Publications

the type ii secretion system: biogenesis, molecular architecture and mechanism.	many gram-negative bacteria use the sophisticated type ii secretion system (t2ss) to translocate a wide range of proteins from the periplasm across the outer membrane. the inner-membrane platform of the t2ss is the nexus of the system and orchestrates the secretion process through its interactions with the periplasmic filamentous pseudopilus, the dodecameric outer-membrane complex and a cytoplasmic secretion atpase. here, recent structural and biochemical information is reviewed to describe our ...	2012	22466878
development of an engineered bioluminescent reporter phage for detection of bacterial blight of crucifers.	bacterial blight, caused by the phytopathogen pseudomonas cannabina pv. alisalensis, is an emerging disease afflicting important members of the brassicaceae family. the disease is often misdiagnosed as pepper spot, a much less severe disease caused by the related pathogen pseudomonas syringae pv. maculicola. we have developed a phage-based diagnostic that can both identify and detect the causative agent of bacterial blight and differentiate the two pathogens. a recombinant "light"-tagged reporte ...	2012	22427491
involvement of two latex-clearing proteins during rubber degradation and insights into the subsequent degradation pathway revealed by the genome sequence of gordonia polyisoprenivorans strain vh2.	the increasing production of synthetic and natural poly(cis-1,4-isoprene) rubber leads to huge challenges in waste management. only a few bacteria are known to degrade rubber, and little is known about the mechanism of microbial rubber degradation. the genome of gordonia polyisoprenivorans strain vh2, which is one of the most effective rubber-degrading bacteria, was sequenced and annotated to elucidate the degradation pathway and other features of this actinomycete. the genome consists of a circ ...	2012	22327575
differential expression of in vivo and in vitro protein profile of outer membrane of acidovorax avenae subsp. avenae.	outer membrane (om) proteins play a significant role in bacterial pathogenesis. in this work, we examined and compared the expression of the om proteins of the rice pathogen acidovorax avenae subsp. avenae strain rs-1, a gram-negative bacterium, both in an in vitro culture medium and in vivo rice plants. global proteomic profiling of a. avenae subsp. avenae strain rs-1 comparing in vivo and in vitro conditions revealed the differential expression of proteins affecting the survival and pathogenic ...	2012	23166741
discovery of an l-fucono-1,5-lactonase from cog3618 of the amidohydrolase superfamily.	a member of the amidohydrolase superfamily, bmulj_04915 from burkholderia multivorans, of unknown function was determined to hydrolyze a series of sugar lactones: l-fucono-1,4-lactone, d-arabino-1,4-lactone, l-xylono-1,4-lactone, d-lyxono-1,4-lactone, and l-galactono-1,4-lactone. the highest activity was shown for l-fucono-1,4-lactone with a k(cat) value of 140 s(-1) and a k(cat)/k(m) value of 1.0 × 10(5) m(-1) s(-1) at ph 8.3. the enzymatic product of an adjacent l-fucose dehydrogenase, bmulj_0 ...	2012	23214453
discovery of an l-fucono-1,5-lactonase from cog3618 of the amidohydrolase superfamily.	a member of the amidohydrolase superfamily, bmulj_04915 from burkholderia multivorans, of unknown function was determined to hydrolyze a series of sugar lactones: l-fucono-1,4-lactone, d-arabino-1,4-lactone, l-xylono-1,4-lactone, d-lyxono-1,4-lactone, and l-galactono-1,4-lactone. the highest activity was shown for l-fucono-1,4-lactone with a k(cat) value of 140 s(-1) and a k(cat)/k(m) value of 1.0 × 10(5) m(-1) s(-1) at ph 8.3. the enzymatic product of an adjacent l-fucose dehydrogenase, bmulj_0 ...	2012	23214453
pseudomonas syringae catalases are collectively required for plant pathogenesis.	the bacterial pathogen pseudomonas syringae pv. tomato dc3000 must detoxify plant-produced hydrogen peroxide (h(2)o(2)) in order to survive in its host plant. candidate enzymes for this detoxification include the monofunctional catalases katb and kate and the bifunctional catalase-peroxidase katg of dc3000. this study shows that katg is the major housekeeping catalase of dc3000 and provides protection against menadione-generated endogenous h(2)o(2). in contrast, katb rapidly and substantially ac ...	2012	22797762
genetic and functional characterization of cyclic lipopeptide white-line-inducing principle (wlip) production by rice rhizosphere isolate pseudomonas putida rw10s2.	the secondary metabolite mediating the gacs-dependent growth-inhibitory effect exerted by the rice rhizosphere isolate pseudomonas putida rw10s2 on phytopathogenic xanthomonas species was identified as white-line-inducing principle (wlip), a member of the viscosin group of cyclic lipononadepsipeptides. wlip producers are commonly referred to by the taxonomically invalid name "pseudomonas reactans," based on their capacity to reveal the presence of a nearby colony of pseudomonas tolaasii by induc ...	2012	22544260
the fleq protein from pseudomonas aeruginosa functions as both a repressor and an activator to control gene expression from the pel operon promoter in response to c-di-gmp.	bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-gmp) modulates the transition between planktonic and biofilm life styles. in response to c-di-gmp, the enhancer binding protein fleq from pseudomonas aeruginosa derepresses the expression of pel exopolysaccharide genes required for biofilm formation when a second protein, flen is present. a model is that binding of c-di-gmp to fleq induces its dissociation from the pela promoter allowing rna polymerase to access this site. to test this, we ...	2012	22581773
structural polymorphism of c-di-gmp bound to an eal domain and in complex with a type ii pilz-domain protein.	cyclic di-gmp (c-di-gmp) is a novel secondary-messenger molecule that is involved in regulating a plethora of important bacterial activities through binding to an unprecedented array of effectors. proteins with a canonical pilz domain that bind c-di-gmp play crucial roles in regulating flagellum-based motility. in contrast, noncanonical type ii pilz domains that do not effectively bind c-di-gmp regulate twitching motility, which is dependent on type iv pili (t4p). recent data indicate that t4p b ...	2012	22993092
dynamic complex formation between hd-gyp, ggdef and pilz domain proteins regulates motility in xanthomonas campestris.	rpfg is a member of a class of wide spread bacterial two-component regulators with an hd-gyp cyclic di-gmp phosphodiesterase domain. in the plant pathogen xanthomonas campestris, rpfg together with the sensor kinase rpfc regulates multiple factors as a response to the cell-to-cell diffusible signalling factor (dsf). a dynamic physical interaction of rpfg with two diguanylate cyclase (ggdef) domain proteins controls motility. here we show that, contrary to expectation, regulation of motility by t ...	2012	22924852
xanthan production by xanthomonas campestris using whey permeate medium.	xanthan gum is a polysaccharide that is widely used as stabilizer and thickener with many industrial applications in food industry. our aim was to estimate the ability of xanthomonas campestris atcc 13951 for the production of xanthan gum by using whey as a growth medium, a by-product of dairy industry. x. campestris atcc 13951 has been studied in batch cultures using a complex medium for the determination of the optimal concentration of glucose, galactose and lactose. in addition, whey was used ...	2012	22806202
