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genomic and evolutionary comparisons of diazotrophic and pathogenic bacteria of the order rhizobiales.species belonging to the rhizobiales are intriguing and extensively researched for including both bacteria with the ability to fix nitrogen when in symbiosis with leguminous plants and pathogenic bacteria to animals and plants. similarities between the strategies adopted by pathogenic and symbiotic rhizobiales have been described, as well as high variability related to events of horizontal gene transfer. although it is well known that chromosomal rearrangements, mutations and horizontal gene tra ...201020144182
predicted class-i aminoacyl trna synthetase-like proteins in non-ribosomal peptide synthesis.recent studies point to a great diversity of non-ribosomal peptide synthesis systems with major roles in amino acid and co-factor biosynthesis, secondary metabolism, and post-translational modifications of proteins by peptide tags. the least studied of these systems are those utilizing trnas or aminoacyl-trna synthetases (aatrs) in non-ribosomal peptide ligation.201020678224
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
a suite of lotus japonicus starch mutants reveals both conserved and novel features of starch metabolism.the metabolism of starch is of central importance for many aspects of plant growth and development. information on leaf starch metabolism other than in arabidopsis (arabidopsis thaliana) is scarce. furthermore, its importance in several agronomically important traits exemplified by legumes remains to be investigated. to address this issue, we have provided detailed information on the genes involved in starch metabolism in lotus japonicus and have characterized a comprehensive collection of forwa ...201020699404
cloning-independent expression and analysis of omega-transaminases by use of a cell-free protein synthesis system.herewith we report the expression and screening of microbial enzymes without involving cloning procedures. computationally predicted putative omega-transaminase (omega-ta) genes were pcr amplified from the bacterial colonies and expressed in a cell-free protein synthesis system for subsequent analysis of their enzymatic activity and substrate specificity. through the cell-free expression analysis of the putative omega-ta genes, a number of enzyme-substrate pairs were identified in a matter of ho ...201020656866
effect of abscisic acid on symbiotic nitrogen fixation activity in the root nodules of lotus japonicus.the phytohormone abscisic acid (aba) is known to be a negative regulator of legume root nodule formation. by screening lotus japonicus seedlings for survival on an agar medium containing 70 μm aba, we obtained mutants that not only showed increased root nodule number, but also enhanced nitrogen fixation. the mutant was designated enf1 (enhanced nitrogen fixation 1) and was confirmed to be monogenic and incompletely dominant. in long-term growth experiments with m. loti, although some yield param ...201020118670
analysis of two potential long-distance signaling molecules, ljcle-rs1/2 and jasmonic acid, in a hypernodulating mutant too much love.legume plants tightly control the number and development of root nodules. this is partly regulated by a long-distance signaling known as auto-regulation of nodulation (aon). aon signaling involves at least two potential long-distance signals: root-derived signal and shoot-derived signal. however, their molecular characteristics and the mode of action remain unclear. in our recent study, we isolated a novel lotus japonicus hypernodulating mutant too much love (tml). based on several grafting expe ...201020061808
glycolysis and the tricarboxylic acid cycle are linked by alanine aminotransferase during hypoxia induced by waterlogging of lotus japonicus.the role of nitrogen metabolism in the survival of prolonged periods of waterlogging was investigated in highly flood-tolerant, nodulated lotus japonicus plants. alanine production revealed to be a critical hypoxic pathway. alanine is the only amino acid whose biosynthesis is not inhibited by nitrogen deficiency resulting from rna interference silencing of nodular leghemoglobin. the metabolic changes that were induced following waterlogging can be best explained by the activation of alanine meta ...201020089769
tertiary alcohol preferred: hydroxylation of trans-3-methyl-l-proline with proline hydroxylases.the enzymatic synthesis of tertiary alcohols by the stereospecific oxidation of tertiary alkyl centers is a most-straightforward but challenging approach, since these positions are sterically hindered. in contrast to p450-monooxygenases, there is little known about the potential of non-heme iron(ii) oxygenases to catalyze such reactions. we have studied the hydroxylation of trans-3-methyl-l-proline with the α-ketoglutarate (α-kg) dependent oxygenases, cis-3-proline hydroxylase type ii and cis-4- ...201122238542
gating of the mlotik1 potassium channel involves large rearrangements of the cyclic nucleotide-binding domains.cyclic nucleotide-regulated ion channels are present in bacteria, plants, vertebrates, and humans. in higher organisms, they are closely involved in signaling networks of vision and olfaction. binding of camp or cgmp favors the activation of these ion channels. despite a wealth of structural and studies, there is a lack of structural data describing the gating process in a full-length cyclic nucleotide-regulated channel. we used high-resolution atomic force microscopy (afm) to directly observe t ...201122135457
characterization of highly efficient heavy-ion mutagenesis in arabidopsis thaliana.heavy-ion mutagenesis is recognised as a powerful technology to generate new mutants, especially in higher plants. heavy-ion beams show high linear energy transfer (let) and thus more effectively induce dna double-strand breaks than other mutagenic techniques. previously, we determined the most effective heavy-ion let (letmax: 30.0 kev μm(-1)) for arabidopsis mutagenesis by analysing the effect of let on mutation induction. however, the molecular structure of mutated dna induced by heavy ions wi ...201122085561
expression screening of fusion partners from an e. coli genome for soluble expression of recombinant proteins in a cell-free protein synthesis system.while access to soluble recombinant proteins is essential for a number of proteome studies, preparation of purified functional proteins is often limited by the protein solubility. in this study, potent solubility-enhancing fusion partners were screened from the repertoire of endogenous e. coli proteins. based on the presumed correlation between the intracellular abundance and folding efficiency of proteins, pcr-amplified orfs of a series of highly abundant e. coli proteins were fused with aggreg ...201122073212
the evolution of function in strictosidine synthase-like proteins.the exponential growth of sequence data provides abundant information for the discovery of new enzyme reactions. correctly annotating the functions of highly diverse proteins can be difficult, however, hindering use of this information. global analysis of large superfamilies of related proteins is a powerful strategy for understanding the evolution of reactions by identifying catalytic commonalities and differences in reaction and substrate specificity, even when only a few members have been bio ...201121948213
