| minimum requirements of flagellation and motility for infection of agrobacterium sp. strain h13-3 by flagellotropic bacteriophage 7-7-1. | the flagellotropic phage 7-7-1 specifically adsorbs to agrobacterium sp. strain h13-3 (formerly rhizobium lupini h13-3) flagella for efficient host infection. the agrobacterium sp. h13-3 flagellum is complex and consists of three flagellin proteins: the primary flagellin flaa, which is essential for motility, and the secondary flagellins flab and flad, which have minor functions in motility. using quantitative infectivity assays, we showed that absence of flad had no effect on phage infection, w ... | 2012 | 22865074 |
| predicting plasmid promiscuity based on genomic signature. | despite the important contribution of self-transmissible plasmids to bacterial evolution, little is understood about the range of hosts in which these plasmids have evolved. our goal was to infer this so-called evolutionary host range. the nucleotide composition, or genomic signature, of plasmids is often similar to that of the chromosome of their current host, suggesting that plasmids acquire their hosts' signature over time. therefore, we examined whether the evolutionary host range of plasmid ... | 2010 | 20851899 |
| sinorhizobium meliloti exor is the target of periplasmic proteolysis. | sinorhizobium meliloti exor regulates the production of succinoglycan and flagella through the exos/chvi two-component regulatory system. exor has been proposed to inhibit the exos sensor through direct interaction in the periplasm. to understand how exor suppression of exos is relieved, which is required for the expression of exos/chvi-regulated symbiosis genes, we characterized wild-type exor and exor95 mutant proteins. in addition to the previously identified precursor and mature forms of exo ... | 2012 | 22636773 |
| light regulates attachment, exopolysaccharide production, and nodulation in rhizobium leguminosarum through a lov-histidine kinase photoreceptor. | rhizobium leguminosarum is a soil bacterium that infects root hairs and induces the formation of nitrogen-fixing nodules on leguminous plants. light, oxygen, and voltage (lov)-domain proteins are blue-light receptors found in higher plants and many algae, fungi, and bacteria. the genome of r. leguminosarum bv. viciae 3841, a pea-nodulating endosymbiont, encodes a sensor histidine kinase containing a lov domain at the n-terminal end (r-lov-hk). r-lov-hk has a typical lov domain absorption spectru ... | 2012 | 22773814 |
| analysis of the sos response of vibrio and other bacteria with multiple chromosomes. | the sos response is a well-known regulatory network present in most bacteria and aimed at addressing dna damage. it has also been linked extensively to stress-induced mutagenesis, virulence and the emergence and dissemination of antibiotic resistance determinants. recently, the sos response has been shown to regulate the activity of integrases in the chromosomal superintegrons of the vibrionaceae, which encompasses a wide range of pathogenic species harboring multiple chromosomes. here we combin ... | 2012 | 22305460 |
| improving microbial genome annotations in an integrated database context. | effective comparative analysis of microbial genomes requires a consistent and complete view of biological data. consistency regards the biological coherence of annotations, while completeness regards the extent and coverage of functional characterization for genomes. we have developed tools that allow scientists to assess and improve the consistency and completeness of microbial genome annotations in the context of the integrated microbial genomes (img) family of systems. all publicly available ... | 2013 | 23424620 |
| reconciliation of sequence data and updated annotation of the genome of agrobacterium tumefaciens c58, and distribution of a linear chromosome in the genus agrobacterium. | two groups independently sequenced the agrobacterium tumefaciens c58 genome in 2001. we report here consolidation of these sequences, updated annotation, and additional analysis of the evolutionary history of the linear chromosome, which is apparently limited to the biovar i group of agrobacterium. | 2013 | 23241979 |
| 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 ... | 2013 | 23144250 |
| protein encoded by oncogene 6b from agrobacterium tumefaciens has a reprogramming potential and histone chaperone-like activity. | crown gall tumors are formed mainly by actions of a group of genes in the t-dna that is transferred from agrobacterium tumefaciens and integrated into the nuclear dna of host plants. these genes encode enzymes for biosynthesis of auxin and cytokinin in plant cells. gene 6b in the t-dna affects tumor morphology and this gene alone is able to induce small tumors on certain plant species. in addition, unorganized calli are induced from leaf disks of tobacco that are incubated on phytohormone-free m ... | 2014 | 25389429 |
