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proteomic profiling of rhizobium tropici prf 81: identification of conserved and specific responses to heat stress.rhizobium tropici strain prf 81 (= semia 4080) has been used in commercial inoculants for application to common-bean crops in brazil since 1998, due to its high efficiency in fixing nitrogen, competitiveness against indigenous rhizobial populations and capacity to adapt to stressful tropical conditions, representing a key alternative to application of n-fertilizers. the objective of our study was to obtain an overview of adaptive responses to heat stress of strain prf 81, by analyzing differenti ...201222647150
conjugal transfer of polychlorinated biphenyl/biphenyl degradation genes in acidovorax sp. strain kks102, which are located on an integrative and conjugative element.a polychlorinated biphenyl (pcb)/biphenyl degradation gene cluster in acidovorax sp. strain kks102, which is very similar to that in tn4371 from cupriavidus oxalaticus a5, was transferred to several proteobacterial strains by conjugation. the mobilized dna fragment consisted of 61,807 bp and carried genes for mating-pair formation (mpf), dna transfer (dtr), integrase (int), and replication-partition proteins (rep-parab). in the transconjugants, transferred dna was integrated at attgcatcag or sim ...201222685277
the plant growth promoting substance, lumichrome, mimics starch, and ethylene-associated symbiotic responses in lotus and tomato roots.symbiosis involves responses that maintain the plant host and symbiotic partner's genetic program; yet these cues are far from elucidated. here we describe the effects of lumichrome, a flavin identified from rhizobium spp., applied to lotus (lotus japonicus) and tomato (solanum lycopersicum). combined transcriptional and metabolite analyses suggest that both species shared common pathways that were altered in response to this application under replete, sterile conditions. these included genes in ...201222701462
structural characterization of a conserved, calcium-dependent periplasmic protease from legionella pneumophila.the bacterial dinucleotide second messenger c-di-gmp has emerged as a central molecule in regulating bacterial behavior, including motility and biofilm formation. proteins for the synthesis and degradation of c-di-gmp and effectors for its signal transmission are widely used in the bacterial domain. previous work established the ggdef-eal domain-containing receptor lapd as a central switch in pseudomonas fluorescens cell adhesion. lapd senses c-di-gmp inside the cytosol and relays this signal to ...201222707706
evidence for horizontally transferred genes involved in the biosynthesis of vitamin b(1), b(5), and b(7) in heterodera glycines.heterodera glycines is a nematode that is highly adapted to manipulate and parasitize plant hosts. the molecular players involved in these interactions have only recently begun to be identified. here, the sequencing of the second stage juvenile transcriptome, followed by a bioinformatic screen for novel genes, identified seven new genes involved in biosynthesis and salvage of vitamins b₁, b₅, and b₇. with no confirmed reports in the literature, each of these biosynthesis pathways is believed to ...200922736827
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
genetic diversity, symbiotic evolution, and proposed infection process of bradyrhizobium strains isolated from root nodules of aeschynomene americana l. in thailand.the diversity of bacteria nodulating aeschynomene americana l. in thailand was determined from phenotypic characteristics and multilocus sequence analysis of the 16s rrna gene and 3 housekeeping genes (dnak, reca, and glnb). the isolated strains were nonphotosynthetic bacteria and were assigned to the genus bradyrhizobium, in which b. yuanmingense was the dominant species. some of the other species, including b. japonicum, b. liaoningense, and b. canariense, were minor species. these isolated st ...201222752179
the bacterium pantoea stewartii uses two different type iii secretion systems to colonize its plant host and insect vector.plant- and animal-pathogenic bacteria utilize phylogenetically distinct type iii secretion systems (t3ss) that produce needle-like injectisomes or pili for the delivery of effector proteins into host cells. pantoea stewartii subsp. stewartii (herein referred to as p. stewartii), the causative agent of stewart's bacterial wilt and leaf blight of maize, carries phylogenetically distinct t3sss. in addition to an hrc-hrp t3ss, known to be essential for maize pathogenesis, p. stewartii has a second t ...201222773631
negative regulation of ccamk is essential for symbiotic infection.one of the earliest responses of legumes to symbiotic signalling is oscillation of the calcium concentration in the nucleoplasm of root epidermal cells. integration and decoding of the calcium-spiking signal involve a calcium- and calmodulin-dependent protein kinase (ccamk) and its phosphorylation substrates, such as cyclops. here we describe the lotus japonicus ccamk-14 mutant that originated from a har1-1 suppressor screen. the ccamk-14 mutation causes a serine to asparagine substitution at po ...201222775286
computational selection, identification and structural analysis of ω-aminotransferases with various substrate specificities from the genome sequence of mesorhizobium loti maff303099.ω-aminotransferase (ω-at) is an important class of enzymes for the synthesis of chiral amines or β-amino acids. family profile analysis was applied to screen putative ω-ats from mesorhizobium loti maff303099, a nitrogen fixation bacterium that has a larger number of ats than other microorganisms. by family profile analysis, we selected 10 putative ω-ats according to e-value. the functions of the putative ω-ats were investigated by examining activities towards amines and/or β-amino acids. 10 puta ...201222785472
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
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
pseudomonas syringae catalases are collectively required for plant pathogenesis.the bacterial pathogen pseudomonas syringae pv. tomato dc3000 must detoxify plant-produced hydrogen peroxide (h(2)o(2)) in order to survive in its host plant. candidate enzymes for this detoxification include the monofunctional catalases katb and kate and the bifunctional catalase-peroxidase katg of dc3000. this study shows that katg is the major housekeeping catalase of dc3000 and provides protection against menadione-generated endogenous h(2)o(2). in contrast, katb rapidly and substantially ac ...201222797762