bacterial community assembly based on functional genes rather than species.the principles underlying the assembly and structure of complex microbial communities are an issue of long-standing concern to the field of microbial ecology. we previously analyzed the community membership of bacterial communities associated with the green macroalga ulva australis, and proposed a competitive lottery model for colonization of the algal surface in an attempt to explain the surprising lack of similarity in species composition across different algal samples. here we extend the prev ...201121825123
peroxiredoxins and nadph-dependent thioredoxin systems in the model legume lotus japonicus.peroxiredoxins (prxs), thioredoxins (trxs), and nadph-thioredoxin reductases (ntrs) constitute central elements of the thiol-disulfide redox regulatory network of plant cells. this study provides a comprehensive survey of this network in the model legume lotus japonicus. the aims were to identify and characterize these gene families and to assess whether the ntr-trx systems are operative in nodules. quantitative reverse transcription-polymerase chain reaction and immunological and proteomic appr ...201121562331
evolution of abscisic acid synthesis and signaling mechanisms.the plant hormone abscisic acid (aba) mediates seed dormancy, controls seedling development and triggers tolerance to abiotic stresses, including drought. core aba signaling components consist of a recently identified group of aba receptor proteins of the pyrabactin resistance (pyr)/regulatory component of aba receptor (rcar) family that act as negative regulators of members of the protein phosphatase 2c (pp2c) family. inhibition of pp2c activity enables activation of snf1-related kinase 2 (snrk ...201121549957
proteinortho: detection of (co-)orthologs in large-scale analysis.orthology analysis is an important part of data analysis in many areas of bioinformatics such as comparative genomics and molecular phylogenetics. the ever-increasing flood of sequence data, and hence the rapidly increasing number of genomes that can be compared simultaneously, calls for efficient software tools as brute-force approaches with quadratic memory requirements become infeasible in practise. the rapid pace at which new data become available, furthermore, makes it desirable to compute ...201121526987
interaction of diverse voltage sensor homologs with lipid bilayers revealed by self-assembly simulations.voltage sensors (vs) domains couple the activation of ion channels/enzymes to changes in membrane voltage. we used molecular dynamics simulations to examine interactions with lipids of several vs homologs. vss in intact channels in the activated state are exposed to phospholipids, leading to a characteristic local distortion of the lipid bilayer which decreases its thickness by ∼10 å. this effect is mediated by a conserved hydrophilic stretch in the s4-s5 segment linking the vs and the pore doma ...201121320431
the repertoire of ice in prokaryotes underscores the unity, diversity, and ubiquity of conjugation.horizontal gene transfer shapes the genomes of prokaryotes by allowing rapid acquisition of novel adaptive functions. conjugation allows the broadest range and the highest gene transfer input per transfer event. while conjugative plasmids have been studied for decades, the number and diversity of integrative conjugative elements (ice) in prokaryotes remained unknown. we defined a large set of protein profiles of the conjugation machinery to scan over 1,000 genomes of prokaryotes. we found 682 pu ...201121876676
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
sequence variability of rhizobiales orthologs and relationship with physico-chemical characteristics of proteins.chromosomal orthologs can reveal the shared ancestral gene set and their evolutionary trends. additionally, physico-chemical properties of encoded proteins could provide information about functional adaptation and ecological niche requirements.201121970442
distribution of genes encoding nucleoid-associated protein homologs in plasmids.bacterial nucleoid-associated proteins (naps) form nucleoprotein complexes and influence the expression of genes. recent studies have shown that some plasmids carry genes encoding nap homologs, which play important roles in transcriptional regulation networks between plasmids and host chromosomes. in this study, we determined the distributions of the well-known naps fis, h-ns, hu, ihf, and lrp and the newly found naps mvat and ndpa among the whole-sequenced 1382 plasmids found in gram-negative b ...201121350637
legume pectate lyase required for root infection by rhizobia.to allow rhizobial infection of legume roots, plant cell walls must be locally degraded for plant-made infection threads (its) to be formed. here we identify a lotus japonicus nodulation pectate lyase gene (ljnpl), which is induced in roots and root hairs by rhizobial nodulation (nod) factors via activation of the nodulation signaling pathway and the nin transcription factor. two ljnpl mutants produced uninfected nodules and most infections arrested as infection foci in root hairs or roots. the ...201122203959
legume pectate lyase required for root infection by rhizobia.to allow rhizobial infection of legume roots, plant cell walls must be locally degraded for plant-made infection threads (its) to be formed. here we identify a lotus japonicus nodulation pectate lyase gene (ljnpl), which is induced in roots and root hairs by rhizobial nodulation (nod) factors via activation of the nodulation signaling pathway and the nin transcription factor. two ljnpl mutants produced uninfected nodules and most infections arrested as infection foci in root hairs or roots. the ...201122203959
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
bacterial transition metal p(1b)-atpases: transport mechanism and roles in virulence.p(1b)-type atpases are polytopic membrane proteins that couple the hydrolysis of atp to the efflux of cytoplasmic transition metals. this paper reviews recent progress in our understanding of the structure and function of these proteins in bacteria. these are members of the p-type superfamily of transport atpases. cu(+)-atpases are the most frequently observed and best-characterized members of this group of transporters. however, bacterial genomes show diverse arrays of p(1b)-type atpases with a ...201121999638
gene transfer into solanum tuberosum via rhizobium spp.agrobacterium tumefaciens-mediated transformation (atmt) is the preferred technique for gene transfer into crops. a major disadvantage of the technology remains the complexity of the patent landscape that surrounds atmt which restricts its use for commercial applications. an alternative system has been described (broothaerts et al. in nature 433:629-633, 2005) detailing the propensity of three rhizobia to transform the model crop arabidopsis thaliana, the non-food crop nicotiana tabacum and, at ...201120582626