analysis of new type iii effectors from xanthomonas uncovers xopb and xops as suppressors of plant immunity.	the pathogenicity of the gram-negative plant-pathogenic bacterium xanthomonas campestris pv. vesicatoria (xcv) is dependent on type iii effectors (t3es) that are injected into plant cells by a type iii secretion system and interfere with cellular processes to the benefit of the pathogen. in this study, we analyzed eight t3es from xcv strain 85-10, six of which were newly identified effectors. genetic studies and protoplast expression assays revealed that xopb and xops contribute to disease sympt ...	2012	22738163
the pepper rna-binding protein carbp1 functions in hypersensitive cell death and defense signaling in the cytoplasm.	the regulation of gene expression via post-transcriptional modification by rna-binding proteins is crucial for plant disease and innate immunity. here, we report the identification of the pepper (capsicum annuum) rna-binding protein1 gene (carbp1) as essential for hypersensitive cell death and defense signaling in the cytoplasm. carbp1 contains an rna recognition motif and is rapidly and strongly induced in pepper by avirulent xanthomonas campestris pv. vesicatoria (xcv) infection. carbp1 displa ...	2012	22640562
a xanthomonas uridine 5'-monophosphate transferase inhibits plant immune kinases.	plant innate immunity is activated on the detection of pathogen-associated molecular patterns (pamps) at the cell surface, or of pathogen effector proteins inside the plant cell. together, pamp-triggered immunity and effector-triggered immunity constitute powerful defences against various phytopathogens. pathogenic bacteria inject a variety of effector proteins into the host cell to assist infection or propagation. a number of effector proteins have been shown to inhibit plant immunity, but the ...	2012	22504181
improved thermostability of aeh by combining b-fit analysis and structure-guided consensus method.	α-amino ester hydrolases (aeh, e.c. 3.1.1.43) catalyze the synthesis and hydrolysis of α-amino β-lactam antibiotics. the aeh enzymes have been shown to feature excellent synthetic capability but suffer from poor thermostability. aeh from xanthomonas campestris exhibits an optimal activity temperature of 25 °c, an observed half-life of 5 min at 30 °c, and a "t-50" value, the temperature at which the half-life is 30 min, of 27 °c. to improve the thermostability of aeh, a modified structure-guided ...	2012	22426092
differential expression of peach erf transcriptional activators in response to signaling molecules and inoculation with xanthomonas campestris pv. pruni.	ethylene response factors (erfs) are a large family of transcription factors (tfs) that have diverse functions in plant development and immunity. however, very little is known about the molecular regulation of these tfs in stone fruits during disease incidence. in the present study, we describe the identification of five peach erfs (pp-erfs), aiming to elucidate their potential roles in defense against xanthomonas campestris pv. pruni (xcp), the causal agent of bacterial spot disease. the phylog ...	2012	22410465
characterization of hrpb2 from xanthomonas campestris pv. vesicatoria identifies protein regions that are essential for type iii secretion pilus formation.	the gram-negative plant-pathogenic bacterium xanthomonas campestris pv. vesicatoria employs a type iii secretion (t3s) system to translocate effector proteins into plant cells. t3s depends on hrpb2, which is essential for assembly of the extracellular t3s pilus and is itself weakly secreted. to characterize the role of hrpb2, we used a transposon mutagenesis approach, which led to the insertion of pentapeptide-encoding sequences into hrpb2. complementation studies with hrpb2 mutant derivatives r ...	2012	22343358
the pepper mlo gene, camlo2, is involved in the susceptibility cell-death response and bacterial and oomycete proliferation.	loss-of-function alleles of the mildew resistance locus o (mlo) gene provide broad-spectrum powdery mildew disease resistance. here, we identified a pepper (capsicum annuum) mlo gene (camlo2) that is transcriptionally induced by xanthomonas campestris pv. vesicatoria (xcv) infection. topology and subcellular localization analyses reveal that camlo2 is a plasma membrane-anchored and amphiphilic ca²⁺-dependent calmodulin-binding protein. camlo2 expression is up-regulated by xcv and salicylic acid, ...	2012	22913752
overexpression of xanthomonas campestris pv. vesicatoria effector avrbst in arabidopsis triggers plant cell death, disease and defense responses.	recognition of bacterial effector proteins by plant cells is crucial for plant disease and defense response signaling. the xanthomonas campestris pv. vesicatoria (xcv) type iii effector protein, avrbst, is secreted into plant cells from xcv strain bv5-4a. here, we demonstrate that dexamethasone (dex): avrbst overexpression triggers cell death signaling in healthy transgenic arabidopsis plants. avrbst overexpression in arabidopsis also reduced susceptibility to infection with the obligate biotrop ...	2012	22678032
simple deletion: a vector- and marker-free method to generate and isolate site-directed deletion mutants.	we have designed a new vector- and marker-free site-directed deletion system for gram-negative bacteria. in this system, a specific dna fragment is amplified from a parental strain by using polymerase chain reaction (pcr), then circularized and introduced back into the parental strain for homologous recombination. the recombinant mutant is then detected and isolated by pcr-based sib selection. unlike conventional methods, our simple deletion method requires no cloning procedures, and no foreign ...	2012	22391971
microbial mats: an ecological niche for fungi.	fungi were documented in tropical hypersaline microbial mats and their role in the degradation of complex carbohydrates (exopolymeric substance - eps) was explored. fungal diversity is higher during the wet season with acremonium, aspergillus, cladosporium, and penicillium among the more common genera. diversity is also higher in the oxic layer and in young and transient mats. enrichments with xanthan (a model eps) show that without antibiotics (full community) degradation is faster than enrichm ...	2012	23577004
microbial mats: an ecological niche for fungi.	fungi were documented in tropical hypersaline microbial mats and their role in the degradation of complex carbohydrates (exopolymeric substance - eps) was explored. fungal diversity is higher during the wet season with acremonium, aspergillus, cladosporium, and penicillium among the more common genera. diversity is also higher in the oxic layer and in young and transient mats. enrichments with xanthan (a model eps) show that without antibiotics (full community) degradation is faster than enrichm ...	2012	23577004
linen most useful: perspectives on structure, chemistry, and enzymes for retting flax.	the components of flax (linum usitatissimum) stems are described and illustrated, with reference to the anatomy and chemical makeup and to applications in processing and products. bast fiber, which is a major economic product of flax along with linseed and linseed oil, is described with particular reference to its application in textiles, composites, and specialty papers. a short history of retting methods, which is the separation of bast fiber from nonfiber components, is presented with emphasi ...	2012	25969769
linen most useful: perspectives on structure, chemistry, and enzymes for retting flax.	the components of flax (linum usitatissimum) stems are described and illustrated, with reference to the anatomy and chemical makeup and to applications in processing and products. bast fiber, which is a major economic product of flax along with linseed and linseed oil, is described with particular reference to its application in textiles, composites, and specialty papers. a short history of retting methods, which is the separation of bast fiber from nonfiber components, is presented with emphasi ...	2012	25969769