| development of scar primers for pcr assay to detect diplodia seriata. | the aim of this study was to develop primer pairs for diplodia seriata identification, one of the most common fungal species associated with grapevine decline in castilla y león (spain). genetic variability of selected isolates of d. seriata was estimated. a molecular marker was generated from a random amplified polymorphic dna (rapd) fragment. pcr products of around 1200 bp were obtained with ope20 primer. the pcr products were cloned and sequenced. the sequences were compared and a fragment of ... | 2014 | 27437468 |
| reduction in pathogen populations at grapevine wound sites is associated with the mechanism underlying the biological control of crown gall by rhizobium vitis strain ark-1. | a nonpathogenic strain of rhizobium (=agrobacterium) vitis, ark-1, limited the development of grapevine crown gall. a co-inoculation with ark-1 and the tumorigenic strain vat07-1 at a 1:1 cell ratio resulted in a higher population of ark-1 than vat07-1 in shoots without tumors, but a significantly lower population of ark-1 than vat07-1 in grapevine shoots with tumors. ark-1 began to significantly suppress the vat07-1 population 2 d after the inoculation. this result indicated that ark-1 reduced ... | 2014 | 25077443 |
| the use of fosmid metagenomic libraries in preliminary screening for various biological activities. | it is generally believed that there are many natural sources of as yet unknown bioactive compounds with a high biotechnological potential. however, the common method based on the use of cell extracts in the preliminary screening for particular molecules or activities is problematic as amounts of obtained compounds may be low, and such experiments are hardly reproducible. therefore, the aim of this work was to test whether a novel strategy to search for previously unknown biological activities ca ... | 2014 | 25048369 |
| agrobacterium tumefaciens responses to plant-derived signaling molecules. | as a special phytopathogen, agrobacterium tumefaciens infects a wide range of plant hosts and causes plant tumors also known as crown galls. the complexity of agrobacterium-plant interaction has been studied for several decades. agrobacterium pathogenicity is largely attributed to its evolved capabilities of precise recognition and response to plant-derived chemical signals. agrobacterium perceives plant-derived signals to activate its virulence genes, which are responsible for transferring and ... | 2014 | 25071805 |
| rhizobial homologs of the fatty acid transporter fadl facilitate perception of long-chain acyl-homoserine lactone signals. | quorum sensing (qs) using n-acyl homoserine lactones (ahls) as signal molecules is a common strategy used by diverse gram-negative bacteria. a widespread mechanism of ahl sensing involves binding of these molecules by cytosolic luxr-type transcriptional regulators, which requires uptake of external ahls. the outer membrane is supposed to be an efficient barrier for diffusion of long-chain ahls. here we report evidence that in sinorhizobium meliloti, sensing of ahls with acyl chains composed of 1 ... | 2014 | 25002473 |
| nopaline-type ti plasmid of agrobacterium encodes a virf-like functional f-box protein. | during agrobacterium-mediated genetic transformation of plants, several bacterial virulence (vir) proteins are translocated into the host cell to facilitate infection. one of the most important of such translocated factors is virf, an f-box protein produced by octopine strains of agrobacterium, which presumably facilitates proteasomal uncoating of the invading t-dna from its associated proteins. the presence of virf also is thought to be involved in differences in host specificity between octopi ... | 2015 | 26586289 |
| succinyl-coa synthetase: new antigen candidate of bartonella bacilliformis. | bartonella bacilliformis is the causative agent of carrion's disease, a neglected illness with mortality rates of 40-85% in the absence of treatment. the lack of a diagnostic technique to overcome misdiagnosis and treat asymptomatic carriers is of note. this study aimed to identify new b. bacilliformis antigenic candidates that could lead to a new diagnostic tool able to be implemented in endemic rural areas. | 2016 | 27627803 |
| prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks. | metabolic pathways in eubacteria and archaea often are encoded by operons and/or gene clusters (genome neighborhoods) that provide important clues for assignment of both enzyme functions and metabolic pathways. we describe a bioinformatic approach (genome neighborhood network; gnn) that enables large scale prediction of the in vitro enzymatic activities and in vivo physiological functions (metabolic pathways) of uncharacterized enzymes in protein families. we demonstrate the utility of the gnn a ... | 2014 | 24980702 |
| molecular characterization of nad+-dependent dna ligase from wolbachia endosymbiont of lymphatic filarial parasite brugia malayi. | the lymphatic filarial parasite, brugia malayi contains wolbachia endobacteria that are essential for development, viability and fertility of the parasite. therefore, wolbachial proteins have been currently seen as the potential antifilarial drug targets. nad(+)-dependent dna ligase is characterized as a promising drug target in several organisms due to its crucial, indispensable role in dna replication, recombination and dna repair. we report here the cloning, expression and purification of nad ... | 2012 | 22815933 |
