cropped worldwide for food production and its agronomic performance can be greatly improved if the benefits from symbiotic nitrogen fixation are maximized. the legume is known for its high promiscuity in nodulating with several rhizobium species, but those belonging to the rhizobium tropici "group" are the most successful and efficient in fixing nitrogen in tropical acid soils. rhizobium leucaenae belongs to this group, which is ab ...	2016	27485828
exopolysaccharide production by sinorhizobium fredii hh103 is repressed by genistein in a nodd1-dependent manner.	in the rhizobia-legume symbiotic interaction, bacterial surface polysaccharides, such as exopolysaccharide (eps), lipopolysaccharide (lps), k-antigen polysaccharide (kps) or cyclic glucans (cg), appear to play crucial roles either acting as signals required for the progression of the interaction and/or preventing host defence mechanisms. the symbiotic significance of each of these polysaccharides varies depending on the specific rhizobia-legume couple. in this work we show that the production of ...	2016	27486751
structures of exopolysaccharides involved in receptor-mediated perception of mesorhizobium loti by lotus japonicus.	in the symbiosis formed between mesorhizobium loti strain r7a and lotus japonicus gifu, rhizobial exopolysaccharide (eps) plays an important role in infection thread formation. mutants of strain r7a affected in early exopolysaccharide biosynthetic steps form nitrogen-fixing nodules on l. japonicus gifu after a delay, whereas mutants affected in mid or late biosynthetic steps induce uninfected nodule primordia. recently, it was shown that a plant receptor-like kinase, epr3, binds low molecular ma ...	2016	27502279
reclassification of strains maff 303099t and r7a into mesorhizobiumjaponicum sp. nov.	in this work we revise the taxonomic status of the lotus-nodulating strains maff 303099t and r7a isolated in japan and new zealand, respectively. their 16s rrna gene sequences are identical and show 98.0, 99.7, 99.8 and 99.9 % similarity values with respect to mesorhizobium loti nzp 2213t, m. jarvisii atcc 33669t, m. huakuii usda 4779t (=ccbau 2609t) and m. erdmanii usda 3471t, respectively. the analysis of reca and glnii gene sequeces showed that m. jarvisii atcc 33669t and m. huakuii usda 4779 ...	2016	27565417
role of the tyr270 residue in 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase from mesorhizobium loti.	the flavoenzyme 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase (mhpco) catalyzes the cleavage of the pyridine ring of 2-methyl-3-hydroxypyridine-5-carboxylic acid (mhpc) in the presence of nadh, molecular oxygen, and water. mhpco also catalyzes the nadh oxidation reaction uncoupled with ring opening in the absence of mhpc (the basal activity). the enzyme shows activity toward not only mhpc but also 5-hydroxynicotinic acid (5hn) and 5-pyridoxic acid (5pa). the reaction rate toward 5pa is ...	2017	27568368
rop6 is involved in root hair deformation induced by nod factors in lotus japonicus.	roots of leguminous plants perceive nod factor signals, and then root hair deformation responses such as swelling and curling are activated. however, very little is known about the molecular mechanisms of such root hair deformation. we have previously shown that ljrop6, a member of the rho family of small gtpases, was identified as an nfr5 (nod factor receptor 5)-interacting protein and participated in symbiotic nodulation in lotus japonicus. in this study, we identified ten ljrop gtpases includ ...	2016	27592173
blue light perception by both roots and rhizobia inhibits nodule formation in lotus japonicus.	in many legumes, roots that are exposed to light do not form nodules. here, we report that blue light inhibits nodulation in lotus japonicus roots inoculated with mesorhizobium loti. using rna interference, we suppressed the expression of the phototropin and cryptochrome genes in l. japonicus hairy roots. under blue light, plants transformed with an empty vector did not develop nodules, whereas plants exhibiting suppressed expression of cry1 and cry2 genes formed nodules. we also measured rhizob ...	2016	27611874
nitrogen fixation and molecular oxygen: comparative genomic reconstruction of transcription regulation in alphaproteobacteria.	biological nitrogen fixation plays a crucial role in the nitrogen cycle. an ability to fix atmospheric nitrogen, reducing it to ammonium, was described for multiple species of bacteria and archaea. the transcriptional regulatory network for nitrogen fixation was extensively studied in several representatives of the class alphaproteobacteria. this regulatory network includes the activator of nitrogen fixation nifa, working in tandem with the alternative sigma-factor rpon as well as oxygen-respons ...	2016	27617010
overexpression of the starch phosphorylase-like gene (pho3) in lotus japonicus has a profound effect on the growth of plants and reduction of transitory starch accumulation.	two isoforms of starch phosphorylase (pho; ec 2.4.1.1), plastidic pho1 and cytosolic pho2, have been found in all plants studied to date. another starch phosphorylase-like gene, pho3, which is an ortholog of chlamydomonas phob, has been detected in some plant lineages. in this study, we identified three pho isoform (ljpho) genes in the lotus japonicus genome. expression of the ljpho3 gene was observed in all tissues tested in l. japonicus, and the ljpho3 protein was located in the chloroplast. o ...	2016	27630651