rsma regulates biofilm formation in xanthomonas campestris through a regulatory network involving cyclic di-gmp and the clp transcription factor.	biofilm formation and dispersal in the black rot pathogen xanthomonas campestris pathovar campestris (xcc) is influenced by a number of factors. the extracellular mannanase mana has been implicated in biofilm dispersal whereas biofilm formation requires a putative glycosyl transferase encoded by the xag gene cluster. previously we demonstrated that the post-transcriptional regulator rsma exerts a negative regulatory influence on biofilm formation in xcc. here we address the mechanisms by which r ...	2012	23285129
structure of the complex of neisseria gonorrhoeae n-acetyl-l-glutamate synthase with a bound bisubstrate analog.	n-acetyl-l-glutamate synthase catalyzes the conversion of accoa and glutamate to coa and n-acetyl-l-glutamate (nag), the first step of the arginine biosynthetic pathway in lower organisms. in mammals, nag is an obligate cofactor of carbamoyl phosphate synthetase i in the urea cycle. we have previously reported the structures of nags from neisseria gonorrhoeae (ngnags) with various substrates bound. here we reported the preparation of the bisubstrate analog, coa-s-acetyl-l-glutamate, the crystal ...	2012	23261468
structure of the complex of neisseria gonorrhoeae n-acetyl-l-glutamate synthase with a bound bisubstrate analog.	n-acetyl-l-glutamate synthase catalyzes the conversion of accoa and glutamate to coa and n-acetyl-l-glutamate (nag), the first step of the arginine biosynthetic pathway in lower organisms. in mammals, nag is an obligate cofactor of carbamoyl phosphate synthetase i in the urea cycle. we have previously reported the structures of nags from neisseria gonorrhoeae (ngnags) with various substrates bound. here we reported the preparation of the bisubstrate analog, coa-s-acetyl-l-glutamate, the crystal ...	2012	23261468
gene family assignment-free comparative genomics.	the comparison of relative gene orders between two genomes offers deep insights into functional correlations of genes and the evolutionary relationships between the corresponding organisms. methods for gene order analyses often require prior knowledge of homologies between all genes of the genomic dataset. since such information is hard to obtain, it is common to predict homologous groups based on sequence similarity. these hypothetical groups of homologous genes are called gene families.	2012	23281826
cell-free production of integral membrane aspartic acid proteases reveals zinc-dependent methyltransferase activity of the pseudomonas aeruginosa prepilin peptidase pild.	integral membrane aspartic acid proteases are receiving growing recognition for their fundamental roles in cellular physiology of eukaryotes and prokaryotes, and may be medically important pharmaceutical targets. the gram-negative pseudomonas aeruginosa pild and the archaeal methanococcus voltae flak were synthesized in the presence of unilamellar liposomes in a cell-free translation system. cosynthesis of pild with its full-length substrate, pila, or of flak with its full-length substrate, flab ...	2012	23255525
cell-free production of integral membrane aspartic acid proteases reveals zinc-dependent methyltransferase activity of the pseudomonas aeruginosa prepilin peptidase pild.	integral membrane aspartic acid proteases are receiving growing recognition for their fundamental roles in cellular physiology of eukaryotes and prokaryotes, and may be medically important pharmaceutical targets. the gram-negative pseudomonas aeruginosa pild and the archaeal methanococcus voltae flak were synthesized in the presence of unilamellar liposomes in a cell-free translation system. cosynthesis of pild with its full-length substrate, pila, or of flak with its full-length substrate, flab ...	2012	23255525
rapa2 is a calcium-binding lectin composed of two highly conserved cadherin-like domains that specifically recognize rhizobium leguminosarum acidic exopolysaccharides.	in silico analyses have revealed a conserved protein domain (chdl) widely present in bacteria that has significant structural similarity to eukaryotic cadherins. a chdl domain was shown to be present in rapa, a protein that is involved in autoaggregation of rhizobium cells, biofilm formation, and adhesion to plant roots as shown by us and others. structural similarity to cadherins suggested calcium-dependent oligomerization of chdl domains as a mechanistic basis for rapa action. here we show by ...	2012	23235153
rapa2 is a calcium-binding lectin composed of two highly conserved cadherin-like domains that specifically recognize rhizobium leguminosarum acidic exopolysaccharides.	in silico analyses have revealed a conserved protein domain (chdl) widely present in bacteria that has significant structural similarity to eukaryotic cadherins. a chdl domain was shown to be present in rapa, a protein that is involved in autoaggregation of rhizobium cells, biofilm formation, and adhesion to plant roots as shown by us and others. structural similarity to cadherins suggested calcium-dependent oligomerization of chdl domains as a mechanistic basis for rapa action. here we show by ...	2012	23235153
the zinc-responsive regulon of neisseria meningitidis comprises 17 genes under control of a zur element.	zinc is a bivalent cation essential for bacterial growth and metabolism. the human pathogen neisseria meningitidis expresses a homologue of the zinc uptake regulator zur, which has been postulated to repress the putative zinc uptake protein znud. in this study, we elucidated the transcriptome of meningococci in response to zinc by microarrays and quantitative real-time pcr (qrt-pcr). we identified 15 genes that were repressed and two genes that were activated upon zinc addition. all transcriptio ...	2012	23043002
transcriptome analysis of symptomatic and recovered leaves of geminivirus-infected pepper (capsicum annuum).	geminiviruses are a large and important family of plant viruses that infect a wide range of crops throughout the world. the begomovirus genus contains species that are transmitted by whiteflies and are distributed worldwide causing disease on an array of horticultural crops. symptom remission, in which newly developed leaves of systemically infected plants exhibit a reduction in symptom severity (recovery), has been observed on pepper (capsicum annuum) plants infected with pepper golden mosaic v ...	2012	23185982
self-produced exopolysaccharide is a signal that stimulates biofilm formation in pseudomonas aeruginosa.	bacteria have a tendency to attach to surfaces and grow as structured communities called biofilms. chronic biofilm infections are a problem because they tend to resist antibiotic treatment and are difficult to eradicate. bacterial biofilms have an extracellular matrix that is usually composed of a mixture of polysaccharides, proteins, and nucleic acids. this matrix has long been assumed to play a passive structural and protective role for resident biofilm cells. here we show that this view is an ...	2012	23175784
accelerated pentose utilization by corynebacterium glutamicum for accelerated production of lysine, glutamate, ornithine and putrescine.	because of their abundance in hemicellulosic wastes arabinose and xylose are an interesting source of carbon for biotechnological production processes. previous studies have engineered several corynebacterium glutamicum strains for the utilization of arabinose and xylose, however, with inefficient xylose utilization capabilities. to improve xylose utilization, different xylose isomerase genes were tested in c. glutamicum. the gene originating from xanthomonas campestris was shown to have the hig ...	2012	23164409