phenotypic and molecular characterization of indigenous rhizobia nodulating chickpea in india.in a combined approach of phenotypic and genotypic characterization, 28 indigenous rhizobial isolates obtained from different chickpea growing regions in peninsular and northern india were analyzed for diversity. the field isolates were compared to two reference strains tal620 and upm-ca142 representing m. ciceri and m. mediterraneum respectively. phenotypic markers such as resistance to antibiotics, tolerance to salinity, temperature, ph, phosphate solubilization ability, growth rate and also s ...201222803324
plant hormonal regulation of nitrogen-fixing nodule organogenesis.legumes have evolved symbiotic interactions with rhizobial bacteria to efficiently utilize nitrogen. recent progress in symbiosis has revealed several key components of host plants required for nitrogen-fixing nodule organogenesis, in which complicated metabolic and signaling pathways in the host plant are reprogrammed to generate nodules in the cortex upon perception of the rhizobial nod factor. following the recognition of nod factors, plant hormones are likely to be essential throughout nodul ...201222820920
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
the histidine kinase pdhs controls cell cycle progression of the pathogenic alphaproteobacterium brucella abortus.bacterial differentiation is often associated with the asymmetric localization of regulatory proteins, such as histidine kinases. pdhs is an essential and polarly localized histidine kinase in the pathogenic alphaproteobacterium brucella abortus. after cell division, pdhs is asymmetrically segregated between the two sibling cells, highlighting a differentiation event. however, the function(s) of pdhs in the b. abortus cell cycle remains unknown. we used an original approach, the pentapeptide sca ...201222843843
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
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
atlast4ss: a curated database for type iv secretion systems.the type iv secretion system (t4ss) can be classified as a large family of macromolecule transporter systems, divided into three recognized sub-families, according to the well-known functions. the major sub-family is the conjugation system, which allows transfer of genetic material, such as a nucleoprotein, via cell contact among bacteria. also, the conjugation system can transfer genetic material from bacteria to eukaryotic cells; such is the case with the t-dna transfer of agrobacterium tumefa ...201222876890
the accessory sec protein asp2 modulates glcnac deposition onto the serine-rich repeat glycoprotein gspb.the accessory sec system is a specialized transport system that exports serine-rich repeat (srr) glycoproteins of gram-positive bacteria. this system contains two homologues of the general secretory (sec) pathway (seca2 and secy2) and several other essential proteins (asp1 to asp5) that share no homology to proteins of known function. in streptococcus gordonii, asp2 is required for the transport of the srr adhesin gspb, but its role in export is unknown. tertiary structure predictions suggest th ...201222885294
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
reactive oxygen species-inducible ecf σ factors of bradyrhizobium japonicum.extracytoplasmic function (ecf) σ factors control the transcription of genes involved in different cellular functions, such as stress responses, metal homeostasis, virulence-related traits, and cell envelope structure. the genome of bradyrhizobium japonicum, the nitrogen-fixing soybean endosymbiont, encodes 17 putative ecf σ factors belonging to nine different ecf σ factor families. the genes for two of them, ecfq (bll1028) and ecff (blr3038), are highly induced in response to the reactive oxyge ...201222916258
comparative genomics of early-diverging brucella strains reveals a novel lipopolysaccharide biosynthesis pathway.brucella species are gram-negative bacteria that infect mammals. recently, two unusual strains (brucella inopinata bo1(t) and b. inopinata-like bo2) have been isolated from human patients, and their similarity to some atypical brucellae isolated from australian native rodent species was noted. here we present a phylogenomic analysis of the draft genome sequences of bo1(t) and bo2 and of the australian rodent strains 83-13 and nf2653 that shows that they form two groups well separated from the ot ...201222930339
phylogenetic analysis of a gene cluster encoding an additional, rhizobial-like type iii secretion system that is narrowly distributed among pseudomonas syringae strains.the central role of type iii secretion systems (t3ss) in bacteria-plant interactions is well established, yet unexpected findings are being uncovered through bacterial genome sequencing. some pseudomonas syringae strains possess an uncharacterized cluster of genes encoding putative components of a second t3ss (t3ss-2) in addition to the well characterized hrc1 t3ss which is associated with disease lesions in host plants and with the triggering of hypersensitive response in non-host plants. the a ...201222937899
methylation--an uncommon modification of glycans.a methyl (me) group on a sugar residue is a rarely reported event. until now, this type of modification has been found in the animal kingdom only in worms and molluscs, whereas it is more frequently present in some species of bacteria, fungi, algae and plants, but not in mammals. the monosaccharides involved as well as the positions of the me groups on the sugar vary with species. methylation appears to play a role in some recognition events, but details are still unknown. this review summarises ...201222944672
agrobacteria lacking ornithine lipids induce more rapid tumour formation.ornithine lipids (ols) are phosphorus-free membrane lipids that are widespread among gram-negative bacteria. their basic structure consists of a 3-hydroxy fatty acyl group attached in amide linkage to the α-amino group of ornithine and a second fatty acyl group ester-linked to the 3-hydroxy position of the first fatty acid. it has been shown that ols can be hydroxylated within the amide-linked fatty acyl moiety, the secondary fatty acyl moiety or within the ornithine moiety. these modifications ...201222958119