efficient inactivation of symbiotic nitrogen fixation related genes in lotus japonicus using crispr-cas9.	the targeted genome editing technique, crispr/cas9 system, has been widely used to modify genes of interest in a predictable and precise manner. in this study, we describe the crispr/cas9-mediated efficient editing of representative snf (symbiotic nitrogen fixation) related genes in the model legume lotus japonicus via agrobacterium-mediated stable or hairy root transformation. we first predicted nine endogenous u6 genes in lotus and then demonstrated the efficacy of the lju6-1 gene promoter in ...	2016	27630657
real-time visualization of conformational changes within single mlok1 cyclic nucleotide-modulated channels.	eukaryotic cyclic nucleotide-modulated (cnm) ion channels perform various physiological roles by opening in response to cyclic nucleotides binding to a specialized cyclic nucleotide-binding domain. despite progress in structure-function analysis, the conformational rearrangements underlying the gating of these channels are still unknown. here, we image ligand-induced conformational changes in single cnm channels from mesorhizobium loti (mlok1) in real-time, using high-speed atomic force microsco ...	2016	27647260
genome analysis and characterisation of the exopolysaccharide produced by bifidobacterium longum subsp. longum 35624™.	the bifibobacterium longum subsp. longum 35624™ strain (formerly named bifidobacterium longum subsp. infantis) is a well described probiotic with clinical efficacy in irritable bowel syndrome clinical trials and induces immunoregulatory effects in mice and in humans. this paper presents (a) the genome sequence of the organism allowing the assignment to its correct subspeciation longum; (b) a comparative genome assessment with other b. longum strains and (c) the molecular structure of the 35624 e ...	2016	27656878
the transcriptional factor ttsi is involved in a negative regulation of swimming motility in mesorhizobium loti maff303099.	mesorhizobium loti maff303099 has a functional type iii secretion system (t3ss) that is involved in the determination of competitiveness for legume nodulation. here we demonstrate that the transcriptional factor ttsi, which positively regulates t3ss genes expression, is involved in a negative regulation of m. loti swimming motility in soft-agar. conditions that induce t3ss expression affect flagella production. the same conditions also affect promoter activity of m. loti visn gene, a homolog to ...	2016	27664056
assembly and transfer of tripartite integrative and conjugative genetic elements.	integrative and conjugative elements (ices) are ubiquitous mobile genetic elements present as "genomic islands" within bacterial chromosomes. symbiosis islands are ices that convert nonsymbiotic mesorhizobia into symbionts of legumes. here we report the discovery of symbiosis ices that exist as three separate chromosomal regions when integrated in their hosts, but through recombination assemble as a single circular ice for conjugative transfer. whole-genome comparisons revealed exconjugants deri ...	2016	27733511
surface properties of wild-type rhizobium leguminosarum bv. trifolii strain 24.2 and its derivatives with different extracellular polysaccharide content.	rhizobium leguminosarum bv. trifolii is a soil bacterium able to establish symbiosis with agriculturally important legumes, i.e., clover plants (trifolium spp.). cell surface properties of rhizobia play an essential role in their interaction with both biotic and abiotic surfaces. physicochemical properties of bacterial cells are underpinned by the chemical composition of their envelope surrounding the cells, and depend on various environmental conditions. in this study, we performed a comprehens ...	2016	27760230
whole-genome sequence of the nitrogen-fixing symbiotic rhizobium mesorhizobium loti strain tono.	mesorhizobium loti is the nitrogen-fixing microsymbiont for legumes of the genus lotus here, we report the whole-genome sequence of a mesorhizobium loti strain, tono, which is used as a symbiont for the model legume lotus japonicus the whole-genome sequence of the strain tono will be a solid platform for comparative genomics analyses and for the identification of genes responsible for the symbiotic properties of mesorhizobium species.	2016	27795235
reclassification of the taxonomic status of semia3007 isolated in mexico b-11a mex as rhizobium leguminosarum bv. viceae by bioinformatic tools.	evidence based on genomic sequences is extremely important to confirm the phylogenetic relationships within the rhizobium group. semia3007 was analyzed within the mesorhizobium groups to define the underlying causes of taxonomic identification. we previously used biochemical tests and phenotypic taxonomic methods to identify bacteria, which can lead to erroneous classification. an improved understanding of bacterial strains such as the mesorhizobium genus would increase our knowledge of classifi ...	2016	27814683
search for nodulation and nodule development-related cystatin genes in the genome of soybean (glycine max).	nodulation, nodule development and senescence directly affects nitrogen fixation efficiency, and previous studies have shown that inhibition of some cysteine proteases delay nodule senescence, so their nature inhibitors, cystatin genes, are very important in nodulation, nodule development, and senescence. although several cystatins are actively transcribed in soybean nodules, their exact roles and functional diversities in legume have not been well explored in genome-wide survey studies. in this ...	2016	27826313