accelerated pentose utilization by corynebacterium glutamicum for accelerated production of lysine, glutamate, ornithine and putrescine.	because of their abundance in hemicellulosic wastes arabinose and xylose are an interesting source of carbon for biotechnological production processes. previous studies have engineered several corynebacterium glutamicum strains for the utilization of arabinose and xylose, however, with inefficient xylose utilization capabilities. to improve xylose utilization, different xylose isomerase genes were tested in c. glutamicum. the gene originating from xanthomonas campestris was shown to have the hig ...	2012	23164409
tmv-gate vectors: gateway compatible tobacco mosaic virus based expression vectors for functional analysis of proteins.	plant viral expression vectors are advantageous for high-throughput functional characterization studies of genes due to their capability for rapid, high-level transient expression of proteins. we have constructed a series of tobacco mosaic virus (tmv) based vectors that are compatible with gateway technology to enable rapid assembly of expression constructs and exploitation of orfeome collections. in addition to the potential of producing recombinant protein at grams per kilogram fw of leaf tiss ...	2012	23166857
in silico biosynthesis of virenose, a methylated deoxy-sugar unique to coxiella burnetii lipopolysaccharide.		2012	23150954
the quorum sensing volatile molecule 2-amino acetophenon modulates host immune responses in a manner that promotes life with unwanted guests.	increasing evidence indicates that bacterial quorum sensing (qs) signals are important mediators of immunomodulation. however, whether microbes utilize these immunomodulatory signals to maintain infection remain unclear. here, we show that the pseudomonas aeruginosa qs-regulated molecule 2-amino acetophenone (2-aa) modulates host immune responses in a manner that increases host ability to cope with this pathogen. mice treated with 2-aa prior to infection had a 90% survival compared to 10% surviv ...	2012	23166496
analysis of tomato gene promoters activated in syncytia induced in tomato and potato hairy roots by globodera rostochiensis.	the potato cyst nematode (globodera rostochiensis) induces feeding sites (syncytia) in tomato and potato roots. in a previous study, 135 tomato genes up-regulated during g. rostochiensis migration and syncytium development were identified. five genes (cyp97a29, dfr, fls, nik and pmei) were chosen for further study to examine their roles in plant-nematode interactions. the promoters of these genes were isolated and potential cis regulatory elements in their sequences were characterized using bioi ...	2012	23129482
analysis of tomato gene promoters activated in syncytia induced in tomato and potato hairy roots by globodera rostochiensis.	the potato cyst nematode (globodera rostochiensis) induces feeding sites (syncytia) in tomato and potato roots. in a previous study, 135 tomato genes up-regulated during g. rostochiensis migration and syncytium development were identified. five genes (cyp97a29, dfr, fls, nik and pmei) were chosen for further study to examine their roles in plant-nematode interactions. the promoters of these genes were isolated and potential cis regulatory elements in their sequences were characterized using bioi ...	2012	23129482
biodegradation of selected nigerian fruit peels by the use of a non-pathogenic rhizobium species cwp g34b.	this study was carried out to determine the ability of rhizobium species cwp g34b to degrade the peels of selected nigerian fruits. the potential of the bacterium to digest some carbon sources (lactose, maltose, sucrose and mannitol) and peels of some nigerian fruits (pineapple, orange, plantain, banana, pawpaw and mango fruits) was investigated by growing the organism on the substances separately after which dnsa reagent method was used to quantify glucose released into the medium. the results ...	2012	23166567
role of escp (orf16) in injectisome biogenesis and regulation of type iii protein secretion in enteropathogenic escherichia coli.	enteropathogenic escherichia coli employs a type iii secretion system (t3ss) to translocate virulence effector proteins directly into enterocyte host cells, leading to diarrheal disease. the t3ss is encoded within the chromosomal locus of enterocyte effacement (lee). the function of some of the lee-encoded proteins remains unknown. here we investigated the role of the orf16 protein in t3ss biogenesis and function. an orf16 deletion mutant showed translocator and effector protein secretion profil ...	2012	22923600
functional divergence of fimx in pilz binding and type iv pilus regulation.	type iv pili (t4p) are polar surface structures that play important roles in bacterial motility, biofilm formation, and pathogenicity. the protein fimx and its orthologs are known to mediate t4p formation in the human pathogen pseudomonas aeruginosa and some other bacterial species. it was reported recently that fimx(xac2398) from xanthomonas axonopodis pv. citri interacts with pilz(xac1133) directly through the nonenzymatic eal domain of fimx(xac2398). here we present experimental data to revea ...	2012	22942245
redox active thiol sensors of oxidative and nitrosative stress.	the reactivity of the thiol in the side chain of cysteines is exploited by bacterial regulatory proteins that sense and respond to reactive oxygen and nitrogen species.	2012	22257022
o-glcnac transferase invokes nucleotide sugar pyrophosphate participation in catalysis.	protein o-glcnacylation is an essential post-translational modification on hundreds of intracellular proteins in metazoa, catalyzed by o-linked β-n-acetylglucosamine (o-glcnac) transferase (ogt) using unknown mechanisms of transfer and substrate recognition. through crystallographic snapshots and mechanism-inspired chemical probes, we define how human ogt recognizes the sugar donor and acceptor peptide and uses a new catalytic mechanism of glycosyl transfer, involving the sugar donor α-phosphate ...	2012	23103942
formation of phosphoglycosides in caenorhabditis elegans: a novel biotransformation pathway.	caenorhabditis elegans (c. elegans) has become a widely used model to explore the effect of food constituents on health as well as on life-span extension. the results imply that besides essential nutrients several flavonoids are able to impact the aging process. what is less investigated is the bioavailability and biotransformation of these compounds in c. elegans. in the present study, we focused on the soy isoflavone genistein and its metabolism in the nematode as a basis for assessing whether ...	2012	23082135
pyrosequencing-based transcriptome analysis of the asian rice gall midge reveals differential response during compatible and incompatible interaction.	the asian rice gall midge (orseolia oryzae) is a major pest responsible for immense loss in rice productivity. currently, very little knowledge exists with regard to this insect at the molecular level. the present study was initiated with the aim of developing molecular resources as well as identifying alterations at the transcriptome level in the gall midge maggots that are in a compatible (sh) or in an incompatible interaction (rh) with their rice host. roche 454 pyrosequencing strategy was us ...	2012	23202939