agrobacteria lacking ornithine lipids induce more rapid tumour formation.ornithine lipids (ols) are phosphorus-free membrane lipids that are widespread among gram-negative bacteria. their basic structure consists of a 3-hydroxy fatty acyl group attached in amide linkage to the α-amino group of ornithine and a second fatty acyl group ester-linked to the 3-hydroxy position of the first fatty acid. it has been shown that ols can be hydroxylated within the amide-linked fatty acyl moiety, the secondary fatty acyl moiety or within the ornithine moiety. these modifications ...201222958119
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
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
robust markers reflecting phylogeny and taxonomy of rhizobia.genomic ani (average nucleotide identity) has been found to be able to replace dna-dna hybridization in prokaryote taxonomy. the ani of each of the core genes that has a phylogeny congruent with the reference species tree of rhizobia was compared to the genomic ani. this allowed us to identify three housekeeping genes (smc00019-trua-thra) whose ani reflected the intraspecies and interspecies genomic ani among rhizobial strains, revealing an ani gap (≥2%) between the inter- and intra-species comp ...201223028691
mesorhizobium qingshengii sp. nov., isolated from effective nodules of astragalus sinicus.in a study on the diversity of rhizobia isolated from root nodules of astragalus sinicus, five strains showed identical 16s rrna gene sequences. they were related most closely to the type strains of mesorhizobium loti, mesorhizobium shangrilense, mesorhizobium ciceri and mesorhizobium australicum, with sequence similarities of 99.6-99.8%. a polyphasic approach, including 16s-23s intergenic spacer (igs) rflp, comparative sequence analysis of 16s rrna, atpd, glnii and reca genes, dna-dna hybridiza ...201323041644
a rubisco-like protein links sam metabolism with isoprenoid biosynthesis.functional assignment of uncharacterized proteins is a challenge in the era of large-scale genome sequencing. here, we combine in extracto nmr, proteomics and transcriptomics with a newly developed (knock-out) metabolomics platform to determine a potential physiological role for a ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco)-like protein from rhodospirillum rubrum. our studies unraveled an unexpected link in bacterial central carbon metabolism between s-adenosylmethionine-dependent ...201223042035
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
global network alignment using multiscale spectral signatures.protein interaction networks provide an important system-level view of biological processes. one of the fundamental problems in biological network analysis is the global alignment of a pair of networks, which puts the proteins of one network into correspondence with the proteins of another network in a manner that conserves their interactions while respecting other evidence of their homology. by providing a mapping between the networks of different species, alignments can be used to inform hypot ...201223047556
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
how membranes shape plant symbioses: signaling and transport in nodulation and arbuscular mycorrhiza.as sessile organisms that cannot evade adverse environmental conditions, plants have evolved various adaptive strategies to cope with environmental stresses. one of the most successful adaptations is the formation of symbiotic associations with beneficial microbes. in these mutualistic interactions the partners exchange essential nutrients and improve their resistance to biotic and abiotic stresses. in arbuscular mycorrhiza (am) and in root nodule symbiosis (rns), am fungi and rhizobia, respecti ...201223060892
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
ethylene in mutualistic symbioses.ethylene (et) is a gaseous phytohormone that participates in various plant physiological processes and essentially contributes to plant immunity. et conducts its functions by regulating the expression of et-responsive genes or in crosstalk with other hormones. several recent studies have shown the significance of et in the establishment and development of plant-microbe interactions. therefore, it is not surprising that pathogens and mutualistic symbionts target et synthesis or signaling to colon ...201223072986
isolation of fucosyltransferase-producing bacteria from marine environments.fucose-containing oligosaccharides on the cell surface of some pathogenic bacteria are thought to be important for host-microbe interactions and to play a major role in the pathogenicity of bacterial pathogens. here, we screened marine bacteria for glycosyltransferases using two methods: a one-pot glycosyltransferase assay method and a lectin-staining method. using this approach, we isolated marine bacteria with fucosyltransferase activity. there have been no previous reports of marine bacteria ...201223100020
a widely conserved molecular switch controls quorum sensing and symbiosis island transfer in mesorhizobium loti through expression of a novel antiactivator.icemlsym(r7a) of mesorhizobium loti is an integrative and conjugative element (ice) that confers the ability to form a nitrogen-fixing symbiosis with lotus species. horizontal transfer is activated by trar and n-acyl-homoserine lactone (ahl), which can stimulate ice excision in 100% of cells. however, in wild-type cultures, the ice is excised at low frequency. here we show that qsem, a widely conserved ice-encoded protein, is an antiactivator of trar. mutation of qsem resulted in trar-dependent ...201323106190
rhizobia with 16s rrna and nifh similar to mesorhizobium huakuii but novel reca, glnii, noda and nodc genes are symbionts of new zealand carmichaelinae.new zealand became geographically isolated about 80 million years ago and this separation gave rise to a unique native flora including four genera of legume, carmichaelia, clianthus and montigena in the carmichaelinae clade, tribe galegeae, and sophora, tribe sophoreae, sub-family papilionoideae. ten bacterial strains isolated from nz carmichaelinae growing in natural ecosystems grouped close to the mesorhizobium huakuii type strain in relation to their 16s rrna and nifh gene sequences. however, ...201223118889
conditional requirement for exopolysaccharide in the mesorhizobium-lotus symbiosis.rhizobial surface polysaccharides are required for nodule formation on the roots of at least some legumes but the mechanisms by which they act are yet to be determined. as a first step to investigate the function of exopolysaccharide (eps) in the formation of determinate nodules, we isolated mesorhizobium loti mutants affected in various steps of eps biosynthesis and characterized their symbiotic phenotypes on two lotus spp. the wild-type m. loti r7a produced both high molecular weight eps and l ...201323134480