mining high-throughput experimental data to link gene and function.nearly 2200 genomes that encode around 6 million proteins have now been sequenced. around 40% of these proteins are of unknown function, even when function is loosely and minimally defined as 'belonging to a superfamily'. in addition to in silico methods, the swelling stream of high-throughput experimental data can give valuable clues for linking these unknowns with precise biological roles. the goal is to develop integrative data-mining platforms that allow the scientific community at large to ...201121310501
contribution of nfp lysm domains to the recognition of nod factors during the medicago truncatula/sinorhizobium meliloti symbiosis.the root nodule nitrogen fixing symbiosis between legume plants and soil bacteria called rhizobia is of great agronomical and ecological interest since it provides the plant with fixed atmospheric nitrogen. the establishment of this symbiosis is mediated by the recognition by the host plant of lipo-chitooligosaccharides called nod factors (nfs), produced by the rhizobia. this recognition is highly specific, as precise nf structures are required depending on the host plant. here, we study the imp ...201122087221
a simple method to evaluate the number of bradyrhizobia on soybean seeds and its implication on inoculant quality control.abstract: soybean seeds are non-sterile and their bacterial population interferes with the enumeration of beneficial bacteria, making it difficult to assess survival under different conditions. within this context, the principal aims of this work were: (1) to improve a selective media for the enumeration of b. japonicum recovered from inoculated soybean seeds; (2) to establish the most representative mathematical function for b. japonicum mortality on soybean seeds after inoculation; (3) to eval ...201121906377
a novel hydrolase identified by genomic-proteomic analysis of phenylurea herbicide mineralization by variovorax sp. strain srs16.the soil bacterial isolate variovorax sp. strain srs16 mineralizes the phenylurea herbicide linuron. the proposed pathway initiates with hydrolysis of linuron to 3,4-dichloroaniline (dca) and n,o-dimethylhydroxylamine, followed by conversion of dca to krebs cycle intermediates. differential proteomic analysis showed a linuron-dependent upregulation of several enzymes that fit into this pathway, including an amidase (liba), a multicomponent chloroaniline dioxygenase, and enzymes associated with a ...201122003008
Identification of a novel gene for biosynthesis of a bacteroid-specific electron carrier menaquinone.Ubiquinone (UQ) has been considered as an electron mediator in electron transfer that generates ATP in Rhizobium under both free-living and symbiosis conditions. When mutated, the dmtH gene has a symbiotic phenotype of forming ineffective nodules on Astragalus sinicus. The gene was isolated from a Mesorhizobium huakuii 7653R transposon-inserted mutant library. The DNA sequence and conserved protein domain analyses revealed that dmtH encodes demethylmenaquinone (DMK) methyltransferase, which cata ...201122194970
nodulin 41, a novel late nodulin of common bean with peptidase activity.the legume-rhizobium symbiosis requires the formation of root nodules, specialized organs where the nitrogen fixation process takes place. nodule development is accompanied by the induction of specific plant genes, referred to as nodulin genes. important roles in processes such as morphogenesis and metabolism have been assigned to nodulins during the legume-rhizobium symbiosis.201121985276
Lotus japonicus nodulation is photomorphogenetically controlled by sensing the red/far red (R/FR) ratio through jasmonic acid (JA) signaling.Light is critical for supplying carbon to the energetically expensive, nitrogen-fixing symbiosis between legumes and rhizobia. Here, we show that phytochrome B (phyB) is part of the monitoring system to detect suboptimal light conditions, which normally suppress Lotus japonicus nodule development after Mesorhizobium loti inoculation. We found that the number of nodules produced by L. japonicus phyB mutants is significantly reduced compared with the number produced of WT Miyakojima MG20. To explo ...201121930895
biological consequences of ancient gene acquisition and duplication in the large genome of candidatus solibacter usitatus ellin6076.members of the bacterial phylum acidobacteria are widespread in soils and sediments worldwide, and are abundant in many soils. acidobacteria are challenging to culture in vitro, and many basic features of their biology and functional roles in the soil have not been determined. candidatus solibacter usitatus strain ellin6076 has a 9.9 mb genome that is approximately 2-5 times as large as the other sequenced acidobacteria genomes. bacterial genome sizes typically range from 0.5 to 10 mb and are in ...201121949776
the rhizome of reclinomonas americana, homo sapiens, pediculus humanus and saccharomyces cerevisiae mitochondria.mitochondria are thought to have evolved from eubacteria-like endosymbionts; however, the origin of the mitochondrion remains a subject of debate. in this study, we investigated the phenomenon of chimerism in mitochondria to shed light on the origin of these organelles by determining which species played a role in their formation. we used the mitochondria of four distinct organisms, reclinomonas americana, homo sapiens, saccharomyces cerevisiae and multichromosome pediculus humanus, and attempte ...201122014084
quantitative trait locus analysis of symbiotic nitrogen fixation activity in the model legume lotus japonicus.many legumes form nitrogen-fixing root nodules. an elevation of nitrogen fixation in such legumes would have significant implications for plant growth and biomass production in agriculture. to identify the genetic basis for the regulation of nitrogen fixation, quantitative trait locus (qtl) analysis was conducted with recombinant inbred lines derived from the cross miyakojima mg-20 × gifu b-129 in the model legume lotus japonicus. this population was inoculated with mesorhizobium loti maff303099 ...201122009016
Is the sequence-specific binding of aminoacyl-tRNAs by EF-Tu universal among bacteria?Three base pairs in the T-stem are primarily responsible for the sequence-specific interaction of tRNA with Escherichia coli and Thermus thermophilus EF-Tu. While the amino acids on the surface of EF-Tu that contact aminoacyl-tRNA (aa-tRNA) are highly conserved among bacteria, the T-stem sequences of individual tRNA are variable, making it unclear whether or not this protein-nucleic acid interaction is also sequence specific in other bacteria. We propose and validate a thermodynamic model that p ...201121893586
structure of the pilus assembly protein tadz from eubacterium rectale: implications for polar localization.the tad (tight adherence) locus encodes a protein translocation system that produces a novel variant of type iv pili. the pilus assembly protein tadz (called cpae in caulobacter crescentus) is ubiquitous in tad loci, but is absent in other type iv pilus biogenesis systems. the crystal structure of tadz from eubacterium rectale (ertadz), in complex with atp and mg(2+) , was determined to 2.1 å resolution. ertadz contains an atypical atpase domain with a variant of a deviant walker-a motif that re ...201122211578
