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minimal genome encoding proteins with constrained amino acid repertoire.minimal bacterial gene set comprises the genetic elements needed for survival of engineered bacterium on a rich medium. this set is estimated to include 300-350 protein-coding genes. one way of simplifying an organism with such a minimal genome even further is to constrain the amino acid content of its proteins. in this study, comparative genomics approaches and the results of gene knockout experiments were used to extrapolate the minimal gene set of mollicutes, and bioinformatics combined with ...201323873957
plant growth promotion potential is equally represented in diverse grapevine root-associated bacterial communities from different biopedoclimatic environments.plant-associated bacteria provide important services to host plants. environmental factors such as cultivar type and pedoclimatic conditions contribute to shape their diversity. however, whether these environmental factors may influence the plant growth promoting (pgp) potential of the root-associated bacteria is not widely understood. to address this issue, the diversity and pgp potential of the bacterial assemblage associated with the grapevine root system of different cultivars in three medit ...201323878810
proteogenomic analysis of bradyrhizobium japonicum usda110 using genosuite, an automated multi-algorithmic pipeline.we present genosuite, an integrated proteogenomic pipeline to validate, refine and discover protein coding genes using high-throughput mass spectrometry (ms) data from prokaryotes. to demonstrate the effectiveness of genosuite, we analyzed proteomics data of bradyrhizobium japonicum (usda110), a model organism to study agriculturally important rhizobium-legume symbiosis. our analysis confirmed 31% of known genes, refined 49 gene models for their translation initiation site (tis) and discovered 5 ...201323882027
disclosure of the differences of mesorhizobium loti under the free-living and symbiotic conditions by comparative proteome analysis without bacteroid isolation.rhizobia are symbiotic nitrogen-fixing soil bacteria that show a symbiotic relationship with their host legume. rhizobia have 2 different physiological conditions: a free-living condition in soil, and a symbiotic nitrogen-fixing condition in the nodule. the lifestyle of rhizobia remains largely unknown, although genome and transcriptome analyses have been carried out. to clarify the lifestyle of bacteria, proteome analysis is necessary because the protein profile directly reflects in vivo reacti ...201323898917
characterization of inta, a bidirectional site-specific recombinase required for conjugative transfer of the symbiotic plasmid of rhizobium etli cfn42.site-specific recombination occurs at short specific sequences, mediated by the cognate recombinases. inta is a recombinase from rhizobium etli cfn42 and belongs to the tyrosine recombinase family. it allows cointegration of plasmid p42a and the symbiotic plasmid via site-specific recombination between attachment regions (atta and attd) located in each replicon. cointegration is needed for conjugative transfer of the symbiotic plasmid. to characterize this system, two plasmids harboring the corr ...201323935046
identification and characterization of ribn, a novel family of riboflavin transporters from rhizobium leguminosarum and other proteobacteria.rhizobia are symbiotic bacteria able to invade and colonize the roots of legume plants, inducing the formation of nodules, where bacteria reduce atmospheric nitrogen (n2) to ammonia (nh3). riboflavin availability influences the capacity of rhizobia to survive in the rhizosphere and to colonize roots. in this study, we identified the rl1692 gene of rhizobium leguminosarum downstream of a flavin mononucleotide (fmn) riboswitch. rl1692 encodes a putative transmembrane permease with two eama domains ...201323935051
genomic and evolutionary aspects of phytoplasmas.parasitic bacteria that infect eukaryotes, such as animals and plants, often have reduced genomes, having lost important metabolic genes as a result of their host-dependent life cycles. genomic sequencing of these bacteria has revealed their survival strategies and adaptations to parasitism. phytoplasmas (class mollicutes, genus 'candidatus phytoplasma') are intracellular bacterial pathogens of plants and insects and cause devastating yield losses in diverse low- and high-value crops worldwide. ...201323966988
argonaute protein as a linker to command center of physiological processes.micrornas (mirnas) post-transcriptionally regulate gene expression by binding to target mrnas with perfect or imperfect complementarity, recruiting an argonaute (ago) protein complex that usually results in degradation or translational repression of the target mrna. ago proteins function as the slicer enzyme in mirna and small interfering rna (sirna) pathways involved in human physiological and pathophysiological processes, such as antiviral responses and disease formation. although the past dec ...201323997530
evolutionary diversification and characterization of the eubacterial gene family encoding dxr type ii, an alternative isoprenoid biosynthetic enzyme.isoprenoids constitute a vast family of natural compounds performing diverse and essential functions in all domains of life. in most eubacteria, isoprenoids are synthesized through the methylerythritol 4-phosphate (mep) pathway. the production of mep is usually catalyzed by deoxyxylulose 5-phosphate reductoisomerase (dxr-i) but a few organisms use an alternative dxr-like enzyme (dxr-ii).201324004839
genetic diversity of indigenous common bean (phaseolus vulgaris l.) rhizobia from the state of minas gerais, brazil.we characterized indigenous common bean rhizobia from five districts of the state of minas gerais, brazil. the isolates were trapped by two common bean varieties, the mineiro precoce (andean origin) and ouro negro (mesoamerican origin). analysis by box-pcr of selected isolates detected a high level of genetic diversity.200924031433
application of representational difference analysis to identify genomic differences between bradyrhizobium elkanii and b. japonicum species.bradyrhizobium elkanii is successfully used in the formulation of commercial inoculants and, together with b. japonicum, it fully supplies the plant nitrogen demands. despite the similarity between b. japonicum and b. elkanii species, several works demonstrated genetic and physiological differences between them. in this work representational difference analysis (rda) was used for genomic comparison between b. elkanii semia 587, a crop inoculant strain, and b. japonicum usda 110, a reference stra ...201024031597
genetic diversity of rhizobia isolates from amazon soils using cowpea (vigna unguiculata) as trap plant.the aim of this work was to characterize rhizobia isolated from the root nodules of cowpea (vigna unguiculata) plants cultivated in amazon soils samples by means of ardra (amplified rdna restriction analysis) and sequencing analysis, to know their phylogenetic relationships. the 16s rrna gene of rhizobia was amplified by pcr (polymerase chain reaction) using universal primers y1 and y3. the amplification products were analyzed by the restriction enzymes hinfi, mspi and ddei and also sequenced wi ...201224031880