| escherichia coli d-malate dehydrogenase, a generalist enzyme active in the leucine biosynthesis pathway. | the enzymes of the β-decarboxylating dehydrogenase superfamily catalyze the oxidative decarboxylation of d-malate-based substrates with various specificities. here, we show that, in addition to its natural function affording bacterial growth on d-malate as a carbon source, the d-malate dehydrogenase of escherichia coli (ecdmla) naturally expressed from its chromosomal gene is capable of complementing leucine auxotrophy in a leub(-) strain lacking the paralogous isopropylmalate dehydrogenase enzy ... | 2014 | 25160617 |
| advancing the development of glycated protein biosensing technology: next-generation sensing molecules. | research advances in biochemical molecules have led to the development of convenient and reproducible biosensing molecules for glycated proteins, such as those based on the enzymes fructosyl amino acid oxidase (faox) or fructosyl peptide oxidase (fpox). recently, more attractive biosensing molecules with potential applications in next-generation biosensing of glycated proteins have been aggressively reported. we review 2 such molecules, fructosamine 6-kinase (fn6k) and fructosyl amino acid-bindi ... | 2015 | 25627465 |
| isolation of a gene responsible for the oxidation of trans-anethole to para-anisaldehyde by pseudomonas putida jyr-1 and its expression in escherichia coli. | a plasmid, pta163, in escherichia coli contained an approximately 34-kb gene fragment from pseudomonas putida jyr-1 that included the genes responsible for the metabolism of trans-anethole to protocatechuic acid. three tn5-disrupted open reading frame 10 (orf 10) mutants of plasmid pta163 lost their abilities to catalyze trans-anethole. heterologously expressed orf 10 (1,047 nucleotides [nt]) under a t7 promoter in e. coli catalyzed oxidative cleavage of a propenyl group of trans-anethole to an ... | 2012 | 22610435 |
| disruption of gene pqqa or pqqb reduces plant growth promotion activity and biocontrol of crown gall disease by rahnella aquatilis hx2. | rahnella aquatilis strain hx2 has the ability to promote maize growth and suppress sunflower crown gall disease caused by agrobacterium vitis, a. tumefaciens, and a. rhizogenes. pyrroloquinoline quinone (pqq), a cofactor of aldose and alcohol dehydrogenases, is required for the synthesis of an antibacterial substance, gluconic acid, by hx2. mutants of hx2 unable to produce pqq were obtained by in-frame deletion of either the pqqa or pqqb gene. in this study, we report the independent functions o ... | 2014 | 25502691 |
| conventional and real-time pcrs for detection of erwinia piriflorinigrans allow its distinction from the fire blight pathogen, erwinia amylovora. | erwinia piriflorinigrans is a new pathogenic species of the bacterial genus erwinia that has been described recently in spain. accurate detection and identification of e. piriflorinigrans are challenging because its symptoms on pear blossoms are similar to those caused by erwinia amylovora, the causal agent of fire blight. moreover, these two species share phenotypic and molecular characteristics. two specific and sensitive conventional and real-time pcr protocols were developed to identify and ... | 2014 | 24509928 |
| whole-genome sequence and annotation of octopine-utilizing pseudomonas kilonensis (previously p. fluorescens) strain 1855-344. | here, we report the whole-genome sequence and annotation of pseudomonas kilonensis 1855-344 (previously known as p. fluorescens 1855-344). the genome contains an octopine oxidase gene cluster consistent with the ability to utilize octopine. a biosynthetic gene cluster was identified for mangotoxin and aryl-polyene using the antismash server. | 2015 | 25977435 |
| algae-bacteria association inferred by 16s rdna similarity in established microalgae cultures. | forty cultivable, visually distinct bacterial cultures were isolated from four baltic microalgal cultures chlorella pyrenoidosa, scenedesmus obliquus, isochrysis sp., and nitzschia microcephala, which have been maintained for several years in the laboratory. bacterial isolates were characterized with respect to morphology, antibiotic susceptibility, and 16s ribosomal dna sequence. a total of 17 unique bacterial strains, almost all belonging to one of three families, rhodobacteraceae, rhizobiacea ... | 2014 | 24799387 |
| genomic characterization of ensifer aridi, a proposed new species of nitrogen-fixing rhizobium recovered from asian, african and american deserts. | nitrogen fixing bacteria isolated from hot arid areas in asia, africa and america but from diverse leguminous plants have been recently identified as belonging to a possible new species of ensifer (sinorhizobium). in this study, 6 strains belonging to this new clade were compared with ensifer species at the genome-wide level. their capacities to utilize various carbon sources and to establish a symbiotic interaction with several leguminous plants were examined. | 2017 | 28088165 |
