Publications

overexpressing cyp71z2 enhances resistance to bacterial blight by suppressing auxin biosynthesis in rice.	the hormone auxin plays an important role not only in the growth and development of rice, but also in its defense responses. we've previously shown that the p450 gene cyp71z2 enhances disease resistance to pathogens through regulation of phytoalexin biosynthesis in rice, though it remains unclear if auxin is involved in this process or not.	2015	25786239
goodness-of-fit tests and model diagnostics for negative binomial regression of rna sequencing data.	this work is about assessing model adequacy for negative binomial (nb) regression, particularly (1) assessing the adequacy of the nb assumption, and (2) assessing the appropriateness of models for nb dispersion parameters. tools for the first are appropriate for nb regression generally; those for the second are primarily intended for rna sequencing (rna-seq) data analysis. the typically small number of biological samples and large number of genes in rna-seq analysis motivate us to address the tr ...	2015	25787144
carnitine in bacterial physiology and metabolism.	carnitine is a quaternary amine compound found at high concentration in animal tissues, particularly muscle, and is most well studied for its contribution to fatty acid transport into mitochondria. in bacteria, carnitine is an important osmoprotectant, and can also enhance thermotolerance, cryotolerance and barotolerance. carnitine can be transported into the cell or acquired from metabolic precursors, where it can serve directly as a compatible solute for stress protection or be metabolized thr ...	2015	25787873
hijacking of the jasmonate pathway by the mycotoxin fumonisin b1 (fb1) to initiate programmed cell death in arabidopsis is modulated by rglg3 and rglg4.	the mycotoxin fumonisin b1 (fb1) is a strong inducer of programmed cell death (pcd) in plants, but its underlying mechanism remains unclear. here, we describe two ubiquitin ligases, ring domain ligase3 (rglg3) and rglg4, which control fb1-triggered pcd by modulating the jasmonate (ja) signalling pathway in arabidopsis thaliana. rglg3 and rglg4 transcription was sensitive to fb1. arabidopsis fb1 sensitivity was suppressed by loss of function of rglg3 and rglg4 and was increased by their overexpre ...	2015	25788731
effect of quorum sensing signals produced by seaweed-associated bacteria on carpospore liberation from gracilaria dura.	epiphytic and endophytic bacteria associated with green macroalgae ulva (u. fasciata and u. lactuca) and red macroalgae gracilaria (g. corticata and g. dura) have been identified from three different seasons to evaluate the effect of quorum sensing (qs) molecules on carpospores liberation from gracilaria dura. the bacterial isolates belonging to the orders bacillales, pseudomonadales, alteromonadales, and vibrionales were present in all seasons, whereas actinomycetales and enterobacteriales were ...	2015	25788899
hrpg and hrpv proteins from the type iii secretion system of erwinia amylovora form a stable heterodimer.	bacterial type iii secretion systems (t3sss) are specialized multicomponent nanomachines that mediate the transport of proteins either to extracellular locations or directly into eukaryotic host cell cytoplasm. erwinia amylovora, the main agent of rosaceous plants fireblight disease, employs an hrp/hrc1 t3ss to accomplish its pathogenesis. the regulatory network that controls the activation of this t3ss is largely unknown in e. amylovora. however, in pseudomonas syringae pathovars, the hrpg/hrpv ...	2015	25790492
draft genome sequence of pseudomonas abietaniphila kf717 (nbrc 110669), isolated from biphenyl-contaminated soil in japan.	pseudomonas abietaniphila kf717 utilizes biphenyl as a sole source of carbon and energy and degrades polychlorinated biphenyls (pcbs). we report here the 6,930,016-bp genome sequence of this strain, which contains 6,323 predicted coding sequences (cdss), including the biphenyl-utilizing bph gene cluster.	2015	25792041
the n-terminal domain of the tomato immune protein prf contains multiple homotypic and pto kinase interaction sites.	resistance to pseudomonas syringae bacteria in tomato (solanum lycopersicum) is conferred by the prf recognition complex, composed of the nucleotide-binding leucine-rich repeats protein prf and the protein kinase pto. the complex is activated by recognition of the p. syringae effectors avrpto and avrptob. the n-terminal domain is responsible for prf homodimerization, which brings two pto kinases into close proximity and holds them in inactive conformation in the absence of either effector. negat ...	2015	25792750
functional genomics of tomato for the study of plant immunity.	tomato (solanum lycopersicum), along with many other economically valuable species, belongs to the solanaceae family. understanding how plants in this family defend themselves against pathogens offers the opportunity of improving yield and quality of their edible products. the use of functional genomics has contributed to this purpose through both traditional and recently developed techniques that allow determination of changes in transcript abundance during pathogen attack. such changes can imp ...	2015	25797691
molecular and functional characterization of recd, a novel member of the sf1 family of helicases, from mycobacterium tuberculosis.	the annotated whole-genome sequence of mycobacterium tuberculosis revealed the presence of a putative recd gene; however, the biochemical characteristics of its encoded protein product (mtrecd) remain largely unknown. here, we show that mtrecd exists in solution as a stable homodimer. protein-dna binding assays revealed that mtrecd binds efficiently to single-stranded dna and linear duplexes containing 5' overhangs relative to the 3' overhangs but not to blunt-ended duplex. furthermore, mtrecd b ...	2015	25802334
functional roles of three cutin biosynthetic acyltransferases in cytokinin responses and skotomorphogenesis.	cytokinins (cks) regulate plant development and growth via a two-component signaling pathway. by forward genetic screening, we isolated an arabidopsis mutant named grow fast on cytokinins 1 (gfc1), whose seedlings grew larger aerial parts on ms medium with ck. gfc1 is allelic to a previously reported cutin mutant defective in cuticular ridges (dcr). gfc1/dcr encodes a soluble bahd acyltransferase (a name based on the first four enzymes characterized in this family: benzylalcohol o-acetyltransfer ...	2015	25803274
the co-4 locus on chromosome pv08 contains a unique cluster of 18 cok-4 genes and is regulated by immune response in common bean.	the common bean locus co - 4, traditionally referred to as an anthracnose-resistant gene, contains a cluster of predicted receptor-like kinases (cok-4 and crrlk1-like), and at least two of these kinases are co-regulated with the plant's basal immunity. genetic resistance to anthracnose, caused by the fungus colletotrichum lindemuthianum (sacc. and magnus) briosi and cavara, is conferred by major loci throughout the phaseolus vulgaris genome, named co. the complex co-4 locus was previously report ...	2015	25805316
