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molecular evolution of urea amidolyase and urea carboxylase in fungi.urea amidolyase breaks down urea into ammonia and carbon dioxide in a two-step process, while another enzyme, urease, does this in a one step-process. urea amidolyase has been found only in some fungal species among eukaryotes. it contains two major domains: the amidase and urea carboxylase domains. a shorter form of urea amidolyase is known as urea carboxylase and has no amidase domain. eukaryotic urea carboxylase has been found only in several fungal species and green algae. in order to elucid ...201121447149
senescence marker protein 30: functional and structural insights to its unknown physiological function.senescence marker protein 30 (smp30) is a multifunctional protein involved in cellular ca(2+) homeostasis and the biosynthesis of ascorbate in non-primate mammals. the primary structure of the protein is highly conserved among vertebrates, suggesting the existence of a significant physiological function common to all mammals, including primates. enzymatic activities of smp30 include aldonolactone and organophosphate hydrolysis. protective effects against apoptosis and oxidative stress have been ...201122844387
senescence marker protein 30: functional and structural insights to its unknown physiological function.senescence marker protein 30 (smp30) is a multifunctional protein involved in cellular ca(2+) homeostasis and the biosynthesis of ascorbate in non-primate mammals. the primary structure of the protein is highly conserved among vertebrates, suggesting the existence of a significant physiological function common to all mammals, including primates. enzymatic activities of smp30 include aldonolactone and organophosphate hydrolysis. protective effects against apoptosis and oxidative stress have been ...201122844387
an approach for searching insertions in bacterial genes leading to the phase shift of triplet periodicity.the concept of the phase shift of triplet periodicity (tp) was used for searching potential dna insertions in genes from 17 bacterial genomes. a mathematical algorithm for detection of these insertions has been developed. this approach can detect potential insertions and deletions with lengths that are not multiples of three bases, especially insertions of relatively large dna fragments (>100 bases). new similarity measure between triplet matrixes was employed to improve the sensitivity for dete ...201122196359
structural and biochemical changes in salicylic-acid-treated date palm roots challenged with fusarium oxysporum f. sp. albedinis.histochemical and ultrastructural analyses were carried out to assess structural and biochemical changes in date palm roots pretreated with salicylic acid (sa) then inoculated with fusarium oxysporum f. sp. albedinis (foa). flavonoids, induced proteins, and peroxidase activity were revealed in root tissues of sa-treated plants after challenge by foa. these reactions were closely associated with plant resistance to foa. host reactions induced after inoculation of sa-treated plants with foa includ ...201122567327
draft genome sequences of xanthomonas sacchari and two banana-associated xanthomonads reveal insights into the xanthomonas group 1 clade.we present draft genome sequences for three strains of xanthomonas species, each of which was associated with banana plants (musa species) but is not closely related to the previously sequenced banana-pathogen xanthomonas campestris pathovar musacearum. strain ncppb4393 had been deposited as xanthomonas campestris pathovar musacearum but in fact falls within the species xanthomonas sacchari. strain ncppb1132 is more distantly related to xanthomonas sacchari whilst strain ncppb 1131 grouped in a ...201124710305
opaque7 encodes an acyl-activating enzyme-like protein that affects storage protein synthesis in maize endosperm.in maize, a series of seed mutants with starchy endosperm could increase the lysine content by decreased amount of zeins, the main storage proteins in endosperm. cloning and characterization of these mutants could reveal regulatory mechanisms for zeins accumulation in maize endosperm. opaque7 (o7) is a classic maize starchy endosperm mutant with large effects on zeins accumulation and high lysine content. in this study, the o7 gene was cloned by map-based cloning and confirmed by transgenic func ...201121954158
effects of xanthan, guar, carrageenan and locust bean gum addition on physical, chemical and sensory properties of meatballs.this study evaluated the effects of xanthan gum, guar gum, carrageenan and locust bean gum on physical, chemical and sensory properties of meatballs. meatball samples were produced with three different formulations including of 0.5, 1, and 1.5% each gum addition and gum added samples were compared with the control meatballs. physical and chemical analyses were carried out on raw and cooked samples separately. moisture contents of raw samples decreased by addition of gums. there were significant ...201124803701
effects of xanthan, guar, carrageenan and locust bean gum addition on physical, chemical and sensory properties of meatballs.this study evaluated the effects of xanthan gum, guar gum, carrageenan and locust bean gum on physical, chemical and sensory properties of meatballs. meatball samples were produced with three different formulations including of 0.5, 1, and 1.5% each gum addition and gum added samples were compared with the control meatballs. physical and chemical analyses were carried out on raw and cooked samples separately. moisture contents of raw samples decreased by addition of gums. there were significant ...201124803701
enhanced resistance to bacterial and fungal pathogens by overexpression of a human cathelicidin antimicrobial peptide (hcap18/ll-37) in chinese cabbage.the human cathelicidin antimicrobial protein hcap18, which includes the c-terminal peptide ll-37, is a multifunctional protein. as a possible approach to enhancing the resistance to plant disease, a dna fragment coding for hcap18/ll-37 was fused at the c-terminal end of the leader sequence of endopolygalacturonase-inhibiting protein under the control of the cauliflower mosaic virus 35s promoter region. the construct was then introduced into brassica rapa. ll-37 expression was confirmed in transg ...201122308171
enhanced resistance to bacterial and fungal pathogens by overexpression of a human cathelicidin antimicrobial peptide (hcap18/ll-37) in chinese cabbage.the human cathelicidin antimicrobial protein hcap18, which includes the c-terminal peptide ll-37, is a multifunctional protein. as a possible approach to enhancing the resistance to plant disease, a dna fragment coding for hcap18/ll-37 was fused at the c-terminal end of the leader sequence of endopolygalacturonase-inhibiting protein under the control of the cauliflower mosaic virus 35s promoter region. the construct was then introduced into brassica rapa. ll-37 expression was confirmed in transg ...201122308171