rhizobia species: a boon for "plant genetic engineering".since past three decades new discoveries in plant genetic engineering have shown remarkable potentials for crop improvement. agrobacterium ti plasmid based dna transfer is no longer the only efficient way of introducing agronomically important genes into plants. recent studies have explored a novel plant genetic engineering tool, rhizobia sp., as an alternative to agrobacterium, thereby expanding the choice of bacterial species in agricultural plant biotechnology. rhizobia sp. serve as an open l ...201123024417
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
a processive glycosyltransferase involved in glycolipid synthesis during phosphate deprivation in mesorhizobium loti.natural habitats are often characterized by a low availability of phosphate. in plants and many bacteria, phosphate deficiency causes different physiological responses, including the replacement of phosphoglycerolipids in the membranes with nonphosphorous lipids. we describe here a processive glycosyltransferase (pgt) in mesorhizobium loti (rhizobiales) involved in the synthesis of di- and triglycosyldiacylglycerols (dglycd and tglycd) during phosphate deprivation. cells of the corresponding δpg ...201121239587
characterization of two novel nodule-enhanced α-type carbonic anhydrases from lotus japonicus.two cdna clones coding for α-type carbonic anhydrases (ca; ec 4.2.1.1) in the nitrogen-fixing nodules of the model legume lotus japonicus were identified. functionality of the full-length proteins was confirmed by heterologous expression in escherichia coli and purification of the encoded polypeptides. the developmental expression pattern of ljcaa1 and ljcaa2 revealed that both genes code for nodule enhanced carbonic anhydrase isoforms, which are induced early during nodule development. the gene ...201121256984
two novel classes of enzymes are required for the biosynthesis of aurofusarin in fusarium graminearum.previous studies have reported the functional characterization of 9 out of 11 genes found in the gene cluster responsible for biosynthesis of the polyketide pigment aurofusarin in fusarium graminearum. here we reanalyze the function of a putative aurofusarin pump (aurt) and the two remaining orphan genes, aurz and aurs. targeted gene replacement of aurz resulted in the discovery that the compound ywa1, rather than nor-rubrofusarin, is the primary product of f. graminearum polyketide synthase 12 ...201121296881
nodulation enhances dark co2 fixation and recycling in the model legume lotus japonicus.during symbiotic nitrogen fixation (snf), the nodule becomes a strong sink for photosynthetic carbon. here, it was studied whether nodule dark co(2) fixation could participate in a mechanism for co(2) recycling through c(4)-type photosynthesis. differences in the natural d(13)c abundance between lotus japonicus inoculated or not with the n-fixing mesorhizobium loti were assessed. (13)c labelling and gene expression of key enzymes of co(2) metabolism were applied in plants inoculated with wild-ty ...201121307384
the crystal structure of sdr-type pyridoxal 4-dehydrogenase of mesorhizobium loti.pyridoxal 4-dehydrogenase catalyzes the irreversible oxidation of pyridoxal to 4-pyridoxolactone and is involved in degradation pathway i of pyridoxine, a vitamin b(6) compound. its crystal structure was elucidated for the first time. molecular replacement with (s)-1-phenylthanol dehydrogenase (pdb code 2ew8) was adopted to determine the tertiary structure of the nad(+)-bound enzyme.201121307574
nitric oxide production induced in roots of lotus japonicus by lipopolysaccharide from mesorhizobium loti.lipopolysaccharide (lps) is a bacterial molecule that induces nitric oxide (no) production and triggers defense systems in plant-pathogen interactions. no production is induced in the roots of lotus japonicus after inoculation of the roots with its microsymbiont mesorhizobium loti. however, the rhizobial molecule that induces no production has not yet been identified. we investigated no production in the roots of l. japonicus by treatment with lps of m. loti. lps was prepared by phenol-hot water ...201121330297
role of baca in lipopolysaccharide synthesis, peptide transport, and nodulation by rhizobium sp. strain ngr234.baca of sinorhizobium meliloti plays an essential role in the establishment of nitrogen-fixing symbioses with medicago plants, where it is involved in peptide import and in the addition of very-long-chain fatty acids (vlcfa) to lipid a of lipopolysaccharide (lps). we investigated the role of baca in rhizobium species strain ngr234 by mutating the baca gene. in the ngr234 baca mutant, peptide import was impaired, but no effect on vlcfa addition was observed. more importantly, the symbiotic abilit ...201121357487
structural insights into conformational changes of a cyclic nucleotide-binding domain in solution from mesorhizobium loti k1 channel.cyclic nucleotide-sensitive ion channels, known as hcn and cng channels, are activated by binding of ligands to a domain (cnbd) located on the cytoplasmic side of the channel. the underlying mechanisms are not well understood. to elucidate the gating mechanism, structures of both the ligand-free and -bound cnbd are required. several crystal structures of the cnbd from hcn2 and a bacterial cng channel (mlok1) have been solved. however, for hcn2, the camp-free and -bound state did not reveal subst ...201121430265
nitric oxide is required for an optimal establishment of the medicago truncatula-sinorhizobium meliloti symbiosis.nitric oxide (no) is a gaseous molecule that participates in numerous plant signalling pathways. it is involved in plant responses to pathogens and development processes such as seed germination, flowering and stomatal closure. using a permeable no-specific fluorescent probe and a bacterial reporter strain expressing the lacz gene under the control of a no-responsive promoter, we detected no production in the first steps, during infection threads growth, of the medicago truncatula-sinorhizobium ...201121457261
housekeeping genes essential for pantothenate biosynthesis are plasmid-encoded in rhizobium etli and rhizobium leguminosarum.a traditional concept in bacterial genetics states that housekeeping genes, those involved in basic metabolic functions needed for maintenance of the cell, are encoded in the chromosome, whereas genes required for dealing with challenging environmental conditions are located in plasmids. exceptions to this rule have emerged from genomic sequence data of bacteria with multipartite genomes. the genome sequence of r. etli cfn42 predicts the presence of panc and panb genes clustered together on the ...201121463532
competing formate- and carbon dioxide-utilizing prokaryotes in an anoxic methane-emitting fen soil.methanogenesis in wetlands is dependent on intermediary substrates derived from the degradation of biopolymers. formate is one such substrate and is stimulatory to methanogenesis and acetogenesis in anoxic microcosms of soil from the fen schlöppnerbrunnen. formate dissimilation also yields co(2) as a potential secondary substrate. the objective of this study was to resolve potential differences between anaerobic formate- and co(2)-utilizing prokaryotes of this fen by stable isotope probing. anox ...201121478308
