| bacteria are not what they eat: that is why they are so diverse. | | 2000 | 10629168 |
| medium- and short-chain dehydrogenase/reductase gene and protein families : the sdr superfamily: functional and structural diversity within a family of metabolic and regulatory enzymes. | short-chain dehydrogenases/reductases (sdrs) constitute a large family of nad(p)(h)-dependent oxidoreductases, sharing sequence motifs and displaying similar mechanisms. sdr enzymes have critical roles in lipid, amino acid, carbohydrate, cofactor, hormone and xenobiotic metabolism as well as in redox sensor mechanisms. sequence identities are low, and the most conserved feature is an alpha/beta folding pattern with a central beta sheet flanked by 2 - 3 alpha-helices from each side, thus a classi ... | 2008 | 19011750 |
| corepression of the p1 addiction operon by phd and doc. | the p1 plasmid addiction operon encodes doc, a toxin that kills plasmid-free segregants, and phd, an unstable antidote that neutralizes the toxin. additionally, these products repress transcription of the operon. the antidote binds to two adjacent sites in the promoter. here we present evidence concerning the regulatory role of the toxin, which we studied with the aid of a mutation, doch66y. the doch66y protein retained the regulatory properties of the wild-type protein, but not its toxicity. in ... | 1998 | 9829946 |
| two-component signal transduction as a target for microbial anti-infective therapy. | | 1998 | 9660978 |
| molecular and biochemical characterization of cytosolic phosphoglucomutase in maize. expression during development and in response to oxygen deprivation. | phosphoglucomutase (pgm) catalyzes the interconversion of glucose (glc)-1- and glc-6-phosphate in the synthesis and consumption of sucrose. we isolated two maize (zea mays l.) cdnas that encode pgm with 98.5% identity in their deduced amino acid sequence. southern-blot analysis with genomic dna from lines with different pgm1 and pgm2 genotypes suggested that the cdnas encode the two known cytosolic pgm isozymes, pgm1 and pgm2. the cytosolic pgms of maize are distinct from a plastidic pgm of spin ... | 1998 | 9662542 |
| production of acylated homoserine lactones by psychrotrophic members of the enterobacteriaceae isolated from foods. | bacteria are able to communicate and gene regulation can be mediated through the production of acylated homoserine lactone (ahl) signal molecules. these signals play important roles in several pathogenic and symbiotic bacteria. the following study was undertaken to investigate whether ahls are produced by bacteria found in food at temperatures and nacl conditions commercially used for food preservation and storage. a minimum of 116 of 154 psychrotrophic enterobacteriaceae strains isolated from c ... | 1999 | 10427034 |
| the arcelin-5 gene of phaseolus vulgaris directs high seed-specific expression in transgenic phaseolus acutifolius and arabidopsis plants. | the regulatory sequences of many genes encoding seed storage proteins have been used to drive seed-specific expression of a variety of proteins in transgenic plants. because the levels at which these transgene-derived proteins accumulate are generally quite low, we investigated the utility of the arcelin-5 regulatory sequences in obtaining high seed-specific expression in transgenic plants. arcelin-5 is an abundant seed protein found in some wild common bean (phaseolus vulgaris l.) genotypes. se ... | 1999 | 10444093 |
| genetic evidence for the role of gdp-mannose in plant ascorbic acid (vitamin c) biosynthesis. | vitamin c (l-ascorbic acid; asa) acts as a potent antioxidant and cellular reductant in plants and animals. asa has long been known to have many critical physiological roles in plants, yet its biosynthesis is only currently being defined. a pathway for asa biosynthesis that features gdp-mannose and l-galactose has recently been proposed for plants. we have isolated a collection of asa-deficient mutants of arabidopsis thaliana that are valuable tools for testing of an asa biosynthetic pathway. th ... | 1999 | 10097187 |
| the bacterial elicitor flagellin activates its receptor in tomato cells according to the address-message concept. | flg22, a peptide corresponding to the most conserved domain of bacterial flagellin, acts as a potent elicitor in plants. here, we have used an iodinated derivative of flg22 ((125)i-labeled tyr-flg22) as a molecular probe for the flagellin receptor in tomato cells. this radioligand showed rapid binding to a single class of specific, saturable, high-affinity receptor sites in intact cells and membrane preparations. binding, although essentially nonreversible under physiological conditions, was not ... | 2000 | 11006347 |
| bacterial quorum sensing in pathogenic relationships. | | 2000 | 10948095 |
| bacterial growth stimulation with exogenous siderophore and synthetic n-acyl homoserine lactone autoinducers under iron-limited and low-nutrient conditions. | the growth of marine bacteria under iron-limited conditions was investigated. neither siderophore production nor bacterial growth was detected for pelagiobacter sp. strain v0110 when fe(iii) was present in the culture medium at a concentration of <1.0 microm. however, the growth of v0110 was strongly stimulated by the presence of trace amounts of exogenous siderophore from an alpha proteobacterium, v0902, and 1 nm n-acyl-octanoylhomoserine lactone (c(8)-hsl), which is known as a quorum-sensing c ... | 2000 | 10877770 |
| how novel methods can help discover more information about foodborne pathogens. | considerable emphasis is being placed on quantitative risk assessment modelling as a basis for regulation of trade in food products. however, for models to be accurate, information about the behaviour of potential pathogens in foods needs to be available. the question is how to obtain this knowledge in a simple and cost effective way. one technique that has great potential is the use of reporter bacteria which have been genetically modified to express a phenotype that can be easily monitored, su ... | 2000 | 18159282 |
| rapid screening technique for class 1 integrons in enterobacteriaceae and nonfermenting gram-negative bacteria and its use in molecular epidemiology. | a screening technique for integrons in members of the family enterobacteriaceae and nonfermenting gram-negative bacteria by real-time pcr is reported. a total of 226 isolates of gram-negative bacteria obtained from a variety of clinical specimens were screened for class 1 integrons by real-time pcr performed on a lightcycler instrument. this technique used a primer pair specific for a 300-bp conserved region at the 5' ends of class 1 integrons. the screening assay was evaluated by comparison wit ... | 2001 | 11257011 |
| seasonal changes in the rhizosphere microbial communities associated with field-grown genetically modified canola (brassica napus). | the introduction of transgenic plants into agricultural ecosystems has raised the question of the ecological impact of these plants on nontarget organisms, such as soil bacteria. although differences in both the genetic structure and the metabolic function of the microbial communities associated with some transgenic plant lines have been established, it remains to be seen whether these differences have an ecological impact on the soil microbial communities. we conducted a 2-year, multiple-site f ... | 2003 | 14660380 |