plant glutathione biosynthesis: diversity in biochemical regulation and reaction products.in plants, exposure to temperature extremes, heavy metal-contaminated soils, drought, air pollutants, and pathogens results in the generation of reactive oxygen species that alter the intracellular redox environment, which in turn influences signaling pathways and cell fate. as part of their response to these stresses, plants produce glutathione. glutathione acts as an anti-oxidant by quenching reactive oxygen species, and is involved in the ascorbate-glutathione cycle that eliminates damaging p ...201122645536
sublethal concentrations of salicylic acid decrease the formation of reactive oxygen species but maintain an increased nitric oxide production in the root apex of the ethylene-insensitive never ripe tomato mutants.the pattern of salicylic acid (sa)-induced production of reactive oxygen species (ros) and nitric oxide (no) were different in the apex of adventitious roots in wild-type and in the ethylene-insensitive never ripe (nr) mutants of tomato (solanum lycopersicum l. cv ailsa craig). ros were upregulated, while no remained at the control level in apical root tissues of wildtype plants exposed to sublethal concentrations of sa. in contrast, nr plants expressing a defective ethylene receptor displayed a ...201121847015
structure-based insights into the catalytic power and conformational dexterity of peroxiredoxins.peroxiredoxins (prxs), some of nature's dominant peroxidases, use a conserved cys residue to reduce peroxides. they are highly expressed in organisms from all kingdoms, and in eukaryotes they participate in hydrogen peroxide signaling. seventy-two prx structures have been determined that cover much of the diversity of the family. we review here the current knowledge and show that prxs can be effectively classified by a structural/evolutionary organization into six subfamilies followed by specifi ...201120969484
minimal phenotypic test for simple differentiation of xanthomonas campestris from other yellow-pigmented bacteria isolated from soil.isolation of xanthomonas campestris from soil has a wide range of applications from monitoring of phytopathogenic populations in soil to screening of improved xanthan-producing strains. identification of xanthomonas campestris and its pathovars requires pathogenicity tests in addition to phenotypic and molecular characterization.201122347588
new culture medium to xanthan production by xanthomonas campestris pv. campestris.xanthan is a important biopolymer for commercial purpose and it is produced in two stages by xanthomonas campestris. in the first one, the bacterium is cultivated in the complex medium enriched in nitrogen and the biomass produced is used as inoculum for the next stage in which the gum is produced in another medium. in this work a new medium for the first stage is proposed in place of currently used ym medium. different formulated growth media were studied and the correspondent biomass produced ...201122754004
catalytic versus inhibitory promiscuity in cytochrome p450s: implications for evolution of new function.catalytically promiscuous enzymes are intermediates in the evolution of new function from an existing pool of protein scaffolds. however, promiscuity will only confer an evolutionary advantage if other useful properties are not compromised or if there is no "negative trade-off" induced by the mutations that yield promiscuity. therefore, identification and characterization of negative trade-offs incurred during the emergence of promiscuity are required to further develop the evolutionary models a ...201121370922
molecular recognition: o-glcnac transfer: size matters. 201121321551
structure and reaction mechanism in the heme dioxygenases.as members of the family of heme-dependent enzymes, the heme dioxygenases are differentiated by virtue of their ability to catalyze the oxidation of l-tryptophan to n-formylkynurenine, the first and rate-limiting step in tryptophan catabolism. in the past several years, there have been a number of important developments that have meant that established proposals for the reaction mechanism in the heme dioxygenases have required reassessment. this focused review presents a summary of these recent ...201121361337
evolutionary origins of brassicaceae specific genes in arabidopsis thaliana.all sequenced genomes contain a proportion of lineage-specific genes, which exhibit no sequence similarity to any genes outside the lineage. despite their prevalence, the origins and functions of most lineage-specific genes remain largely unknown. as more genomes are sequenced opportunities for understanding evolutionary origins and functions of lineage-specific genes are increasing.201121332978
minimal absent words in prokaryotic and eukaryotic genomes.minimal absent words have been computed in genomes of organisms from all domains of life. here, we explore different sets of minimal absent words in the genomes of 22 organisms (one archaeota, thirteen bacteria and eight eukaryotes). we investigate if the mutational biases that may explain the deficit of the shortest absent words in vertebrates are also pervasive in other absent words, namely in minimal absent words, as well as to other organisms. we find that the compositional biases observed f ...201121386877
extended fujita approach to the molecular weight distribution of polysaccharides and other polymeric systems.in 1962 h. fujita (h. fujita, mathematical theory of sedimentation analysis, academic press, new york, 1962) examined the possibility of transforming a quasi-continuous distribution g(s) of sedimentation coefficient s into a distribution f(m) of molecular weight m for linear polymers using the relation f(m)=g(s)·(ds/dm) and showed that this could be done if information about the relation between s and m is available from other sources. fujita provided the transformation based on the scaling rela ...201121276851
sumo and sumoylation in plants.the traditional focus on the central dogma of molecular biology, from gene through rna to protein, has now been replaced by the recognition of an additional mechanism. the new regulatory mechanism, post-translational modifications to proteins, can actively alter protein function or activity introducing additional levels of functional complexity by altering cellular and sub-cellular location, protein interactions and the outcome of biochemical reaction chains. modifications by ubiquitin (ub) and ...201121912873
synthesis, production, and biotechnological applications of exopolysaccharides and polyhydroxyalkanoates by archaea.extreme environments, generally characterized by atypical temperatures, ph, pressure, salinity, toxicity, and radiation levels, are inhabited by various microorganisms specifically adapted to these particular conditions, called extremophiles. among these, the microorganisms belonging to the archaea domain are of significant biotechnological importance as their biopolymers possess unique properties that offer insights into their biology and evolution. particular attention has been devoted to two ...201122007151