genetic diversity of root nodule bacteria nodulating lotus corniculatus and anthyllis vulneraria in sweden.very little is known about the genetic diversity and phylogeny of rhizobia nodulating lotus species in northern temperate regions. we have therefore studied the genetic diversity among a total of 61 root nodule bacteria isolated from lotus corniculatus and anthyllis vulneraria from different geographic sites and habitats in sweden by restriction fragment length polymorphism (rflp) of the internal transcribed spacer between their 16s rrna and 23s rrna (igs) region. a high diversity consisting of ...201121497473
identification of mesorhizobium loti genes relevant to symbiosis by using signature-tagged mutants.signature-tagged mutagenesis was applied to mesorhizobium loti, a nitrogen-fixing root-nodule symbiont of the leguminous plant lotus japonicus. we arranged 1,887 non-redundant mutant strains of m. loti into 75 sets, each consisting of 24 to 26 strains with a different tag in each strain. these sets were each inoculated en masse onto l. japonicus plants. comparative analysis of total dna extracted from inoculants and resulting nodules based on quantitative pcr led to the selection of 69 strains a ...201121502733
plant growth-promoting fungus, trichoderma koningi suppresses isoflavonoid phytoalexin vestitol production for colonization on/in the roots of lotus japonicus.the relationship between the colonization of lotus japonicus by plant growth-promoting fungi (pgpf) and biosynthesis of the isoflavonoid phytoalexin vestitol, a major defensive response of leguminous plants, was analyzed. when pgpf including trichoderma koningi, fusarium equiseti, and penicillium simplicissimum were inoculated onto l. japonicus roots, only t. koningi colonized the roots long-term and increased plant dry weight (126%). microscopic observations of transverse sections of roots colo ...201121502738
bioinformatic characterization of the trimeric intracellular cation-specific channel protein family.trimeric intracellular cation-specific (tric) channels are integral to muscle excitation-contraction coupling. tric channels provide counter-ionic flux when calcium is rapidly transported from intracellular stores to the cell cytoplasm. until recently, knowledge of the presence of these proteins was limited to animals. we analyzed the tric family and identified a profusion of prokaryotic family members with topologies and motifs similar to those of their eukaryotic counterparts. prokaryotic memb ...201121519847
isolation of xylose isomerases by sequence- and function-based screening from a soil metagenome library.abstract: background: xylose isomerase (xi) catalyses the isomerization of xylose to xylulose in bacteria and some fungi. currently, only a limited number of xi genes have been functionally expressed in saccharomyces cerevisiae, the microorganism of choice for lignocellulosic ethanol production. the objective of the present study was to search for novel xi genes in the vastly diverse microbial habitat present in soil. as the exploitation of microbial diversity is impaired by the ability to culti ...201121545702
annotation and structural analysis of sialylated human milk oligosaccharides.sialylated human milk oligosaccharides (shmos) are important components of human milk oligosaccharides. sialic acids are typically found on the nonreducing end and are known binding sites for pathogens and aid in neonates' brain development. due to their negative charge and hydrophilic nature, they also help modulate cell-cell interactions. it has also been shown that sialic acids are involved in regulating the immune response and aid in brain development. in this study, the enriched shmos from ...201121133381
characterization of mesorhizobium loti l-rhamnose isomerase and its application to l-talose production.the l-rhamnose isomerase gene (rhi) of mesorhizobium loti was cloned and expressed in escherichia coli, and then characterized. the enzyme exhibited activity with respect to various aldoses, including d-allose and l-talose. application of it in l-talose production from galactitol was achieved by a two-step reaction, indicating that it can be utilized in the large-scale production of l-talose.201121597169
s-adenosylmethionine-binding properties of a bacterial phospholipid n-methyltransferase.the presence of the membrane lipid phosphatidylcholine (pc) in the bacterial membrane is critically important for many host-microbe interactions. the phospholipid n-methyltransferase pmta from the plant pathogen agrobacterium tumefaciens catalyzes the formation of pc by a three-step methylation of phosphatidylethanolamine via monomethyl-phosphatidylethanolamine and dimethylphosphatidylethanolamine. the methyl group is provided by s-adenosylmethionine (sam), which is converted to s-adenosylhomocy ...201121602340
crystal structure of a novel esterase rv0045c from mycobacterium tuberculosis.there are at least 250 enzymes in mycobacterium tuberculosis (m. tuberculosis) involved in lipid metabolism. some of the enzymes are required for bacterial survival and full virulence. the esterase rv0045c shares little amino acid sequence similarity with other members of the esterase/lipase family. here, we report the 3d structure of rv0045c. our studies demonstrated that rv0045c is a novel member of α/β hydrolase fold family. the structure of esterase rv0045c contains two distinct domains: the ...201121637775
multiple loci are involved in quorum quenching of autoinducer i molecules in the nitrogen-fixing symbiont (sino-) rhizobium sp. ngr234.rhizobium sp. ngr234 is a unique α-proteobacterium (order - rhizobiales) that forms nitrogen-fixing nodules with more legumes than any other micro-symbiont. since we have previously described the complete genome sequence of ngr234, we now report on a genome wide functional analysis of the genes and enzymes involved in autoinducer i hydrolysis in this microbe. altogether we identified five cosmid clones that repeatedly gave a positive result in our function-based approach for the detection of aut ...201121642401
systems biology of bacterial nitrogen fixation: high-throughput technology and its integrative description with constraint-based modeling.abstract: background: bacterial nitrogen fixation is the biological process by which atmospheric nitrogen is uptaken by bacteroids located in plant root nodules and converted into ammonium through the enzymatic activity of nitrogenase. in practice, this biological process serves as a natural form of fertilization and its optimization has significant implications in sustainable agricultural programs. currently, the advent of high-throughput technology supplies with valuable data that contribute t ...201121801415
a monogalactosyldiacylglycerol synthase found in the green sulfur bacterium chlorobaculum tepidum reveals important roles for galactolipids in photosynthesis.monogalactosyldiacylglycerol (mgdg), which is conserved in almost all photosynthetic organisms, is the most abundant natural polar lipid on earth. in plants, mgdg is highly accumulated in the chloroplast membranes and is an important bulk constituent of thylakoid membranes. however, precise functions of mgdg in photosynthesis have not been well understood. here, we report a novel mgdg synthase from the green sulfur bacterium chlorobaculum tepidum. this enzyme, mgda, catalyzes mgdg synthesis usin ...201121764989