multilocus sequence analysis (mlsa) of bradyrhizobium strains: revealing high diversity of tropical diazotrophic symbiotic bacteria.symbiotic association of several genera of bacteria collectively called as rhizobia and plants belonging to the family leguminosae (=fabaceae) results in the process of biological nitrogen fixation, playing a key role in global n cycling, and also bringing relevant contributions to the agriculture. bradyrhizobium is considered as the ancestral of all nitrogen-fixing rhizobial species, probably originated in the tropics. the genus encompasses a variety of diverse bacteria, but the diversity captu ...201224031882
haemophilus parainfluenzae expresses diverse lipopolysaccharide o-antigens using abc transporter and wzy polymerase-dependent mechanisms.lipopolysaccharide o-antigens are the basis of serotyping schemes for gram negative bacteria and help to determine the nature of host-bacterial interactions. haemophilus parainfluenzae is a normal commensal of humans but is also an occasional pathogen. the prevalence, diversity and biosynthesis of o-antigens were investigated in this species for the first time. 18/18 commensal h. parainfluenzae isolates contain a o-antigen biosynthesis gene cluster flanked by glna and pepb, the same position as ...201324035104
absence of ancient dna in sub-fossil insect inclusions preserved in 'anthropocene' colombian copal.insects preserved in copal, the sub-fossilized resin precursor of amber, have potential value in molecular ecological studies of recently-extinct species and of extant species that have never been collected as living specimens. the objective of the work reported in this paper was therefore to determine if ancient dna is present in insects preserved in copal. we prepared dna libraries from two stingless bees (apidae: meliponini: trigonisca ameliae) preserved in 'anthropocene' colombian copal, dat ...201324039876
prerequisites for amplicon pyrosequencing of microbial methanol utilizers in the environment.the commercial availability of next generation sequencing (ngs) technologies facilitated the assessment of functional groups of microorganisms in the environment with high coverage, resolution, and reproducibility. soil methylotrophs were among the first microorganisms in the environment that were assessed with molecular tools, and nowadays, as well with ngs technologies. studies in the past years re-attracted notice to the pivotal role of methylotrophs in global conversions of methanol, which m ...201324046766
hijacking of leguminous nodulation signaling by the rhizobial type iii secretion system.root-nodule symbiosis between leguminous plants and nitrogen-fixing bacteria (rhizobia) involves molecular communication between the two partners. key components for the establishment of symbiosis are rhizobium-derived lipochitooligosaccharides (nod factors; nfs) and their leguminous receptors (nfrs) that initiate nodule development and bacterial entry. here we demonstrate that the soybean microsymbiont bradyrhizobium elkanii uses the type iii secretion system (t3ss), which is known for its deli ...201324082124
optimization of dairy sludge for growth of rhizobium cells.in this study dairy sludge was evaluated as an alternative cultivation medium for rhizobium. growth of bacterial strains at different concentrations of dairy sludge was monitored. maximum growth of all strains was observed at 60% dairy sludge concentration. at 60% optical density (od) values are 0.804 for rhizobium trifolii (mtcc905), 0.825 for rhizobium trifolii (mtcc906), and 0.793 for rhizobium meliloti (mtcc100). growth pattern of strains was observed at 60% dairy sludge along with different ...201324089690
the lysr-type transcription factor hbrl is a global regulator of iron homeostasis and porphyrin synthesis in rhodobacter capsulatus.the purple bacterium rhodobacter capsulatus is unique among rhodobacteriacae as it contains a putative iron response regulator (irr) but does not possess a copy of the ferric uptake regulator (fur). interestingly, an in-frame deletion mutant of irr shows no major role in iron homeostasis. instead, we showed that the previously identified activator of haem gene expression hbrl is a crucial regulator of iron homeostasis. we demonstrated that an hbrl deletion strain is unable to grow in iron-limite ...201324134691
functional conservation of the capacity for ent-kaurene biosynthesis and an associated operon in certain rhizobia.bacterial interactions with plants are accompanied by complex signal exchange processes. previously, the nitrogen-fixing symbiotic (rhizo)bacterium bradyrhizobium japonicum was found to carry adjacent genes encoding two sequentially acting diterpene cyclases that together transform geranylgeranyl diphosphate to ent-kaurene, the olefin precursor to the gibberellin plant hormones. species from the three other major genera of rhizobia were found to have homologous terpene synthase genes. cloning an ...201424142247
the trehalose utilization gene thua ortholog in mesorhizobium loti does not influence competitiveness for nodulation on lotus spp.competitiveness for nodulation is a desirable trait in rhizobia strains used as inoculant. in sinorhizobium meliloti 1021 mutation in either of the trehalose utilization genes thua or thub influences its competitiveness for root colonization and nodule occupancy depending on the interacting host. we have therefore investigated whether mutation in the thua ortholog in mesorhizobium loti maff303099 also leads to a similar competitive phenotype on its hosts. the results show that m. loti thua mutan ...201424142427
mechanistic aspects of carotenoid biosynthesis. 201324175570
mechanistic aspects of carotenoid biosynthesis. 201324175570
an underground tale: contribution of microbial activity to plant iron acquisition via ecological processes.iron (fe) deficiency in crops is a worldwide agricultural problem. plants have evolved several strategies to enhance fe acquisition, but increasing evidence has shown that the intrinsic plant-based strategies alone are insufficient to avoid fe deficiency in fe-limited soils. soil micro-organisms also play a critical role in plant fe acquisition; however, the mechanisms behind their promotion of fe acquisition remain largely unknown.201324265348
an underground tale: contribution of microbial activity to plant iron acquisition via ecological processes.iron (fe) deficiency in crops is a worldwide agricultural problem. plants have evolved several strategies to enhance fe acquisition, but increasing evidence has shown that the intrinsic plant-based strategies alone are insufficient to avoid fe deficiency in fe-limited soils. soil micro-organisms also play a critical role in plant fe acquisition; however, the mechanisms behind their promotion of fe acquisition remain largely unknown.201324265348
cyanobase and rhizobase: databases of manually curated annotations for cyanobacterial and rhizobial genomes.to understand newly sequenced genomes of closely related species, comprehensively curated reference genome databases are becoming increasingly important. we have extended cyanobase (http://genome.microbedb.jp/cyanobase), a genome database for cyanobacteria, and newly developed rhizobase (http://genome.microbedb.jp/rhizobase), a genome database for rhizobia, nitrogen-fixing bacteria associated with leguminous plants. both databases focus on the representation and reusability of reference genome a ...201324275496