st proteins, a new family of plant tandem repeat proteins with a duf2775 domain mainly found in fabaceae and asteraceae.many proteins with tandem repeats in their sequence have been described and classified according to the length of the repeats: i) repeats of short oligopeptides (from 2 to 20 amino acids), including structural cell wall proteins and arabinogalactan proteins. ii) repeats that range in length from 20 to 40 residues, including proteins with a well-established three-dimensional structure often involved in mediating protein-protein interactions. (iii) longer repeats in the order of 100 amino acids th ...201223134664
rhizobial and mycorrhizal symbioses in lotus japonicus require lectin nucleotide phosphohydrolase, which acts upstream of calcium signaling.nodulation in legumes requires the recognition of rhizobially made nod factors. genetic studies have revealed that the perception of nod factors involves lysm domain receptor-like kinases, while biochemical approaches have identified lectin nucleotide phosphohydrolase (lnp) as a nod factor-binding protein. here, we show that antisense inhibition of lnp blocks nodulation in lotus japonicus. this absence of nodulation was due to a defect in nod factor signaling based on the observations that the e ...201223136382
rhizobial and mycorrhizal symbioses in lotus japonicus require lectin nucleotide phosphohydrolase, which acts upstream of calcium signaling.nodulation in legumes requires the recognition of rhizobially made nod factors. genetic studies have revealed that the perception of nod factors involves lysm domain receptor-like kinases, while biochemical approaches have identified lectin nucleotide phosphohydrolase (lnp) as a nod factor-binding protein. here, we show that antisense inhibition of lnp blocks nodulation in lotus japonicus. this absence of nodulation was due to a defect in nod factor signaling based on the observations that the e ...201223136382
the national bioresource project (nbrp) lotus and glycine in japan.the objective of the national bioresource project (nbrp) in japan is to collect, conserve and distribute biological materials for life sciences research. the project consists of twenty-eight bioresources, including animal, plant, microorganism and dna resources. nbrp lotus and glycine aims to support the development of legume research through the collection, conservation, and distribution of these bioresources. lotus japonicus is a perennial legume that grows naturally throughout japan and is wi ...201223136485
genetic characterization of a novel rhizobial plasmid conjugation system in rhizobium leguminosarum bv. viciae strain vf39sm.rhizobium leguminosarum strain vf39sm contains two plasmids that have previously been shown to be self-transmissible by conjugation. one of these plasmids, prlevf39b, is shown in this study to carry a set of plasmid transfer genes that differs significantly from conjugation systems previously studied in the rhizobia but is similar to an uncharacterized set of genes found in r. leguminosarum bv. trifolii strain wsm2304. the entire sequence of the transfer region on prlevf39b was determined as par ...201323144250
contribution of lateral gene transfers to the genome composition and parasitic ability of root-knot nematodes.lateral gene transfers (lgt), species to species transmission of genes by means other than direct inheritance from a common ancestor, have played significant role in shaping prokaryotic genomes and are involved in gain or transfer of important biological processes. whether lgt significantly contributed to the composition of an animal genome is currently unclear. in nematodes, multiple lgt are suspected to have favored emergence of plant-parasitism. with the availability of whole genome sequences ...201223226415
cloning of a novel 6-chloronicotinic acid chlorohydrolase from the newly isolated 6-chloronicotinic acid mineralizing bradyrhizobiaceae strain sg-6c.a 6-chloronicotinic acid mineralizing bacterium was isolated from enrichment cultures originating from imidacloprid-contaminated soil samples. this bradyrhizobiaceae, designated strain sg-6c, hydrolytically dechlorinated 6-chloronicotinic acid to 6-hydroxynicotinic acid, which was then further metabolised via the nicotinic acid pathway. this metabolic pathway was confirmed by growth and resting cell assays using hplc and lc-ms studies. a candidate for the gene encoding the initial dechlorination ...201223226482
mechanistic studies of fosb: a divalent-metal-dependent bacillithiol-s-transferase that mediates fosfomycin resistance in staphylococcus aureus.fosb is a divalent-metal-dependent thiol-s-transferase implicated in fosfomycin resistance among many pathogenic gram-positive bacteria. in the present paper, we describe detailed kinetic studies of fosb from staphylococcus aureus (safosb) that confirm that bacillithiol (bsh) is its preferred physiological thiol substrate. safosb is the first to be characterized among a new class of enzyme (bacillithiol-s-transferases), which, unlike glutathione transferases, are distributed among many low-g+c g ...201323256780
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
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
elucidation of a novel lipid a α-(1,1)-gala transferase gene (rgtf) from mesorhizobium loti: heterologous expression of rgtf causes rhizobium etli to synthesize lipid a with α-(1,1)-gala.an unusual α-(1,1)-galacturonic acid (gala) lipid a modification has been reported in the lipopolysaccharide of a number of interesting gram-negative bacteria, including the nitrogen-fixing bacteria azospirillum lipoferum, mesorhizobium huakuii and m. loti, the stalk-forming bacterium caulobacter crescentus and the hyperthermophilic bacterium aquifex aeolicus. however, the α-(1,1)-gala transferase (galat) gene, which we have named rgtf, was not identified. species of the rhizobium genera produce ...201323283001
catalytic mechanism of short ethoxy chain nonylphenol dehydrogenase belonging to a polyethylene glycol dehydrogenase group in the gmc oxidoreductase family.ethoxy (eo) chain nonylphenol dehydrogenase (npeo-dh) from ensifer sp. as08 and eo chain octylphenol dehydrogenase from pseudomonas putida share common molecular characteristics with polyethylene glycol (peg) dehydrogenases (peg-dh) and comprise a peg-dh subgroup in the family of glucose-methanol-choline (gmc) oxidoreductases that includes glucose/alcohol oxidase and glucose/choline dehydrogenase. three-dimensional (3d) molecular modeling suggested that differences in the size, secondary structu ...201323306149