identification of xanthomonas fragariae, xanthomonas axonopodis pv. phaseoli, and xanthomonas fuscans subsp. fuscans with novel markers and using a dot blot platform coupled with automatic data analysis.phytosanitary regulations and the provision of plant health certificates still rely mainly on long and laborious culture-based methods of diagnosis, which are frequently inconclusive. dna-based methods of detection can circumvent many of the limitations of currently used screening methods, allowing a fast and accurate monitoring of samples. the genus xanthomonas includes 13 phytopathogenic quarantine organisms for which improved methods of diagnosis are needed. in this work, we propose 21 new xa ...201121705524
expression and characterization of a mycoplasma genitalium glycosyltransferase in membrane glycolipid biosynthesis. potential target against mycoplasma infections.mycoplasmas contain glycoglycerolipids in their plasma membrane as key structural components involved in bilayer properties and stability. a membrane-associated glycosyltransferase, gt mg517, has been identified in mycoplasma genitalium, which sequentially produces monoglycosyl- and diglycosyldiacylglycerols (mgdag and dgdag). when recombinantly expressed in e. coli, the enzyme was functional in vivo and yielded membrane glycolipids from which glc+¦1,6glc+¦dag was identified as the main product. ...201121835921
horizontal gene exchange in environmental microbiota.horizontal gene transfer (hgt) plays an important role in the evolution of life on the earth. this view is supported by numerous occasions of hgt that are recorded in the genomes of all three domains of living organisms. hgt-mediated rapid evolution is especially noticeable among the bacteria, which demonstrate formidable adaptability in the face of recent environmental changes imposed by human activities, such as the use of antibiotics, industrial contamination, and intensive agriculture. at th ...201121845185
phylogenetic analysis reveals gene conversions in multigene families of rhizobia.gene families are an important and intrinsic trait of rhizobial species. these gene copies can participate in non-reciprocal recombination events, also called gene conversions. gene conversion has diverse roles, but it is usually implicated in the evolution of multigene families. here, we searched for gene conversions in multigene families of six representative rhizobial genomes. we identified 11 gene families with different numbers of copies, genome location and function in cfn42 and ciat652 st ...201121823087
photorespiratory metabolism and nodule function: behavior of lotus japonicus mutants deficient in plastid glutamine synthetase.two photorespiratory mutants of lotus japonicus deficient in plastid glutamine synthetase (gs(2)) were examined for their capacity to establish symbiotic association with mesorhizobium loti bacteria. biosynthetic glutamine synthetase (gs) activity was reduced by around 40% in crude nodule extracts from mutant plants as compared with the wild type (wt). western blot analysis further confirmed the lack of gs(2) polypeptide in mutant nodules. the decrease in gs activity affected the nodular carbon ...201122007601
Recent Progress in Development of Tnt1 Functional Genomics Platform for Medicago truncatula and Lotus japonicus in Bulgaria.Legumes, as protein-rich crops, are widely used for human food, animal feed and vegetable oil production. Over the past decade, two legume species, Medicago truncatula and Lotus japonicus, have been adopted as model legumes for genomics and physiological studies. The tobacco transposable element, Tnt1, is a powerful tool for insertional mutagenesis and gene inactivation in plants. A large collection of Tnt1-tagged lines of M. truncatula cv. Jemalong was generated during the course of the project ...201121966253
excision of an unstable pathogenicity island in salmonella enterica serovar enteritidis is induced during infection of phagocytic cells.the availability of the complete genome sequence of several salmonella enterica serovars has revealed the presence of unstable genetic elements in these bacteria, such as pathogenicity islands and prophages. this is the case of salmonella enterica serovar enteritidis (s. enteritidis), a bacterium that causes gastroenteritis in humans and systemic infection in mice. the whole genome sequence analysis for s. enteritidis unveiled the presence of several genetic regions that are absent in other salm ...201122039432
sequence and role in virulence of the three plasmid complement of the model tumor-inducing bacterium pseudomonas savastanoi pv. savastanoi ncppb 3335.pseudomonas savastanoi pv. savastanoi ncppb 3335 is a model for the study of the molecular basis of disease production and tumor formation in woody hosts, and its draft genome sequence has been recently obtained. here we closed the sequence of the plasmid complement of this strain, composed of three circular molecules of 78,357 nt (ppsv48a), 45,220 nt (ppsv48b), and 42,103 nt (ppsv48c), all belonging to the ppt23a-like family of plasmids widely distributed in the p. syringae complex. a total of ...201122022435
identification of a eukaryotic reductive dechlorinase and characterization of its mechanism of action on its natural substrate.chlorinated compounds are important environmental pollutants whose biodegradation may be limited by inefficient dechlorinating enzymes. dictyostelium amoebae produce a chlorinated alkyl phenone called dif which induces stalk cell differentiation during their multicellular development. here we describe the identification of dif dechlorinase. dif dechlorinase is active when expressed in bacteria, and activity is lost from dictyostelium cells when its gene, drca, is knocked out. it has a k(m) for d ...201122035794
a novel interaction between ccamk and a protein containing the scythe_n ubiquitin-like domain in lotus japonicus.in the rhizobium-legume symbiosis, calcium/calmodulin-dependent protein kinase (ccamk) is a key regulator for both rhizobial infection and nodule organogenesis. deregulation of ccamk by either a point mutation in the autophosphorylation site or the deletion of the carboxyl-terminal regulatory domain results in spontaneous nodule formation without rhizobia. however, the underlying biochemical mechanisms are poorly understood. here, using the kinase domain of ccamk as a bait in yeast two-hybrid sc ...201121209278
cyclic gmp controls rhodospirillum centenum cyst development.adenylyl cyclases are widely distributed across all kingdoms whereas guanylyl cyclases are generally thought to be restricted to eukaryotes. here we report that the α-proteobacterium rhodospirillum centenum secretes cgmp when developing cysts and that a guanylyl cyclase deletion strain fails to synthesize cgmp and is defective in cyst formation. the r. centenum cyclase was purified and shown to effectively synthesize cgmp from gtp in vitro, demonstrating that it is a functional guanylyl cyclase. ...201121214648
azorhirobial chromosome partition gene (para) is involved in the onset of bacteroid differentiation in sesbania rostrata stem-nodule development.a para gene in-frame deletion mutant of azorhizobium caulinodans ors571 (ors571-δpara) was constructed to evaluate the roles of the chromosome partitioning gene on various bacterial traits and on the development of stem-positioned nodules. the δpara mutant showed a pleiomorphic cell shape phenotype, and was polyploidy with differences in nucleoid sizes due to dramatic defects in chromosome partitioning. upon inoculating the δpara mutant onto the stem of sesbania rostrata, three types of immature ...201121571889