the intracellular scots pine shoot symbiont methylobacterium extorquens dsm13060 aggregates around the host nucleus and encodes eukaryote-like proteins.	endophytes are microbes that inhabit plant tissues without any apparent signs of infection, often fundamentally altering plant phenotypes. while endophytes are typically studied in plant roots, where they colonize the apoplast or dead cells, methylobacterium extorquens strain dsm13060 is a facultatively intracellular symbiont of the meristematic cells of scots pine (pinus sylvestris l.) shoot tips. the bacterium promotes host growth and development without the production of known plant growth-st ...	2015	25805725
molecular, physiological and phenotypic characterization of paracoccus denitrificans atcc 19367 mutant strain p-87 producing improved coenzyme q10.	coenzyme q10 (coq10) is a blockbuster nutraceutical molecule which is often used as an oral supplement in the supportive therapy for cardiovascular diseases, cancer and neurodegenerative diseases. it is commercially produced by fermentation process, hence constructing the high yielding coq10 producing strains is a pre-requisite for cost effective production. paracoccus denitrificans atcc 19367, a biochemically versatile organism was selected to carry out the studies on coq10 yield improvement. t ...	2014	25805905
molecular, physiological and phenotypic characterization of paracoccus denitrificans atcc 19367 mutant strain p-87 producing improved coenzyme q10.	coenzyme q10 (coq10) is a blockbuster nutraceutical molecule which is often used as an oral supplement in the supportive therapy for cardiovascular diseases, cancer and neurodegenerative diseases. it is commercially produced by fermentation process, hence constructing the high yielding coq10 producing strains is a pre-requisite for cost effective production. paracoccus denitrificans atcc 19367, a biochemically versatile organism was selected to carry out the studies on coq10 yield improvement. t ...	2014	25805905
roles and programming of arabidopsis argonaute proteins during turnip mosaic virus infection.	in eukaryotes, argonaute proteins (agos) associate with micrornas (mirnas), short interfering rnas (sirnas), and other classes of small rnas to regulate target rna or target loci. viral infection in plants induces a potent and highly specific antiviral rna silencing response characterized by the formation of virus-derived sirnas. arabidopsis thaliana has ten ago genes of which ago1, ago2, and ago7 have been shown to play roles in antiviral defense. a genetic analysis was used to identify and cha ...	2015	25806948
the cost of phage resistance in a plant pathogenic bacterium is context-dependent.	parasites are ubiquitous features of living systems and many parasites severely reduce the fecundity or longevity of their hosts. this parasite-imposed selection on host populations should strongly favor the evolution of host resistance, but hosts typically face a trade-off between investment in reproductive fitness and investment in defense against parasites. the magnitude of such a trade-off is likely to be context-dependent, and accordingly costs that are key in shaping evolution in nature ma ...	2015	25809535
a duplex pcr assay for the detection of ralstonia solanacearum phylotype ii strains in musa spp.	banana wilt outbreaks that are attributable to moko disease-causing strains of the pathogen ralstonia solanacearum (rs) remain a social and economic burden for both multinational corporations and subsistence farmers. all known moko strains belong to the phylotype ii lineage, which has been previously recognized for its broad genetic basis. moko strains are paraphyletic and are distributed among seven related but distinct phylogenetic clusters (sequevars) that are potentially major threats to mus ...	2015	25811378
dimeric c-di-gmp is required for post-translational regulation of alginate production in pseudomonas aeruginosa.	pseudomonas aeruginosa is an opportunistic human pathogen that secretes the exopolysaccharide alginate during infection of the respiratory tract of individuals afflicted with cystic fibrosis and chronic obstructive pulmonary disease. among the proteins required for alginate production, alg44 has been identified as an inner membrane protein whose bis-(3',5')-cyclic dimeric guanosine monophosphate (c-di-gmp) binding activity post-translationally regulates alginate secretion. in this study, we repo ...	2015	25817996
chemical diversity of microbial volatiles and their potential for plant growth and productivity.	microbial volatile organic compounds (mvocs) are produced by a wide array of microorganisms ranging from bacteria to fungi. a growing body of evidence indicates that mvocs are ecofriendly and can be exploited as a cost-effective sustainable strategy for use in agricultural practice as agents that enhance plant growth, productivity, and disease resistance. as naturally occurring chemicals, mvocs have potential as possible alternatives to harmful pesticides, fungicides, and bactericides as well as ...	2015	25821453
transgenic expression of the dicotyledonous pattern recognition receptor efr in rice leads to ligand-dependent activation of defense responses.	plant plasma membrane localized pattern recognition receptors (prrs) detect extracellular pathogen-associated molecules. prrs such as arabidopsis efr and rice xa21 are taxonomically restricted and are absent from most plant genomes. here we show that rice plants expressing efr or the chimeric receptor efr::xa21, containing the efr ectodomain and the xa21 intracellular domain, sense both escherichia coli- and xanthomonas oryzae pv. oryzae (xoo)-derived elf18 peptides at sub-nanomolar concentratio ...	2015	25821973
transcriptomic profiling of arabidopsis thaliana mutant pad2.1 in response to combined cold and osmotic stress.	the contribution of glutathione (gsh) in stress tolerance, defense response and antioxidant signaling is an established fact. in this study transcriptome analysis of pad2.1, an arabidopsis thaliana mutant, after combined osmotic and cold stress treatment has been performed to explore the intricate position of gsh in the stress and defense signaling network in planta. microarray data revealed the differential regulation of about 1674 genes in pad2.1 amongst which 973 and 701 were significantly up ...	2015	25822199
inhibition of cell differentiation in bacillus subtilis by pseudomonas protegens.	interspecies interactions have been described for numerous bacterial systems, leading to the identification of chemical compounds that impact bacterial physiology and differentiation for processes such as biofilm formation. here, we identified soil microbes that inhibit biofilm formation and sporulation in the common soil bacterium bacillus subtilis. we did so by creating a reporter strain that fluoresces when the transcription of a biofilm-specific gene is repressed. using this reporter in a co ...	2015	25825426
regulation of coronafacoyl phytotoxin production by the pas-luxr family regulator cfar in the common scab pathogen streptomyces scabies.	potato common scab is an economically important crop disease that is characterized by the formation of superficial, raised or pitted lesions on the potato tuber surface. the most widely distributed causative agent of the disease is streptomyces scabies, which produces the phytotoxic secondary metabolite thaxtomin a that serves as a key virulence factor for the organism. recently, it was demonstrated that s. scabies can also produce the phytotoxic secondary metabolite coronafacoyl-l-isoleucine (c ...	2015	25826255