cyanobase and rhizobase: databases of manually curated annotations for cyanobacterial and rhizobial genomes.to understand newly sequenced genomes of closely related species, comprehensively curated reference genome databases are becoming increasingly important. we have extended cyanobase (http://genome.microbedb.jp/cyanobase), a genome database for cyanobacteria, and newly developed rhizobase (http://genome.microbedb.jp/rhizobase), a genome database for rhizobia, nitrogen-fixing bacteria associated with leguminous plants. both databases focus on the representation and reusability of reference genome a ...201324275496
global transcriptional response to heat shock of the legume symbiont mesorhizobium loti maff303099 comprises extensive gene downregulation.rhizobia, the bacterial legume symbionts able to fix atmospheric nitrogen inside root nodules, have to survive in varied environmental conditions. the aim of this study was to analyse the transcriptional response to heat shock of mesorhizobium loti maff303099, a rhizobium with a large multipartite genome of 7.6 mb that nodulates the model legume lotus japonicus. using microarray analysis, extensive transcriptomic changes were detected in response to heat shock: 30% of the protein-coding genes we ...201324277738
global transcriptional response to heat shock of the legume symbiont mesorhizobium loti maff303099 comprises extensive gene downregulation.rhizobia, the bacterial legume symbionts able to fix atmospheric nitrogen inside root nodules, have to survive in varied environmental conditions. the aim of this study was to analyse the transcriptional response to heat shock of mesorhizobium loti maff303099, a rhizobium with a large multipartite genome of 7.6 mb that nodulates the model legume lotus japonicus. using microarray analysis, extensive transcriptomic changes were detected in response to heat shock: 30% of the protein-coding genes we ...201324277738
knockdown of ljipt3 influences nodule development in lotus japonicus.cytokinins play important roles in legume-rhizobia symbiosis. here we report isolation of six genes encoding isopentenyl transferase (ipt) from lotus japonicus, which catalyze the rate-limiting step of cytokinin biosynthesis. the ljipt3 gene was found to be up-regulated in infected roots and mature nodules. histochemical analysis demonstrated expression of pro(ljipt3):gus (β-glucuronidase) in vegetative and reproductive organs, and was especially high in the vascular bundles of roots. when inocu ...201424285753
structural insight into l-ribulose 3-epimerase from mesorhizobium loti.l-ribulose 3-epimerase (l-re) from mesorhizobium loti has been identified as the first ketose 3-epimerase that shows the highest observed activity towards ketopentoses. in the present study, the crystal structure of the enzyme was determined to 2.7 å resolution. the asymmetric unit contained two homotetramers with the monomer folded into an (α/β)8-barrel carrying four additional short α-helices. the overall structure of m. loti l-re showed significant similarity to the structures of ketose 3-epi ...201324311575
engineering rhizobial bioinoculants: a strategy to improve iron nutrition.under field conditions, inoculated rhizobial strains are at a survival disadvantage as compared to indigenous strains. in order to out-compete native rhizobia it is not only important to develop strong nodulation efficiency but also increase their competence in the soil and rhizosphere. competitive survival of the inoculated strain may be improved by employing strain selection and by genetic engineering of superior nitrogen fixing strains. iron sufficiency is an important factor determining the ...201324319357
aliphatic, cyclic, and aromatic organic acids, vitamins, and carbohydrates in soil: a review.organic acids, vitamins, and carbohydrates represent important organic compounds in soil. aliphatic, cyclic, and aromatic organic acids play important roles in rhizosphere ecology, pedogenesis, food-web interactions, and decontamination of sites polluted by heavy metals and organic pollutants. carbohydrates in soils can be used to estimate changes of soil organic matter due to management practices, whereas vitamins may play an important role in soil biological and biochemical processes. the aim ...201324319374
rhizobial infection does not require cortical expression of upstream common symbiosis genes responsible for the induction of ca(2+) spiking.for the establishment of an effective root nodule symbiosis, a coordinated regulation of the infection processes between the epidermis and cortex is required. however, it remains unclear whether the symbiotic genes identified so far are involved in epidermal and/or cortical infection, e.g. epidermal and cortical infection thread formation or cortical cell division. to analyze the symbiotic gene requirements of the infection process, we have developed an epidermis-specific expression system (pepi ...201324329948
rhizobial infection does not require cortical expression of upstream common symbiosis genes responsible for the induction of ca(2+) spiking.for the establishment of an effective root nodule symbiosis, a coordinated regulation of the infection processes between the epidermis and cortex is required. however, it remains unclear whether the symbiotic genes identified so far are involved in epidermal and/or cortical infection, e.g. epidermal and cortical infection thread formation or cortical cell division. to analyze the symbiotic gene requirements of the infection process, we have developed an epidermis-specific expression system (pepi ...201324329948
comparative phylogenomics and evolution of the brucellae reveal a path to virulence.brucella species include important zoonotic pathogens that have a substantial impact on both agriculture and human health throughout the world. brucellae are thought of as "stealth pathogens" that escape recognition by the host innate immune response, modulate the acquired immune response, and evade intracellular destruction. we analyzed the genome sequences of members of the family brucellaceae to assess its evolutionary history from likely free-living soil-based progenitors into highly success ...201424336939
endoplasmic reticulum-targeted gfp reveals er remodeling in mesorhizobium-treated lotus japonicus root hairs during root hair curling and infection thread formation.the endoplasmic reticulum (er) of the model legume lotus japonicus was visualized using green fluorescent protein (gfp) fused with the kdel sequence to investigate the changes in the root hair cortical er in the presence or absence of mesorhizobium loti using live fluorescence imaging. uninoculated root hairs displayed dynamic forms of er, ranging from a highly condensed form to an open reticulum. in the presence of m. loti, a highly dynamic condensed form of the er linked with the nucleus was f ...201424337802
cris-a novel camp-binding protein controlling spermiogenesis and the development of flagellar bending.the second messengers camp and cgmp activate their target proteins by binding to a conserved cyclic nucleotide-binding domain (cnbd). here, we identify and characterize an entirely novel cnbd-containing protein called cris (cyclic nucleotide receptor involved in sperm function) that is unrelated to any of the other members of this protein family. cris is exclusively expressed in sperm precursor cells. cris-deficient male mice are either infertile due to a lack of sperm resulting from spermatogen ...201324339785