| the repabc plasmids with quorum-regulated transfer systems in members of the rhizobiales divide into two structurally and separately evolving groups. | the large repabc plasmids of the order rhizobiales with class i quorum-regulated conjugative transfer systems often define the nature of the bacterium that harbors them. these otherwise diverse plasmids contain a core of highly conserved genes for replication and conjugation raising the question of their evolutionary relationships. in an analysis of 18 such plasmids these elements fall into two organizational classes, group i and group ii, based on the sites at which cargo dna is located. cladog ... | 2015 | 26590210 |
| molecular and phenotypic characterization of agrobacterium species from vineyards allows identification of typical agrobacterium vitis and atypical biovar 1 strains. | to molecularly and phenotypically characterize a selection of agrobacterium-like isolates from grapevine canes, crowns, soil and tumours in plants grown under cold conditions. | 2015 | 25752332 |
| chemical composition and antibacterial activity of methanolic extract and essential oil of iranian teucrium polium against some of phytobacteria. | the antibacterial activity of essential oil and methanolic extract of teucrium polium was determined against pseudomonas aeruginosa, pantoea agglomerans, brenneria nigrifluens, rhizobium radiobacter, rhizobium vitis, streptomyces scabies, ralstonia solanacearum, xanthomonas campestris and pectobacterium cartovorum by disc diffusion method. minimum inhibitory concentration and minimum bactericidal concentration were determined by using the serial dilution method. chemical composition of essential ... | 2015 | 25583240 |
| silencing agrobacterium oncogenes in transgenic grapevine results in strain-specific crown gall resistance. | grapevine rootstock transformed with an agrobacterium oncogene-silencing transgene was resistant to certain agrobacterium strains but sensitive to others. thus, genetic diversity of agrobacterium oncogenes may limit engineering crown gall resistance. | 2013 | 23903949 |
| rhizobium oryziradicis sp. nov., isolated from the root of rice. | two gram-negative, aerobic, rod-shaped endophytic bacterial strains, n19t and n11-2, were isolated from fresh rice (oryza sativa) root during investigating the rice endophytic bacterial diversity. the 16s rrna gene sequence results indicated that the similarity between strains n19t and n11-2 was 100 %. both of them phylogenetically belong to the genus rhizobium, with close similarity to rhizobium taibaishanense ccnwsx 0483t (97.7 %), followed by rhizobium vitis ncppb 3554t (97.5 %). the sequence ... | 2016 | 27959784 |
| 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 ... | 2011 | 21876676 |
| illumina-based analysis of microbial community diversity. | microbes commonly exist in milieus of varying complexity and diversity. although cultivation-based techniques have been unable to accurately capture the true diversity within microbial communities, these deficiencies have been overcome by applying molecular approaches that target the universally conserved 16s ribosomal rna gene. the recent application of 454 pyrosequencing to simultaneously sequence thousands of 16s rdna sequences (pyrotags) has revolutionized the characterization of complex mic ... | 2011 | 21677692 |
| illumina-based analysis of microbial community diversity. | microbes commonly exist in milieus of varying complexity and diversity. although cultivation-based techniques have been unable to accurately capture the true diversity within microbial communities, these deficiencies have been overcome by applying molecular approaches that target the universally conserved 16s ribosomal rna gene. the recent application of 454 pyrosequencing to simultaneously sequence thousands of 16s rdna sequences (pyrotags) has revolutionized the characterization of complex mic ... | 2011 | 21677692 |
| identification of tissue-specific, abiotic stress-responsive gene expression patterns in wine grape (vitis vinifera l.) based on curation and mining of large-scale est data sets. | abiotic stresses, such as water deficit and soil salinity, result in changes in physiology, nutrient use, and vegetative growth in vines, and ultimately, yield and flavor in berries of wine grape, vitis vinifera l. large-scale expressed sequence tags (ests) were generated, curated, and analyzed to identify major genetic determinants responsible for stress-adaptive responses. although roots serve as the first site of perception and/or injury for many types of abiotic stress, est sequencing in roo ... | 2011 | 21592389 |
| role of trehalose in heat and desiccation tolerance in the soil bacterium rhizobium etli. | the compatible solute trehalose is involved in the osmostress response of rhizobium etli, the microsymbiont of phaseolus vulgaris. in this work, we reconstructed trehalose metabolism in r. etli, and investigated its role in cellular adaptation and survival to heat and desiccation stress under free living conditions. | 2012 | 22985230 |
| genome sequence of novosphingobium sp. strain rr 2-17, a nopaline crown gall-associated bacterium isolated from vitis vinifera l. grapevine. | novosphingobium sp. strain rr 2-17 is an n-acyl homoserine lactone (ahl)-producing bacterium isolated from the crown gall tumor of a grapevine. to our knowledge, this is the first draft genome announcement of a plant-associated strain from the genus novosphingobium. | 2012 | 22933764 |