new structural and functional contexts of the dx[dn]xdg linear motif: insights into evolution of calcium-binding proteins.binding of calcium ions (ca²⁺) to proteins can have profound effects on their structure and function. common roles of calcium binding include structure stabilization and regulation of activity. it is known that diverse families--ef-hands being one of at least twelve--use a dx[dn]xdg linear motif to bind calcium in near-identical fashion. here, four novel structural contexts for the motif are described. existing experimental data for one of them, a thermophilic archaeal subtilisin, demonstrate fo ...201121720552
the enzymes of bacterial census and censorship.n-acyl-l-homoserine lactones (ahls) are a major class of quorum-sensing signals used by gram-negative bacteria to regulate gene expression in a population-dependent manner, thereby enabling group behavior. enzymes capable of generating and catabolizing ahl signals are of significant interest for the study of microbial ecology and quorum-sensing pathways, for understanding the systems that bacteria have evolved to interact with small-molecule signals, and for their possible use in therapeutic and ...201122099187
the enzymes of bacterial census and censorship.n-acyl-l-homoserine lactones (ahls) are a major class of quorum-sensing signals used by gram-negative bacteria to regulate gene expression in a population-dependent manner, thereby enabling group behavior. enzymes capable of generating and catabolizing ahl signals are of significant interest for the study of microbial ecology and quorum-sensing pathways, for understanding the systems that bacteria have evolved to interact with small-molecule signals, and for their possible use in therapeutic and ...201122099187
a plethora of virulence strategies hidden behind nuclear targeting of microbial effectors.plant immune responses depend on the ability to couple rapid recognition of the invading microbe to an efficient response. during evolution, plant pathogens have acquired the ability to deliver effector molecules inside host cells in order to manipulate cellular and molecular processes and establish pathogenicity. following translocation into plant cells, microbial effectors may be addressed to different subcellular compartments. intriguingly, a significant number of effector proteins from diffe ...201122639625
the comprehensive phytopathogen genomics resource: a web-based resource for data-mining plant pathogen genomes.the comprehensive phytopathogen genomics resource (cpgr) provides a web-based portal for plant pathologists and diagnosticians to view the genome and trancriptome sequence status of 806 bacterial, fungal, oomycete, nematode, viral and viroid plant pathogens. tools are available to search and analyze annotated genome sequences of 74 bacterial, fungal and oomycete pathogens. oomycete and fungal genomes are obtained directly from genbank, whereas bacterial genome sequences are downloaded from the a ...201122120664
nuclear dynamics during plant innate immunity. 201121951465
nuclear dynamics during plant innate immunity. 201121951465
lrr conservation mapping to predict functional sites within protein leucine-rich repeat domains.computational prediction of protein functional sites can be a critical first step for analysis of large or complex proteins. contemporary methods often require several homologous sequences and/or a known protein structure, but these resources are not available for many proteins. leucine-rich repeats (lrrs) are ligand interaction domains found in numerous proteins across all taxonomic kingdoms, including immune system receptors in plants and animals. we devised repeat conservation mapping (rcm), ...201121789174
interactions of bacterial proteins with host eukaryotic ubiquitin pathways.ubiquitination is a post-translational modification in which one or more 76 amino acid polypeptide ubiquitin molecules are covalently linked to the lysine residues of target proteins. ubiquitination is the main pathway for protein degradation that governs a variety of eukaryotic cellular processes, including the cell-cycle, vesicle trafficking, antigen presentation, and signal transduction. not surprisingly, aberrations in the system have been implicated in the pathogenesis of many diseases incl ...201121772834
of pamps and effectors: the blurred pti-eti dichotomy.typically, pathogen-associated molecular patterns (pamps) are considered to be conserved throughout classes of microbes and to contribute to general microbial fitness, whereas effectors are species, race, or strain specific and contribute to pathogen virulence. both types of molecule can trigger plant immunity, designated pamp-triggered and effector-triggered immunity (pti and eti, respectively). however, not all microbial defense activators conform to the common distinction between pamps and ef ...201121278123
glycoalkaloid metabolism1 is required for steroidal alkaloid glycosylation and prevention of phytotoxicity in tomato.steroidal alkaloids (sas) are triterpene-derived specialized metabolites found in members of the solanaceae family that provide plants with a chemical barrier against a broad range of pathogens. their biosynthesis involves the action of glycosyltransferases to form steroidal glycoalkaloids (sgas). to elucidate the metabolism of sgas in the solanaceae family, we examined the tomato (solanum lycopersicum) glycoalkaloid metabolism1 (game1) gene. our findings imply that game1 is a galactosyltransfer ...201122180624
chromatin configuration as a battlefield in plant-bacteria interactions. 201121825106
cell wall damage-induced lignin biosynthesis is regulated by a reactive oxygen species- and jasmonic acid-dependent process in arabidopsis.the plant cell wall is a dynamic and complex structure whose functional integrity is constantly being monitored and maintained during development and interactions with the environment. in response to cell wall damage (cwd), putatively compensatory responses, such as lignin production, are initiated. in this context, lignin deposition could reinforce the cell wall to maintain functional integrity. lignin is important for the plant's response to environmental stress, for reinforcement during secon ...201121546454
programmed cell death in the plant immune system.cell death has a central role in innate immune responses in both plants and animals. besides sharing striking convergences and similarities in the overall evolutionary organization of their innate immune systems, both plants and animals can respond to infection and pathogen recognition with programmed cell death. the fact that plant and animal pathogens have evolved strategies to subvert specific cell death modalities emphasizes the essential role of cell death during immune responses. the hyper ...201121475301
the role of the plasma membrane h+-atpase in plant-microbe interactions.plasma membrane (pm) h+-atpases are the primary pumps responsible for the establishment of cellular membrane potential in plants. in addition to regulating basic aspects of plant cell function, these enzymes contribute to signaling events in response to diverse environmental stimuli. here, we focus on the roles of the pm h+-atpase during plant-pathogen interactions. pm h+-atpases are dynamically regulated during plant immune responses and recent quantitative proteomics studies suggest complex sp ...201121300757