ltma, a novel cyclic di-gmp-responsive activator, broadly regulates the expression of lipid transport and metabolism genes in mycobacterium smegmatis.	in a bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-gmp)/transcription factor binding screen, we identified mycobacterium smegmatis ms6479 as the first c-di-gmp-responsive transcriptional factor in mycobacteria. ms6479 could specifically bind with c-di-gmp and recognize the promoters of 37 lipid transport and metabolism genes. c-di-gmp could enhance the ability of ms6479 to bind to its target dna. furthermore, our results establish ms6479 as a global activator that positively regulates ...	2012	23047950
fractionation, stability, and isolate-specificity of qtl for resistance to phytophthora infestans in cultivated tomato (solanum lycopersicum).	cultivated tomato (solanum lycopersicum) is susceptible to late blight, a major disease caused by phytophthora infestans, but quantitative resistance exists in the wild tomato species s. habrochaites. previously, we mapped several quantitative trait loci (qtl) from s. habrochaites and then introgressed each individually into s. lycopersicum. near-isogenic lines (nils) were developed, each containing a single introgressed qtl on chromosome 5 or 11. nils were used to create two recombinant sub-nil ...	2012	23050225
peroxide-sensing transcriptional regulators in bacteria.	the ability to maintain intracellular concentrations of toxic reactive oxygen species (ros) within safe limits is essential for all aerobic life forms. in bacteria, as well as other organisms, ros are produced during the normal course of aerobic metabolism, necessitating the constitutive expression of ros scavenging systems. however, bacteria can also experience transient high-level exposure to ros derived either from external sources, such as the host defense response, or as a secondary effect ...	2012	22797754
expression, purification and crystallization of the outer membrane lipoprotein gumb from xanthomonas campestris.	gumb is a predicted outer membrane lipoprotein that is involved in the synthesis and/or secretion of xanthan gum. this exopolysaccharide, produced by xanthomonas campestris, is valuable in industry because of its important rheological properties. solution of the gumb structure will provide insight into the polymerization and/or secretion mechanisms of xanthan gum. gumb was overexpressed and purified and diffraction-quality crystals of native gumb were obtained. a complete data set was collected ...	2012	23027761
crystallization and preliminary x-ray diffraction studies of xanthomonas campestris pnpase in the presence of c-di-gmp.	bacterial polynucleotide phosphorylase (pnpase) is a 3'-5' processive exoribonuclease that participates in mrna turnover and quality control of rrna precursors in many bacterial species. it also associates with the rnase e scaffold and other components to form a multi-enzyme rna degradasome machinery that performs a wider regulatory role in degradation, quality control and maturation of mrna and noncoding rna. several crystal structures of bacterial pnpases, as well as some biological activity s ...	2012	23027759
analysis of tir- and non-tir-nbs-lrr disease resistance gene analogous in pepper: characterization, genetic variation, functional divergence and expression patterns.	pepper (capsicum annuum l.) is one of the most important vegetable crops worldwide. however, its yield and fruit quality can be severely threatened by several pathogens. the plant nucleotide-binding site (nbs)-leucine-rich repeat (lrr) gene family is the largest class of known disease resistance genes (r genes) effective against such pathogens. therefore, the isolation and identification of such r gene homologues from pepper will provide a critical foundation for improving disease resistance bre ...	2012	22998579
functional studies of ssdna binding ability of marr family protein tcar from staphylococcus epidermidis.	the negative transcription regulator of the ica locus, tcar, regulates proteins involved in the biosynthesis of poly-n-acetylglucosamine (pnag). absence of tcar increases pnag production and promotes biofilm formation in staphylococci. previously, the 3d structure of tcar in its apo form and its complex structure with several antibiotics have been analyzed. however, the detailed mechanism of multiple antibiotic resistance regulator (marr) family proteins such as tcar is unclear and only restrict ...	2012	23029170
the oxidation-sensing regulator (mosr) is a new redox-dependent transcription factor in mycobacterium tuberculosis.	mycobacterium tuberculosis thrives in oxidative environments such as the macrophage. to survive, the bacterium must sense and adapt to the oxidative conditions. several antioxidant defenses including a thick cell wall, millimolar concentrations of small molecule thiols, and protective enzymes are known to help the bacterium withstand the oxidative stress. however, oxidation-sensing regulators that control these defenses have remained elusive. in this study, we report a new oxidation-sensing regu ...	2012	22992749
mapping the active site helix-to-strand conversion of cxxxxc peroxiredoxin q enzymes.	peroxiredoxins (prx) make up a family of enzymes that reduce peroxides using a peroxidatic cysteine residue; among these, members of the prxq subfamily are proposed to be the most ancestral-like yet are among the least characterized. in many prxq enzymes, a second "resolving" cysteine is located five residues downstream from the peroxidatic cys, and these residues form a disulfide during the catalytic cycle. here, we describe three hyperthermophilic prxq crystal structures originally determined ...	2012	22928725
structure and assembly of a trans-periplasmic channel for type iv pili in neisseria meningitidis.	type iv pili are polymeric fibers which protrude from the cell surface and play a critical role in adhesion and invasion by pathogenic bacteria. the secretion of pili across the periplasm and outer membrane is mediated by a specialized secretin protein, pilq, but the way in which this large channel is formed is unknown. using nmr, we derived the structures of the periplasmic domains from n. meningitidis pilq: the n-terminus is shown to consist of two β-domains, which are unique to the type iv pi ...	2012	23028322
characterization of genes encoding for acquired bacitracin resistance in clostridium perfringens.	phenotypic bacitracin resistance has been reported in clostridium perfringens. however, the genes responsible for the resistance have not yet been characterized. ninety-nine c. perfringens isolates recovered from broilers and turkeys were tested for phenotypic bacitracin resistance. bacitracin mic(90) (>256 µg/ml) was identical for both turkey and chicken isolates; whereas mic(50) was higher in turkey isolates (6 µg/ml) than in chicken isolates (3 µg/ml). twenty-four of the 99 isolates showed hi ...	2012	22970221
cis-2-dodecenoic acid receptor rpfr links quorum-sensing signal perception with regulation of virulence through cyclic dimeric guanosine monophosphate turnover.	many bacterial pathogens produce diffusible signal factor (dsf)-type quorum sensing (qs) signals in modulation of virulence and biofilm formation. previous work on xanthomonas campestris showed that the rpfc/rpfg two-component system is involved in sensing and responding to dsf signals, but little is known in other microorganisms. here we show that in burkholderia cenocepacia the dsf-family signal cis-2-dodecenoic acid (bdsf) negatively controls the intracellular cyclic dimeric guanosine monopho ...	2012	22949660
proteomic analysis of survival of rhodococcus jostii rha1 during carbon starvation.	rhodococcus jostii rha1, a catabolically diverse soil actinomycete, is highly resistant to long-term nutrient starvation. after 2 years of carbon starvation, 10% of the bacterial culture remained viable. to study the molecular basis of such resistance, we monitored the abundance of about 1,600 cytosolic proteins during a 2-week period of carbon source (benzoate) starvation. hierarchical cluster analysis elucidated 17 major protein clusters and showed that most changes occurred during transition ...	2012	22798368