Interplay of flg22-induced defence responses and nodulation in Lotus japonicus.In this study the interplay between the symbiotic and defence signalling pathways in Lotus japonicus was investigated by comparing the responses to Mesorhizobium loti, the symbiotic partner of L. japonicus, and the elicitor flg22, a conserved peptide motif present in flagellar protein of a wide range of bacteria. It was found that defence and symbiotic pathways overlap in the interaction between L. japonicus and M. loti since similar responses were induced by the mutualistic bacteria and flg22. ...201221934117
Interplay of flg22-induced defence responses and nodulation in Lotus japonicus.In this study the interplay between the symbiotic and defence signalling pathways in Lotus japonicus was investigated by comparing the responses to Mesorhizobium loti, the symbiotic partner of L. japonicus, and the elicitor flg22, a conserved peptide motif present in flagellar protein of a wide range of bacteria. It was found that defence and symbiotic pathways overlap in the interaction between L. japonicus and M. loti since similar responses were induced by the mutualistic bacteria and flg22. ...201221934117
wide variation in antibiotic resistance proteins identified by functional metagenomic screening of a soil dna library.most genes for antibiotic resistance present in soil microbes remain unexplored because most environmental microbes cannot be cultured. only recently has the identification of these genes become feasible through the use of culture-independent methods. we screened a soil metagenomic dna library in an escherichia coli host for genes that can confer resistance to kanamycin, gentamicin, rifampin, trimethoprim, chloramphenicol, or tetracycline. the screen revealed 41 genes that encode novel protein v ...201222247132
structure of l-rhamnose isomerase in complex with l-rhamnopyranose demonstrates the sugar-ring opening mechanism and the role of a substrate sub-binding site.l-rhamnose isomerase (l-rhi) catalyzes the reversible isomerization of l-rhamnose to l-rhamnulose. previously determined x-ray structures of l-rhi showed a hydride-shift mechanism for the isomerization of substrates in a linear form, but the mechanism for opening of the sugar-ring is still unclear. to elucidate this mechanism, we determined x-ray structures of a mutant l-rhi in complex with l-rhamnopyranose and d-allopyranose. results suggest that a catalytic water molecule, which acts as an aci ...201223772372
structure of l-rhamnose isomerase in complex with l-rhamnopyranose demonstrates the sugar-ring opening mechanism and the role of a substrate sub-binding site.l-rhamnose isomerase (l-rhi) catalyzes the reversible isomerization of l-rhamnose to l-rhamnulose. previously determined x-ray structures of l-rhi showed a hydride-shift mechanism for the isomerization of substrates in a linear form, but the mechanism for opening of the sugar-ring is still unclear. to elucidate this mechanism, we determined x-ray structures of a mutant l-rhi in complex with l-rhamnopyranose and d-allopyranose. results suggest that a catalytic water molecule, which acts as an aci ...201223772372
crystallization and preliminary x-ray analysis of pyridoxine 4-oxidase, the first enzyme in pyridoxine degradation pathway i.vitamin b(6)-degradation pathway i has recently been identified in mesorhizobium loti maff303099. pyridoxine 4-oxidase, an fad-dependent enzyme, is the first enzyme in this pathway and catalyzes the irreversible oxidation of pyridoxine to pyridoxal. the enzyme was overexpressed in escherichia coli with a his(6) tag and purified. the recombinant enzyme was crystallized at 277 k by the sitting-drop vapour-diffusion method using peg 4000 as the precipitant. the crystal, which belonged to space grou ...201222232175
crystallization and preliminary x-ray analysis of pyridoxine 4-oxidase, the first enzyme in pyridoxine degradation pathway i.vitamin b(6)-degradation pathway i has recently been identified in mesorhizobium loti maff303099. pyridoxine 4-oxidase, an fad-dependent enzyme, is the first enzyme in this pathway and catalyzes the irreversible oxidation of pyridoxine to pyridoxal. the enzyme was overexpressed in escherichia coli with a his(6) tag and purified. the recombinant enzyme was crystallized at 277 k by the sitting-drop vapour-diffusion method using peg 4000 as the precipitant. the crystal, which belonged to space grou ...201222232175
the aspergillus fumigatus dihydroxyacid dehydratase ilv3a/ilvc is required for full virulence.dihydroxyacid dehydratase (dhad) is a key enzyme in the branched-chain amino acid biosynthetic pathway that exists in a variety of organisms, including fungi, plants and bacteria, but not humans. in this study we identified four putative dhad genes from the filamentous fungus aspergillus fumigatus by homology to saccharomyces cerevisiae ilv3. two of these genes, afua_2g14210 and afua_1g03550, initially designated afilv3a and afilv3b for this study, clustered in the same group as s. cerevisiae il ...201223028460
characterization of nitric oxide-inducing lipid a derived from mesorhizobium loti lipopolysaccharide.mesorhizobium loti is a member of the rhizobia and forms nitrogen-fixing symbioses with several lotus species. recently, it was reported that m. loti bacterial cells and their lipopolysaccharide (lps) preparations transiently induced nitric oxide (no) production in the roots of l. japonicus. we subsequently found that polysaccharides and the lipid a moiety were responsible for this no induction. in this study, we elucidated the chemical structure of m. loti lipid a and characterized its no-induc ...201223059724
cubic time algorithms of amalgamating gene trees and building evolutionary scenarios.a long recognized problem is the inference of the supertree s that amalgamates a given set {g(j)} of trees g(j), with leaves in each g(j) being assigned homologous elements. we ground on an approach to find the tree s by minimizing the total cost of mappings α(j) of individual gene trees g(j) into s. traditionally, this cost is defined basically as a sum of duplications and gaps in each α(j). the classical problem is to minimize the total cost, where s runs over the set of all trees that contain ...201223259766
meta-analysis of general bacterial subclades in whole-genome phylogenies using tree topology profiling.in the last two decades, a large number of whole-genome phylogenies have been inferred to reconstruct the tree of life (tol). underlying data models range from gene or functionality content in species to phylogenetic gene family trees and multiple sequence alignments of concatenated protein sequences. diversity in data models together with the use of different tree reconstruction techniques, disruptive biological effects and the steadily increasing number of genomes have led to a huge diversity ...201222915837