phospholipases in action during plant defense signaling.eukaryotic organisms rely on intricate signaling networks to connect recognition of microbes with the activation of efficient defense reactions. accumulating evidence indicates that phospholipids are more than mere structural components of biological membranes. indeed, phospholipid-based signal transduction is widely used in plant cells to relay perception of extracellular signals. upon perception of the invading microbe, several phospholipid hydrolyzing enzymes are activated that contribute to ...201121248491
the tomato rlk superfamily: phylogeny and functional predictions about the role of the lrrii-rlk subfamily in antiviral defense.receptor-like kinases (rlks) play key roles during development and in responses to the environment. despite the relevance of the rlk family and the completion of the tomato genome sequencing, the tomato rlk family has not yet been characterized, and a framework for functional predictions of the members of the family is lacking.201223198823
hrcq provides a docking site for early and late type iii secretion substrates from xanthomonas.pathogenicity of many gram-negative bacteria depends on a type iii secretion (t3s) system which translocates bacterial effector proteins into eukaryotic cells. the membrane-spanning secretion apparatus is associated with a cytoplasmic atpase complex and a predicted cytoplasmic (c) ring structure which is proposed to provide a substrate docking platform for secreted proteins. in this study, we show that the putative c ring component hrcq from the plant pathogenic bacterium xanthomonas campestris ...201223226460
involvement of bacterial tonb-dependent signaling in the generation of an oligogalacturonide damage-associated molecular pattern from plant cell walls exposed to xanthomonas campestris pv. campestris pectate lyases.efficient perception of attacking pathogens is essential for plants. plant defense is evoked by molecules termed elicitors. endogenous elicitors or damage-associated molecular patterns (damps) originate from plant materials upon injury or pathogen activity. while there are comparably well-characterized examples for damps, often oligogalacturonides (ogas), generated by the activity of fungal pathogens, endogenous elicitors evoked by bacterial pathogens have been rarely described. in particular, t ...201223082751
catecholate siderophores protect bacteria from pyochelin toxicity.bacteria produce small molecule iron chelators, known as siderophores, to facilitate the acquisition of iron from the environment. the synthesis of more than one siderophore and the production of multiple siderophore uptake systems by a single bacterial species are common place. the selective advantages conferred by the multiplicity of siderophore synthesis remains poorly understood. however, there is growing evidence suggesting that siderophores may have other physiological roles besides their ...201223071628
an amino acid substitution inhibits specialist herbivore production of an antagonist effector and recovers insect-induced plant defenses.plants respond to insect herbivory through the production of biochemicals that function as either direct defenses or indirect defenses via the attraction of natural enemies. while attack by closely related insect pests can result in distinctive levels of induced plant defenses, precise biochemical mechanisms responsible for differing responses remain largely unknown. cowpea (vigna unguiculata) responds to fall armyworm (spodoptera frugiperda) herbivory through the detection of fragments of chlor ...201223008466
diversities in virulence, antifungal activity, pigmentation and dna fingerprint among strains of burkholderia glumae.burkholderia glumae is the primary causal agent of bacterial panicle blight of rice. in this study, 11 naturally avirulent and nine virulent strains of b. glumae native to the southern united states were characterized in terms of virulence in rice and onion, toxofalvin production, antifungal activity, pigmentation and genomic structure. virulence of b. glumae strains on rice panicles was highly correlated to virulence on onion bulb scales, suggesting that onion bulb can be a convenient alternati ...201223028972
disease resistance to pectobacterium carotovorum is negatively modulated by the arabidopsis lectin receptor kinase lecrk-v.5.plant stomata function in disease resistance by restricting bacteria entry inside leaves. during plant-bacteria interactions, stomatal closure is initiated by the recognition of microbe-associated molecular patterns (mamps). recently, we have shown that the lectin receptor kinase v.5 (lecrk-v.5) negatively regulates bacterium- and mamp-induced stomatal closure upstream of reactive oxygen species (ros) production mediated by abscisic acid signaling. closed stomata in lecrk-v.5 mutants are correla ...201222899085
hspro controls early nicotiana attenuata seedling growth during interaction with the fungus piriformospora indica.in a previous study aimed at identifying regulators of nicotiana attenuata responses against chewing insects, a 26-nucleotide tag matching the hspro (ortholog of sugar beet hs1(pro)(-)(1)) gene was found to be strongly induced after simulated herbivory (gilardoni et al., 2010). here we characterized the function of hspro during biotic interactions in transgenic n. attenuata plants silenced in its expression (ir-hspro). in wild-type plants, hspro expression was not only induced during simulated h ...201222892352
the prolific atl family of ring-h2 ubiquitin ligases.an abundant class of e3 ubiquitin ligases encodes the ring-finger domain. the ring finger binds to the e2 ubiquitin-conjugating enzyme and brings together both the e2 and substrate. it is predicted that 477 ring finger e3 ligases exist in arabidopsis thaliana. a particular family among them, named arabidopsis tóxicos en levadura (atl), consists of 91 members that contain the ring-h2 variation and a hydrophobic domain located at the n-terminal end. transmembrane e3 ligases are important in severa ...201222827943
expanded roles for multicargo and class 1b effector chaperones in type iii secretion.bacterial type iii secretion systems (t3ss) are complex protein assemblies that mediate the secretion of protein substrates outside the cell. type iii secretion chaperones (t3sc) are always found associated with t3ss, and they serve in multiple roles to ensure that protein substrates are efficiently targeted for secretion. bacterial pathogens with t3ss express t3sc proteins that bind effectors, a process important for effector protein delivery into eukaryotic cells during infection. in this mini ...201222636784
the novel kasugamycin 2'-n-acetyltransferase gene aac(2')-iia, carried by the incp island, confers kasugamycin resistance to rice-pathogenic bacteria.kasugamycin (ksm), a unique aminoglycoside antibiotic, has been used in agriculture for many years to control not only rice blast caused by the fungus magnaporthe grisea but also rice bacterial grain and seedling rot or rice bacterial brown stripe caused by burkholderia glumae or acidovorax avenae subsp. avenae, respectively. since both bacterial pathogens are seed-borne and cause serious injury to rice seedlings, the emergence of ksm-resistant b. glumae and a. avenae isolates highlights the urg ...201222660700