quorum sensing and self-quorum quenching in the intracellular pathogen brucellamelitensis.brucella quorum sensing has been described as an important regulatory system controlling crucial virulence determinants such as the virb type iv secretion system and the flagellar genes. however, the basis of quorum sensing, namely the production of autoinducers in brucella has been questioned. here, we report data obtained from the use of a genetic tool allowing the in situ detection of long-chain n-acyl-homoserine lactones (ahl) activity at single bacterium level in brucella melitensis. these ...201324349302
isolation and characterization of two novel bacteria afipia cberi and mesorhizobium hominis from blood of a patient afflicted with fatal pulmonary illness.we recently isolated and discovered new bradyrhizobiaceae microbes from the cryopreserved culture broth of blood samples from 3 patients with poorly defined illnesses using modified sp4 media and culture conditions coupled with genomic sequencing. using a similar protocol, we studied a previously cryopreserved culture broth of blood sample from a patient who had succumbed to an acute onset of fulminant pulmonary illness. we report that two phases of microbial growth were observed in the re-initi ...201324367538
molecular characterization of a novel n-acetyltransferase from chryseobacterium sp.n-acetyltransferase from chryseobacterium sp. strain 5-3b is an acetyl coenzyme a (acetyl-coa)-dependent enzyme that catalyzes the enantioselective transfer of an acetyl group from acetyl-coa to the amino group of l-2-phenylglycine to produce (2s)-2-acetylamino-2-phenylacetic acid. we purified the enzyme from strain 5-3b and deduced the n-terminal amino acid sequence. the gene, designated nata, was cloned with two other hypothetical protein genes; the three genes probably form a 2.5-kb operon. t ...201424375143
iron homeostasis in the rhodobacter genus.metals are utilized for a variety of critical cellular functions and are essential for survival. however cells are faced with the conundrum of needing metals coupled with e fact that some metals, iron in particular are toxic if present in excess. maintaining metal homeostasis is therefore of critical importance to cells. in this review we have systematically analyzed sequenced genomes of three members of the rhodobacter genus, r. capsulatus sb1003, r. sphaeroides 2.4.1 and r. ferroxidans sw2 to ...201324382933
characterization of rhizobium grahamii extrachromosomal replicons and their transfer among rhizobia.rhizobium grahamii belongs to a new phylogenetic group of rhizobia together with rhizobium mesoamericanum and other species. r. grahamii has a broad-host-range that includes leucaena leucocephala and phaseolus vulgaris, although it is a poor competitor for p. vulgaris nodulation in the presence of rhizobium etli or rhizobium phaseoli strains. this work analyzed the genome sequence and transfer properties of r. grahamii plasmids.201424397311
rep-pcr mediated genomic fingerprinting of rhizobia and computer-assisted phylogenetic pattern analysis.a rapid and reproducible method has been developed for genomic fingerprinting of rhizobia and other soil microbes interacting with plants. the method is based on the use of oligonucleotide primers, corresponding to conserved motifs in naturally occurring interspersed repetitive dna elements in bacteria (rep-elements), and the polymerase chain reaction (rep-pcr). rep-pcr results in the amplification of inter-element genomic dna fragments of characteristic lengths and thereby generates a genomic f ...199624415164
performance of chickpea, lentil and lupin nodulated with indigenous or inoculated rhizobia micropartners under nitrogen, boron, cobalt and molybdenum fertilization schedules.chickpea (cicer arietinum), lentil (lens esculenta) and lupin (lupinus albus) responded to inoculation with their respective symbiotants:rhizobium loti, rhizobium leguminosarum biovarviceae andbradyrhizobium sp. (lupinus) alone or with (nh4)2so4 at 30 ppm n. soil application of na2moo4.2h2o at 3 ppm mo, cocl2.6h2o at 2 ppm co(2+) or na2b4o7.10h2o at 1 ppm b with 0 and 30 ppm n increased nodule weight and plant dry weight and n-content 60 days after sowing and seed yield, seed size and the n and ...199224425609
ligand-induced structural changes in the cyclic nucleotide-modulated potassium channel mlok1.cyclic nucleotide-modulated ion channels are important for signal transduction and pacemaking in eukaryotes. the molecular determinants of ligand gating in these channels are still unknown, mainly because of a lack of direct structural information. here we report ligand-induced conformational changes in full-length mlok1, a cyclic nucleotide-modulated potassium channel from the bacterium mesorhizobium loti, analysed by electron crystallography and atomic force microscopy. upon camp binding, the ...201424469021
glutamine synthetase i-deficiency in mesorhizobium loti differentially affects nodule development and activity in lotus japonicus.in this study, we focused on the effect of glutamine synthetase (gsi) activity in mesorhizobium loti on the symbiosis between the host plant, lotus japonicus, and the bacteroids. we used a signature-tagged mutant of m. loti (stm30) with a transposon inserted into the gsi (mll0343) gene. the l. japonicus plants inoculated with stm30 had significantly more nodules, and the occurrence of senesced nodules was much higher than in plants inoculated with the wild-type. the acetylene reduction activity ...201424484964
microtubule array formation during root hair infection thread initiation and elongation in the mesorhizobium-lotus symbiosis.nuclear migration during infection thread (it) development in root hairs is essential for legume-rhizobium symbiosis. however, little is known about the relationships between it formation, nuclear migration, and microtubule dynamics. to this aim, we used transgenic lotus japonicus expressing a fusion of the green fluorescent protein and tubulin-α6 from arabidopsis thaliana to visualize in vivo dynamics of cortical microtubules (cmt) and endoplasmic microtubules (emts) in root hairs in the presen ...201424488109
crystal structure of an (r)-selective ω-transaminase from aspergillus terreus.chiral amines are important building blocks for the synthesis of pharmaceutical products, fine chemicals, and agrochemicals. ω-transaminases are able to directly synthesize enantiopure chiral amines by catalysing the transfer of an amino group from a primary amino donor to a carbonyl acceptor with pyridoxal 5'-phosphate (plp) as cofactor. in nature, (s)-selective amine transaminases are more abundant than the (r)-selective enzymes, and therefore more information concerning their structures is av ...201424498081
a kcsa/mlok1 chimeric ion channel has lipid-dependent ligand-binding energetics.cyclic nucleotide-modulated ion channels play crucial roles in signal transduction in eukaryotes. the molecular mechanism by which ligand binding leads to channel opening remains poorly understood, due in part to the lack of a robust method for preparing sufficient amounts of purified, stable protein required for structural and biochemical characterization. to overcome this limitation, we designed a stable, highly expressed chimeric ion channel consisting of the transmembrane domains of the well ...201424515111
evolutionary insights about bacterial glxrs from whole genome analyses: is glurs2 a chimera?evolutionary histories of glutamyl-trna synthetase (glurs) and glutaminyl-trna synthetase (glnrs) in bacteria are convoluted. after the divergence of eubacteria and eukarya, bacterial glurs glutamylated both trnagln and trnaglu until glnrs appeared by horizontal gene transfer (hgt) from eukaryotes or a duplicate copy of glurs (glurs2) that only glutamylates trnagln appeared. the current understanding is based on limited sequence data and not always compatible with available experimental results. ...201424521160