a tangled web: regulatory connections between quorum sensing and cyclic di-gmp.	bacteria sense and respond to environmental cues to control important developmental processes. two widely conserved and important strategies that bacteria employ to sense changes in population density and local environmental conditions are quorum sensing (qs) and cyclic di-gmp (c-di-gmp) signaling, respectively. the importance of these pathways in controlling a broad variety of functions, including virulence, biofilm formation, and motility, has been recognized in many species. recent research h ...	2012	22661686
genome sequence of xanthomonas campestris jx, an industrially productive strain for xanthan gum.	xanthomonas campestris jx, a soil bacterium, is an industrially productive strain for xanthan gum. here we present a 5.0-mb assembly of its genome sequence. we have annotated 12 coding sequences (cdss) responsible for xanthan gum biosynthesis, 346 cdss encoding carbohydrate metabolism, and 69 cdss related to virulence, defense, and plant disease.	2012	22887662
i-pfop3i: a novel nicking hnh homing endonuclease encoded in the group i intron of the dna polymerase gene in phormidium foveolarum phage pf-wmp3.	homing endonucleases encoded in a group i self-splicing intron in a protein-coding gene in cyanophage genomes have not been reported, apart from some free-standing homing edonucleases. in this study, a nicking dna endonuclease, i-pfop3i, encoded in a group ia2 intron in the dna polymerase gene of a t7-like cyanophage pf-wmp3, which infects the freshwater cyanobacterium phormidium foveolarum is described. the pf-wmp3 intron splices efficiently in vivo and self-splices in vitro simultaneously duri ...	2012	22952751
aggregation by depletion attraction in cultures of bacteria producing exopolysaccharide.	in bacteria, the production of exopolysaccharides--polysaccharides secreted by the cells into their growth medium--is integral to the formation of aggregates and biofilms. these exopolysaccharides often form part of a matrix that holds the cells together. investigating the bacterium sinorhizobium meliloti, we found that a mutant that overproduces the exopolysaccharide succinoglycan showed enhanced aggregation, resulting in phase separation of the cultures. however, the aggregates did not appear ...	2012	22896568
yghg (gspsβ) is a novel pilot protein required for localization of the gspsβ type ii secretion system secretin of enterotoxigenic escherichia coli.	the enterotoxigenic escherichia coli (etec) pathotype, characterized by the prototypical strain h10407, is a leading cause of morbidity and mortality in the developing world. a major virulence factor of etec is the type ii secretion system (t2ss) responsible for secretion of the diarrheagenic heat-labile enterotoxin (lt). in this study, we have characterized the two type ii secretion systems, designated alpha (t2ss(α)) and beta (t2ss(β)), encoded in the h10407 genome and describe the prevalence ...	2012	22585966
crystal structure of a catalytically active gg(d/e)ef diguanylate cyclase domain from marinobacter aquaeolei with bound c-di-gmp product.	recent studies of signal transduction in bacteria have revealed a unique second messenger, bis-(3'-5')-cyclic dimeric gmp (c-di-gmp), which regulates transitions between motile states and sessile states, such as biofilms. c-di-gmp is synthesized from two gtp molecules by diguanylate cyclases (dgc). the catalytic activity of dgcs depends on a conserved gg(d/e)ef domain, usually part of a larger multi-domain protein organization. the domains other than the gg(d/e)ef domain often control dgc activa ...	2012	22843345
structures of the peld cyclic diguanylate effector involved in pellicle formation in pseudomonas aeruginosa pao1.	the second messenger bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-gmp) plays a vital role in the global regulation in bacteria. here, we describe structural and biochemical characterization of a novel c-di-gmp effector peld that is critical to the formation of pellicles by pseudomonas aeruginosa. we present high-resolution structures of a cytosolic fragment of peld in apo form and its complex with c-di-gmp. the structure contains a bi-domain architecture composed of a gaf domain (com ...	2012	22810222
quantification of high-specificity cyclic diguanylate signaling.	cyclic di-gmp (c-di-gmp) is a second messenger molecule that regulates the transition between sessile and motile lifestyles in bacteria. bacteria often encode multiple diguanylate cyclase (dgc) and phosphodiesterase (pde) enzymes that produce and degrade c-di-gmp, respectively. because of multiple inputs into the c-di-gmp-signaling network, it is unclear whether this system functions via high or low specificity. high-specificity signaling is characterized by individual dgcs or pdes that are spec ...	2012	22802636
contribution of phe-7 to tat-dependent export of β-lactamase in xanthomonas campestris.	strains of xanthomonas campestris pv. campestris isolated in taiwan are commonly resistant to ampicillin owing to the constitutive expression of a chromosomally encoded β-lactamase that is secreted into the periplasm. in this study, we found that levels of β-lactamase vary among x. campestris pv. campestris strains, a difference that can be attributed to amino acid substitutions at least at positions 7 and 206, with the former having the major impact. bioinformatic and pcr analyses indicated tha ...	2012	22526303
antibiofilm polysaccharides.	bacterial extracellular polysaccharides have been shown to mediate many of the cell-to-cell and cell-to-surface interactions that are required for the formation, cohesion and stabilization of bacterial biofilms. however, recent studies have identified several bacterial polysaccharides that inhibit biofilm formation by a wide spectrum of bacteria and fungi both in vitro and in vivo. this review discusses the composition, modes of action and potential biological roles of antibiofilm polysaccharide ...	2012	22730907
antibiofilm polysaccharides.	bacterial extracellular polysaccharides have been shown to mediate many of the cell-to-cell and cell-to-surface interactions that are required for the formation, cohesion and stabilization of bacterial biofilms. however, recent studies have identified several bacterial polysaccharides that inhibit biofilm formation by a wide spectrum of bacteria and fungi both in vitro and in vivo. this review discusses the composition, modes of action and potential biological roles of antibiofilm polysaccharide ...	2012	22730907
in silico model of dsf synthase rpff protein from xanthomonas oryzae pv. oryzae: a novel target for bacterial blight of rice disease.	rice plant diseases play a major role as biological constraints on production. one of such rice disease is bacterial leaf blight, caused by xanthomonas oryzae pv. oryzae (xoo). the diffusible signal factor (dsf) synthesized by xoo has a major role in virulence to rice plant. the dsf synthase rpff protein, which is related to crotonase superfamily is responsible for the maintaining concentration of dsf. dsf-dependent quorum sensing (qs) system adopts protein- protein interaction mechanism to auto ...	2012	22829719