| rational genomics i: antisense open reading frames and codon bias in short-chain oxido reductase enzymes and the evolution of the genetic code. | the short-chain oxidoreductase (scor) family of enzymes includes over 6000 members, extending from bacteria and archaea to humans. nucleic acid sequence analysis reveals that significant numbers of these genes are remarkably free of stopcodons in reading frames other than the coding frame, including those on the antisense strand. the genes from this subset also use almost entirely the gc-rich half of the 64 codons. analysis of a million hypothetical genes having random nucleotide composition sho ... | 2005 | 16245321 |
| controlled clinical comparison of plastic versus glass bottles of bact/alert pf medium for culturing blood from children. | the plastic pediatric bact/alert (biomérieux, durham, n.c.) pf (ppf) is a new nonvented aerobic culture medium in a clear plastic bottle designed to prevent breakage. we compared the performance of the new ppf bottle to that of the present glass bact/alert pf bottle for the recovery of microorganisms as well as for the time to detection of growth in samples of blood obtained for culture from children. we found that the ppf and pf bottles were comparable for recovery of microorganisms and that th ... | 2005 | 15635011 |
| comparative genomics of pakd4, the prototype incp-1delta plasmid with a complete backbone. | plasmids of the incompatibility group incp-1 are important agents of horizontal gene transfer and contribute to the spread of antibiotic resistance and xenobiotic degradation within bacterial communities. even though some prototype plasmids have been studied in much detail, the diversity of this plasmid group was still greatly underestimated until recently, as only two of the five currently known divergent sub-groups had been described. to further improve our insight into the diversity and evolu ... | 2009 | 20018208 |
| validation of vitek 2 nonfermenting gram-negative cards and vitek 2 version 4.02 software for identification and antimicrobial susceptibility testing of nonfermenting gram-negative rods from patients with cystic fibrosis. | accurate identification and antimicrobial susceptibility testing (ast) of nonfermenters from cystic fibrosis patients are essential for appropriate antimicrobial treatment. this study examined the ability of the newly designed vitek 2 nonfermenting gram-negative card (ngnc) (new gram-negative identification card; biomérieux, marcy-l'etoile, france) to identify nonfermenting gram-negative rods from cystic fibrosis patients in comparison to reference methods and the accuracy of the new vitek 2 ver ... | 2009 | 19710272 |
| genomics of plant-associated microbes. | | 2009 | 21255272 |
| infectious complications associated with monoclonal antibodies and related small molecules. | biologics are increasingly becoming part of routine disease management. as more agents are developed, the challenge of keeping track of indications and side effects is growing. while biologics represent a milestone in targeted and specific therapy, they are not without drawbacks, and the judicious use of these "magic bullets" is essential if their full potential is to be realized. infectious complications in particular are not an uncommon side effect of therapy, whether as a direct consequence o ... | 2009 | 19366915 |
| future research trends in the major chemical language of bacteria. | microbiology was revolutionized in the 1990's by the discovery that many different bacterial species coordinate their behavior when they form a group. in fact, bacteria are now considered multicellular organisms capable of communicating and changing behavior in relation to their cell-density; since 1994 this has been called quorum sensing. this group behavior ensures survival and propagation of the community in many natural environments. bacterial intercellular communication is mediated by diffe ... | 2009 | 19794815 |
| in vitro antibacterial activity of cysteine protease inhibitor from kiwifruit (actinidia deliciosa). | the need for replacing traditional pesticides with alternative agents for the management of agricultural pathogens is rising worldwide. in this study, a cysteine proteinase inhibitor (cpi), 11 kda in size, was purified from green kiwifruit to homogeneity. we examined the growth inhibition of three plant pathogenic gram-negative bacterial strains by kiwi cpi and attempted to elucidate the potential mechanism of the growth inhibition. cpi influenced the growth of phytopathogenic bacteria agrobacte ... | 2012 | 24426085 |
| detection, characterization, and biological effect of quorum-sensing signaling molecules in peanut-nodulating bradyrhizobia. | bacteria of the genus bradyrhizobium are able to establish a symbiotic relationship with peanut (arachis hypogaea) root cells and to fix atmospheric nitrogen by converting it to nitrogenous compounds. quorum sensing (qs) is a cell-cell communication mechanism employed by a variety of bacterial species to coordinate behavior at a community level through regulation of gene expression. the qs process depends on bacterial production of various signaling molecules, among which the n-acylhomoserine la ... | 2012 | 22736981 |
| conformational sampling, catalysis, and evolution of the bacterial phosphotriesterase. | to efficiently catalyze a chemical reaction, enzymes are required to maintain fast rates for formation of the michaelis complex, the chemical reaction and product release. these distinct demands could be satisfied via fluctuation between different conformational substates (css) with unique configurations and catalytic properties. however, there is debate as to how these rapid conformational changes, or dynamics, exactly affect catalysis. as a model system, we have studied bacterial phosphotriest ... | 2009 | 19966226 |
| transient expression of organophosphorus hydrolase to enhance the degrading activity of tomato fruit on coumaphos. | we constructed an expression cassette of the organophosphorus pesticide degrading (opd) gene under the control of the e8 promoter. then opd was transformed into tomato fruit using an agroinfiltration transient expression system. beta-glucuronidase (gus) staining, reverse transcription-polymerase chain reaction (rt-pcr), wavelength scanning, and fluorescent reaction were performed to examine the expression of the opd gene and the hydrolysis activity on coumaphos of organophosphorus hydrolase (oph ... | 2009 | 19235273 |
| in vivo self-assembly of stable green fluorescent protein fusion particles and their uses in enzyme immobilization. | bacterial inclusion bodies are aggregations of mostly inactive and misfolded proteins. however, previously the in vivo self-assembly of green fluorescent protein (gfp) fusions into fluorescent particles which displayed specific binding sites suitable for applications in bioseparation and diagnostics was demonstrated. here, the suitability of gfp particles for enzyme immobilization was assessed. the enzymes tested were a thermostable α-amylase from bacillus licheniformis, n-acetyl-d-neuraminic ac ... | 2014 | 24610847 |