direct exchange of vitamin b12 is demonstrated by modelling the growth dynamics of algal-bacterial cocultures.the growth dynamics of populations of interacting species in the aquatic environment is of great importance, both for understanding natural ecosystems and in efforts to cultivate these organisms for industrial purposes. here we consider a simple two-species system wherein the bacterium mesorhizobium loti supplies vitamin b12 (cobalamin) to the freshwater green alga lobomonas rostrata, which requires this organic micronutrient for growth. in return, the bacterium receives photosynthate from the a ...201424522262
a bifunctional glycosyltransferase from agrobacterium tumefaciens synthesizes monoglucosyl and glucuronosyl diacylglycerol under phosphate deprivation.glycolipids are mainly found in phototrophic organisms (like plants and cyanobacteria), in gram-positive bacteria, and a few other bacterial phyla. besides the function as bulk membrane lipids, they often play a role under phosphate deprivation as surrogates for phospholipids. the gram-negative agrobacterium tumefaciens accumulates four different glycolipids under phosphate deficiency, including digalactosyl diacylglycerol and glucosylgalactosyl diacylglycerol synthesized by a processive glycosy ...201424558041
corbi: a new r package for biological network alignment and querying.in the last decade, plenty of biological networks are built from the large scale experimental data produced by the rapidly developing high-throughput techniques as well as literature and other sources. but the huge amount of network data have not been fully utilized due to the limited biological network analysis tools. as a basic and essential bioinformatics method, biological network alignment and querying have been applied in many fields such as predicting new protein-protein interactions (ppi ...201324565104
lotus japonicus cytokinin receptors work partially redundantly to mediate nodule formation.previous analysis of the lotus histidine kinase1 (lhk1) cytokinin receptor gene has shown that it is required and also sufficient for nodule formation in lotus japonicus. the l. japonicus mutant carrying the loss-of-function lhk1-1 allele is hyperinfected by its symbiotic partner, mesorhizobium loti, in the initial absence of nodule organogenesis. at a later time point following bacterial infection, lhk1-1 develops a limited number of nodules, suggesting the presence of an lhk1-independent mecha ...201424585837
a proteomic approach of bradyrhizobium/aeschynomene root and stem symbioses reveals the importance of the fixa locus for symbiosis.rhizobia are soil bacteria that are able to form symbiosis with plant hosts of the legume family. these associations result in the formation of organs, called nodules in which bacteria fix atmospheric nitrogen to the benefit of the plant. most of our knowledge on the metabolism and the physiology of the bacteria during symbiosis derives from studying roots nodules of terrestrial plants. here we used a proteomics approach to investigate the bacterial physiology of photosynthetic bradyrhizobium sp ...201424590127
fixating on metals: new insights into the role of metals in nodulation and symbiotic nitrogen fixation.symbiotic nitrogen fixation is one of the most promising and immediate alternatives to the overuse of polluting nitrogen fertilizers for improving plant nutrition. at the core of this process are a number of metalloproteins that catalyze and provide energy for the conversion of atmospheric nitrogen to ammonia, eliminate free radicals produced by this process, and create the microaerobic conditions required by these reactions. in legumes, metal cofactors are provided to endosymbiotic rhizobia wit ...201424592271
evolution of tryptophan biosynthetic pathway in microbial genomes: a comparative genetic study.biosynthetic pathway evolution needs to consider the evolution of a group of genes that code for enzymes catalysing the multiple chemical reaction steps leading to the final end product. tryptophan biosynthetic pathway has five chemical reaction steps that are highly conserved in diverse microbial genomes, though the genes of the pathway enzymes show considerable variations in arrangements, operon structure (gene fusion and splitting) and regulation. we use a combined bioinformatic and statistic ...201324592292
evolution of tryptophan biosynthetic pathway in microbial genomes: a comparative genetic study.biosynthetic pathway evolution needs to consider the evolution of a group of genes that code for enzymes catalysing the multiple chemical reaction steps leading to the final end product. tryptophan biosynthetic pathway has five chemical reaction steps that are highly conserved in diverse microbial genomes, though the genes of the pathway enzymes show considerable variations in arrangements, operon structure (gene fusion and splitting) and regulation. we use a combined bioinformatic and statistic ...201324592292
bacterial genome instability.bacterial genomes are remarkably stable from one generation to the next but are plastic on an evolutionary time scale, substantially shaped by horizontal gene transfer, genome rearrangement, and the activities of mobile dna elements. this implies the existence of a delicate balance between the maintenance of genome stability and the tolerance of genome instability. in this review, we describe the specialized genetic elements and the endogenous processes that contribute to genome instability. we ...201424600039
utilization of glyphosate as phosphate source: biochemistry and genetics of bacterial carbon-phosphorus lyase.after several decades of use of glyphosate, the active ingredient in weed killers such as roundup, in fields, forests, and gardens, the biochemical pathway of transformation of glyphosate phosphorus to a useful phosphorus source for microorganisms has been disclosed. glyphosate is a member of a large group of chemicals, phosphonic acids or phosphonates, which are characterized by a carbon-phosphorus bond. this is in contrast to the general phosphorus compounds utilized and metabolized by microor ...201424600043
the growth of steroidobacter agariperforans sp. nov., a novel agar-degrading bacterium isolated from soil, is enhanced by the diffusible metabolites produced by bacteria belonging to rhizobiales.an agar-degrading bacterium was isolated from soil collected in a vegetable cropping field. the growth of this isolate was enhanced by supplying culture supernatants of bacteria belonging to the order rhizobiales. phylogenetic analysis based on 16s rrna gene sequences indicated the novel bacterium, strain ka5-b(t), belonged to the genus steroidobacter in gammaproteobacteria, but differed from its closest relative, steroidobacter denitrificans fs(t), at the species level with 96.5% similarity. st ...201424621511
a second-generation protein-protein interaction network of helicobacter pylori.helicobacter pylori infections cause gastric ulcers and play a major role in the development of gastric cancer. in 2001, the first protein interactome was published for this species, revealing over 1500 binary protein interactions resulting from 261 yeast two-hybrid screens. here we roughly double the number of previously published interactions using an orfeome-based, proteome-wide yeast two-hybrid screening strategy. we identified a total of 1515 protein-protein interactions, of which 1461 are ...201424627523