the structure of mlc titration factor a (mtfa/yeei) reveals a prototypical zinc metallopeptidase related to anthrax lethal factor.	mtfa of escherichia coli (formerly yeei) was previously identified as a regulator of the phosphoenolpyruvate (pep)-dependent:glucose phosphotransferase system. mtfa homolog proteins are highly conserved, especially among beta- and gammaproteobacteria. we determined the crystal structures of the full-length mtfa apoenzyme from klebsiella pneumoniae and its complex with zinc (holoenzyme) at 2.2 and 1.95 å, respectively. mtfa contains a conserved h(149)e(150)xxh(153)+e(212)+y(205) metallopeptidase ...	2012	22467785
functional dissection of n-acetylglutamate synthase (arga) of pseudomonas aeruginosa and restoration of its ancestral n-acetylglutamate kinase activity.	in many microorganisms, the first step of arginine biosynthesis is catalyzed by the classical n-acetylglutamate synthase (nags), an enzyme composed of n-terminal amino acid kinase (aak) and c-terminal histone acetyltransferase (gnat) domains that bind the feedback inhibitor arginine and the substrates, respectively. in nags, three aak domain dimers are interlinked by their n-terminal helices, conforming a hexameric ring, whereas each gnat domain sits on the aak domain of an adjacent dimer. the a ...	2012	22447897
beta-glucans improve growth, viability and colonization of probiotic microorganisms.	probiotics, prebiotics and synbiotics are frequently-used components for the elaboration of functional food. currently, most of the commercialized probiotics are limited to a few strains of the genera bifidobacteria, lactobacillus and streptococcus, most of which produce exopolysaccharides (eps). this suggests that the beneficial properties of these microorganisms may be related to the biological activities of these biopolymers. in this work we report that a 2-substituted-(1,3)-β-d-glucan of non ...	2012	22754347
crystal structures of xanthomonas campestris olea reveal features that promote head-to-head condensation of two long-chain fatty acids.	olea is a thiolase superfamily enzyme that has been shown to catalyze the condensation of two long-chain fatty acyl-coenzyme a (coa) substrates. the enzyme is part of a larger gene cluster responsible for generating long-chain olefin products, a potential biofuel precursor. in thiolase superfamily enzymes, catalysis is achieved via a ping-pong mechanism. the first substrate forms a covalent intermediate with an active site cysteine that is followed by reaction with the second substrate. for olea ...	2012	22524624
staphylococcus aureus cymr is a new thiol-based oxidation-sensing regulator of stress resistance and oxidative response.	as a human pathogen, staphylococcus aureus must cope with oxidative stress generated by the human immune system. here, we report that cymr utilizes its sole cys-25 to sense oxidative stress. oxidation followed by thiolation of this cysteine residue leads to dissociation of cymr from its cognate promoter dna. in contrast, the dna binding of the cymrc25s mutant was insensitive to oxidation and thiolation, suggesting that cymr senses oxidative stress through oxidation of its sole cysteine to form a ...	2012	22553203
leaf microbiota in an agroecosystem: spatiotemporal variation in bacterial community composition on field-grown lettuce.	the presence, size and importance of bacterial communities on plant leaf surfaces are widely appreciated. however, information is scarce regarding their composition and how it changes along geographical and seasonal scales. we collected 106 samples of field-grown romaine lettuce from commercial production regions in california and arizona during the 2009-2010 crop cycle. total bacterial populations averaged between 10(5) and 10(6) per gram of tissue, whereas counts of culturable bacteria were on ...	2012	22534606
functional dissection of ssef, a membrane-integral effector protein of intracellular salmonella enterica.	during intracellular life, the bacterial pathogen salmonella enterica translocates a complex cocktail of effector proteins by means of the spi2-encoded type iii secretions system. the effectors jointly modify the endosomal system and vesicular transport in host cells. ssef and sseg are two effectors encoded by genes within salmonella pathogenicity island 2 and both effector associate with endosomal membranes and microtubules and are involved in the formation of salmonella-induced filaments. our ...	2012	22529968
insight on an arginine synthesis metabolon from the tetrameric structure of yeast acetylglutamate kinase.	n-acetyl-l-glutamate kinase (nagk) catalyzes the second, generally controlling, step of arginine biosynthesis. in yeasts, nagk exists either alone or forming a metabolon with n-acetyl-l-glutamate synthase (nags), which catalyzes the first step and exists only within the metabolon. yeast nagk (ynagk) has, in addition to the amino acid kinase (aak) domain found in other nagks, a ~150-residue c-terminal domain of unclear significance belonging to the duf619 domain family. we deleted this domain, pr ...	2012	22529931
aconitase b is required for optimal growth of xanthomonas campestris pv. vesicatoria in pepper plants.	the aerobic plant pathogenic bacterium xanthomonas campestris pv. vesicatoria (xcv) colonizes the intercellular spaces of pepper and tomato. one enzyme that might contribute to the successful proliferation of xcv in the host is the iron-sulfur protein aconitase, which catalyzes the conversion of citrate to isocitrate in the tricarboxylic acid (tca) cycle and might also sense reactive oxygen species (ros) and changes in cellular iron levels. xcv contains three putative aconitases, two of which, a ...	2012	22493725
sumoylation at the host-pathogen interface.	many viral proteins have been shown to be sumoylated with corresponding regulatory effects on their protein function, indicating that this host cell modification process is widely exploited by viral pathogens to control viral activity. in addition to using sumoylation to regulate their own proteins, several viral pathogens have been shown to modulate overall host sumoylation levels. given the large number of cellular targets for sumo addition and the breadth of critical cellular processes that a ...	2012	23795346
an alginate-layer technique for culture of brassica oleracea l. protoplasts.	ten accessions belonging to the brassica oleracea subspecies alba and rubra, and to b. oleracea var. sabauda were used in this study. protoplasts were isolated from leaves and hypocotyls of in vitro grown plants. the influence of selected factors on the yield, viability, and mitotic activity of protoplasts immobilized in calcium alginate layers was investigated. the efficiency of protoplast isolation from hypocotyls was lower (0.7 ± 0.1 × 10(6) ml(-1)) than for protoplasts isolated from leaf mes ...	2012	22593638
genomes-based phylogeny of the genus xanthomonas.	the genus xanthomonas comprises several plant pathogenic bacteria affecting a wide range of hosts. despite the economic, industrial and biological importance of xanthomonas, the classification and phylogenetic relationships within the genus are still under active debate. some of the relationships between pathovars and species have not been thoroughly clarified, with old pathovars becoming new species. a change in the genus name has been recently suggested for xanthomonas albilineans, an early br ...	2012	22443110
metal transport across biomembranes: emerging models for a distinct chemistry.	transition metals are essential components of important biomolecules, and their homeostasis is central to many life processes. transmembrane transporters are key elements controlling the distribution of metals in various compartments. however, due to their chemical properties, transition elements require transporters with different structural-functional characteristics from those of alkali and alkali earth ions. emerging structural information and functional studies have revealed distinctive fea ...	2012	22389499