ketoglutarate transport protein kgtp is secreted through the type iii secretion system and contributes to virulence in xanthomonas oryzae pv. oryzae.the phytopathogenic prokaryote xanthomonas oryzae pv. oryzae is the causal agent of bacterial leaf blight (bb) of rice and utilizes a type iii secretion system (t3ss) to deliver t3ss effectors into rice cells. in this report, we show that the ketoglutarate transport protein (kgtp) is secreted in an hpab-independent manner through the t3ss of x. oryzae pv. oryzae pxo99(a) and localizes to the host cell membrane for α-ketoglutaric acid export. kgtp contained an imperfect pip box (plant-inducible p ...201222685129
genetic and physical mapping of candidate genes for resistance to fusarium oxysporum f.sp. tracheiphilum race 3 in cowpea [vigna unguiculata (l.) walp].fusarium oxysporum f.sp. tracheiphilum (fot) is a soil-borne fungal pathogen that causes vascular wilt disease in cowpea. fot race 3 is one of the major pathogens affecting cowpea production in california. identification of fot race 3 resistance determinants will expedite delivery of improved cultivars by replacing time-consuming phenotypic screening with selection based on perfect markers, thereby generating successful cultivars in a shorter time period. resistance to fot race 3 was studied in ...201222860000
genome-wide identification of pseudomonas aeruginosa virulence-related genes using a caenorhabditis elegans infection model.pseudomonas aeruginosa strain pa14 is an opportunistic human pathogen capable of infecting a wide range of organisms including the nematode caenorhabditis elegans. we used a non-redundant transposon mutant library consisting of 5,850 clones corresponding to 75% of the total and approximately 80% of the non-essential pa14 orfs to carry out a genome-wide screen for attenuation of pa14 virulence in c. elegans. we defined a functionally diverse 180 mutant set (representing 170 unique genes) necessar ...201222911607
effector-triggered post-translational modifications and their role in suppression of plant immunity.plant-pathogen interactions feature complex signaling exchanges between host and microbes that ultimately determine association outcomes. plants deploy pattern recognition receptors to perceive pathogen-associated molecular patterns, mount pattern-triggered immunity (pti), and fend off potential pathogens. in recent years an increasing number of defense-signaling components have been identified along with a mechanistic understanding of their regulation during immune responses. post-translational ...201222811685
variation in extragenic repetitive dna sequences in pseudomonas syringae and potential use of modified rep primers in the identification of closely related isolates.in this study, pseudomonas syringe pathovars isolated from olive, tomato and bean were identified by species-specific pcr and their genetic diversity was assessed by repetitive extragenic palindromic (rep)-pcr. reverse universal primers for rep-pcr were designed by using the bases of a, t, g or c at the positions of 1, 4 and 11 to identify additional polymorphism in the banding patterns. binding of the primers to different annealing sites in the genome revealed additional fingerprint patterns in ...201223055805
tomato tft1 is required for pamp-triggered immunity and mutations that prevent t3s effector xopn from binding to tft1 attenuate xanthomonas virulence.xopn is a type iii effector protein from xanthomonas campestris pathovar vesicatoria that suppresses pamp-triggered immunity (pti) in tomato. previous work reported that xopn interacts with the tomato 14-3-3 isoform tft1; however, tft1's role in pti and/or xopn virulence was not determined. here we show that tft1 functions in pti and is a xopn virulence target. virus-induced gene silencing of tft1 mrna in tomato leaves resulted in increased growth of xcv δxopn and xcv δhrpf demonstrating that tf ...201222719257
novel phakopsora pachyrhizi extracellular proteins are ideal targets for immunological diagnostic assays.phakopsora pachyrhizi, the causal agent of asian soybean rust (asr), continues to spread across the southeast and midsouth regions of the united states, necessitating the use of fungicides by producers. our objective in this research was to identify asr proteins expressed early during infection for the development of immunodiagnostic assays. we have identified and partially characterized a small gene family encoding extracellular proteins in the p. pachyrhizi urediniospore wall, termed pheps (fo ...201222447596
complete genome sequence, lifestyle, and multi-drug resistance of the human pathogen corynebacterium resistens dsm 45100 isolated from blood samples of a leukemia patient.corynebacterium resistens was initially recovered from human infections and recognized as a new coryneform species that is highly resistant to antimicrobial agents. bacteremia associated with this organism in immunocompromised patients was rapidly fatal as standard minocycline therapies failed. c. resistens dsm 45100 was isolated from a blood culture of samples taken from a patient with acute myelocytic leukemia. the complete genome sequence of c. resistens dsm 45100 was determined by pyrosequen ...201222524407
requirement of the cytosolic interaction between pathogenesis-related protein10 and leucine-rich repeat protein1 for cell death and defense signaling in pepper.plants recruit innate immune receptors such as leucine-rich repeat (lrr) proteins to recognize pathogen attack and activate defense genes. here, we identified the pepper (capsicum annuum) pathogenesis-related protein10 (pr10) as a leucine-rich repeat protein1 (lrr1)-interacting partner. bimolecular fluorescence complementation and coimmunoprecipitation assays confirmed the specific interaction between lrr1 and pr10 in planta. avirulent xanthomonas campestris pv vesicatoria infection induces pr10 ...201222492811
large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events.an increasing amount of evidence from experimental and computational analysis suggests that rare codon clusters are functionally important for protein activity. most of the studies on rare codon clusters were performed on a limited number of proteins or protein families. in the present study, we present the sherlocc program and how it can be used for large scale protein family analysis of evolutionarily conserved rare codon clusters and their relation to protein function and structure. this larg ...201222467916
identification of immunogenic microbial patterns takes the fast lane. 201222403065
erwinia amylovora expresses fast and simultaneously hrp/dsp virulence genes during flower infection on apple trees.pathogen entry through host blossoms is the predominant infection pathway of the gram-negative bacterium erwinia amylovora leading to manifestation of the disease fire blight. like in other economically important plant pathogens, e. amylovora pathogenicity depends on a type iii secretion system encoded by hrp genes. however, timing and transcriptional order of hrp gene expression during flower infections are unknown.201222412891