comparative genomic analysis of n2-fixing and non-n2-fixing paenibacillus spp.: organization, evolution and expression of the nitrogen fixation genes.we provide here a comparative genome analysis of 31 strains within the genus paenibacillus including 11 new genomic sequences of n2-fixing strains. the heterogeneity of the 31 genomes (15 n2-fixing and 16 non-n2-fixing paenibacillus strains) was reflected in the large size of the shell genome, which makes up approximately 65.2% of the genes in pan genome. large numbers of transposable elements might be related to the heterogeneity. we discovered that a minimal and compact nif cluster comprising ...201424651173
lotus japonicus sunergos1 encodes a predicted subunit a of a dna topoisomerase vi that is required for nodule differentiation and accommodation of rhizobial infection.a symbiotic mutant of lotus japonicus, called sunergos1-1 (suner1-1), originated from a har1-1 suppressor screen. suner1-1 supports epidermal infection by mesorhizobium loti and initiates cell divisions for organogenesis of nodule primordia. however, these processes appear to be temporarily stalled early during symbiotic interaction, leading to a low nodule number phenotype. this defect is ephemeral and near wild-type nodule numbers are reached by suner1-1 at a later point after infection. using ...201424661810
biotechnology of polyketides: new breath of life for the novel antibiotic genetic pathways discovery through metagenomics.the discovery of secondary metabolites produced by microorganisms (e.g., penicillin in 1928) and the beginning of their industrial application (1940) opened new doors to what has been the main medication source for the treatment of infectious diseases and tumors. in fact, approximately 80 years after the discovery of the first antibiotic compound, and despite all of the warnings about the failure of the "goose that laid the golden egg," the potential of this wealth is still inexorable: simply ad ...201424688489
biotechnology of polyketides: new breath of life for the novel antibiotic genetic pathways discovery through metagenomics.the discovery of secondary metabolites produced by microorganisms (e.g., penicillin in 1928) and the beginning of their industrial application (1940) opened new doors to what has been the main medication source for the treatment of infectious diseases and tumors. in fact, approximately 80 years after the discovery of the first antibiotic compound, and despite all of the warnings about the failure of the "goose that laid the golden egg," the potential of this wealth is still inexorable: simply ad ...201424688489
rna-seq and microarrays analyses reveal global differential transcriptomes of mesorhizobium huakuii 7653r between bacteroids and free-living cells.mesorhizobium huakuii 7653r occurs either in nitrogen-fixing symbiosis with its host plant, astragalus sinicus, or free-living in the soil. the m. huakuii 7653r genome has recently been sequenced. to better understand the complex biochemical and developmental changes that occur in 7653r during bacteroid development, rna-seq and microarrays were used to investigate the differential transcriptomes of 7653r bacteroids and free-living cells. the two approaches identified several thousand differentia ...201424695521
structure of 4-pyridoxolactonase from mesorhizobium loti.4-pyridoxolactonase from mesorhizobium loti catalyzes the zinc-dependent lactone-ring hydrolysis of 4-pyridoxolactone (4pal) to 4-pyridoxic acid (4pa) in vitamin b6 degradation pathway i. the crystal structures of 4-pyridoxolactonase and its complex with 5-pyridoxolactone (5pal; the competitive inhibitor) were determined. the overall structure was an αβ/βα sandwich fold, and two zinc ions were coordinated. this strongly suggested that the enzyme belongs to subclass b3 of the class b β-lactamases ...201424699732
the genetics of symbiotic nitrogen fixation: comparative genomics of 14 rhizobia strains by resolution of protein clusters.the symbiotic relationship between legumes and nitrogen fixing bacteria is critical for agriculture, as it may have profound impacts on lowering costs for farmers, on land sustainability, on soil quality, and on mitigation of greenhouse gas emissions. however, despite the importance of the symbioses to the global nitrogen cycling balance, very few rhizobial genomes have been sequenced so far, although there are some ongoing efforts in sequencing elite strains. in this study, the genomes of fourt ...201224704847
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 ...201224704978
common symbiosis genes cerberus and nsp1 provide additional insight into the establishment of arbuscular mycorrhizal and root nodule symbioses in lotus japonicus.arbuscular mycorrhizal symbiosis (ams) and root nodule symbiosis (rns) share several common symbiotic components, and many of the common symbiosis mutants block the entry of symbionts into the roots. we recently reported that cerberus (an e3 ubiquitin ligase) and nsp1 (a gras family transcription factor), required for rns, also modulate ams development in lotus japonicus. the novel common symbiosis mutants, cerberus and nsp1, have low colonization of arbuscular mycorrhiza (am) fungi, caused by a ...201424705023
genome sequence of ensifer adhaerens ov14 provides insights into its ability as a novel vector for the genetic transformation of plant genomes.recently it has been shown that ensifer adhaerens can be used as a plant transformation technology, transferring genes into several plant genomes when equipped with a ti plasmid. for this study, we have sequenced the genome of ensifer adhaerens ov14 (ov14) and compared it with those of agrobacterium tumefaciens c58 (c58) and sinorhizobium meliloti 1021 (1021); the latter of which has also demonstrated a capacity to genetically transform crop genomes, albeit at significantly reduced frequencies.201424708309
complete genome sequence of the soybean symbiont bradyrhizobium japonicum strain usda6t.the complete nucleotide sequence of the genome of the soybean symbiont bradyrhizobium japonicum strain usda6t was determined. the genome of usda6t is a single circular chromosome of 9,207,384 bp. the genome size is similar to that of the genome of another soybean symbiont, b. japonicum usda110 (9,105,828 bp). comparison of the whole-genome sequences of usda6t and usda110 showed colinearity of major regions in the two genomes, although a large inversion exists between them. a significantly high l ...201124710291
annotation of protein domains reveals remarkable conservation in the functional make up of proteomes across superkingdoms.the functional repertoire of a cell is largely embodied in its proteome, the collection of proteins encoded in the genome of an organism. the molecular functions of proteins are the direct consequence of their structure and structure can be inferred from sequence using hidden markov models of structural recognition. here we analyze the functional annotation of protein domain structures in almost a thousand sequenced genomes, exploring the functional and structural diversity of proteomes. we find ...201124710297
conservation and occurrence of trans-encoded srnas in the rhizobiales.post-transcriptional regulation by trans-encoded srnas, for example via base-pairing with target mrnas, is a common feature in bacteria and influences various cell processes, e.g., response to stress factors. several studies based on computational and rna-seq approaches identified approximately 180 trans-encoded srnas in sinorhizobium meliloti. the initial point of this report is a set of 52 trans-encoded srnas derived from the former studies. sequence homology combined with structural conservat ...201124710299