marr-type transcriptional regulator chlr activates expression of tetrapyrrole biosynthesis genes in response to low-oxygen conditions in cyanobacteria.	oxygen is required for three enzyme reactions in chlorophyll and bilin biosynthesis pathways: coproporphyrinogen iii oxidase (hemf), heme oxygenase (ho1), and mg-protoporphyrin ix monomethylester cyclase (chla(i)). the cyanobacterium synechocystis sp. pcc 6803 has alternative enzymes, hemn, ho2, and chla(ii), to supply chlorophyll/bilins even under low-oxygen environments. the three genes form an operon, chla(ii)-ho2-hemn, that is induced in response to low-oxygen conditions to bypass the oxygen ...	2012	22375005
crystallization and preliminary x-ray diffraction characterization of the xccfimx(eal)-c-di-gmp and xccfimx(eal)-c-di-gmp-xccpilz complexes from xanthomonas campestris.	c-di-gmp is a major secondary-messenger molecule in regulation of bacterial pathogenesis. therefore, the c-di-gmp-mediated signal transduction network is of considerable interest. the pilz domain was the first c-di-gmp receptor to be predicted and identified. however, every pilz domain binds c-di-gmp with a different binding affinity. intriguingly, a noncanonical pilz domain has recently been found to serve as a mediator to link fimx(eal) to the pilb or pilt atpase to control the function of typ ...	2012	22442228
characterization of catalase from psychrotolerant psychrobacter piscatorii t-3 exhibiting high catalase activity.	a psychrotolerant bacterium, strain t-3 (identified as psychrobacter piscatorii), that exhibited an extraordinarily high catalase activity was isolated from the drain pool of a plant that uses h(2)o(2) as a bleaching agent. its cell extract exhibited a catalase activity (19,700 u·mg protein(-1)) that was higher than that of micrococcus luteus used for industrial catalase production. catalase was approximately 10% of the total proteins in the cell extract of the strain. the catalase (pkta) was pu ...	2012	22408420
identification of the protein sequence of the type iii effector xopd from the b100 strain of xanthomonas campestris pv campestris.	during evolution, pathogens have developed sophisticated strategies to suppress plant defense responses and promote successful colonization of their hosts. in their attempt to quell host resistance, gram-negative phytopathogenic bacteria inject type iii effectors (t3es) into plant cells, where they typically target plant components essential for the establishment of defense responses. we have recently shown that the xopd t3e from the strain b100 of xanthomonas campestris pathovar campestris (xop ...	2012	22353870
global regulation of gene expression by oxyr in an important human opportunistic pathogen.	most bacteria control oxidative stress through the h(2)o(2)-responsive transactivator oxyr, a member of the lttr family (lysr type transcriptional regulators), which activates the expression of defensive genes such as those encoding catalases, alkyl hydroperoxide reductases and superoxide dismutases. in the human opportunistic pathogen pseudomonas aeruginosa, oxyr positively regulates expression of the oxidative stress response genes kata, katb, ahpb and ahpcf. to identify additional targets of ...	2012	22275523
the arabidopsis o-linked n-acetylglucosamine transferase spindly interacts with class i tcps to facilitate cytokinin responses in leaves and flowers.	o-linked n-acetylglucosamine (o-glcnac) modifications regulate the posttranslational fate of target proteins. the arabidopsis thaliana o-glcnac transferase (ogt) spindly (spy) suppresses gibberellin signaling and promotes cytokinin (ck) responses by unknown mechanisms. here, we present evidence that two closely related class i tcp transcription factors, tcp14 and tcp15, act with spy to promote ck responses. tcp14 and tcp15 interacted with spy in yeast two-hybrid and in vitro pull-down assays and ...	2012	22267487
the mycobacterial lysr-type regulator oxys responds to oxidative stress and negatively regulates expression of the catalase-peroxidase gene.	protection against oxidative stress is one of the primary defense mechanisms contributing to the survival of mycobacterium tuberculosis in the host. in this study, we provide evidence that oxys, a lysr-type transcriptional regulator functions as an oxidative stress response regulator in mycobacteria. overexpression of oxys lowers expression of the catalase-peroxidase (katg) gene in m. smegmatis. oxys binds directly with the katg promoter region and a conserved, gc-rich t-n(11)-a motif for oxys b ...	2012	22272299
smart sensor for real-time quantification of common symptoms present in unhealthy plants.	plant responses to physiological function disorders are called symptoms and they are caused principally by pathogens and nutritional deficiencies. plant symptoms are commonly used as indicators of the health and nutrition status of plants. nowadays, the most popular method to quantify plant symptoms is based on visual estimations, consisting on evaluations that raters give based on their observation of plant symptoms; however, this method is inaccurate and imprecise because of its obvious subjec ...	2012	22368496
production of quorum sensing inhibitors in growing onion bulbs infected with pseudomonas aeruginosa e (hq324110).	eighteen organic compounds were present in growing onion bulbs cultivar giza 6 infected with p. aeruginosa, but only fourteen of them are present in dry infected onion bulbs; however, four compounds were missing in dry onion. the missing compounds in dry infected onion bulbs are pantolactone, 4,5-dihydro-4,5-dimethylfuran-2(3h)-one, myristic acid, and linoleic acid. all of them were detected in growing onion (living cell) during pseudomonas aeruginosa infection, and it is hypothesized that it ma ...	2012	23724316
expression of four methionine sulfoxide reductases in staphylococcus aureus.	staphylococcus aureus possesses three msra enzymes (msra1, msra2, msra3) that reduce the s-epimer of methionine sulfoxide (meto) and an msrb enzyme that reduces r-meto. the four msr genes are expressed from three different promoters. the msra1/msrb genes are coexpressed. to determine the expression pattern of msr genes, three independent reporter strains were constructed where msr promoter was cloned in front of a promoterless lacz and the resulting construct was integrated in the chromosome. us ...	2012	22272204
trojan horse strategies used by pathogens to influence the small ubiquitin-like modifier (sumo) system of host eukaryotic cells.	a remarkable feature of pathogenic organisms is their ability to utilize the cellular machinery of host cells to their advantage in facilitating their survival and propagation. posttranslational modification of proteins offers a quick way to achieve changes in the localization, binding partners or functions of a target protein. it is no surprise then that pathogens have evolved multiple ways to interfere with host posttranslational modifications and hijack them for their own purposes. recently, ...	2012	22223032
the importance of the interaction of ched with chec and the chemoreceptors compared to its enzymatic activity during chemotaxis in bacillus subtilis.	bacillus subtilis use three systems for adaptation during chemotaxis. one of these systems involves two interacting proteins, chec and ched. ched binds to the receptors and increases their ability to activate the chea kinase. ched also binds chec, and the strength of this interaction is increased by phosphorylated chey. chec is believed to control the binding of ched to the receptors in response to the levels of phosphorylated chey. in addition to their role in adaptation, chec and ched also hav ...	2012	23226535