the nifa-rpon regulon of mesorhizobium loti strain r7a and its symbiotic activation by a novel laci/galr-family regulator.mesorhizobium loti is the microsymbiont of lotus species, including the model legume l. japonicus. m. loti differs from other rhizobia in that it contains two copies of the key nitrogen fixation regulatory gene nifa, nifa1 and nifa2, both of which are located on the symbiosis island icemlsym(r7a). m. loti r7a also contains two rpon genes, rpon1 located on the chromosome outside of icemlsym(r7a) and rpon2 that is located on icemlsym(r7a). the aims of the current work were to establish how nifa ex ...201323308282
how does (e)-2-(acetamidomethylene)succinate bind to its hydrolase? from the binding process to the final result.the binding of (e)-2-(acetamidomethylene)succinate (e-2ams) to e-2ams hydrolase is crucial for biological function of the enzyme and the last step reaction of vitamin b(6) biological degradation. in the present study, several molecular simulation methods, including molecular docking, conventional molecular dynamics (md), steered md (smd), and free energy calculation methods, were properly integrated to investigate the detailed binding process of e-2ams to its hydrolase and to assign the optimal ...201323308285
mesorhizobium sangaii sp. nov., isolated from the root nodules of astragalus luteolus and astragalus ernestii.our previous published data indicated that the two rhizobial strains scau7(t) and scau27, which were isolated from the root nodules of astragalus luteolus and astragalus ernestii respectively, in sichuan province, china, might be novel species of the genus mesorhizobium. their exact taxonomic position was determined in the present study by using polyphasic approaches. comparative analysis of nearly full-length 16s rrna gene sequences showed that these strains belonged to the genus mesorhizobium, ...201323315406
kinetics of ligand-receptor interaction reveals an induced-fit mode of binding in a cyclic nucleotide-activated protein.many receptors and ion channels are activated by ligands. one key question concerns the binding mechanism. does the ligand induce conformational changes in the protein via the induced-fit mechanism? or does the protein preexist as an ensemble of conformers and the ligand selects the most complementary one, via the conformational selection mechanism? here, we study ligand binding of a tetrameric cyclic nucleotide-gated channel from mesorhizobium loti and of its monomeric binding domain (cnbd) usi ...201323332059
grafting analysis indicates that malfunction of tricot in the root causes a nodulation-deficient phenotype in lotus japonicus.leguminous plants develop root nodules in symbiosis with soil rhizobia. nodule formation occurs following rhizobial infection of the host root that induces dedifferentiation of some cortical cells and the initiation of a new developmental program to form nodule primordia. in a recent study, we identified a novel gene, tricot (tco), that acts as a positive regulator of nodulation in lotus japonicus. in addition to its role in nodulation, tco mutant plants display pleiotropic defects including abn ...201323333956
down-regulation of nsp2 expression in developmentally young regions of lotus japonicus roots in response to rhizobial inoculation.during the early 1980s, bauer and associates reported that nodulation potential in primary roots of soybean seedlings following inoculation with rhizobia was significantly reduced in developmentally younger regions. they suggested that this phenomenon might be due to a fast-acting regulatory mechanism in the host that prevented excessive nodulation. however, the molecular mechanism of this fast-acting regulatory response remains uncertain. here, we sought to elucidate components of this regulato ...201323335614
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
reconstruction of phyletic trees by global alignment of multiple metabolic networks.in the last decade, a considerable amount of research has been devoted to investigating the phylogenetic properties of organisms from a systems-level perspective. most studies have focused on the classification of organisms based on structural comparison and local alignment of metabolic pathways. in contrast, global alignment of multiple metabolic networks complements sequence-based phylogenetic analyses and provides more comprehensive information.201323368411
profligate biotin synthesis in α-proteobacteria - a developing or degenerating regulatory system?biotin (vitamin h) is a key enzyme cofactor required in all three domains of life. although this cofactor was discovered over 70 years ago and has long been recognized as an essential nutrient for animals, our knowledge of the strategies bacteria use to sense biotin demand is very limited. the paradigm mechanism is that of escherichia coli in which bira protein, the prototypical bi-functional biotin protein ligase, both covalently attaches biotin to the acceptor proteins of central metabolism an ...201323387333
genome analysis suggests that the soil oligotrophic bacterium agromonas oligotrophica (bradyrhizobium oligotrophicum) is a nitrogen-fixing symbiont of aeschynomene indica.agromonas oligotrophica (bradyrhizobium oligotrophicum) s58(t) is a nitrogen-fixing oligotrophic bacterium isolated from paddy field soil that is able to grow in extra-low-nutrient environments. here, the complete genome sequence of s58 was determined. the s58 genome was found to comprise a circular chromosome of 8,264,165 bp with an average gc content of 65.1% lacking nodabc genes and the typical symbiosis island. the genome showed a high level of similarity to the genomes of bradyrhizobium sp. ...201323396330
voltage sensor ring in a native structure of a membrane-embedded potassium channel.voltage-gated ion channels support electrochemical activity in cells and are largely responsible for information flow throughout the nervous systems. the voltage sensor domains in these channels sense changes in transmembrane potential and control ion flux across membranes. the x-ray structures of a few voltage-gated ion channels in detergents have been determined and have revealed clear structural variations among their respective voltage sensor domains. more recent studies demonstrated that li ...201323401554