| aerobic growth on nitroglycerin as the sole carbon, nitrogen, and energy source by a mixed bacterial culture. | nitroglycerin (glycerol trinitrate [gtn]), an explosive and vasodilatory compound, was metabolized by mixed microbial cultures from aeration tank sludge previously exposed to gtn. aerobic enrichment cultures removed gtn rapidly in the absence of a supplemental carbon source. complete denitration of gtn, provided as the sole c and n source, was observed in aerobic batch cultures and proceeded stepwise via the dinitrate and mononitrate isomers, with successive steps occurring at lower rates. the d ... | 1998 | 9726874 |
| analysis of biolog gn substrate utilization patterns by microbial communities. | biolog gn plates are increasingly used to characterize microbial communities by determining the ability of the communities to oxidize various carbon sources. studies were done to determine whether the biolog gn plate assay accurately reflects the catabolic potential of the inoculum used. to gain insight into which populations of microbial communities contribute to the biolog patterns, denaturing gradient gel electrophoresis and temperature gradient gel electrophoresis (tgge) were used to assess ... | 1998 | 16349535 |
| jasmonic acid signaling modulates ozone-induced hypersensitive cell death. | recent studies suggest that cross-talk between salicylic acid (sa)-, jasmonic acid (ja)-, and ethylene-dependent signaling pathways regulates plant responses to both abiotic and biotic stress factors. earlier studies demonstrated that ozone (o(3)) exposure activates a hypersensitive response (hr)-like cell death pathway in the arabidopsis ecotype cvi-0. we now have confirmed the role of sa and ja signaling in influencing o(3)-induced cell death. expression of salicylate hydroxylase (nahg) in cvi ... | 2000 | 11006337 |
| naphthalene and donor cell density influence field conjugation of naphthalene catabolism plasmids. | we examined transfer of naphthalene-catabolic genes from donor microorganisms native to a contaminated site to site-derived, rifampin-resistant recipient bacteria unable to grow on naphthalene. horizontal gene transfer (hgt) was demonstrated in filter matings using groundwater microorganisms as donors. two distinct but similar plasmid types, closely related to pdtg1, were retrieved. in laboratory-incubated sediment matings, the addition of naphthalene stimulated hgt. however, recipient bacteria ... | 2000 | 10877811 |
| cell wall and membrane-associated exo-beta-d-glucanases from developing maize seedlings. | a beta-d-glucan exohydrolase was purified from the cell walls of developing maize (zea mays l.) shoots. the cell wall enzyme preferentially hydrolyzes the non-reducing terminal glucosyl residue from (1-->3)-beta-d-glucans, but also hydrolyzes (1-->2)-, (1-->6)-, and (1-->4)-beta-d-glucosyl units in decreasing order of activity. polyclonal antisera raised against the purified exo-beta-d-glucanase (exgase) were used to select partial-length cdna clones, and the complete sequence of 622 amino acid ... | 2000 | 10859178 |
| the arabidopsis thaliana-pseudomonas syringae interaction. | | 2002 | 22303207 |
| horizontally transferred genes in plant-parasitic nematodes: a high-throughput genomic approach. | published accounts of horizontally acquired genes in plant-parasitic nematodes have not been the result of a specific search for gene transfer per se, but rather have emerged from characterization of individual genes. we present a method for a high-throughput genome screen for horizontally acquired genes, illustrated using expressed sequence tag (est) data from three species of root-knot nematode, meloidogyne species. | 2003 | 12801413 |
| a novel family of p-loop ntpases with an unusual phyletic distribution and transmembrane segments inserted within the ntpase domain. | recent sequence-structure studies on p-loop-fold ntpases have substantially advanced the existing understanding of their evolution and functional diversity. these studies provide a framework for characterization of novel lineages within this fold and prediction of their functional properties. | 2004 | 15128444 |
| growing and analyzing static biofilms. | many bacteria can exist as surface-attached aggregations known as biofilms. presented in this unit are several approaches for the study of these communities. the focus here is on static biofilm systems, which are particularly useful for examination of the early stages of biofilm formation, including initial adherence to the surface and microcolony formation. furthermore, most of the techniques presented are easily adapted to the study of biofilms under a variety of conditions and are suitable fo ... | 2005 | 18770545 |
| molecular characterization of resistance-nodulation-division transporters from solvent- and drug-resistant bacteria in petroleum-contaminated soil. | pcr assays for analyzing resistance-nodulation-division transporters from solvent- and drug-resistant bacteria in soil were developed. sequence analysis of amplicons showed that the pcr successfully retrieved transporter gene fragments from soil. most of the genes retrieved from petroleum-contaminated soils formed a cluster (cluster pcs) that was distantly related to known transporter genes. competitive pcr showed that the abundance of pcs genes is increased in petroleum-contaminated soil. | 2005 | 15640241 |
| messing with bacterial quorum sensing. | quorum sensing is widely recognized as an efficient mechanism to regulate expression of specific genes responsible for communal behavior in bacteria. several bacterial phenotypes essential for the successful establishment of symbiotic, pathogenic, or commensal relationships with eukaryotic hosts, including motility, exopolysaccharide production, biofilm formation, and toxin production, are often regulated by quorum sensing. interestingly, eukaryotes produce quorum-sensing-interfering (qsi) compo ... | 2006 | 17158701 |
| the epidermis-specific extracellular bodyguard controls cuticle development and morphogenesis in arabidopsis. | the outermost epidermal cell wall is specialized to withstand pathogens and natural stresses, and lipid-based cuticular polymers are the major barrier against incursions. the arabidopsis thaliana mutant bodyguard (bdg), which exhibits defects characteristic of the loss of cuticle structure not attributable to a lack of typical cutin monomers, unexpectedly accumulates significantly more cell wall-bound lipids and epicuticular waxes than wild-type plants. pleiotropic effects of the bdg mutation on ... | 2006 | 16415209 |
| antimicrobial activities of essential oil and methanol extract of teucrium montanum. | this study was designed to examine the chemical composition of essential oil and the in vitro antimicrobial activities of essential oil and methanol extract of teucrium montanum. the inhibitory effects of essential oil and methanol extracts of t. montanum were tested against 13 bacterial and three fungal species by using disc-diffusion method. gc/ms analyses revealed that essential oil contains mainly delta-cadinene (17.19%), beta-selinene (8.16%) alpha-calacorene (4.97%), 1,6-dimethyl-4-(1-meth ... | 2007 | 18227926 |