phenotypic characterization of astragalus glycyphyllos symbionts and their phylogeny based on the 16s rdna sequences and rflp of 16s rrna gene.in this study, the nitrogen fixing astragalus glycyphyllos symbionts were characterized by phenotypic properties, restriction fragment length polymorphism (rflp), and sequences of 16s rdna. the generation time of a. glycyphyllos rhizobia in yeast extract mannitol medium was in the range 4-6 h. the studied isolates exhibited a low resistance to antibiotics, a moderate tolerance to nacl, assimilated di- and trisaccharides, and produced acid in medium containing mannitol as a sole carbon source. in ...201424710996
a positive regulator of nodule organogenesis, nodule inception, acts as a negative regulator of rhizobial infection in lotus japonicus.legume-rhizobium symbiosis occurs in specialized root organs called nodules. to establish the symbiosis, two major genetically controlled events, rhizobial infection and organogenesis, must occur. for a successful symbiosis, it is essential that the two phenomena proceed simultaneously in different root tissues. although several symbiotic genes have been identified during genetic screenings of nonsymbiotic mutants, most of the mutants harbor defects in both infection and organogenesis pathways, ...201424722550
membrane lipids in agrobacterium tumefaciens: biosynthetic pathways and importance for pathogenesis.many cellular processes critically depend on the membrane composition. in this review, we focus on the biosynthesis and physiological roles of membrane lipids in the plant pathogen agrobacterium tumefaciens. the major components of a. tumefaciens membranes are the phospholipids (pls), phosphatidylethanolamine (pe), phosphatidylglycerol, phosphatidylcholine (pc) and cardiolipin, and ornithine lipids (ols). under phosphate-limited conditions, the membrane composition shifts to phosphate-free lipid ...201424723930
commonalities and differences of t3sss in rhizobia and plant pathogenic bacteria.plant pathogenic bacteria and rhizobia infect higher plants albeit the interactions with their hosts are principally distinct and lead to completely different phenotypic outcomes, either pathogenic or mutualistic, respectively. bacterial protein delivery to plant host plays an essential role in determining the phenotypic outcome of plant-bacteria interactions. the involvement of type iii secretion systems (t3sss) in mediating animal- and plant-pathogen interactions was discovered in the mid-80's ...201424723933
genomic analysis of cyclic-di-gmp-related genes in rhizobial type strains and functional analysis in rhizobium etli.rhizobia are soil bacteria that can fix nitrogen in symbiosis with leguminous plants or exist free living in the rhizosphere. crucial to their complex lifestyle is the ability to sense and respond to diverse environmental stimuli, requiring elaborate signaling pathways. in the majority of bacteria, the nucleotide-based second messenger cyclic diguanosine monophosphate (c-di-gmp) is involved in signal transduction. surprisingly, little is known about the importance of c-di-gmp signaling in rhizob ...201424728599
the role of symbiotic nitrogen fixation in sustainable production of biofuels.with the ever-increasing population of the world (expected to reach 9.6 billion by 2050), and altered life style, comes an increased demand for food, fuel and fiber. however, scarcity of land, water and energy accompanied by climate change means that to produce enough to meet the demands is getting increasingly challenging. today we must use every avenue from science and technology available to address these challenges. the natural process of symbiotic nitrogen fixation, whereby plants such as l ...201424786096
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 ...201424794560
knockdown of ljald1, agd2-like defense response protein 1, influences plant growth and nodulation in lotus japonicus.the discovery of the enzyme l,l-diaminopimelate aminotransferase (ll-dap-at, ec 2.6.1.83) uncovered a unique step in the l-lysine biosynthesis pathway in plants. in arabidopsis thaliana, ll-dap-at has been shown to play a key role in plant-pathogen interactions by regulation of the salicylic acid (sa) signaling pathway. here, a full-length cdna of ll-dap-at named as ljald1 from lotus japonicus (regel) larsen was isolated. the deduced amino acid sequence shares 67% identity with the arabidopsis a ...201424797909
structural characterization and function determination of a nonspecific carboxylate esterase from the amidohydrolase superfamily with a promiscuous ability to hydrolyze methylphosphonate esters.the uncharacterized protein rsp3690 from rhodobacter sphaeroides is a member of the amidohydrolase superfamily of enzymes. in this investigation the gene for rsp3690 was expressed in escherichia coli and purified to homogeneity, and the three-dimensional structure was determined to a resolution of 1.8 å. the protein folds as a distorted (β/α)8-barrel, and the subunits associate as a homotetramer. the active site is localized to the c-terminal end of the β-barrel and is highlighted by the formati ...201424832101
metagenomic analyses reveal phylogenetic diversity of carboxypeptidase gene sequences in activated sludge of a wastewater treatment plant in shanghai, china.activated sludge of wastewater treatment plants carries a diverse microflora. however, up to 80-90 % of microorganisms in activated sludge cannot be cultured by current laboratory techniques, leaving an enzyme reservoir largely unexplored. in this study, we investigated carboxypeptidase diversity in activated sludge of a wastewater treatment plant in shanghai, china, by a culture-independent metagenomic approach. three sets of consensus degenerate hybrid oligonucleotide primers (codehops) target ...201324860282
metagenomic analyses reveal phylogenetic diversity of carboxypeptidase gene sequences in activated sludge of a wastewater treatment plant in shanghai, china.activated sludge of wastewater treatment plants carries a diverse microflora. however, up to 80-90 % of microorganisms in activated sludge cannot be cultured by current laboratory techniques, leaving an enzyme reservoir largely unexplored. in this study, we investigated carboxypeptidase diversity in activated sludge of a wastewater treatment plant in shanghai, china, by a culture-independent metagenomic approach. three sets of consensus degenerate hybrid oligonucleotide primers (codehops) target ...201324860282
comparative genomics of bradyrhizobium japonicum cpac 15 and bradyrhizobium diazoefficiens cpac 7: elite model strains for understanding symbiotic performance with soybean.the soybean-bradyrhizobium symbiosis can be highly efficient in fixing nitrogen, but few genomic sequences of elite inoculant strains are available. here we contribute with information on the genomes of two commercial strains that are broadly applied to soybean crops in the tropics. b. japonicum cpac 15 (=semia 5079) is outstanding in its saprophytic capacity and competitiveness, whereas b. diazoefficiens cpac 7 (=semia 5080) is known for its high efficiency in fixing nitrogen. both are well ada ...201424888481