cessation of photosynthesis in lotus japonicus leaves leads to reprogramming of nodule metabolism.symbiotic nitrogen fixation (snf) involves global changes in gene expression and metabolite accumulation in both rhizobia and the host plant. in order to study the metabolic changes mediated by leaf-root interaction, photosynthesis was limited in leaves by exposure of plants to darkness, and subsequently gene expression was profiled by real-time reverse transcription-pcr (rt-pcr) and metabolite levels by gas chromatography-mass spectrometry in the nodules of the model legume lotus japonicus. pho ...201323404899
comparative genomics of the core and accessory genomes of 48 sinorhizobium strains comprising five genospecies.the sinorhizobia are amongst the most well studied members of nitrogen-fixing root nodule bacteria and contribute substantial amounts of fixed nitrogen to the biosphere. while the alfalfa symbiont sinorhizobium meliloti rm 1021 was one of the first rhizobial strains to be completely sequenced, little information is available about the genomes of this large and diverse species group.201323425606
phylogenetic analysis of erythritol catabolic loci within the rhizobiales and proteobacteria.the ability to use erythritol as a sole carbon source is not universal among the rhizobiaceae. based on the relatedness to the catabolic genes in brucella it has been suggested that the eryabcd operon may have been horizontally transferred into rhizobium. during work characterizing a locus necessary for the transport and catabolism of erythritol, adonitol and l-arabitol in sinorhizobium meliloti, we became interested in the differences between the erythritol loci of s. meliloti and r. leguminosa ...201323432981
the shoct domain: a widespread domain under-represented in model organisms.we have identified a new protein domain, which we have named the shoct domain (short c-terminal domain). this domain is widespread in bacteria with over a thousand examples. but we found it is missing from the most commonly studied model organisms, despite being present in closely related species. it's predominantly c-terminal location, co-occurrence with numerous other domains and short size is reminiscent of the gram-positive anchor motif, however it is present in a much wider range of species ...201323451277
mutualistic co-evolution of type iii effector genes in sinorhizobium fredii and bradyrhizobium japonicum.two diametric paradigms have been proposed to model the molecular co-evolution of microbial mutualists and their eukaryotic hosts. in one, mutualist and host exhibit an antagonistic arms race and each partner evolves rapidly to maximize their own fitness from the interaction at potential expense of the other. in the opposing model, conflicts between mutualist and host are largely resolved and the interaction is characterized by evolutionary stasis. we tested these opposing frameworks in two line ...201323468637
gene cloning and characterization of l-ribulose 3-epimerase from mesorhizobium loti and its application to rare sugar production.a gene encoding l-ribulose 3-epimerase (l-re) from mesorhizobium loti, an important enzyme for rare sugar production by the izumoring strategy, was cloned and overexpressed. the enzyme showed highest activity toward l-ribulose (230 u/mg) among keto-pentoses and keto-hexoses. this is the first report on a ketose 3-epimerase showing highest activity toward keto-pentose. the optimum enzyme reaction conditions for l-re were determined to be sodium phosphate buffer (ph 8.0) at 60 °c. the enzyme showe ...201323470755
crystal structure of pyridoxine 4-oxidase from mesorhizobium loti.pyridoxine 4-oxidase (pnox) from mesorhizobium loti is a monomeric glucose-methanol-choline (gmc) oxidoreductase family enzyme, catalyzes fad-dependent oxidation of pyridoxine (pn) into pyridoxal, and is the first enzyme in pathway i for the degradation of pn. the tertiary structures of pnox with a c-terminal his6-tag and pnox-pyridoxamine (pm) complex were determined at 2.2å and at 2.1å resolutions, respectively. the overall structure consisted of fad-binding and substrate-binding domains. in t ...201323501672
myo-inositol and d-ribose ligand discrimination in an abc periplasmic binding protein.the periplasmic binding protein (pbp) ibpa mediates the uptake of myo-inositol by the iatp-iata atp-binding cassette transmembrane transporter. we report a crystal structure of caulobacter crescentus ibpa bound to myo-inositol at 1.45 å resolution. this constitutes the first structure of a pbp bound to inositol. ibpa adopts a type i pbp fold consisting of two α-β lobes that surround a central hinge. a pocket positioned between the lobes contains the myo-inositol ligand, which binds with submicro ...201323504019
arylamine n-acetyltransferases: a structural perspective.arylamine n-acetyltransferase (nat) plays an important role in metabolism and detoxification of many compounds including drugs and environmental carcinogens through chemical modification of the amine group with an acetyl group. recent studies have suggested that nats are also involved in cancer cell growth and inhibition of the enzymes may be a potential target for cancer chemotherapy. three-dimensional (3d) structures are available for nats from both prokaryotes and eukaryotes. these structures ...201323517104
spatio-temporal expression patterns of arabidopsis thaliana and medicago truncatula defensin-like genes.plant genomes contain several hundred defensin-like (defl) genes that encode short cysteine-rich proteins resembling defensins, which are well known antimicrobial polypeptides. little is known about the expression patterns or functions of many defls because most were discovered recently and hence are not well represented on standard microarrays. we designed a custom affymetrix chip consisting of probe sets for 317 and 684 defls from arabidopsis thaliana and medicago truncatula, respectively for ...201323527067
modularity of plant metabolic gene clusters: a trio of linked genes that are collectively required for acylation of triterpenes in oat.operon-like gene clusters are an emerging phenomenon in the field of plant natural products. the genes encoding some of the best-characterized plant secondary metabolite biosynthetic pathways are scattered across plant genomes. however, an increasing number of gene clusters encoding the synthesis of diverse natural products have recently been reported in plant genomes. these clusters have arisen through the neo-functionalization and relocation of existing genes within the genome, and not by hori ...201323532069