| unusual long-chain n-acyl homoserine lactone production by and presence of quorum quenching activity in bacterial isolates from diseased tilapia fish. | growth-dependent cell-cell communication termed quorum sensing is a key regulatory system in bacteria for controlling gene expression including virulence factors. in this study five potential bacterial pathogens including bacillus sp. w2.2, klebsiella sp. w4.2, pseudomonas sp. w3 and w3.1 and serratia sp. w2.3 were isolated from diseased tilapia fish in malaysia, supplied by the leading global fish supplier. proteolytic activity assays confirmed that with the exception of klebsiella sp. w4.2, al ... | 2012 | 22952864 |
| grapevine rootstock effects on scion sap phenolic levels, resistance to xylella fastidiosa infection, and progression of pierce's disease. | the xylem-limited bacterium xylella fastidiosa (xf) causes pierce's disease (pd), an important disease of grapevine, vitis vinifera l. grapevine rootstocks were developed to provide increased resistance to root disease, but rootstock effects on cane and vine diseases remain unclear. grapevines that consisted of cabernet sauvignon or chardonnay grafted to 13 different rootstocks were inoculated with xf and evaluated for pd severity and xf titer after 6 months. a subset of six rootstock/scion comb ... | 2013 | 24376452 |
| structure-guided discovery of new deaminase enzymes. | a substantial challenge for genomic enzymology is the reliable annotation for proteins of unknown function. described here is an interrogation of uncharacterized enzymes from the amidohydrolase superfamily using a structure-guided approach that integrates bioinformatics, computational biology, and molecular enzymology. previously, tm0936 from thermotoga maritima was shown to catalyze the deamination of s-adenosylhomocysteine (sah) to s-inosylhomocysteine (sih). homologues of tm0936 homologues we ... | 2013 | 23968233 |
| crystal structures of malonyl-coenzyme a decarboxylase provide insights into its catalytic mechanism and disease-causing mutations. | malonyl-coenzyme a decarboxylase (mcd) is found from bacteria to humans, has important roles in regulating fatty acid metabolism and food intake, and is an attractive target for drug discovery. we report here four crystal structures of mcd from human, rhodopseudomonas palustris, agrobacterium vitis, and cupriavidus metallidurans at up to 2.3 å resolution. the mcd monomer contains an n-terminal helical domain involved in oligomerization and a c-terminal catalytic domain. the four structures exhib ... | 2013 | 23791943 |
| biological control of crown gall on grapevine and root colonization by nonpathogenic rhizobium vitis strain ark-1. | a nonpathogenic strain of rhizobium vitis ark-1 was tested as a biological control agent for grapevine crown gall. when grapevine roots were soaked in a cell suspension of strain ark-1 before planting in the field, the number of plants with tumors was reduced. the results from seven field trials from 2009 to 2012 were combined in a meta-analysis. the integrated relative risk after treatment with ark-1 was 0.15 (95% confidence interval: 0.07-0.29, p<symbol></symbol>0.001), indicating that the dis ... | 2013 | 23708779 |
| genetic relatedness and recombination analysis of allorhizobium vitis strains associated with grapevine crown gall outbreaks in europe. | to analyse genetic diversity and epidemiological relationships among 54 strains of allorhizobium vitis isolated in europe during an 8-year period and to assess the relative contribution of mutation and recombination in shaping their diversity. | 2015 | 26032990 |
| the calcium-stimulated lipid a 3-o deacylase from rhizobium etli is not essential for plant nodulation. | the lipid a component of lipopolysaccharide from the nitrogen-fixing plant endosymbiont, rhizobium etli, is structurally very different from that found in most enteric bacteria. the lipid a from free-living r. etli is structurally heterogeneous and exists as a mixture of species which are either pentaacylated or tetraacylated. in contrast, the lipid a from r. etli bacteroids is reported to consist exclusively of tetraacylated lipid a species. the tetraacylated lipid a species in both cases lack ... | 2013 | 23583844 |
| polyketide synthase gene diversity within the microbiome of the sponge arenosclera brasiliensis, endemic to the southern atlantic ocean. | microbes associated with marine sponges are considered important producers of bioactive, structurally unique polyketides. the synthesis of such secondary metabolites involves type i polyketide synthases (pkss), which are enzymes that reach a maximum complexity degree in bacteria. the haplosclerida sponge arenosclera brasiliensis hosts a complex microbiota and is the source of arenosclerins, alkaloids with cytotoxic and antibacterial activity. in the present investigation, we performed high-throu ... | 2013 | 23275501 |