| native bacterial endophytes promote host growth in a species-specific manner; phytohormone manipulations do not result in common growth responses. | all plants in nature harbor a diverse community of endophytic bacteria which can positively affect host plant growth. changes in plant growth frequently reflect alterations in phytohormone homoeostasis by plant-growth-promoting (pgp) rhizobacteria which can decrease ethylene (et) levels enzymatically by 1-aminocyclopropane-1-carboxylate (acc) deaminase or produce indole acetic acid (iaa). whether these common pgp mechanisms work similarly for different plant species has not been rigorously teste ... | 2008 | 18628963 |
| the metacyc database of metabolic pathways and enzymes and the biocyc collection of pathway/genome databases. | the metacyc database (metacyc.org) is a comprehensive and freely accessible resource for metabolic pathways and enzymes from all domains of life. the pathways in metacyc are experimentally determined, small-molecule metabolic pathways and are curated from the primary scientific literature. with more than 1400 pathways, metacyc is the largest collection of metabolic pathways currently available. pathways reactions are linked to one or more well-characterized enzymes, and both pathways and enzymes ... | 2009 | 19850718 |
| the role of microbial signals in plant growth and development. | plant growth and development involves a tight coordination of the spatial and temporal organization of cell division, cell expansion and cell differentiation. orchestration of these events requires the exchange of signaling molecules between the root and shoot, which can be affected by both biotic and abiotic factors. the interactions that occur between plants and their associated microorganisms have long been of interest, as knowledge of these processes could lead to the development of novel ag ... | 2009 | 19820333 |
| nitrilase enzymes and their role in plant-microbe interactions. | nitrilase enzymes (nitrilases) catalyse the hydrolysis of nitrile compounds to the corresponding carboxylic acid and ammonia, and have a wide range of industrial and biotechnological applications, including the synthesis of industrially important carboxylic acids and bioremediation of cyanide and toxic nitriles. nitrilases are produced by a wide range of organisms, including plants, bacteria and fungi, but despite their biotechnological importance, the role of these enzymes in living organisms i ... | 2009 | 21255276 |
| life of microbes that interact with plants. | | 2009 | 21255273 |
| signals, regulatory networks, and materials that build and break bacterial biofilms. | biofilms are communities of microorganisms that live attached to surfaces. biofilm formation has received much attention in the last decade, as it has become clear that virtually all types of bacteria can form biofilms and that this may be the preferred mode of bacterial existence in nature. our current understanding of biofilm formation is based on numerous studies of myriad bacterial species. here, we review a portion of this large body of work including the environmental signals and signaling ... | 2009 | 19487730 |
| induced resistance triggered by piriformospora indica. | | 2009 | 19721753 |
| integration of bioinformatics and synthetic promoters leads to the discovery of novel elicitor-responsive cis-regulatory sequences in arabidopsis. | a combination of bioinformatic tools, high-throughput gene expression profiles, and the use of synthetic promoters is a powerful approach to discover and evaluate novel cis-sequences in response to specific stimuli. with arabidopsis (arabidopsis thaliana) microarray data annotated to the pathoplant database, 732 different queries with a focus on fungal and oomycete pathogens were performed, leading to 510 up-regulated gene groups. using the binding site estimation suite of tools, best, 407 conse ... | 2012 | 22744985 |
| recent advances in soybean transformation and their application to molecular breeding and genomic analysis. | herbicide-resistant transgenic soybean plants hold a leading market share in the usa and other countries, but soybean has been regarded as recalcitrant to transformation for many years. the cumulative and, at times, exponential advances in genetic manipulation have made possible further choices for soybean transformation. the most widely and routinely used transformation systems are cotyledonary node-agrobacterium-mediated transformation and somatic embryo-particle-bombardment-mediated transform ... | 2012 | 23136488 |
| celr, an ortholog of the diguanylate cyclase pled of caulobacter, regulates cellulose synthesis in agrobacterium tumefaciens. | cellulose fibrils play a role in attachment of agrobacterium tumefaciens to its plant host. while the genes for cellulose biosynthesis in the bacterium have been identified, little is known concerning the regulation of the process. the signal molecule cyclic di-gmp (c-di-gmp) has been linked to the regulation of exopolysaccharide biosynthesis in many bacterial species, including a. tumefaciens. in this study, we identified two putative diguanylate cyclase genes, celr (atu1297) and atu1060, that ... | 2013 | 24038703 |
| the structure of glycerol trinitrate reductase nera from agrobacterium radiobacter reveals the molecular reason for nitro- and ene-reductase activity in oye homologues. | in recent years, old yellow enzymes (oyes) and their homologues have found broad application in the efficient asymmetric hydrogenation of activated c=c bonds with high selectivities and yields. members of this class of enzymes have been found in many different organisms and are rather diverse on the sequence level, with pairwise identities as low as 20 %, but they exhibit significant structural similarities with the adoption of a conserved (αβ)(8)-barrel fold. some oyes have been shown not only ... | 2013 | 23606302 |
| quorum sensing in some representative species of halomonadaceae. | cell-to-cell communication, or quorum-sensing (qs), systems are employed by bacteria for promoting collective behaviour within a population. an analysis to detect qs signal molecules in 43 species of the halomonadaceae family revealed that they produced n-acyl homoserine lactones (ahls), which suggests that the qs system is widespread throughout this group of bacteria. thin-layer chromatography (tlc) analysis of crude ahl extracts, using agrobacterium tumefaciens ntl4 (pzlr4) as biosensor strain ... | 2013 | 25371343 |
| inhibitory and toxic effects of volatiles emitted by strains of pseudomonas and serratia on growth and survival of selected microorganisms, caenorhabditis elegans, and drosophila melanogaster. | in previous research, volatile organic compounds (vocs) emitted by various bacteria into the chemosphere were suggested to play a significant role in the antagonistic interactions between microorganisms occupying the same ecological niche and between bacteria and target eukaryotes. moreover, a number of volatiles released by bacteria were reported to suppress quorum-sensing cell-to-cell communication in bacteria, and to stimulate plant growth. here, volatiles produced by pseudomonas and serratia ... | 2014 | 25006575 |