hyperspectral and thermal imaging of oilseed rape (brassica napus) response to fungal species of the genus alternaria.	in this paper, thermal (8-13 µm) and hyperspectral imaging in visible and near infrared (vnir) and short wavelength infrared (swir) ranges were used to elaborate a method of early detection of biotic stresses caused by fungal species belonging to the genus alternaria that were host (alternaria alternata, alternaria brassicae, and alternaria brassicicola) and non-host (alternaria dauci) pathogens to oilseed rape (brassica napus l.). the measurements of disease severity for chosen dates after inoc ...	2015	25826369
cytoplastic glyceraldehyde-3-phosphate dehydrogenases interact with atg3 to negatively regulate autophagy and immunity in nicotiana benthamiana.	autophagy as a conserved catabolic pathway can respond to reactive oxygen species (ros) and plays an important role in degrading oxidized proteins in plants under various stress conditions. however, how ros regulates autophagy in response to oxidative stresses is largely unknown. here, we show that autophagy-related protein 3 (atg3) interacts with the cytosolic glyceraldehyde-3-phosphate dehydrogenases (gapcs) to regulate autophagy in nicotiana benthamiana plants. we found that oxidative stress ...	2015	25829441
involvement of the caleosin/peroxygenase rd20 in the control of cell death during arabidopsis responses to pathogens.	caleosins, mostly found in lipid droplets of seeds and leaves, are believed to play physiological roles through their enzymatic capacities to produce oxylipins. we recently identified the caleosin rd20 as a peroxygenase reducing endogenous fatty acid hydroperoxides into their corresponding alcohols. such oxylipins confer tolerance to oxidative stress by decreasing reactive oxygen species accumulation and by minimizing cell death. rd20 expression being induced by pathogens, we have examined the m ...	2015	25830533
novel disease susceptibility factors for fungal necrotrophic pathogens in arabidopsis.	host cells use an intricate signaling system to respond to invasions by pathogenic microorganisms. although several signaling components of disease resistance against necrotrophic fungal pathogens have been identified, our understanding for how molecular components and host processes contribute to plant disease susceptibility is rather sparse. here, we identified four transcription factors (tfs) from arabidopsis that limit pathogen spread. arabidopsis mutants defective in any of these tfs displa ...	2015	25830627
regulation of bacterial virulence by csr (rsm) systems.	most bacterial pathogens have the remarkable ability to flourish in the external environment and in specialized host niches. this ability requires their metabolism, physiology, and virulence factors to be responsive to changes in their surroundings. it is no surprise that the underlying genetic circuitry that supports this adaptability is multilayered and exceedingly complex. studies over the past 2 decades have established that the csra/rsma proteins, global regulators of posttranscriptional ge ...	2015	25833324
bactericidal compounds controlling growth of the plant pathogen pseudomonas syringae pv. actinidiae, which forms biofilms composed of a novel exopolysaccharide.	pseudomonas syringae pv. actinidiae is the major cause of bacterial canker and is a severe threat to kiwifruit production worldwide. many aspects of the disease caused by p. syringae pv. actinidiae, such as the pathogenicity-relevant formation of a biofilm composed of extracellular polymeric substances (epss), are still unknown. here, a highly virulent strain of p. syringae pv. actinidiae, nz v-13, was studied with respect to biofilm formation and architecture using a flow cell system combined w ...	2015	25841017
nuclear processes associated with plant immunity and pathogen susceptibility.	plants are sessile organisms that have evolved exquisite and sophisticated mechanisms to adapt to their biotic and abiotic environment. plants deploy receptors and vast signalling networks to detect, transmit and respond to a given biotic threat by inducing properly dosed defence responses. genetic analyses and, more recently, next-generation -omics approaches have allowed unprecedented insights into the mechanisms that drive immunity. similarly, functional genomics and the emergence of pathogen ...	2015	25846755
lipopolysaccharide perception leads to dynamic alterations in the microtranscriptome of arabidopsis thaliana cells and leaf tissues.	micrornas (mirnas) are non-coding rna molecules which have recently emerged as important gene regulators in plants and their gene expression analysis is becoming increasingly important. mirnas regulate gene expression at the post-transcriptional level by translational repression or target degradation of specific mrnas and gene silencing. in order to profile the microtranscriptome of arabidopsis thaliana leaf and callus tissues in response to bacterial lipopolysaccharide (lps), small rna librarie ...	2015	25848807
the physcomitrella patens unique alpha-dioxygenase participates in both developmental processes and defense responses.	plant α-dioxygenases catalyze the incorporation of molecular oxygen into polyunsaturated fatty acids leading to the formation of oxylipins. in flowering plants, two main groups of α-doxs have been described. while the α-dox1 isoforms are mainly involved in defense responses against microbial infection and herbivores, the α-dox2 isoforms are mostly related to development. to gain insight into the roles played by these enzymes during land plant evolution, we performed biochemical, genetic and mole ...	2015	25848849
a novel pyrimidin-like plant activator stimulates plant disease resistance and promotes growth.	plant activators are chemicals that induce plant defense responses to a broad spectrum of pathogens. here, we identified a new potential plant activator, 5-(cyclopropylmethyl)-6-methyl-2-(2-pyridyl)pyrimidin-4-ol, named ppa (pyrimidin-type plant activator). compared with benzothiadiazole s-methyl ester (bth), a functional analog of salicylic acid (sa), ppa was fully soluble in water and increased fresh weight of rice (oryza sativa) and arabidopsis plants at low concentrations. in addition, ppa a ...	2015	25849038
histone chaperones in arabidopsis and rice: genome-wide identification, phylogeny, architecture and transcriptional regulation.	histone chaperones modulate chromatin architecture and hence play a pivotal role in epigenetic regulation of gene expression. in contrast to their animal and yeast counterparts, not much is known about plant histone chaperones. to gain insights into their functions in plants, we sought to identify histone chaperones from two model plant species and investigated their phylogeny, domain architecture and transcriptional profiles to establish correlation between their expression patterns and potenti ...	2015	25849155
the e3 ligase ospub15 interacts with the receptor-like kinase pid2 and regulates plant cell death and innate immunity.	rice blast disease is one of the most destructive diseases of rice worldwide. we previously cloned the rice blast resistance gene pid2, which encodes a transmembrane receptor-like kinase containing an extracellular b-lectin domain and an intracellular serine/threonine kinase domain. however, little is known about pid2-mediated signaling.	2015	25849162