| insights into the activity and substrate binding of xylella fastidiosa polygalacturonase by modification of a unique qmk amino acid motif using protein chimeras. | polygalacturonases (ec 3.2.1.15) catalyze the random hydrolysis of 1, 4-alpha-d-galactosiduronic linkages in pectate and other galacturonans. xylella fastidiosa possesses a single polygalacturonase gene, pgla (pd1485), and x. fastidiosa mutants deficient in the production of polygalacturonase are non-pathogenic and show a compromised ability to systemically infect grapevines. these results suggested that grapevines expressing sufficient amounts of an inhibitor of x. fastidiosa polygalacturonase ... | 2015 | 26571265 |
| nitrite-oxidizing bacterium nitrobacter winogradskyi produces n-acyl-homoserine lactone autoinducers. | nitrobacter winogradskyi is a chemolithotrophic bacterium that plays a role in the nitrogen cycle by oxidizing nitrite to nitrate. here, we demonstrate a functional n-acyl-homoserine lactone (acyl-hsl) synthase in this bacterium. the n. winogradskyi genome contains genes encoding a putative acyl-hsl autoinducer synthase (nwi0626, nwii) and a putative acyl-hsl autoinducer receptor (nwi0627, nwir) with amino acid sequences 38 to 78% identical to those in rhodopseudomonas palustris and other rhizob ... | 2015 | 26092466 |
| characterization of leaf blade- and leaf sheath-associated bacterial communities and assessment of their responses to environmental changes in co₂, temperature, and nitrogen levels under field conditions. | rice shoot-associated bacterial communities at the panicle initiation stage were characterized and their responses to elevated surface water-soil temperature (et), low nitrogen (ln), and free-air co2 enrichment (face) were assessed by clone library analyses of the 16s rrna gene. principal coordinate analyses combining all sequence data for leaf blade- and leaf sheath-associated bacteria revealed that each bacterial community had a distinct structure, as supported by pc1 (61.5%), that was mainly ... | 2015 | 25740174 |
| profiling of disease-related metabolites in grapevine internode tissues infected with agrobacterium vitis. | green shoot cuttings of 10 different grapevine species were inoculated with agrobacterium vitis to find disease-related metabolites in the grapevine. crown galls formed 60 days after inoculation varied in gall severity (gs) evaluated by gall incidence (gi) and gall diameter (gd), which were classified into three response types as rr (low gi and small gd), sr (high gi and small gd), and ss (high gi and large gd), corresponding to resistant, moderately resistant, and susceptible responses, respect ... | 2016 | 27904455 |
| genome-wide analyses of chitin synthases identify horizontal gene transfers towards bacteria and allow a robust and unifying classification into fungi. | chitin, the second most abundant biopolymer on earth after cellulose, is found in probably all fungi, many animals (mainly invertebrates), several protists and a few algae, playing an essential role in the development of many of them. this polysaccharide is produced by type 2 glycosyltransferases, called chitin synthases (chs). there are several contradictory classifications of chs isoenzymes and, as regards their evolutionary history, their origin and diversity is still a matter of debate. | 2016 | 27881071 |
| the absence of the n-acyl-homoserine-lactone autoinducer synthase genes trai and ngri increases the copy number of the symbiotic plasmid in sinorhizobium fredii ngr234. | plant-released flavonoids induce the transcription of symbiotic genes in rhizobia and one of the first bacterial responses is the synthesis of so called nod factors. they are responsible for the initial root hair curling during onset of root nodule development. this signal exchange is believed to be essential for initiating the plant symbiosis with rhizobia affiliated with the alphaproteobacteria. here, we provide evidence that in the broad host range strain sinorhizobium fredii ngr234 the compl ... | 2016 | 27917168 |
| leaf treatments with a protein-based resistance inducer partially modify phyllosphere microbial communities of grapevine. | protein derivatives and carbohydrates can stimulate plant growth, increase stress tolerance, and activate plant defense mechanisms. however, these molecules can also act as a nutritional substrate for microbial communities living on the plant phyllosphere and possibly affect their biocontrol activity against pathogens. we investigated the mechanisms of action of a protein derivative (nutrient broth, nb) against grapevine downy mildew, specifically focusing on the effects of foliar treatments on ... | 2016 | 27486468 |
| characterization of an indole-3-acetamide hydrolase from alcaligenes faecalis subsp. parafaecalis and its application in efficient preparation of both enantiomers of chiral building block 2,3-dihydro-1,4-benzodioxin-2-carboxylic acid. | both the enantiomers of 2,3-dihydro-1,4-benzodioxin-2-carboxylic acid are valuable chiral synthons for enantiospecific synthesis of therapeutic agents such as (s)-doxazosin mesylate, wb 4101, mkc 242, 2,3-dihydro-2-hydroxymethyl-1,4-benzodioxin, and n-[2,4-oxo-1,3-thiazolidin-3-yl]-2,3-dihydro-1,4-benzodioxin-2-carboxamide. pharmaceutical applications require these enantiomers in optically pure form. however, currently available methods suffer from one drawback or other, such as low efficiency, ... | 2016 | 27391673 |