sinorhizobium fredii hh103 invades lotus burttii by crack entry in a nod factor-and surface polysaccharide-dependent manner.	sinorhizobium fredii hh103-rif(r), a broad host range rhizobial strain, induces nitrogen-fixing nodules in lotus burttii but ineffective nodules in l. japonicus. confocal microscopy studies showed that mesorhizobium loti maff303099 and s. fredii hh103-rif(r) invade l. burttii roots through infection threads or epidermal cracks, respectively. infection threads in root hairs were not observed in l. burttii plants inoculated with s. fredii hh103-rif(r). a s. fredii hh103-rif(r) noda mutant failed t ...	2016	27827003
root nodule symbiosis in lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities.	lotus japonicus has been used for decades as a model legume to study the establishment of binary symbiotic relationships with nitrogen-fixing rhizobia that trigger root nodule organogenesis for bacterial accommodation. using community profiling of 16s rrna gene amplicons, we reveal that in lotus, distinctive nodule- and root-inhabiting communities are established by parallel, rather than consecutive, selection of bacteria from the rhizosphere and root compartments. comparative analyses of wild-t ...	2016	27864511
iron-induced nitric oxide leads to an increase in the expression of ferritin during the senescence of lotus japonicus nodules.	iron is an essential nutrient for legume-rhizobium symbiosis and accumulates abundantly in the nodules. however, the concentration of free iron in the cells is strictly controlled to avoid toxicity. it is known that ferritin accumulates in the cells as an iron storage protein. during nodule senescence, the expression of the ferritin gene, ljfer1, was induced in lotus japonicus. we investigated a signal transduction pathway leading to the increase of ljfer1 in the nodule. the ljfer1 promoter of l ...	2017	27889519
genome-wide discovery of putative srnas in paracoccus denitrificans expressed under nitrous oxide emitting conditions.	nitrous oxide (n2o) is a stable, ozone depleting greenhouse gas. emissions of n2o into the atmosphere continue to rise, primarily due to the use of nitrogen-containing fertilizers by soil denitrifying microbes. it is clear more effective mitigation strategies are required to reduce emissions. one way to help develop future mitigation strategies is to address the currently poor understanding of transcriptional regulation of the enzymes used to produce and consume n2o. with this ultimate aim in mi ...	2016	27895629
discovery and structural characterisation of new fold type iv-transaminases exemplify the diversity of this enzyme fold.	transaminases are useful biocatalysts for the production of amino acids and chiral amines as intermediates for a broad range of drugs and fine chemicals. here, we describe the discovery and characterisation of new transaminases from microorganisms which were enriched in selective media containing (r)-amines as sole nitrogen source. while most of the candidate proteins were clearly assigned to known subgroups of the fold iv family of plp-dependent enzymes by sequence analysis and characterisation ...	2016	27905516
structural and catalytic properties of s1 nuclease from aspergillus oryzae responsible for substrate recognition, cleavage, non-specificity, and inhibition.	the single-strand-specific s1 nuclease from aspergillus oryzae is an archetypal enzyme of the s1-p1 family of nucleases with a widespread use for biochemical analyses of nucleic acids. we present the first x-ray structure of this nuclease along with a thorough analysis of the reaction and inhibition mechanisms and of its properties responsible for identification and binding of ligands. seven structures of s1 nuclease, six of which are complexes with products and inhibitors, and characterization ...	2016	28036383
crystal structure of stna for the biosynthesis of antitumor drug streptonigrin reveals a unique substrate binding mode.	streptonigrin methylesterase a (stna) is one of the tailoring enzymes that modify the aminoquinone skeleton in the biosynthesis pathway of streptomyces species. although stna has no significant sequence homology with the reported α/β-fold hydrolases, it shows typical hydrolytic activity in vivo and in vitro. in order to reveal its functional characteristics, the crystal structures of the selenomethionine substituted stna (semet-stna) and the complex (s185a mutant) with its substrate were resolve ...	2017	28074848
high-quality draft genome sequence of rhizobium mesoamericanum strain stm6155, a mimosa pudica microsymbiont from new caledonia.	rhizobium mesoamericanum stm6155 (inscd = atyy01000000) is an aerobic, motile, gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as an effective nitrogen fixing microsymbiont of the legume mimosa pudica l.. stm6155 was isolated in 2009 from a nodule of the trap host m. pudica grown in nickel-rich soil collected near mont dore, new caledonia. r. mesoamericanum stm6155 was selected as part of the doe joint genome institute 2010 genomic encyclopedia for bacteria and archae ...	2017	28116041