nodule inception directly targets nf-y subunit genes to regulate essential processes of root nodule development in lotus japonicus.the interactions of legumes with symbiotic nitrogen-fixing bacteria cause the formation of specialized lateral root organs called root nodules. it has been postulated that this root nodule symbiosis system has recruited factors that act in early signaling pathways (common sym genes) partly from the ancestral mycorrhizal symbiosis. however, the origins of factors needed for root nodule organogenesis are largely unknown. nodule inception (nin) is a nodulation-specific gene that encodes a putative ...201323555278
a gene transfer agent and a dynamic repertoire of secretion systems hold the keys to the explosive radiation of the emerging pathogen bartonella.gene transfer agents (gtas) randomly transfer short fragments of a bacterial genome. a novel putative gta was recently discovered in the mouse-infecting bacterium bartonella grahamii. although gtas are widespread in phylogenetically diverse bacteria, their role in evolution is largely unknown. here, we present a comparative analysis of 16 bartonella genomes ranging from 1.4 to 2.6 mb in size, including six novel genomes from bartonella isolated from a cow, two moose, two dogs, and a kangaroo. a ...201323555299
carotenoid cleavage dioxygenase 7 modulates plant growth, reproduction, senescence, and determinate nodulation in the model legume lotus japonicus.strigolactones (sls) are newly identified hormones that regulate multiple aspects of plant development, infection by parasitic weeds, and mutualistic symbiosis in the roots. in this study, the role of sls was studied for the first time in the model plant lotus japonicus using transgenic lines silenced for carotenoid cleavage dioxygenase 7 (ljccd7), the orthologue of arabidopsis more axillary growth 3. transgenic ljccd7-silenced plants displayed reduced height due to shorter internodes, and more ...201323567864
atomic force microscopy: a multifaceted tool to study membrane proteins and their interactions with ligands.membrane proteins are embedded in lipid bilayers and facilitate the communication between the external environment and the interior of the cell. this communication is often mediated by the binding of ligands to the membrane protein. understanding the nature of the interaction between a ligand and a membrane protein is required to both understand the mechanism of action of these proteins and for the development of novel pharmacological drugs. the highly hydrophobic nature of membrane proteins and ...201323603221
atomic force microscopy: a multifaceted tool to study membrane proteins and their interactions with ligands.membrane proteins are embedded in lipid bilayers and facilitate the communication between the external environment and the interior of the cell. this communication is often mediated by the binding of ligands to the membrane protein. understanding the nature of the interaction between a ligand and a membrane protein is required to both understand the mechanism of action of these proteins and for the development of novel pharmacological drugs. the highly hydrophobic nature of membrane proteins and ...201323603221
comparative genomic analysis of the genus nocardiopsis provides new insights into its genetic mechanisms of environmental adaptability.the genus nocardiopsis, a widespread group in phylum actinobacteria, has received much attention owing to its ecological versatility, pathogenicity, and ability to produce a rich array of bioactive metabolites. its high environmental adaptability might be attributable to its genome dynamics, which can be estimated through comparative genomic analysis targeting microorganisms with close phylogenetic relationships but different phenotypes. to shed light on speciation, gene content evolution, and e ...201323626695
two lotus japonicus symbiosis mutants impaired at distinct steps of arbuscule development.arbuscular mycorrhiza (am) fungi form nutrient-acquiring symbioses with the majority of higher plants. nutrient exchange occurs via arbuscules, highly branched hyphal structures that are formed within root cortical cells. with a view to identifying host genes involved in am development, we isolated lotus japonicus am-defective mutants via a microscopic screen of an ethyl methanesulfonate-mutagenized population. a standardized mapping procedure was developed that facilitated positioning of the de ...201323627596
genome-wide transcriptional responses of two metal-tolerant symbiotic mesorhizobium isolates to zinc and cadmium exposure.mesorhizobium metallidurans stm 2683t and mesorhizobium sp. strain stm 4661 were isolated from nodules of the metallicolous legume anthyllis vulneraria from distant mining spoils. they tolerate unusually high zinc and cadmium concentrations as compared to other mesorhizobia. this work aims to study the gene expression profiles associated with zinc or cadmium exposure and to identify genes involved in metal tolerance in these two metallicolous mesorhizobium strains of interest for mine phytostabi ...201323631387
commonalities and differences among symbiosis islands of three mesorhizobium loti strains.to shed light on the breadth of the host range of mesorhizobium loti strain nzp2037, we determined the sequence of the nzp2037 symbiosis island and compared it with those of strain maff303099 and r7a islands. the determined 533 kb sequence of nzp2037 symbiosis island, on which 504 genes were predicted, implied its integration into a phenylalanine-trna gene and subsequent genome rearrangement. comparative analysis revealed that the core regions of the three symbiosis islands consisted of 165 gene ...201323666538
carbohydrate kinase (rhak)-dependent abc transport of rhamnose in rhizobium leguminosarum demonstrates genetic separation of kinase and transport activities.in rhizobium leguminosarum the abc transporter responsible for rhamnose transport is dependent on rhak, a sugar kinase that is necessary for the catabolism of rhamnose. this has led to a working hypothesis that rhak has two biochemical functions: phosphorylation of its substrate and affecting the activity of the rhamnose abc transporter. to address this hypothesis, a linker-scanning random mutagenesis of rhak was carried out. thirty-nine linker-scanning mutations were generated and mapped. allel ...201323708135
biotransformation of trichoderma spp. and their tolerance to aromatic amines, a major class of pollutants.trichoderma spp. are cosmopolitan soil fungi that are highly resistant to many toxic compounds. here, we show that trichoderma virens and t. reesei are tolerant to aromatic amines (aa), a major class of pollutants including the highly toxic pesticide residue 3,4-dichloroaniline (3,4-dca). in a previous study, we provided proof-of-concept remediation experiments in which another soil fungus, podospora anserina, detoxifies 3,4-dca through its arylamine n-acetyltransferase (nat), a xenobiotic-metab ...201323728813