| grapevine pathogenic microorganisms: understanding infection strategies and host response scenarios. | grapevine (vitis vinifera l.) is one of the most important fruit crop worldwide. commercial cultivars are greatly affected by a large number of pathogenic microorganisms that cause diseases during pre- and/or post-harvest periods, affecting production, processing and export, along with fruit quality. among the potential threats, we can find bacteria, fungi, oomycete, or viruses with different life cycles, infection mechanisms and evasion strategies. while plant-pathogen interactions are cycles o ... | 2016 | 27066032 |
| bacterial associations across house fly life history: evidence for transstadial carriage from managed manure. | house flies (diptera: muscidae; musca domestica l.) associate with microbe-rich substrates throughout life history. because larvae utilize bacteria as a food source, most taxa present in the larval substrate, e.g., manure, are digested or degraded. however, some species survive and are present as third-instar larvae begin pupation. during metamorphosis, many bacteria are again lost during histolysis of the larval gut and subsequent remodeling to produce the gut of the imago. it has been previous ... | 2016 | 26798138 |
| phylogeny of the rhizobium-allorhizobium-agrobacterium clade supports the delineation of neorhizobium gen. nov. | the genera agrobacterium, allorhizobium, and rhizobium belong to the family rhizobiaceae. however, the placement of a phytopathogenic group of bacteria, the genus agrobacterium, among the nitrogen-fixing bacteria and the unclear position of rhizobium galegae have caused controversy in previous taxonomic studies. to resolve uncertainties in the taxonomy and nomenclature within this family, the phylogenetic relationships of generic members of rhizobiaceae were studied, but with particular emphasis ... | 2014 | 24581678 |
| grapevine (vitis vinifera) crown galls host distinct microbiota. | crown gall disease of grapevine is caused by virulent agrobacterium strains and establishes a suitable habitat for agrobacteria and, potentially, other bacteria. the microbial community associated with grapevine plants has not been investigated with respect to this disease, which frequently results in monetary losses. this study compares the endophytic microbiota of organs from grapevine plants with or without crown gall disease and the surrounding vineyard soil over the growing seasons of 1 yea ... | 2016 | 27371584 |
| structure of an abc transporter solute-binding protein specific for the amino sugars glucosamine and galactosamine. | the uptake of exogenous solutes by prokaryotes is mediated by transport systems embedded in the plasma membrane. in many cases, a solute-binding protein (sbp) is utilized to bind ligands with high affinity and deliver them to the membrane-bound components responsible for translocation into the cytoplasm. in the present study, avi_5305, an agrobacterium vitis sbp belonging to pfam13407, was screened by differential scanning fluorimetry (dsf) and found to be stabilized by d-glucosamine and d-galac ... | 2016 | 27303900 |
| inhibition of grape crown gall by agrobacterium vitis f2/5 requires two nonribosomal peptide synthetases and one polyketide synthase. | agrobacterium vitis nontumorigenic strain f2/5 is able to inhibit crown gall disease on grapevines. the mechanism of grape tumor inhibition (gti) by f2/5 has not been fully determined. in this study, we demonstrate that two nonribosomal peptide synthetase (nrps) genes (f-avi3342 and f-avi5730) and one polyketide synthase gene (f-avi4330) are required for gti. knockout of any one of them resulted in f/25 losing gti capacity. we previously reported that f-avi3342 and f-avi4330 but not f-avi5730 ar ... | 2016 | 26575143 |
| screening bactericidal effect of pectobacterium carotovorum subsp. carotovorum strains against causal agent of potato soft rot. | this study focuses on the potential of pectobacterium carotovorum subsp. carotovorum (pcc) strains producing bacteriocin as a tool to control potato soft rot disease. thirty out of 48 purified bacterial strains were characterized as pcc using specific pcr and phenotypic tests. the pathogenicity and pectate degrading assays were recorded positive for 13 strains. bacteriocin typing clustered producers into three groups according to their antimicrobial spectra. majority of the producers except stra ... | 2016 | 26523939 |
| a phage display-selected peptide inhibitor of agrobacterium vitis polygalacturonase. | agrobacterium vitis, the causal agent of crown gall of grapevine, is a threat to viticulture worldwide. a major virulence factor of this pathogen is polygalacturonase, an enzyme that degrades pectin components of the xylem cell wall. a single gene encodes for the polygalacturonase gene. disruption of the polygalacturonase gene results in a mutant that is less pathogenic and produces significantly fewer root lesions on grapevines. thus, the identification of peptides or proteins that could inhibi ... | 2016 | 26177065 |