| gene-splitting technology: a novel approach for the containment of transgene flow in nicotiana tabacum. | the potential impact of transgene escape on the environment and food safety is a major concern to the scientists and public. this work aimed to assess the effect of intein-mediated gene splitting on containment of transgene flow. two fusion genes, epspsn-in and ic-epspsc, were constructed and integrated into n. tabacum, using agrobacterium tumefaciens-mediated transformation. epspsn-in encodes the first 295 aa of the herbicide resistance gene 5-enolpyruvyl shikimate-3-phosphate synthase (epsps) ... | 2014 | 24915192 |
| low agrobacterium tumefaciens inoculum levels and a long co-culture period lead to reduced plant defense responses and increase transgenic shoot production of sunflower (helianthus annuus l.). | agrobacterium-mediated plant transformation is typically conducted by inoculating plant tissues with an agrobacterium suspension containing approximately 10(8)-10(9) bacteria ml(-1), followed by a 2-3-d co-culture period. use of longer co-culture periods could potentially increase transformation efficiencies by allowing more time for agrobacterium to interact with plant cells, but bacterial overgrowth is likely to occur, leading to severe tissue browning and reduced transformation and regenerati ... | 2016 | 27746666 |
| coordinated regulation of species-specific hydroxycinnamic acid degradation and siderophore biosynthesis pathways in agrobacterium fabrum. | the rhizosphere-inhabiting species agrobacterium fabrum (genomospecies g8 of the agrobacterium tumefaciens species complex) is known to degrade hydroxycinnamic acids (hcas), especially ferulic acid and p-coumaric acid, via the novel a. fabrum hca degradation pathway. gene expression profiles of a. fabrum strain c58 were investigated in the presence of hcas, using a c58 whole-genome oligoarray. both ferulic acid and p-coumaric acid caused variations in the expression of more than 10% of the c58 g ... | 2016 | 27060117 |
| microbial diversity and activity in the nematostella vectensis holobiont: insights from 16s rrna gene sequencing, isolate genomes, and a pilot-scale survey of gene expression. | we have characterized the molecular and genomic diversity of the microbiota of the starlet sea anemone nematostella vectensis, a cnidarian model for comparative developmental and functional biology and a year-round inhabitant of temperate salt marshes. molecular phylogenetic analysis of 16s rrna gene clone libraries revealed four ribotypes associated with n. vectensis at multiple locations and times. these associates include two novel ribotypes within the ε-proteobacterial order campylobacterale ... | 2015 | 26388838 |
| root-associated bacterial endophytes from ralstonia solanacearum resistant and susceptible tomato cultivars and their pathogen antagonistic effects. | this study was undertaken to assess if the root-associated native bacterial endophytes in tomato have any bearing in governing the host resistance to the wilt pathogen ralstonia solanacearum. internal colonization of roots by bacterial endophytes was confirmed through confocal imaging after syto-9 staining. endophytes were isolated from surface-sterilized roots of 4-weeks-old seedlings of known wilt resistant (r) tomato cultivar arka abha and susceptible (s) cv. arka vikas on nutrient agar after ... | 2015 | 25926818 |
| widespread occurrence of a novel division of bacteria identified by 16s rrna gene sequences originally found in deep marine sediments. | phylogenetic analysis of 16s rrna gene sequences from deep marine sediments identified a deeply branching clade, designated candidate division js1. primers for pcr amplification of partial 16s rrna genes that target the js1 division were developed and used to detect js1 sequences in dna extracted from various sedimentary environments, including, for the first time, coastal marine and brackish sediments. | 2004 | 15345467 |
| impact of unusual fatty acid synthesis on futile cycling through beta-oxidation and on gene expression in transgenic plants. | arabidopsis expressing the castor bean (ricinus communis) oleate 12-hydroxylase or the crepis palaestina linoleate 12-epoxygenase in developing seeds typically accumulate low levels of ricinoleic acid and vernolic acid, respectively. we have examined the presence of a futile cycle of fatty acid degradation in developing seeds using the synthesis of polyhydroxyalkanoate (pha) from the intermediates of the peroxisomal beta-oxidation cycle. both the quantity and monomer composition of the pha synth ... | 2004 | 14671017 |
| one-component systems dominate signal transduction in prokaryotes. | two-component systems that link environmental signals to cellular responses are viewed as the primary mode of signal transduction in prokaryotes. by analyzing information encoded by 145 prokaryotic genomes, we found that the majority of signal transduction systems consist of a single protein that contains input and output domains but lacks phosphotransfer domains typical of two-component systems. one-component systems are evolutionarily older, more widely distributed among bacteria and archaea, ... | 2005 | 15680762 |
| bacterial stationary-state mutagenesis and mammalian tumorigenesis as stress-induced cellular adaptations and the role of epigenetics. | mechanisms of cellular adaptation may have some commonalities across different organisms. revealing these common mechanisms may provide insight in the organismal level of adaptation and suggest solutions to important problems related to the adaptation. an increased rate of mutations, referred as the mutator phenotype, and beneficial nature of these mutations are common features of the bacterial stationary-state mutagenesis and of the tumorigenic transformations in mammalian cells. we argue that ... | 2006 | 18369407 |
| identification and characterization of arabidopsis indole-3-butyric acid response mutants defective in novel peroxisomal enzymes. | genetic evidence suggests that indole-3-butyric acid (iba) is converted to the active auxin indole-3-acetic acid (iaa) by removal of two side-chain methylene units in a process similar to fatty acid beta-oxidation. previous studies implicate peroxisomes as the site of iba metabolism, although the enzymes that act in this process are still being identified. here, we describe two iba-response mutants, ibr1 and ibr10. like the previously described ibr3 mutant, which disrupts a putative peroxisomal ... | 2008 | 18725356 |
| expanding dialogues: from natural autoinducers to non-natural analogues that modulate quorum sensing in gram-negative bacteria. | bacteria are capable of "communicating" their local population densities via a process termed quorum sensing (qs). gram-negative bacteria use n-acylated l-homoserine lactones (ahls), in conjunction with their cognate luxr-type receptors, as their primary signalling circuit for qs. in this critical review, we examine ahl signalling in gram-negative bacteria with a primary focus on the design of non-natural ahls, their structure-activity relationships, and their application in chemical biological ... | 2008 | 18568169 |