xylella fastidiosa comparative genomic database is an information resource to explore the annotation, genomic features, and biology of different strains.the xylella fastidiosa comparative genomic database is a scientific resource with the aim to provide a user-friendly interface for accessing high-quality manually curated genomic annotation and comparative sequence analysis, as well as for identifying and mapping prophage-like elements, a marked feature of xylella genomes. here we describe a database and tools for exploring the biology of this important plant pathogen. the hallmarks of this database are the high quality genomic annotation, the f ...201222481888
identification of innate immunity elicitors using molecular signatures of natural selection.the innate immune system is an ancient and broad-spectrum defense system found in all eukaryotes. the detection of microbial elicitors results in the up-regulation of defense-related genes and the elicitation of inflammatory and apoptotic responses. these innate immune responses are the front-line barrier against disease because they collectively suppress the growth of the vast majority of invading microbes. despite their critical role, we know remarkably little about the diversity of immune eli ...201222323605
type iii secretion and effectors shape the survival and growth pattern of pseudomonas syringae on leaf surfaces.the bacterium pseudomonas syringae pv syringae b728a (psyb728a) uses a type iii secretion system (t3ss) to inject effector proteins into plant cells, a process that modulates the susceptibility of different plants to infection. analysis of green fluorescent protein-expressing psyb728a after spray inoculation without additives under moderate relative humidity conditions permitted (1) a detailed analysis of this strain's survival and growth pattern on host (nicotiana benthamiana) and nonhost (toma ...201222319072
plant stress surveillance monitored by aba and disease signaling interactions.abiotic and biotic stresses are the major factors that negatively impact plant growth. in response to abiotic environmental stresses such as drought, plants generate resistance responses through abscisic acid (aba) signal transduction. in addition to the major role of aba in abiotic stress signaling, aba signaling was reported to downregulate biotic stress signaling. conversely recent findings provide evidence that initial activation of plant immune signaling inhibits subsequent aba signal trans ...201222314325
glycolate oxidase modulates reactive oxygen species-mediated signal transduction during nonhost resistance in nicotiana benthamiana and arabidopsis.in contrast to gene-for-gene disease resistance, nonhost resistance governs defense responses to a broad range of potential pathogen species. to identify specific genes involved in the signal transduction cascade associated with nonhost disease resistance, we used a virus-induced gene-silencing screen in nicotiana benthamiana, and identified the peroxisomal enzyme glycolate oxidase (gox) as an essential component of nonhost resistance. gox-silenced n. benthamiana and arabidopsis thaliana gox t-d ...201222286136
the potential of effector-target genes in breeding for plant innate immunity.increasing numbers of infectious crop diseases that are caused by fungi and oomycetes urge the need to develop alternative strategies for resistance breeding. as an alternative for the use of resistance (r) genes, the application of mutant susceptibility (s) genes has been proposed as a potentially more durable type of resistance. identification of s genes is hampered by their recessive nature. here we explore the use of pathogen-derived effectors as molecular probes to identify s genes. effecto ...201223279965
the potential of effector-target genes in breeding for plant innate immunity.increasing numbers of infectious crop diseases that are caused by fungi and oomycetes urge the need to develop alternative strategies for resistance breeding. as an alternative for the use of resistance (r) genes, the application of mutant susceptibility (s) genes has been proposed as a potentially more durable type of resistance. identification of s genes is hampered by their recessive nature. here we explore the use of pathogen-derived effectors as molecular probes to identify s genes. effecto ...201223279965
tal effectors: function, structure, engineering and applications.tal effectors are proteins secreted by bacterial pathogens into plant cells, where they enter the nucleus and activate expression of individual genes. tal effectors display a modular architecture that includes a central dna-binding region comprising a tandem array of nearly identical repeats that are almost all 34 residues long. residue number 13 in each tal repeat (one of two consecutive polymorphic amino acids that are termed 'repeat variable diresidues', or 'rvds') specifies the identity of a ...201223265998
tal effectors: function, structure, engineering and applications.tal effectors are proteins secreted by bacterial pathogens into plant cells, where they enter the nucleus and activate expression of individual genes. tal effectors display a modular architecture that includes a central dna-binding region comprising a tandem array of nearly identical repeats that are almost all 34 residues long. residue number 13 in each tal repeat (one of two consecutive polymorphic amino acids that are termed 'repeat variable diresidues', or 'rvds') specifies the identity of a ...201223265998
community structure and functional gene profile of bacteria on healthy and diseased thalli of the red seaweed delisea pulchra.disease is increasingly viewed as a major factor in the ecology of marine communities and its impact appears to be increasing with environmental change, such as global warming. the temperate macroalga delisea pulchra bleaches in southeast australia during warm summer periods, a phenomenon which previous studies have indicated is caused by a temperature induced bacterial disease. in order to better understand the ecology of this disease, the bacterial communities associated with threes type of sa ...201223226544
contribution of lateral gene transfers to the genome composition and parasitic ability of root-knot nematodes.lateral gene transfers (lgt), species to species transmission of genes by means other than direct inheritance from a common ancestor, have played significant role in shaping prokaryotic genomes and are involved in gain or transfer of important biological processes. whether lgt significantly contributed to the composition of an animal genome is currently unclear. in nematodes, multiple lgt are suspected to have favored emergence of plant-parasitism. with the availability of whole genome sequences ...201223226415
rna-seq pinpoints a xanthomonas tal-effector activated resistance gene in a large-crop genome.transcription activator-like effector (tale) proteins of the plant pathogenic bacterial genus xanthomonas bind to and transcriptionally activate host susceptibility genes, promoting disease. plant immune systems have taken advantage of this mechanism by evolving tale binding sites upstream of resistance (r) genes. for example, the pepper bs3 and rice xa27 genes are hypersensitive reaction plant r genes that are transcriptionally activated by corresponding tales. both r genes have a hallmark expr ...201223132937