| [detection of pathogenic bacteria rhizobium vitis in vineyards of the south of ukraine]. | the total number of microbiota from grape crown gall tissues ranged from (2,3 ± 0.8) x 10(3) to (7.3 ± 0.4) x 10(5) cfu/g. the amount of bacteria from rhizobium genus reached from (1.2 ±0.2) x 10(2) to (2.1 ± 0.2) x 10(4) cfu/g depending on a tested plant. it was found out that only a small percentage of the strains (3.1 - 4.9%) were oncogenic. new pathogenic strains (r. vitis onu388, r. vitis onu389 and r. vitis onu390) possessing plasmid genes of pathogenicity virc, ipt and vird2 were isolated ... | 2015 | 26036030 |
| characterization of a new pathovar of agrobacterium vitis causing banana leaf blight in china. | a new banana leaf blight was found in nanning city, china, during a 7-year survey (2003-2009) of the bacterial diseases on banana plants. eight bacterial strains were isolated from affected banana leaves, and identified as an intraspecific taxon of agrobacterium vitis based on their 16s rdna sequence similarities with those of 37 randomly selected bacterial strains registered in genbank database. the representative strain ag-1 was virulent on banana leaves and shared similar growth and biochemic ... | 2015 | 23828501 |
| an sfp-type pptase and associated polyketide and nonribosomal peptide synthases in agrobacterium vitis are essential for induction of tobacco hypersensitive response and grape necrosis. | an sfp-type phosphopantetheinyl transferase (pptase) encoding gene f-avi5813 in agrobacterium vitis f2/5 was found to be required for the induction of a tobacco hypersensitive response (hr) and grape necrosis. sfp-type pptases are post-translation modification enzymes that activate acyl-carry protein (acp) domains in polyketide synthases (pks) and peptidyl-carrier protein (pcp) domains of nonribosomal peptide synthases (nrps). mutagenesis of pks and nrps genes in a. vitis led to the identificati ... | 2013 | 23581823 |
| development of a magnetic capture hybridization real-time pcr assay for detection of tumorigenic agrobacterium vitis in grapevines. | agrobacterium vitis, the causal agent of grape crown gall, can have severe economic effects on grape production. the bacterium survives systemically in vines and, therefore, is disseminated in propagation material. we developed an assay for use in indexing programs that is efficient and sensitive for detecting a. vitis in grape tissue. initially, real-time polymerase chain reaction (pcr) primers specific for diverse tumorigenic strains of a. vitis were developed using the vird2 gene sequence. to ... | 2013 | 23324046 |
| a host-specific biological control of grape crown gall by agrobacterium vitis strain f2/5: its regulation and population dynamics. | nontumorigenic agrobacterium vitis strain f2/5 is able to prevent crown gall caused by tumorigenic a. vitis on grape but not on other plant species such as tobacco. mutations in a quorum-sensing transcription factor, avir, and in caseinolytic protease (clp) component genes clpa and clpp1 resulted in reduced or loss of biological control. all mutants were complemented; however, restoration of biological control by complemented clpa and clpp1 mutants was dependent on the copy number of vector that ... | 2013 | 23252969 |
| a transient expression assay for the in planta efficacy screening of an antimicrobial peptide against grapevine bacterial pathogens. | natural and synthetic antimicrobial peptides (amps) are of increasing interest as potential resistance conferring elements in plants against pathogen infection. the efficacy of amps against pathogens is prescreened by in vitro assays, and promising amp candidates are introduced as transgenes into plants. as in vitro and in planta environments differ, a prescreening procedure of the amp efficacy in the plant environment is desired. here, we report the efficacy of the purified synthetic peptide d4 ... | 2012 | 22435990 |
| modification of a bi-functional diguanylate cyclase-phosphodiesterase to efficiently produce cyclic diguanylate monophosphate. | cyclic-digmp is a bacterial messenger that regulates many physiological processes, including many attributed to pathogenicity. bacteria synthesize cyclic-digmp from gtp using diguanylate cyclases; its hydrolysis is catalyzed by phosphodiesterases. here we report the over-expression and purification of a bi-functional diguanylate cyclase-phosphodiesterase from agrobacterium vitis s4. using homology modeling and primary structure alignment, we identify several amino acids predicted to participate ... | 2015 | 28626712 |
| revised phylogeny of rhizobiaceae: proposal of the delineation of pararhizobium gen. nov., and 13 new species combinations. | the family rhizobiaceae accommodates the seven genera rhizobium, neorhizobium, allorhizobium, agrobacterium, ensifer (syn. sinorhizobium), shinella and ciceribacter. however, several so-called rhizobium species do not exhibit robust phylogenetic positions. rhizobium is extremely heterogeneous and is in need of major revision. therefore, a phylogenetic examination of the family rhizobiaceae by multilocus sequence analysis (mlsa) of four housekeeping genes among 100 strains of the family was under ... | 2015 | 25595870 |