| genomic and functional characterization of the modular broad-host-range ra3 plasmid, the archetype of the incu group. | incu plasmids are a distinctive group of mobile elements with highly conserved backbone functions and variable antibiotic resistance gene cassettes. the incu archetype is conjugative plasmid ra3, whose sequence (45,909 bp) shows it to be a mosaic, modular replicon with a class i integron different from that of other incu replicons. functional analysis demonstrated that ra3 possesses a broad host range and can efficiently self-transfer, replicate, and be maintained stably in alpha-, beta-, and ga ... | 2008 | 18502921 |
| evolution of efficient pathways for degradation of anthropogenic chemicals. | anthropogenic compounds used as pesticides, solvents and explosives often persist in the environment and can cause toxicity to humans and wildlife. the persistence of anthropogenic compounds is due to their recent introduction into the environment; microbes in soil and water have had relatively little time to evolve efficient mechanisms for degradation of these new compounds. some anthropogenic compounds are easily degraded, whereas others are degraded very slowly or only partially, leading to a ... | 2009 | 19620997 |
| genetic diversity of siderophore-producing bacteria of tobacco rhizosphere. | the genetic diversity of siderophore-producing bacteria of tobacco rhizosphere was studied by amplified ribosomal dna restriction analysis (ardra), 16s rrna sequence homology and phylogenetics analysis methods. studies demonstrated that 85% of the total 354 isolates produced siderophores in iron limited liquid medium. a total of 28 ardra patterns were identified among the 299 siderophore-producing bacterial isolates. the 28 ardra patterns represented bacteria of 14 different genera belonging to ... | 2009 | 24031358 |
| involvement of rpon in regulating bacterial arsenite oxidation. | in this study with the model organism agrobacterium tumefaciens, we used a combination of lacz gene fusions, reverse transcriptase pcr (rt-pcr), and deletion and insertional inactivation mutations to show unambiguously that the alternative sigma factor rpon participates in the regulation of as(iii) oxidation. a deletion mutation that removed the rpon binding site from the aioba promoter and an aacc3 (gentamicin resistance) cassette insertional inactivation of the rpon coding region eliminated ai ... | 2012 | 22660703 |
| dynamics of seed-borne rice endophytes on early plant growth stages. | bacterial endophytes are ubiquitous to virtually all terrestrial plants. with the increasing appreciation of studies that unravel the mutualistic interactions between plant and microbes, we increasingly value the beneficial functions of endophytes that improve plant growth and development. however, still little is known on the source of established endophytes as well as on how plants select specific microbial communities to establish associations. here, we used cultivation-dependent and -indepen ... | 2012 | 22363438 |
| host range diversification within the incp-1 plasmid group. | broad-host-range plasmids play a critical role in the spread of antibiotic resistance and other traits. in spite of increasing information about the genomic diversity of closely related plasmids, the relationship between sequence divergence and host range remains unclear. incp-1 plasmids are currently classified into six subgroups based on the genetic distance of backbone genes. we investigated whether plasmids from two subgroups exhibit a different host range, using two incp-1γ plasmids, an inc ... | 2013 | 24002747 |
| in vivo analysis of dna binding and ligand interaction of blcr, an iclr-type repressor from agrobacterium tumefaciens. | agrobacterium tumefaciens blcr represses transcription of the blcabc operon, which is involved in metabolism of γ-butyrolactone, and this repression is alleviated by succinate semialdehyde (ssa). blcr exists as a homodimer, and the blcabc promoter dna contains two blcr-binding sites (ir1 and ir2) that correspond to two blcr dimers. in this study, we established an in vivo system to examine the ssa-responsive control of blcr transcriptional regulation. the endogenous blcr, encoded in the patc58 p ... | 2013 | 23449918 |
| plant-agrobacterium interaction mediated by ethylene and super-agrobacterium conferring efficient gene transfer. | agrobacterium tumefaciens has a unique ability to transfer genes into plant genomes. this ability has been utilized for plant genetic engineering. however, the efficiency is not sufficient for all plant species. several studies have shown that ethylene decreased the agrobacterium-mediated transformation frequency. thus, a. tumefaciens with an ability to suppress ethylene evolution would increase the efficiency of agrobacterium-mediated transformation. some studies showed that plant growth-promot ... | 2014 | 25520733 |
| 6-hydroxy-3-succinoylpyridine hydroxylase catalyzes a central step of nicotine degradation in agrobacterium tumefaciens s33. | nicotine is a main alkaloid in tobacco and is also the primary toxic compound in tobacco wastes. it can be degraded by bacteria via either pyridine pathway or pyrrolidine pathway. previously, a fused pathway of the pyridine pathway and the pyrrolidine pathway was proposed for nicotine degradation by agrobacterium tumefaciens s33, in which 6-hydroxy-3-succinoylpyridine (hsp) is a key intermediate connecting the two pathways. we report here the purification and properties of an nadh-dependent hsp ... | 2014 | 25054198 |
| agrobacterium tumefaciens deploys a superfamily of type vi secretion dnase effectors as weapons for interbacterial competition in planta. | the type vi secretion system (t6ss) is a widespread molecular weapon deployed by many proteobacteria to target effectors/toxins into both eukaryotic and prokaryotic cells. we report that agrobacterium tumefaciens, a soil bacterium that triggers tumorigenesis in plants, produces a family of type vi dnase effectors (tde) that are distinct from previously known polymorphic toxins and nucleases. tde exhibits an antibacterial dnase activity that relies on a conserved hxxd motif and can be counteracte ... | 2014 | 24981331 |
| characterization of uronate dehydrogenases catalysing the initial step in an oxidative pathway. | uronate dehydrogenases catalyse the oxidation of uronic acids to aldaric acids, which represent 'top value-added chemicals' that have the potential to substitute petroleum-derived chemicals. the identification and annotation of three uronate dehydrogenases derived from fulvimarina pelagi htcc2506, streptomyces viridochromogenes dsm 40736 and oceanicola granulosus dsm 15982 via sequence analysis is described. characterization and comparison with two known uronate dehydrogenases in regard to subst ... | 2015 | 25884328 |