the interaction of arabidopsis with piriformospora indica shifts from initial transient stress induced by fungus-released chemical mediators to a mutualistic interaction after physical contact of the two symbionts.	piriformospora indica, an endophytic fungus of sebacinales, colonizes the roots of many plant species including arabidopsis thaliana. the symbiotic interaction promotes plant performance, growth and resistance/tolerance against abiotic and biotic stress.	2015	25849363
the f-box protein max2 contributes to resistance to bacterial phytopathogens in arabidopsis thaliana.	the arabidopsis thaliana f-box protein more axillary growth2 (max2) has previously been characterized for its role in plant development. max2 appears essential for the perception of the newly characterized phytohormone strigolactone, a negative regulator of polar auxin transport in arabidopsis.	2015	25849639
rpon1, but not rpon2, is required for twitching motility, natural competence, growth on nitrate, and virulence of ralstonia solanacearum.	the plant pathogen ralstonia solanacearum has two genes encoding for the sigma factor σ(54): rpon1, located in the chromosome and rpon2, located in a distinct "megaplasmid" replicon. in this study, individual mutants as well as a double mutant of rpon were created in r. solanacearum strain gmi1000 in order to determine the extent of functional overlap between these two genes. by virulence assay we observed that rpon1 is required for virulence whereas rpon2 is not. in addition rpon1 controls othe ...	2015	25852679
transcriptomic profiling of linolenic acid-responsive genes in ros signaling from rna-seq data in arabidopsis.	linolenic acid (ln) released from chloroplast membrane galactolipids is a precursor of the phytohormone jasmonic acid (ja). the involvement of this hormone in different plant biological processes, such as responses to biotic stress conditions, has been extensively studied. however, the role of ln in the regulation of gene expression during abiotic stress situations mediated by cellular redox changes and/or by oxidative stress processes remains poorly understood. an rna-seq approach has increased ...	2015	25852698
osmotin: a plant sentinel and a possible agonist of mammalian adiponectin.	osmotin is a stress responsive antifungal protein belonging to the pathogenesis-related (pr)-5 family that confers tolerance to both biotic and abiotic stresses in plants. protective efforts of osmotin in plants range from high temperature to cold and salt to drought. it lyses the plasma membrane of the pathogens. it is widely distributed in fruits and vegetables. it is a differentially expressed and developmentally regulated protein that protects the cells from osmotic stress and invading patho ...	2015	25852715
interconnection between flowering time control and activation of systemic acquired resistance.	the ability to avoid or neutralize pathogens is inherent to all higher organisms including plants. plants recognize pathogens through receptors, and mount resistance against the intruders, with the help of well-elaborated defense arsenal. in response to some localinfections, plants develop systemic acquired resistance (sar), which provides heightened resistance during subsequent infections. infected tissues generate mobile signaling molecules that travel to the systemic tissues, where they epige ...	2015	25852723
lathyrus sativus transcriptome resistance response to ascochyta lathyri investigated by deepsupersage analysis.	lathyrus sativus (grass pea) is a temperate grain legume crop with a great potential for expansion in dry areas or zones that are becoming more drought-prone. it is also recognized as a potential source of resistance to several important diseases in legumes, such as ascochyta blight. nevertheless, the lack of detailed genomic and/or transcriptomic information hampers further exploitation of grass pea resistance-related genes in precision breeding. to elucidate the pathways differentially regulat ...	2015	25852725
identification and functional analysis of genome mutations in a fluoride-resistant streptococcus mutans strain.	it is known that fluoride-resistant microorganisms are different from fluoride-sensitive ones in growth, adherence and metabolic activity. it was hypothesized that these phenotypic differences were due to stable genotypic changes in the fluoride-resistant strains. however, until now, no studies have reported these genotypic changes. the aim of this study is to identify such changes in a fluoride-resistant streptococcus mutans strain (c180-2fr) using whole-genome shotgun (wgs) sequencing and to e ...	2015	25856576
genome sequence of a pseudomonas syringae pv. tabaci strain, yuexi-1, causing wildfire disease in tobacco.	we determined the draft genome sequence of the pseudomonas syringae pv. tabaci strain yuexi-1. it was isolated from tobacco sample of yuexi-1, sichuan province, china, by our laboratory. the genome contains 6,232,497 bp and has a g+c content of 58.2 mol%.	2015	25858831
how salicylic acid takes transcriptional control over jasmonic acid signaling.	transcriptional regulation is a central process in plant immunity. the induction or repression of defense genes is orchestrated by signaling networks that are directed by plant hormones of which salicylic acid (sa) and jasmonic acid (ja) are the major players. extensive cross-communication between the hormone signaling pathways allows for fine tuning of transcriptional programs, determining resistance to invaders and trade-offs with plant development. here, we give an overview of how sa can cont ...	2015	25859250
biotechnological and agronomic potential of endophytic pink-pigmented methylotrophic methylobacterium spp.	the genus methylobacterium is composed of pink-pigmented facultative methylotrophic (ppfm) bacteria, which are able to synthesize carotenoids and grow on reduced organic compounds containing one carbon (c1), such as methanol and methylamine. due to their high phenotypic plasticity, these bacteria are able to colonize different habitats, such as soil, water, and sediment, and different host plants as both endophytes and epiphytes. in plant colonization, the frequency and distribution may be influ ...	2015	25861650
a novel function for arabidopsis cyclase1 in programmed cell death revealed by isobaric tags for relative and absolute quantitation (itraq) analysis of extracellular matrix proteins.	programmed cell death is essential for plant development and stress adaptation. a detailed understanding of the signal transduction pathways that regulate plant programmed cell death requires identification of the underpinning protein networks. here, we have used a protagonist and antagonist of programmed cell death triggered by fumonisin b1 as probes to identify key cell death regulatory proteins in arabidopsis. our hypothesis was that changes in the abundance of cell death-regulatory proteins ...	2015	25862728
t346hunter: a novel web-based tool for the prediction of type iii, type iv and type vi secretion systems in bacterial genomes.	t346hunter (type three, four and six secretion system hunter) is a web-based tool for the identification and localisation of type iii, type iv and type vi secretion systems (t3ss, t4ss and t6ss, respectively) clusters in bacterial genomes. non-flagellar t3ss (nf-t3ss) and t6ss are complex molecular machines that deliver effector proteins from bacterial cells into the environment or into other eukaryotic or prokaryotic cells, with significant implications for pathogenesis of the strains encoding ...	2015	25867189