new insights into 1-aminocyclopropane-1-carboxylate (acc) deaminase phylogeny, evolution and ecological significance.the main objective of this work is the study of the phylogeny, evolution and ecological importance of the enzyme 1-aminocyclopropane-1-carboxylate (acc) deaminase, the activity of which represents one of the most important and studied mechanisms used by plant growth-promoting microorganisms. the acc deaminase gene and its regulatory elements presence in completely sequenced organisms was verified by multiple searches in diverse databases, and based on the data obtained a comprehensive analysis w ...201424905353
functional surface engineering by nucleotide-modulated potassium channel insertion into polymer membranes attached to solid supports.planar solid-supported membranes based on amphiphilic block copolymers represent promising systems for the artificial creation of structural surfaces. here we introduce a method for engineering functional planar solid-supported membranes through insertion of active biomolecules. we show that membranes based on poly(dimethylsiloxane)-block-poly(2-methyl-2-oxazoline) (pdms-b-pmoxa) amphiphilic diblock copolymers, which mimic natural membranes, are suitable for hosting biomolecules. our strategy al ...201424912817
structural basis for catalysis in a cdp-alcohol phosphotransferase.the cdp-alcohol phosphotransferase (cdp-ap) family of integral membrane enzymes catalyses the transfer of a substituted phosphate group from a cdp-linked donor to an alcohol acceptor. this is an essential reaction for phospholipid biosynthesis across all kingdoms of life, and it is catalysed solely by cdp-aps. here we report the 2.0 å resolution crystal structure of a representative cdp-ap from archaeoglobus fulgidus. the enzyme (af2299) is a homodimer, with each protomer consisting of six trans ...201424923293
genes commonly involved in acid tolerance are not overexpressed in the plant microsymbiont mesorhizobium loti maff303099 upon acidic shock.rhizobia are legume bacterial symbionts that fix nitrogen in the root nodules of plants. the aim of the present study was to investigate the global transcriptional response of rhizobia upon an acidic shock. changes in the transcriptome of cells of mesorhizobium loti strain maff303099 upon an acidic shock at ph 3 for 30 min were analysed. from a total of 7,231 protein-coding genes, 433 were found to be differentially expressed upon acidic shock, of which 322 were overexpressed. although most of t ...201424931309
conserved evolutionary units in the heme-copper oxidase superfamily revealed by novel homologous protein families.the heme-copper oxidase (hco) superfamily includes hcos in aerobic respiratory chains and nitric oxide reductases (nors) in the denitrification pathway. the hco/nor catalytic subunit has a core structure consisting of 12 transmembrane helices (tmhs) arranged in three-fold rotational pseudosymmetry, with six conserved histidines for heme and metal binding. using sensitive sequence similarity searches, we detected a number of novel hco/nor homologs and named them hco homology (hcoh) proteins. seve ...201424931479
identification of a dominant gene in medicago truncatula that restricts nodulation by sinorhizobium meliloti strain rm41.leguminous plants are able to form a root nodule symbiosis with nitrogen-fixing soil bacteria called rhizobia. this symbiotic association shows a high level of specificity. beyond the specificity for the legume family, individual legume species/genotypes can only interact with certain restricted group of bacterial species or strains. specificity in this system is regulated by complex signal exchange between the two symbiotic partners and thus multiple genetic mechanisms could be involved in the ...201424934080
genome sequencing of two neorhizobium galegae strains reveals a noet gene responsible for the unusual acetylation of the nodulation factors.the species neorhizobium galegae comprises two symbiovars that induce nodules on galega plants. strains of both symbiovars, orientalis and officinalis, induce nodules on the same plant species, but fix nitrogen only in their own host species. the mechanism behind this strict host specificity is not yet known. in this study, genome sequences of representatives of the two symbiovars were produced, providing new material for studying properties of n. galegae, with a special interest in genomic diff ...201424948393
the first complete genome sequence of the class fimbriimonadia in the phylum armatimonadetes.in this study, we present the complete genome of fimbriimonas ginsengisoli gsoil 348t belonging to the class fimbriimonadia of the phylum armatimonadetes, formerly called as candidate phylum op10. the complete genome contains a single circular chromosome of 5.23 mb including a 45.5 kb prophage. of the 4820 open reading frames (orfs), 3,000 (62.2%) genes could be classified into clusters of orthologous groups (cog) families. with the split of rrna genes, strain gsoil 348t had no typical 16s-23s-5 ...201424967843
land-use influences the distribution and activity of high affinity co-oxidizing bacteria associated to type i-coxl genotype in soil.soil carboxydovore bacteria are the biological sink of atmospheric carbon monoxide (co). the initial oxidation of co is catalyzed by a co-dehydrogenase (codh), and the gene coxl encodes the large subunit of the enzyme. only a few carboxydovore isolates were shown to oxidize atmospheric co and little is known about the potential impact of global change on the ecophysiology of this functional group. the main objective of this study was to assess the impact of land-use and soil properties on coxl g ...201424971077
the complete genome of burkholderia phenoliruptrix strain br3459a, a symbiont of mimosa flocculosa: highlighting the coexistence of symbiotic and pathogenic genes.burkholderia species play an important ecological role related to xenobiosis, the promotion of plant growth, the biocontrol of agricultural diseases, and symbiotic and non-symbiotic biological nitrogen fixation. here, we highlight our study as providing the first complete genome of a symbiotic strain of b. phenoliruptrix, br3459a (=cla1), which was originally isolated in brazil from nodules of mimosa flocculosa and is effective in fixing nitrogen in association with this leguminous species.201424972629
diversity of nitrogen-fixing bacteria associated with switchgrass in the native tallgrass prairie of northern oklahoma.switchgrass (panicum virgatum l.) is a perennial c4 grass native to north america that is being developed as a feedstock for cellulosic ethanol production. industrial nitrogen fertilizers enhance switchgrass biomass production but add to production and environmental costs. a potential sustainable alternative source of nitrogen is biological nitrogen fixation. as a step in this direction, we studied the diversity of nitrogen-fixing bacteria (nfb) associated with native switchgrass plants from the ...201425002418
differing courses of genetic evolution of bradyrhizobium inoculants as revealed by long-term molecular tracing in acacia mangium plantations.introducing nitrogen-fixing bacteria as an inoculum in association with legume crops is a common practice in agriculture. however, the question of the evolution of these introduced microorganisms remains crucial, both in terms of microbial ecology and agronomy. we explored this question by analyzing the genetic and symbiotic evolution of two bradyrhizobium strains inoculated on acacia mangium in malaysia and senegal 15 and 5 years, respectively, after their introduction. based on typing of sever ...201425002434
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