| two distinct cardiolipin synthases operate in agrobacterium tumefaciens. | cardiolipin (cl) is a universal component of energy generating membranes. in most bacteria, it is synthesized via the condensation of two molecules phosphatidylglycerol (pg) by phospholipase d-type cardiolipin synthases (pld-type cls). in the plant pathogen and natural genetic engineer agrobacterium tumefaciens cl comprises up to 15% of all phospholipids in late stationary growth phase. a. tumefaciens harbors two genes, atu1630 (cls1) and atu2486 (cls2), coding for pld-type cls. heterologous exp ... | 2016 | 27472399 |
| regulatory activities of four arsr proteins in agrobacterium tumefaciens 5a. | arsr is a well-studied transcriptional repressor that regulates microbe-arsenic interactions. most microorganisms have an arsr gene, but in cases where multiple copies exist, the respective roles or potential functional overlap have not been explored. we examined the repressors encoded by arsr1 and arsr2 (ars1 operon) and by arsr3 and arsr4 (ars2 operon) in agrobacterium tumefaciens 5a. arsr1 and arsr4 are very similar in their primary sequences and diverge phylogenetically from arsr2 and arsr3, ... | 2016 | 27037117 |
| agricultural microbes genome 2: first glimpses into the genomes of plant-associated microbes. | | 2001 | 11251088 |
| targets of atwrky6 regulation during plant senescence and pathogen defense. | in arabidopsis, wrky factors comprise a large gene family of plant-specific transcriptional regulators controlling several types of plant stress responses. to understand the regulatory role of wrky proteins during such processes, we identified targets of the senescence- and defense-associated wrky6 factor. wrky6 was found to suppress its own promoter activity as well as that of a closely related wrky family member, indicating negative autoregulation. on the other hand, wrky6 positively influence ... | 2002 | 12000796 |
| laf3, a novel factor required for normal phytochrome a signaling. | phytochrome a (phya) is the photolabile plant light receptor that mediates broad spectrum very low-fluence responses and high irradiance responses to continuous far-red light (frc). an arabidopsis mutant laf3-1 (long after far-red 3) was recovered from a screen for transposon-tagged mutants that exhibit reduced inhibition of hypocotyl elongation in frc. the laf phenotype correlated well with a strongly attenuated disappearance of xtr7 transcript in frc. the effects of laf3-1 on phya-controlled c ... | 2003 | 14645728 |
| genome-wide analysis of arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis. | the complete sequence of the arabidopsis thaliana genome revealed thousands of previously unsuspected genes, many of which cannot be ascribed even putative functions. one of the largest and most enigmatic gene families discovered in this way is characterized by tandem arrays of pentatricopeptide repeats (pprs). we describe a detailed bioinformatic analysis of 441 members of the arabidopsis ppr family plus genomic and genetic data on the expression (microarray data), localization (green fluoresce ... | 2004 | 15269332 |
| evaluation of monocot and eudicot divergence using the sugarcane transcriptome. | over 40,000 sugarcane (saccharum officinarum) consensus sequences assembled from 237,954 expressed sequence tags were compared with the protein and dna sequences from other angiosperms, including the genomes of arabidopsis and rice (oryza sativa). approximately two-thirds of the sugarcane transcriptome have similar sequences in arabidopsis. these sequences may represent a core set of proteins or protein domains that are conserved among monocots and eudicots and probably encode for essential angi ... | 2004 | 15020759 |
| bacterial elicitation and evasion of plant innate immunity. | recent research on plant responses to bacterial attack has identified extracellular and intracellular host receptors that recognize conserved pathogen-associated molecular patterns and more specialized virulence proteins, respectively. these findings have shed light on our understanding of the molecular mechanisms by which bacteria elicit host defences and how pathogens have evolved to evade or suppress these defences. | 2006 | 16936700 |
| pathogen virulence factors as molecular probes of basic plant cellular functions. | to successfully colonize plants, pathogens have evolved a myriad of virulence factors that allow them to manipulate host cellular pathways in order to gain entry into, multiply and move within, and eventually exit the host for a new infection cycle. in the past few years, substantial progress has been made in characterizing the host targets of viral and bacterial virulence factors, providing unique insights into basic plant cellular processes such as gene silencing, vesicle trafficking, hormone ... | 2007 | 17884715 |
| genomic islands: tools of bacterial horizontal gene transfer and evolution. | bacterial genomes evolve through mutations, rearrangements or horizontal gene transfer. besides the core genes encoding essential metabolic functions, bacterial genomes also harbour a number of accessory genes acquired by horizontal gene transfer that might be beneficial under certain environmental conditions. the horizontal gene transfer contributes to the diversification and adaptation of microorganisms, thus having an impact on the genome plasticity. a significant part of the horizontal gene ... | 2008 | 19178566 |
| genomic islands: tools of bacterial horizontal gene transfer and evolution. | bacterial genomes evolve through mutations, rearrangements or horizontal gene transfer. besides the core genes encoding essential metabolic functions, bacterial genomes also harbour a number of accessory genes acquired by horizontal gene transfer that might be beneficial under certain environmental conditions. the horizontal gene transfer contributes to the diversification and adaptation of microorganisms, thus having an impact on the genome plasticity. a significant part of the horizontal gene ... | 2008 | 19178566 |
| lifestyles of the effector rich: genome-enabled characterization of bacterial plant pathogens. | | 2009 | 19515788 |
| underexplored niches in research on plant pathogenic bacteria. | | 2009 | 19561122 |
| the pepper extracellular xyloglucan-specific endo-β-1,4-glucanase inhibitor protein gene, caxegip1, is required for plant cell death and defense responses. | plants produce various proteinaceous inhibitors to protect themselves against microbial pathogen attack. a xyloglucan-specific endo-β-1,4-glucanase inhibitor1 gene, caxegip1, was isolated and functionally characterized in pepper (capsicum annuum) plants. caxegip1 was rapidly and strongly induced in pepper leaves infected with avirulent xanthomonas campestris pv vesicatoria, and purified caxegip1 protein significantly inhibited the hydrolytic activity of the glycoside hydrolase74 family xylogluca ... | 2012 | 23093361 |
| transgenic pearl millet male fertility restorer line (icmp451) and hybrid (icmh451) expressing brassica juncea nonexpressor of pathogenesis related genes 1 (bjnpr1) exhibit resistance to downy mildew disease. | brassica juncea nonexpressor of pathogenesis-related genes 1 (bjnpr1) has been introduced into pearl millet male fertility restorer line icmp451 by agrobacterium tumefaciens-mediated genetic transformation. transgenic pearl millet plants were regenerated from the phosphinothricin-resistant calli obtained after co-cultivation with a. tumefaciens strain lba4404 harbouring ti plasmid psb111-bar-bjnpr1. molecular analyses confirmed the stable integration and expression of bjnpr1 in transgenic pearl ... | 2014 | 24603762 |