gmca is a putative glucose-methanol-choline oxidoreductase required for the induction of asexual development in aspergillus nidulans.aspergillus nidulans asexual differentiation is induced by upstream developmental activators (udas) that include the bzip-type transcription factor (tf) flbb. a 2d-page/ms-ms-coupled screen for proteins differentially expressed in the presence and absence of flbb identified 18 candidates. most candidates belong to go term classes involved in osmotic and/or oxidative stress response. among these, we focused on gmca, a putative glucose-methanol-choline oxidoreductase which is upregulated in a δflb ...201222792266
multiple mechanisms contribute to lateral transfer of an organophosphate degradation (opd) island in sphingobium fuliginis atcc 27551.the complete sequence of ppdl2 (37,317 bp), an indigenous plasmid of sphingobium fuliginis atcc 27551 that encodes genes for organophosphate degradation (opd), revealed the existence of a site-specific integrase (int) gene with an attachment site attp, typically seen in integrative mobilizable elements (ime). in agreement with this sequence information, site-specific recombination was observed between ppdl2 and an artificial plasmid having a temperature-sensitive replicon and a cloned attb site ...201223275877
novel amidases of two aminobacter sp. strains: biotransformation experiments and elucidation of gene sequences.the amidase activities of two aminobacter sp. strains (dsm24754 and dsm24755) towards the aryl-substituted substrates phenylhydantoin, indolylmethyl hydantoin, d,l-6-phenyl-5,6-dihydrouracil (phedu) and para-chloro-d,l-6-phenyl-5,6-dihydrouracil were compared. both strains showed hydantoinase and dihydropyrimidinase activity by hydrolyzing all substrates to the corresponding n-carbamoyl-α- or n-carbamoyl-β-amino acids. however, carbamoylase activity and thus a further degradation of these produc ...201222738219
a fosmid cloning strategy for detecting the widest possible spectrum of microbes from the international space station drinking water system.in this study, fosmid cloning strategies were used to assess the microbial populations in water from the international space station (iss) drinking water system (henceforth referred to as prebiocide and tank a water samples). the goals of this study were: to compare the sensitivity of the fosmid cloning strategy with that of traditional culture-based and 16s rrna-based approaches and to detect the widest possible spectrum of microbial populations during the water purification process. initially, ...201223346038
ader, a pucr-type transcription factor, activates expression of l-alanine dehydrogenase and is required for sporulation of bacillus subtilis.the bacillus subtilis ald gene encodes l-alanine dehydrogenase, which catalyzes the nad(+)-dependent deamination of l-alanine to pyruvate for the generation of energy and is required for normal sporulation. the transcription of ald is induced by alanine, but the mechanism underlying alanine induction remains unknown. here we report that a gene (formerly yukf and now designated ader) located upstream of ald is essential for the basal and alanine-inducible expression of ald. the disruption of the ...201222797752
conservation of gene order and content in the circular chromosomes of 'candidatus liberibacter asiaticus' and other rhizobiales.'ca. liberibacter asiaticus,' an insect-vectored, obligate intracellular bacterium associated with citrus-greening disease, also called "hlb," is a member of the rhizobiales along with nitrogen-fixing microsymbionts sinorhizobium meliloti and bradyrhizobium japonicum, plant pathogen agrobacterium tumefaciens and facultative intracellular mammalian pathogen bartonella henselae. comparative analyses of their circular chromosomes identified 514 orthologous genes shared among all five species. share ...201222496839
metabolomics of forage plants: a review.forage plant breeding is under increasing pressure to deliver new cultivars with improved yield, quality and persistence to the pastoral industry. new innovations in dna sequencing technologies mean that quantitative trait loci analysis and marker-assisted selection approaches are becoming faster and cheaper, and are increasingly used in the breeding process with the aim to speed it up and improve its precision. high-throughput phenotyping is currently a major bottle neck and emerging technologi ...201222351485
two micrornas linked to nodule infection and nitrogen-fixing ability in the legume lotus japonicus.legumes overcome nitrogen shortage by developing root nodules in which symbiotic bacteria fix atmospheric nitrogen in exchange for host-derived carbohydrates and mineral nutrients. nodule development involves the distinct processes of nodule organogenesis, bacterial infection, and the onset of nitrogen fixation. these entail profound, dynamic gene expression changes, notably contributed to by micrornas (mirnas). here, we used deep-sequencing, candidate-based expression studies and a selection of ...201223071252
two putative-aquaporin genes are differentially expressed during arbuscular mycorrhizal symbiosis in lotus japonicus.arbuscular mycorrhizas (am) are widespread symbioses that provide great advantages to the plant, improving its nutritional status and allowing the fungus to complete its life cycle. nevertheless, molecular mechanisms that lead to the development of am symbiosis are not yet fully deciphered. here, we have focused on two putative aquaporin genes, ljnip1 and ljxip1, which resulted to be upregulated in a transcriptomic analysis performed on mycorrhizal roots of lotus japonicus.201223046713
lotus japonicus arpc1 is required for rhizobial infection.remodeling of the plant cell cytoskeleton precedes symbiotic entry of nitrogen-fixing bacteria within the host plant roots. here we identify a lotus japonicus gene encoding a predicted actin-related protein component1 (arpc1) as essential for rhizobial infection but not for arbuscular mycorrhiza symbiosis. in other organisms arpc1 constitutes a subunit of the arp2/3 complex, the major nucleator of y-branched actin filaments. the l. japonicus arpc1 mutant showed a distorted trichome phenotype and ...201222864583
the snare protein syp71 expressed in vascular tissues is involved in symbiotic nitrogen fixation in lotus japonicus nodules.soluble n-ethylmaleimide sensitive factor attachment protein receptor (snare) proteins are crucial for signal transduction and development in plants. here, we investigate a lotus japonicus symbiotic mutant defective in one of the snare proteins. when in symbiosis with rhizobia, the growth of the mutant was retarded compared with that of the wild-type plant. although the mutant formed nodules, these exhibited lower nitrogen fixation activity than the wild type. the rhizobia were able to invade no ...201222858633
a ubiquitin ligase of symbiosis receptor kinase involved in nodule organogenesis.the symbiosis receptor kinase (symrk) is required for morphological changes of legume root hairs triggered by rhizobial infection. how protein turnover of symrk is regulated and how the nodulation factor signals are transduced downstream of symrk are not known. in this report, a symrk-interacting e3 ubiquitin ligase (sie3) was shown to bind and ubiquitinate symrk. the sie3-symrk interaction and the ubiquitination of symrk were shown to occur in vitro and in planta. sie3 represents a new class of ...201222822209
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
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