plant immunity triggered by engineered in vivo release of oligogalacturonides, damage-associated molecular patterns.	oligogalacturonides (ogs) are fragments of pectin that activate plant innate immunity by functioning as damage-associated molecular patterns (damps). we set out to test the hypothesis that ogs are generated in planta by partial inhibition of pathogen-encoded polygalacturonases (pgs). a gene encoding a fungal pg was fused with a gene encoding a plant polygalacturonase-inhibiting protein (pgip) and expressed in transgenic arabidopsis plants. we show that expression of the pgip-pg chimera results i ...	2015	25870275
the dominant negative arm domain uncovers multiple functions of pub13 in arabidopsis immunity, flowering, and senescence.	regulating the intensity and duration of immune responses is crucial to combat infections without deleterious side effects. arabidopsis fls2, the receptor for bacterial flagellin, activates immune signalling by association with its partner bak1. upon flagellin (flg22) perception, the plant u-box e3 ubiquitin ligases pub12 and pub13 complex with fls2 in a bak1-dependent manner, and ubiquitinate fls2 for protein degradation, thereby down-regulating flagellin signalling. domain deletion analysis in ...	2015	25873653
pepper aldehyde dehydrogenase caaldh1 interacts with xanthomonas effector avrbst and promotes effector-triggered cell death and defence responses.	xanthomonas type iii effector avrbst induces hypersensitive cell death and defence responses in pepper (capsicum annuum) and nicotiana benthamiana. little is known about the host factors that interact with avrbst. here, we identified pepper aldehyde dehydrogenase 1 (caaldh1) as an avrbst-interacting protein. bimolecular fluorescence complementation and co-immunoprecipitation assays confirmed the interaction between caaldh1 and avrbst in planta. caaldh1:smgfp fluorescence was detected in the cyto ...	2015	25873668
differential effects of lesion mimic mutants in barley on disease development by facultative pathogens.	lesion mimic mutants display spontaneous necrotic spots and chlorotic leaves as a result of mis-regulated cell death programmes. typically these mutants have increased resistance to biotrophic pathogens but their response to facultative fungi that cause necrotrophic diseases is less well studied. the effect of altered cell death regulation on the development of disease caused by ramularia collo-cygni, fusarium culmorum and oculimacula yallundae was explored using a collection of barley necrotic ...	2015	25873675
unmasking host and microbial strategies in the agrobacterium-plant defense tango.	coevolutionary forces drive adaptation of both plant-associated microbes and their hosts. eloquently captured in the red queen hypothesis, the complexity of each plant-pathogen relationship reflects escalating adversarial strategies, but also external biotic and abiotic pressures on both partners. innate immune responses are triggered by highly conserved pathogen-associated molecular patterns, or pamps, that are harbingers of microbial presence. upon cell surface receptor-mediated recognition of ...	2015	25873923
de novo assembly and transcriptomic profiling of the grazing response in stipa grandis.	stipa grandis (poaceae) is one of the dominant species in a typical steppe of the inner mongolian plateau. however, primarily due to heavy grazing, the grasslands have become seriously degraded, and s. grandis has developed a special growth-inhibition phenotype against the stressful habitat. because of the lack of transcriptomic and genomic information, the understanding of the molecular mechanisms underlying the grazing response of s. grandis has been prohibited.	2015	25875617
the upr branch ire1-bzip60 in plants plays an essential role in viral infection and is complementary to the only upr pathway in yeast.	the unfolded protein response (upr) signaling network encompasses two pathways in plants, one mediated by inositol-requiring protein-1 (ire1)-bzip60 mrna and the other by site-1/site-2 proteases (s1p/s2p)-bzip17/bzip28. as the major sensor of upr in eukaryotes, ire1, in response to endoplasmic reticulum (er) stress, catalyzes the unconventional splicing of hac1 in yeast, bzip60 in plants and xbp1 in metazoans. recent studies suggest that ire1p and hac1 mrna, the only upr pathway found in yeast, ...	2015	25875739
synthesis, characterization, and application of microbe-triggered controlled-release kasugamycin-pectin conjugate.	the controlled and targeted release of pesticides with high water solubility has been a challenge for integrated pest management. in this paper, kasugamycin, an antibiotic broadly used in plant disease control, was covalently conjugated to pectin to form a kasugamycin-pectin conjugate by an amide bond. the conjugate was structurally characterized by fourier transform infrared spectroscopy, ultraviolet spectrophotometry, and thermal gravimetric analysis. the results showed that the conjugate was ...	2015	25876441
how bacterial cells keep ribonucleases under control.	ribonucleases (rnases) play an essential role in essentially every aspect of rna metabolism, but they also can be destructive enzymes that need to be regulated to avoid unwanted degradation of rna molecules. as a consequence, cells have evolved multiple strategies to protect rnas against rnase action. they also utilize a variety of mechanisms to regulate the rnases themselves. these include post-transcriptional regulation, post-translational modification, trans-acting inhibitors, cellular locali ...	2015	25878039
wrky proteins: signaling and regulation of expression during abiotic stress responses.	wrky proteins are emerging players in plant signaling and have been thoroughly reported to play important roles in plants under biotic stress like pathogen attack. however, recent advances in this field do reveal the enormous significance of these proteins in eliciting responses induced by abiotic stresses. wrky proteins act as major transcription factors, either as positive or negative regulators. specific wrky factors which help in the expression of a cluster of stress-responsive genes are bei ...	2015	25879071
phylogenetic spectrum and analysis of antibacterial activities of leaf extracts from plants of the genus rhododendron.	plants are traditionally used for medicinal treatment of numerous human disorders including infectious diseases caused by microorganisms. due to the increasing resistance of many pathogens to commonly used antimicrobial agents, there is an urgent need for novel antimicrobial compounds. plants of the genus rhododendron belong to the woody representatives of the family ericaceae, which are typically used in a range of ethno-medical applications. there are more than one thousand rhododendron specie ...	2015	25879877
ecological genomics in xanthomonas: the nature of genetic adaptation with homologous recombination and host shifts.	comparative genomics provides insights into the diversification of bacterial species. bacterial speciation usually takes place with lasting homologous recombination, which not only acts as a cohering force between diverging lineages but brings advantageous alleles favored by natural selection, and results in ecologically distinct species, e.g., frequent host shift in xanthomonas pathogenic to various plants.	2015	25879893