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 ...201223093361
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 ...201223093361
synergistic activation of the pathogenicity-related proline iminopeptidase gene in xanthomonas campestris pv. campestris by hrpx and a luxr homolog.xanthomonas campestris pv. campestris strain 8004 contains an orphan quorum-sensing (qs) locus, xccr-pip(xcc), in which the proline iminopeptidase (pip(xcc)) gene (where "xcc" indicates that the pip gene is from x. campestris pv. campestris) is positively regulated by the luxr homologue xccr by binding to the luxxc box of the pip(xcc) promoter. the disruption of pip(xcc) significantly attenuated the virulence of x. campestris pv. campestris. an imperfect plant-inducible promoter (pip) box is loc ...201222865058
phylogenetic analysis of a gene cluster encoding an additional, rhizobial-like type iii secretion system that is narrowly distributed among pseudomonas syringae strains.the central role of type iii secretion systems (t3ss) in bacteria-plant interactions is well established, yet unexpected findings are being uncovered through bacterial genome sequencing. some pseudomonas syringae strains possess an uncharacterized cluster of genes encoding putative components of a second t3ss (t3ss-2) in addition to the well characterized hrc1 t3ss which is associated with disease lesions in host plants and with the triggering of hypersensitive response in non-host plants. the a ...201222937899
the bacterium pantoea stewartii uses two different type iii secretion systems to colonize its plant host and insect vector.plant- and animal-pathogenic bacteria utilize phylogenetically distinct type iii secretion systems (t3ss) that produce needle-like injectisomes or pili for the delivery of effector proteins into host cells. pantoea stewartii subsp. stewartii (herein referred to as p. stewartii), the causative agent of stewart's bacterial wilt and leaf blight of maize, carries phylogenetically distinct t3sss. in addition to an hrc-hrp t3ss, known to be essential for maize pathogenesis, p. stewartii has a second t ...201222773631
srfj, a salmonella type iii secretion system effector regulated by phop, rcsb, and iolr.virulence-related type iii secretion systems are present in many gram-negative bacterial pathogens. these complex devices translocate proteins, called effectors, from the bacterium into the eukaryotic host cell. here, we identify the product of srfj, a salmonella enterica serovar typhimurium gene regulated by ssrb, as a new substrate of the type iii secretion system encoded by salmonella pathogenicity island 2. the n-terminal 20-amino-acid segment of srfj was recognized as a functional secretion ...201222661691
identification of acquired antimicrobial resistance genes.identification of antimicrobial resistance genes is important for understanding the underlying mechanisms and the epidemiology of antimicrobial resistance. as the costs of whole-genome sequencing (wgs) continue to decline, it becomes increasingly available in routine diagnostic laboratories and is anticipated to substitute traditional methods for resistance gene identification. thus, the current challenge is to extract the relevant information from the large amount of generated data.201222782487
genome-wide sequencing reveals two major sub-lineages in the genetically monomorphic pathogen xanthomonas campestris pathovar musacearum.the bacterium xanthomonas campestris pathovar musacearum (xcm) is the causal agent of banana xanthomonas wilt (bxw). this disease has devastated economies based on banana and plantain crops (musa species) in east africa. here we use genome-wide sequencing to discover a set of single-nucleotide polymorphisms (snps) among east african isolates of xcm. these snps have potential as molecular markers for phylogeographic studies of the epidemiology and spread of the pathogen. our analysis reveals two ...201224704974
genomics of aerobic cellulose utilization systems in actinobacteria.cellulose degrading enzymes have important functions in the biotechnology industry, including the production of biofuels from lignocellulosic biomass. anaerobes including clostridium species organize cellulases and other glycosyl hydrolases into large complexes known as cellulosomes. in contrast, aerobic actinobacteria utilize systems comprised of independently acting enzymes, often with carbohydrate binding domains. numerous actinobacterial genomes have become available through the genomic ency ...201222723998
ubiquitination during plant immune signaling. 201222689893
housekeeping gene sequencing and multilocus variable-number tandem-repeat analysis to identify subpopulations within pseudomonas syringae pv. maculicola and pseudomonas syringae pv. tomato that correlate with host specificity.pseudomonas syringae pv. maculicola causes bacterial spot on brassicaceae worldwide, and for the last 10 years severe outbreaks have been reported in the loire valley, france. p. syringae pv. maculicola resembles p. syringae pv. tomato in that it is also pathogenic for tomato and causes the same types of symptoms. we used a collection of 106 strains of p. syringae to characterize the relationships between p. syringae pv. maculicola and related pathovars, paying special attention to p. syringae p ...201222389364
functional and computational analysis of amino acid patterns predictive of type iii secretion system substrates in pseudomonas syringae.bacterial type iii secretion systems (t3sss) deliver proteins called effectors into eukaryotic cells. although n-terminal amino acid sequences are required for translocation, the mechanism of substrate recognition by the t3ss is unknown. almost all actively deployed t3ss substrates in the plant pathogen pseudomonas syringae pathovar tomato strain dc3000 possess characteristic patterns, including (i) greater than 10% serine within the first 50 amino acids, (ii) an aliphatic residue or proline at ...201222558318
genetic and genomic approaches for r-gene mediated disease resistance in tomato: retrospects and prospects.tomato (solanum lycopersicum) is one of the world's most important vegetable crops. managing the health of this crop can be particularly challenging; crop resistance may be overcome by new pathogen races while new pathogens have been introduced by global agricultural markets. tomato is extensively used as a model plant for resistance studies and much has been attained through both genetic and biotechnological approaches. in this paper, we illustrate genomic methods currently employed to preserve ...201222350316
a bacterial acetyltransferase destroys plant microtubule networks and blocks secretion.the eukaryotic cytoskeleton is essential for structural support and intracellular transport, and is therefore a common target of animal pathogens. however, no phytopathogenic effector has yet been demonstrated to specifically target the plant cytoskeleton. here we show that the pseudomonas syringae type iii secreted effector hopz1a interacts with tubulin and polymerized microtubules. we demonstrate that hopz1a is an acetyltransferase activated by the eukaryotic co-factor phytic acid. activated h ...201222319451