brucella bior regulator defines a complex regulatory mechanism for bacterial biotin metabolism.the enzyme cofactor biotin (vitamin h or b7) is an energetically expensive molecule whose de novo biosynthesis requires 20 atp equivalents. it seems quite likely that diverse mechanisms have evolved to tightly regulate its biosynthesis. unlike the model regulator bira, a bifunctional biotin protein ligase with the capability of repressing the biotin biosynthetic pathway, bior has been recently reported by us as an alternative machinery and a new type of gntr family transcriptional factor that ca ...201323729648
the sinorhizobium meliloti essential porin ropa1 is a target for numerous bacteriophages.the symbiotic nitrogen-fixing bacterium sinorhizobium meliloti harbors a gene, smc02396, which encodes a predicted outer membrane porin that is conserved in many symbiotic and pathogenic bacteria in the order rhizobiales. here, this gene (renamed ropa1) is shown to be required for infection by two commonly utilized transducing bacteriophages (φm12 and n3). mapping of s. meliloti mutations conferring resistance to φm12, n3, or both phages simultaneously revealed diverse mutations mapping within t ...201323749981
interaction of medicago truncatula lysin motif receptor-like kinases, nfp and lyk3, produced in nicotiana benthamiana induces defence-like responses.receptor(-like) kinases with lysin motif (lysm) domains in their extracellular region play crucial roles during plant interactions with microorganisms; e.g. arabidopsis thaliana cerk1 activates innate immunity upon perception of fungal chitin/chitooligosaccharides, whereas medicago truncatula nfp and lyk3 mediate signalling upon perception of bacterial lipo-chitooligosaccharides, termed nod factors, during the establishment of mutualism with nitrogen-fixing rhizobia. however, little is still kno ...201323750228
the thuefgkab operon of rhizobia and agrobacterium tumefaciens codes for transport of trehalose, maltitol, and isomers of sucrose and their assimilation through the formation of their 3-keto derivatives.the thu operon (thuefgkab) in sinorhizobium meliloti codes for transport and utilization functions of the disaccharide trehalose. sequenced genomes of members of the rhizobiaceae reveal that some rhizobia and agrobacterium possess the entire thu operon in similar organizations and that mesorhizobium loti maff303099 lacks the transport (thuefgk) genes. in this study, we show that this operon is dedicated to the transport and assimilation of maltitol and isomers of sucrose (leucrose, palatinose, a ...201323772075
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
structure and function of a bacterial fasciclin i domain protein elucidates function of related cell adhesion proteins such as tgfbip and periostin.fasciclin i (fas1) domains have important roles in cell adhesion, which are not understood despite many structural and functional studies. examples of fas1 domain proteins include tgfbip (βig-h3) and periostin, which function in angiogenesis and development of cornea and bone, and are also highly expressed in cancer tissues. here we report the structure of a single-domain bacterial fasciclin i protein, fdp, in the free-living photosynthetic bacterium rhodobacter sphaeroides, and show that it con ...201323772377
structure and catalytic mechanism of yeast 4-amino-4-deoxychorismate lyase.saccharomyces cerevisiae abz2 is a pyridoxal 5'-phosphate (plp)-dependent lyase that converts 4-amino-4-deoxychorismate (adc) to para-aminobenzoate and pyruvate. to investigate the catalytic mechanism, we determined the 1.9 å resolution crystal structure of abz2 complexed with plp, representing the first eukaryotic adc lyase structure. unlike escherichia coli adc lyase, whose dimerization is critical to the formation of the active site, the overall structure of abz2 displays as a monomer of two ...201323818518
subglacial lake vostok (antarctica) accretion ice contains a diverse set of sequences from aquatic, marine and sediment-inhabiting bacteria and eukarya.lake vostok, the 7(th) largest (by volume) and 4(th) deepest lake on earth, is covered by more than 3,700 m of ice, making it the largest subglacial lake known. the combination of cold, heat (from possible hydrothermal activity), pressure (from the overriding glacier), limited nutrients and complete darkness presents extreme challenges to life. here, we report metagenomic/metatranscriptomic sequence analyses from four accretion ice sections from the vostok 5g ice core. two sections accreted in t ...201323843994
small rna pathways and diversity in model legumes: lessons from genomics.small non-coding rnas (smrna) participate in the regulation of development, cell differentiation, adaptation to environmental constraints and defense responses in plants. they negatively regulate gene expression by degrading specific mrna targets, repressing their translation or modifying chromatin conformation through homologous interaction with target loci. micrornas (mirna) and short-interfering rnas (sirna) are generated from long double stranded rna (dsrna) that are cleaved into 20-24-nucle ...201323847640
comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea.metal sulfide mineral dissolution during bioleaching and acid mine drainage (amd) formation creates an environment that is inhospitable to most life. despite dominance by a small number of bacteria, amd microbial biofilm communities contain a notable variety of coexisting and closely related euryarchaea, most of which have defied cultivation efforts. for this reason, we used metagenomics to analyze variation in gene content that may contribute to niche differentiation among co-occurring amd arch ...201323865623
independent activity of the homologous small regulatory rnas abcr1 and abcr2 in the legume symbiont sinorhizobium meliloti.the legume symbiont sinorhizobium meliloti expresses a plethora of small noncoding rnas (srnas) whose function is mostly unknown. here, we have functionally characterized two tandemly encoded s. meliloti rm1021 srnas that are similar in sequence and structure. homologous srnas (designated abcr1 and abcr2) have been shown to regulate several abc transporters in the related α-proteobacteria agrobacterium tumefaciens and brucella abortus. in rm1021, abcr1 and abcr2 exhibit divergent unlinked regula ...201323869210
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