small rnas in plants: recent development and application for crop improvement.	the phenomenon of rna interference (rnai) which involves sequence-specific gene regulation by small non-coding rnas, i.e., small interfering rna (sirna) and microrna (mirna) has emerged as one of most powerful approaches for crop improvement. rnai based on sirna is one of the widely used tools of reverse genetics which aid in revealing gene functions in many species. this technology has been extensively applied to alter the gene expression in plants with an aim to achieve desirable traits. rnai ...	2015	25883599
characterization of uronate dehydrogenases catalysing the initial step in an oxidative pathway.	uronate dehydrogenases catalyse the oxidation of uronic acids to aldaric acids, which represent 'top value-added chemicals' that have the potential to substitute petroleum-derived chemicals. the identification and annotation of three uronate dehydrogenases derived from fulvimarina pelagi htcc2506, streptomyces viridochromogenes dsm 40736 and oceanicola granulosus dsm 15982 via sequence analysis is described. characterization and comparison with two known uronate dehydrogenases in regard to subst ...	2015	25884328
lipopeptide biosynthesis in pseudomonas fluorescens is regulated by the protease complex clpap.	lipopeptides (lp) are structurally diverse compounds with potent surfactant and broad-spectrum antibiotic activities. in pseudomonas and other bacterial genera, lp biosynthesis is governed by large multimodular nonribosomal peptide synthetases (nrps). to date, relatively little is known about the regulatory genetic network of lp biosynthesis.	2015	25885431
streptophyte phytochromes exhibit an n-terminus of cyanobacterial origin and a c-terminus of proteobacterial origin.	phytochromes are red light-sensitive photoreceptors that control a variety of developmental processes in plants, algae, bacteria and fungi. prototypical phytochromes exhibit an n-terminal tridomain (pgp) consisting of pas, gaf and phy domains and a c-terminal histidine kinase (hk).	2015	25886068
expression of extra-cellular levansucrase in pseudomonas syringae is controlled by the in planta fitness-promoting metabolic repressor hexr.	pseudomonas syringae pv. glycinea pg4180 causes bacterial blight on soybean plants and enters the leaf tissue through stomata or open wounds, where it encounters a sucrose-rich milieu. sucrose is utilized by invading bacteria via the secreted enzyme, levansucrase (lsc), liberating glucose and forming the polyfructan levan. p. syringae pg4180 possesses two functional lsc alleles transcribed at virulence-promoting low temperatures.	2015	25886911
proteomic analysis of citrus sinensis roots and leaves in response to long-term magnesium-deficiency.	magnesium (mg)-deficiency is frequently observed in citrus plantations and is responsible for the loss of productivity and poor fruit quality. knowledge on the effects of mg-deficiency on upstream targets is scarce. seedlings of 'xuegan' [citrus sinensis (l.) osbeck] were irrigated with mg-deficient (0 mm mgso4) or mg-sufficient (1 mm mgso4) nutrient solution for 16 weeks. thereafter, we first investigated the proteomic responses of c. sinensis roots and leaves to mg-deficiency using two-dimensi ...	2015	25887480
structure and function of a short lov protein from the marine phototrophic bacterium dinoroseobacter shibae.	light, oxygen, voltage (lov) domains are widely distributed in plants, algae, fungi, bacteria, and represent the photo-responsive domains of various blue-light photoreceptor proteins. their photocycle involves the blue-light triggered adduct formation between the c(4a) atom of a non-covalently bound flavin chromophore and the sulfur atom of a conserved cysteine in the lov sensor domain. lov proteins show considerable variation in the structure of n- and c-terminal elements which flank the lov co ...	2015	25887755
transcriptional profile of sweet orange in response to chitosan and salicylic acid.	resistance inducers have been used in annual crops as an alternative for disease control. wood perennial fruit trees, such as those of the citrus species, are candidates for treatment with resistance inducers, such as salicylic acid (sa) and chitosan (chi). however, the involved mechanisms in resistance induced by elicitors in citrus are currently few known.	2015	25887907
role of acsr in expression of the acetyl-coa synthetase gene in vibrio vulnificus.	vars/vara is one of the global factors regulating diverse aspects of the metabolism and virulence of bacteria including pathogenic vibrio spp. an experiment to identify the vars/vara-regulon in v. vulnificus revealed that a putative luxr-type transcriptional regulator was down-regulated in δvara mutant. to investigate the roles of this regulatory cascade, the target gene regulated by a luxr-regulator was identified and its expression was characterized.	2015	25887971
wheat homologs of yeast atg6 function in autophagy and are implicated in powdery mildew immunity.	autophagy-related atg6 proteins are pleiotropic proteins functioning in autophagy and the phosphatidylinositol 3-phosphate-signaling pathways. arabidopsis atg6 regulates normal plant growth, pollen development and germination, and plant responses to biotic/abiotic stresses. however, the atg6 functions in wheat (triticum aestivum l.), an important food crop, are lacking.	2015	25888209
comparative genomic analysis of ralstonia solanacearum reveals candidate genes for host specificity.	ralstonia solanacearum is a vascular soil-borne plant pathogen with an unusually broad host range. this economically destructive and globally distributed bacterium has thousands of distinct lineages within a heterogeneous and taxonomically disputed species complex. some lineages include highly host-adapted strains (ecotypes), such as the banana moko disease-causing strains, the cold-tolerant potato brown rot strains (also known as r3bv2) and the recently emerged not pathogenic to banana (npb) st ...	2015	25888333
phylogeny and evolution of plant macrophage migration inhibitory factor/d-dopachrome tautomerase-like proteins.	the human (homo sapiens) chemokine-like protein macrophage migration inhibitory factor (hsmif) is a pivotal mediator of inflammatory, infectious and immune diseases including septic shock, colitis, malaria, rheumatoid arthritis, and atherosclerosis, as well as tumorigenesis. hsmif has been found to exhibit several sequential and three-dimensional sequence motifs that in addition to its receptor binding sites include catalytic sites for oxidoreductase and tautomerase activity, which provide this ...	2015	25888527
a secreted effector protein of ustilago maydis guides maize leaf cells to form tumors.	the biotrophic smut fungus ustilago maydis infects all aerial organs of maize (zea mays) and induces tumors in the plant tissues. u. maydis deploys many effector proteins to manipulate its host. previously, deletion analysis demonstrated that several effectors have important functions in inducing tumor expansion specifically in maize leaves. here, we present the functional characterization of the effector see1 (seedling efficient effector1). see1 is required for the reactivation of plant dna syn ...	2015	25888589
the role of transition metal transporters for iron, zinc, manganese, and copper in the pathogenesis of yersinia pestis.	yersinia pestis, the causative agent of bubonic, septicemic and pneumonic plague, encodes a multitude of fe transport systems. some of these are defective due to frameshift or is element insertions, while others are functional in vitro but have no established role in causing infections. indeed only 3 fe transporters (ybt, yfe and feo) have been shown to be important in at least one form of plague. the yersiniabactin (ybt) system is essential in the early dermal/lymphatic stages of bubonic plague ...	2015	25891079