bacterial effectors target the plant cell nucleus to subvert host transcription.in order to promote virulence, gram-negative bacteria have evolved the ability to inject so-called type iii effector proteins into host cells. the plant cell nucleus appears to be a subcellular compartment repeatedly targeted by bacterial effectors. in agreement with this observation, mounting evidence suggests that manipulation of host transcription is a major strategy developed by bacteria to counteract plant defense responses. it has been suggested that bacterial effectors may adopt at least ...201222353865
bacteriophages and their implications on future biotechnology: a review.recently it has been recognized that bacteriophages, the natural predators of bacteria can be used efficiently in modern biotechnology. they have been proposed as alternatives to antibiotics for many antibiotic resistant bacterial strains. phages can be used as biocontrol agents in agriculture and petroleum industry. moreover phages are used as vehicles for vaccines both dna and protein, for the detection of pathogenic bacterial strain, as display system for many proteins and antibodies. bacteri ...201222234269
multiple mechanisms contribute to lateral transfer of an organophosphate degradation (opd) island in sphingobium fuliginis atcc 27551.the complete sequence of ppdl2 (37,317 bp), an indigenous plasmid of sphingobium fuliginis atcc 27551 that encodes genes for organophosphate degradation (opd), revealed the existence of a site-specific integrase (int) gene with an attachment site attp, typically seen in integrative mobilizable elements (ime). in agreement with this sequence information, site-specific recombination was observed between ppdl2 and an artificial plasmid having a temperature-sensitive replicon and a cloned attb site ...201223275877
the entner-doudoroff pathway is obligatory for gluconate utilization and contributes to the pathogenicity of vibrio cholerae.the entner-doudoroff (ed) pathway has recently been shown to play an important role in sugar catabolism for many organisms although very little information is available on the functionality of this pathway in vibrio cholerae, the causative agent of cholera. in this study, activation of the genes edd and eda, encoding 6-phosphogluconate dehydratase and 2-keto-3-deoxy-6-phosphogluconate aldolase, was used as a marker of a functional ed pathway in v. cholerae. transcriptional activation analyses an ...201222544275
structural characterization of zn(ii)-, co(ii)-, and mn(ii)-loaded forms of the arge-encoded n-acetyl-l-ornithine deacetylase from escherichia coli.the zn, co, and mn k-edge extended x-ray absorption fine structure (exafs) spectra of the n-acetyl-l-ornithine deacetylase (arge) from escherichia coli, loaded with one or two equivalents of divalent metal ions (i.e., [zn(ii)_(arge)], [zn(ii)zn(ii)(arge)], [co(ii)_(arge)], [co(ii)co(ii)(arge)], [mn(ii)_(arge)], and [mn(ii)mn(ii)(arge)]), were recorded. the fourier transformed data (ft) for [zn(ii)_(arge)], [zn(ii)zn(ii)(arge)], [co(ii)_(arge)] and [co(ii)co(ii)(arge)] are dominated by a peak at ...201222459917
top 10 plant pathogenic bacteria in molecular plant pathology.many plant bacteriologists, if not all, feel that their particular microbe should appear in any list of the most important bacterial plant pathogens. however, to our knowledge, no such list exists. the aim of this review was to survey all bacterial pathologists with an association with the journal molecular plant pathology and ask them to nominate the bacterial pathogens they would place in a 'top 10' based on scientific/economic importance. the survey generated 458 votes from the international ...201222672649
ssef, a type iii effector protein from the mammalian pathogen salmonella enterica, requires resistance-gene-mediated signalling to activate cell death in the model plant nicotiana benthamiana.type iii effector proteins (t3es) of many gram-negative pathogenic bacteria manipulate highly conserved cellular processes, indicating conservation in virulence mechanisms during the infection of hosts of divergent evolutionary origin. in order to identify conserved effector functions, we used a cross-kingdom approach in which we expressed selected t3es from the mammalian pathogen salmonella enterica in leaves of nicotiana benthamiana and searched for possible virulence or avirulence phenotypes. ...201222471508
evaluation of rhizospheric pseudomonas and bacillus as biocontrol tool for xanthomonas campestris pv campestris.xanthomonas campestris pv campestris (xcc), causing black rot, is one of the most yield-limiting and destructive pathogens of cruciferous crops. the intention of this study was to evaluate the potential of rhizobacteria in black rot management. fifty-four isolates from rhizosphere soil of brassica campestris were screened against xcc. two isolates namely, ka19 and se, with inhibition radius >11 mm were selected. the combined use of them produced an average inhibition zone of 18.1 ± 1.4 mm radius ...201222806865
intestinal microbial community diversity between healthy and orally infected rabbit with entamoeba histolytica by eric-pcr.enterobacterial repetitive intergenic consensus (eric)-pcr was applied to analyze the difference of intestinal microbial community diversity between healthy and orally infected rabbits with entamoeba histolytica. the dynamic changes in different parts of digestive system including the duodenum, jejunum, ileum, caecum, and rectum in healthy and infected rabbits at different time points were also tested. the intestinal microbial community of the control healthy rabbits was steady, and the total nu ...201222562215
a low-temperature-active alkaline pectate lyase from xanthomonas campestris accc 10048 with high activity over a wide ph range.alkaline pectate lyases are favorable for the textile industry. here, we report the gene cloning and expression of a low-temperature-active alkaline pectate lyase (pl d) from xanthomonas campestris accc 10048. deduced pl d consists of a putative 27-residue signal peptide and a catalytic domain of 320 residues belonging to family pf09492. recombinant pl d (r-pl d) produced in escherichia coli was purified to electrophoretic homogeneity with a single step of ni(2+)-nta affinity chromatography and ...201222983714
freezing activities of flavonoids in solutions containing different ice nucleators.in this study, we examined the effects on freezing of 26 kinds of flavonoid compounds, which were randomly selected as compounds with structures similar to those of flavonoid compounds existing in deep supercooling xylem parenchyma cells (xpcs) in trees, in solutions containing different kinds of ice nucleators, including the ice nucleation bacterium (inb) erwinia ananas, inb xanthomonas campestris, silver iodide, phloroglucinol and unidentified airborne impurities in buffered milli-q water (bmq ...201222406212
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