| water extract from spent mushroom substrate of hericium erinaceus suppresses bacterial wilt disease of tomato. | culture filtrates of six different edible mushroom species were screened for antimicrobial activity against tomato wilt bacteria ralstonia solanacearum b3. hericium erinaceus, lentinula edodes (sanjo 701), grifola frondosa, and hypsizygus marmoreus showed antibacterial activity against the bacteria. water, n-butanol, and ethyl acetate extracts of spent mushroom substrate (sms) of h. erinaceus exhibited high antibacterial activity against different phytopathogenic bacteria: pectobacterium carotov ... | 2015 | 26539048 |
| inter-organ defense networking: leaf whitefly sucking elicits plant immunity to crown gall disease caused by agrobacterium tumefaciens. | plants have elaborate defensive machinery to protect against numerous pathogens and insects. plant hormones function as modulators of defensive mechanisms to maintain plant resistance to natural enemies. our recent study suggests that salicylic acid (sa) is the primary phytohormone regulating plant responses to agrobacterium tumefaciens infection. tobacco (nicotiana benthamiana domin.) immune responses against agrobacterium-mediated crown gall disease were activated by exposure to the sucking in ... | 2015 | 26357873 |
| new polyphenols from a deep sea spiromastix sp. fungus, and their antibacterial activities. | eleven new polyphenols namely spiromastols a-k (1-11) were isolated from the fermentation broth of a deep sea-derived fungus spiromastix sp. mccc 3a00308. their structures were determined by extensive nmr data and mass spectroscopic analysis in association with chemical conversion. the structures are classified as diphenyl ethers, diphenyl esters and isocoumarin derivatives, while the n-propyl group in the analogues is rarely found in natural products. compounds 1-3 exhibited potent inhibitory e ... | 2015 | 25913707 |
| the phylogenetically-related pattern recognition receptors efr and xa21 recruit similar immune signaling components in monocots and dicots. | during plant immunity, surface-localized pattern recognition receptors (prrs) recognize pathogen-associated molecular patterns (pamps). the transfer of prrs between plant species is a promising strategy for engineering broad-spectrum disease resistance. thus, there is a great interest in understanding the mechanisms of prr-mediated resistance across different plant species. two well-characterized plant prrs are the leucine-rich repeat receptor kinases (lrr-rks) efr and xa21 from arabidopsis thal ... | 2015 | 25607985 |
| the antibacterial activity of chitosan products blended with monoterpenes and their biofilms against plant pathogenic bacteria. | this study focuses on the biological activities of eleven chitosan products with a viscosity-average molecular weight ranging from 22 to 846 kda in combination with the most active monoterpenes (geraniol and thymol), out of 10 tested, against four plant pathogenic bacteria, agrobacterium tumefaciens, erwinia carotovora, corynebacterium fascians, and pseudomonas solanacearum. the antibacterial activity was evaluated in vitro by the agar dilution technique as a minimum inhibitory concentration (mi ... | 2016 | 27127676 |
| involvement of agrobacterium tumefaciens galacturonate tripartite atp-independent periplasmic (trap) transporter gaapqm in virulence gene expression. | monosaccharides capable of serving as nutrients for the soil bacterium agrobacterium tumefaciens are also inducers of the vir regulon present in the tumor-inducing (ti) plasmid of this plant pathogen. one such monosaccharide is galacturonate, the predominant monomer of pectin found in plant cell walls. this ligand is recognized by the periplasmic sugar binding protein chve, which interacts with the vira histidine kinase that controls vir gene expression. although chve is also a member of the chv ... | 2016 | 26637603 |
| investigation of atomic level patterns in protein--small ligand interactions. | shape complementarity and non-covalent interactions are believed to drive protein-ligand interaction. to date protein-protein, protein-dna, and protein-rna interactions were systematically investigated, which is in contrast to interactions with small ligands. we investigate the role of covalent and non-covalent bonds in protein-small ligand interactions using a comprehensive dataset of 2,320 complexes. | 2009 | 19221587 |
| significance of bacteria in oviposition and larval development of the sand fly lutzomyia longipalpis. | microbial ecology of phlebotomine sand flies is not well understood although bacteria likely play an important role in the sand fly biology and vector capacity for leishmania parasites. in this study, we assessed the significance of the microbial community of rabbit feces in oviposition and larval development of lutzomyia longipalpis as well as bacterial colonization of the gut of freshly emerged flies. | 2012 | 22827861 |
| the biosynthesis of salicylic acid in potato plants | spraying potato (solanum tuberosum l.) leaves with arachidonic acid (aa) at 1500 &mgr;g ml-1 led to a rapid local synthesis of salicylic acid (sa) and accumulation of a sa conjugate, which was shown to be 2-o-beta-glucopyranosylsalicylic acid. radiolabeling studies with untreated leaves showed that sa was synthesized from phenylalanine and that both cinnamic and benzoic acid were intermediates in the biosynthesis pathway. using radiolabeled phenylalanine as a precursor, the specific activity of ... | 1998 | 9662552 |
| the involvement of hydrogen peroxide in the differentiation of secondary walls in cotton fibers | h2o2 is a widespread molecule in many biological systems. it is created enzymatically in living cells during various oxidation reactions and by leakage of electrons from the electron transport chains. depending on the concentration h2o2 can induce cell protective responses, programmed cell death, or necrosis. here we provide evidence that h2o2 may function as a developmental signal in the differentiation of secondary walls in cotton (gossypium hirsutum) fibers. three lines of evidence support th ... | 1999 | 10069824 |
| characterization of p69e and p69f, two differentially regulated genes encoding new members of the subtilisin-like proteinase family from tomato plants. | subtilisin-like proteins represent an ancient family of serine proteases that are extremely widespread in living organisms. we report here the structure and genomic organization of two new transcriptionally active genes encoding proteins that belong to the p69 family of subtilisin-like proteases from tomato (lycopersicon esculentum) plants. the two new members, p69e and p69f, are organized in a cluster and arranged in a tandem form. mrna expression analysis and studies of transgenic arabidopsis ... | 2000 | 10631250 |