bacterial modulation of plant ethylene levels.	a focus on the mechanisms by which acc deaminase-containing bacteria facilitate plant growth.bacteria that produce the enzyme 1-aminocyclopropane-1-carboxylate (acc) deaminase, when present either on the surface of plant roots (rhizospheric) or within plant tissues (endophytic), play an active role in modulating ethylene levels in plants. this enzyme activity facilitates plant growth especially in the presence of various environmental stresses. thus, plant growth-promoting bacteria that express ...	2015	25897004
a vamp-associated protein, pva31 is involved in leaf senescence in arabidopsis.	vamp-associated proteins (vaps) are highly conserved among eukaryotes. here, we report a functional analysis of one of the vaps, pva31, and demonstrate its novel function on leaf senescence in arabidopsis. the expression of pva31 is highly induced in senescence leaves, and localizes to the plasma membrane as well as the ara7-positive endosomes. yeast two-hybrid analysis demonstrates that pva31 is interacted with the plasma membrane localized-vamp proteins, vamp721/722/724 but not with the endoso ...	2015	25897470
the tyrosine aminomutase tam1 is required for β-tyrosine biosynthesis in rice.	non-protein amino acids, often isomers of the standard 20 protein amino acids, have defense-related functions in many plant species. a targeted search for jasmonate-induced metabolites in cultivated rice (oryza sativa) identified (r)-β-tyrosine, an isomer of the common amino acid (s)-α-tyrosine in the seeds, leaves, roots, and root exudates of the nipponbare cultivar. assays with 119 diverse cultivars showed a distinct presence/absence polymorphism, with β-tyrosine being most prevalent in temper ...	2015	25901084
production of the non-protein amino acid β-tyrosine in rice.		2015	25901086
early response to nanoparticles in the arabidopsis transcriptome compromises plant defence and root-hair development through salicylic acid signalling.	the impact of nano-scaled materials on photosynthetic organisms needs to be evaluated. plants represent the largest interface between the environment and biosphere, so understanding how nanoparticles affect them is especially relevant for environmental assessments. nanotoxicology studies in plants allude to quantum size effects and other properties specific of the nano-stage to explain increased toxicity respect to bulk compounds. however, gene expression profiles after exposure to nanoparticles ...	2015	25903678
cyp94-mediated jasmonoyl-isoleucine hormone oxidation shapes jasmonate profiles and attenuates defence responses to botrytis cinerea infection.	induced resistance to the necrotrophic pathogen botrytis cinerea depends on jasmonate metabolism and signalling in arabidopsis. we have presented here extensive jasmonate profiling in this pathosystem and investigated the impact of the recently reported jasmonoyl-isoleucine (ja-ile) catabolic pathway mediated by cytochrome p450 (cyp94) enzymes. using a series of mutant and overexpressing (oe) plant lines, we showed that cyp94b3 and cyp94c1 are integral components of the fungus-induced jasmonate ...	2015	25903915
atp-sulfurylase, sulfur-compounds, and plant stress tolerance.	sulfur (s) stands fourth in the list of major plant nutrients after n, p, and k. sulfate (so4 (2-)), a form of soil-s taken up by plant roots is metabolically inert. as the first committed step of s-assimilation, atp-sulfurylase (atp-s) catalyzes so4 (2-)-activation and yields activated high-energy compound adenosine-5(')-phosphosulfate that is reduced to sulfide (s(2-)) and incorporated into cysteine (cys). in turn, cys acts as a precursor or donor of reduced s for a range of s-compounds such a ...	2015	25904923
perception of pathogenic or beneficial bacteria and their evasion of host immunity: pattern recognition receptors in the frontline.	plants are continuously monitoring the presence of microorganisms to establish an adapted response. plants commonly use pattern recognition receptors (prrs) to perceive microbe- or pathogen-associated molecular patterns (mamps/pamps) which are microorganism molecular signatures. located at the plant plasma membrane, the prrs are generally receptor-like kinases (rlks) or receptor-like proteins (rlps). mamp detection will lead to the establishment of a plant defense program called mamp-triggered i ...	2015	25904927
deficient plastidic fatty acid synthesis triggers cell death by modulating mitochondrial reactive oxygen species.	programmed cell death (pcd) is of fundamental importance to development and defense in animals and plants. in plants, a well-recognized form of pcd is hypersensitive response (hr) triggered by pathogens, which involves the generation of reactive oxygen species (ros) and other signaling molecules. while the mitochondrion is a master regulator of pcd in animals, the chloroplast is known to regulate pcd in plants. arabidopsis mosaic death 1 (mod1), an enoyl-acyl carrier protein (acp) reductase esse ...	2015	25906995
small molecule fluoride toxicity agonists.	fluoride is a ubiquitous anion that inhibits a wide variety of metabolic processes. here, we report the identification of a series of compounds that enhance fluoride toxicity in escherichia coli and streptococcus mutans. these molecules were isolated by using a high-throughput screen (hts) for compounds that increase intracellular fluoride levels as determined via a fluoride riboswitch reporter fusion construct. a series of derivatives were synthesized to examine structure-activity relationships ...	2015	25910244
induced autoprocessing of the cytopathic makes caterpillars floppy-like effector domain of the vibrio vulnificus martx toxin.	the multifunctional-autoprocessing repeats-in-toxin (martx(vv)) toxin that harbours a varied repertoire of effector domains is the primary virulence factor of vibrio vulnificus. although ubiquitously present among biotype i toxin variants, the 'makes caterpillars floppy-like' effector domain (mcf(vv)) is previously unstudied. using transient expression and protein delivery, mcf(vv) and mcf(ah) from the aeromonas hydrophila martx(ah)) toxin are shown for the first time to induce cell rounding. al ...	2015	25912102
the divergent roles of staygreen (sgr) homologs in chlorophyll degradation.	degradation of chlorophyll (chl) by chl catabolic enzymes (cces) causes the loss of green color that typically occurs during senescence of leaves. in addition to cces, staygreen1 (sgr1) functions as a key regulator of chl degradation. although sgr1 mutants in many plant species exhibit a stay-green phenotype, the biochemical function of the sgr1 protein remains elusive. many recent studies have examined the physiological and molecular roles of sgr1 and its homologs (sgr2 and sgr-like) in chl met ...	2015	25913011
the zinc-binding nuclear protein hipp3 acts as an upstream regulator of the salicylate-dependent plant immunity pathway and of flowering time in arabidopsis thaliana.	biotic and abiotic stress responses of plants are linked to developmental programs. proteins involved in different signaling pathways are the molecular basis of this concerted interplay. in our study, we show that arabidopsis thaliana heavy metal-associated isoprenylated plant protein3 (hipp3; at5g60800) acts as an upstream regulator of stress- and development-related regulatory networks. localization, metal-binding and stress-responsive gene expression of hipp3 were analyzed via microscopy, pro ...	2015	25913773
a taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data.	in recent years a large number of isolates were obtained from saline environments that are phylogenetically related to distinct clades of oligotrophic marine gammaproteobacteria, which were originally identified in seawater samples using cultivation independent methods and are characterized by high seasonal abundances in coastal environments. to date a sound taxonomic framework for the classification of these ecologically important isolates and related species in accordance with their evolutiona ...	2015	25914684
involvement of nitric oxide in the jasmonate-dependent basal defense against root-knot nematode in tomato plants.	jasmonic acid (ja) and nitric oxide (no) are well-characterized signaling molecules in plant defense responses. however, their roles in plant defense against root-knot nematode (rkn, meloidogyne incognita) infection are largely unknown. in this study, we found that the transcript levels of the ja- and no-related biosynthetic and signaling component genes were induced after rkn infection. application of exogenous ja and sodium nitroprusside (snp; a no donor) significantly decreased the number of ...	2015	25914698
vacuolar processing enzyme in plant programmed cell death.	vacuolar processing enzyme (vpe) is a cysteine proteinase originally identified as the proteinase responsible for the maturation and activation of vacuolar proteins in plants, and it is known to be an ortholog of animal asparaginyl endopeptidase (aep/vpe/legumain). vpe has been shown to exhibit enzymatic properties similar to that of caspase 1, which is a cysteine protease that mediates the programmed cell death (pcd) pathway in animals. although there is limited sequence identity between vpe an ...	2015	25914711
integrating data on the arabidopsis npr1/npr3/npr4 salicylic acid receptors; a differentiating argument.	salicylic acid (sa) is a mandatory plant metabolite in the deployment of systemic acquired resistance (sar), a broad-spectrum systemic immune response induced by local inoculation with avirulent pathogens. the npr1 transcription co-activator is the central node positively regulating sar. sa was the last of the major hormones to be without a known receptor. recently, npr1 was shown to be the direct link between sa and gene activation. this discovery seems to be controversial. npr1 being an sa-rec ...	2015	25914712
infection processes of xylem-colonizing pathogenic bacteria: possible explanations for the scarcity of qualitative disease resistance genes against them in crops.	disease resistance against xylem-colonizing pathogenic bacteria in crops. plant pathogenic bacteria cause destructive diseases in many commercially important crops. among these bacteria, eight pathogens, ralstonia solanacearum, xanthomonas oryzae pv. oryzae, x. campestris pv. campestris, erwinia amylovora, pantoea stewartii subsp. stewartii, clavibacter michiganensis subsp. michiganensis, pseudomonas syringae pv. actinidiae, and xylella fastidiosa, infect their host plants through different infe ...	2015	25917599
the pseudomonas aeruginosa pa14 abc transporter nppa1a2bcd is required for uptake of peptidyl nucleoside antibiotics.	analysis of the genome sequence of pseudomonas aeruginosa pa14 revealed the presence of an operon encoding an abc-type transporter (nppa1a2bcd) showing homology to the yej transporter of escherichia coli. the yej transporter is involved in the uptake of the peptide-nucleotide antibiotic microcin c, a translation inhibitor that targets the enzyme aspartyl-trna synthetase. furthermore, it was recently shown that the opp transporter from p. aeruginosa pao1, which is identical to npp, is required fo ...	2015	25917903
signal regulators of systemic acquired resistance.	salicylic acid (sa) is an important phytohormone that plays a vital role in a number of physiological responses, including plant defense. the last two decades have witnessed a number of breakthroughs related to biosynthesis, transport, perception and signaling mediated by sa. these findings demonstrate that sa plays a crictical role in both local and systemic defense responses. systemic acquired resistance (sar) is one such sa-dependent response. sar is a long distance signaling mechanism that p ...	2015	25918514
beyond glycolysis: gapdhs are multi-functional enzymes involved in regulation of ros, autophagy, and plant immune responses.	glyceraldehyde-3-phosphate dehydrogenase (gapdh) is an important enzyme in energy metabolism with diverse cellular regulatory roles in vertebrates, but few reports have investigated the importance of plant gapdh isoforms outside of their role in glycolysis. while animals possess one gapdh isoform, plants possess multiple isoforms. in this study, cell biological and genetic approaches were used to investigate the role of gapdhs during plant immune responses. individual arabidopsis gapdh knockouts ...	2015	25918875
cnl disease resistance genes in soybean and their evolutionary divergence.	disease resistance genes (r-genes) encode proteins involved in detecting pathogen attack and activating downstream defense molecules. recent availability of soybean genome sequences makes it possible to examine the diversity of gene families including disease-resistant genes. the objectives of this study were to identify coiled-coil nbs-lrr (= cnl) r-genes in soybean, infer their evolutionary relationships, and assess structural as well as functional divergence of the r-genes. profile hidden mar ...	2015	25922568
secondary structural entropy in rna switch (riboswitch) identification.	rna regulatory elements play a significant role in gene regulation. riboswitches, a widespread group of regulatory rnas, are vital components of many bacterial genomes. these regulatory elements generally function by forming a ligand-induced alternative fold that controls access to ribosome binding sites or other regulatory sites in rna. riboswitch-mediated mechanisms are ubiquitous across bacterial genomes. a typical class of riboswitch has its own unique structural and biological complexity, m ...	2015	25928324
novptmenzy: a database for enzymes involved in novel post-translational modifications.	with the recent discoveries of novel post-translational modifications (ptms) which play important roles in signaling and biosynthetic pathways, identification of such ptm catalyzing enzymes by genome mining has been an area of major interest. unlike well-known ptms like phosphorylation, glycosylation, sumoylation, no bioinformatics resources are available for enzymes associated with novel and unusual ptms. therefore, we have developed the novptmenzy database which catalogs information on the seq ...	2015	25931459
whole-genome sequencing of 10 pseudomonas syringae strains representing different host range spectra.	pseudomonas syringae is a ubiquitous bacterium that readily persists in environmental habitats as a saprophyte and also is responsible for numerous diseases of crops. here, we report the whole-genome sequences of 10 strains isolated from both woody and herbaceous plants that will contribute to the elucidation of the determinants of their host ranges.	2015	25931602