Publications

dissemination of 6s rna among bacteria.	6s rna is a highly abundant small non-coding rna widely spread among diverse bacterial groups. by competing with dna promoters for binding to rna polymerase (rnap), the rna regulates transcription on a global scale. rnap produces small product rnas derived from 6s rna as template, which rearranges the 6s rna structure leading to dissociation of 6s rna:rnap complexes. although 6s rna has been experimentally analysed in detail for some species, such as escherichia coli and bacillus subtilis, and w ...	2014	25483037
a brief review: the z-curve theory and its application in genome analysis.	in theoretical physics, there exist two basic mathematical approaches, algebraic and geometrical methods, which, in most cases, are complementary. in the area of genome sequence analysis, however, algebraic approaches have been widely used, while geometrical approaches have been less explored for a long time. the z-curve theory is a geometrical approach to genome analysis. the z-curve is a three-dimensional curve that represents a given dna sequence in the sense that each can be uniquely reconst ...	2014	24822026
microbial peptidyl-prolyl cis/trans isomerases (ppiases): virulence factors and potential alternative drug targets.	initially discovered in the context of immunomodulation, peptidyl-prolyl cis/trans isomerases (ppiases) were soon identified as enzymes catalyzing the rate-limiting protein folding step at peptidyl bonds preceding proline residues. intense searches revealed that ppiases are a superfamily of proteins consisting of three structurally distinguishable families with representatives in every described species of prokaryote and eukaryote and, recently, even in some giant viruses. despite the clear-cut ...	2014	25184565
polybacterial human disease: the ills of social networking.	polybacterial diseases involve multiple organisms that act collectively to facilitate disease progression. although this phenomenon was highlighted early in the 20th century, recent technological advances in diagnostics have led to the appreciation that many infections are far more complex than originally believed. furthermore, it is apparent that although most treatments focus on the dominant bacterial species in an infection, other microbes, including commensals, can have a profound impact on ...	2014	24938173
unique aspects of fiber degradation by the ruminal ethanologen ruminococcus albus 7 revealed by physiological and transcriptomic analysis.	bacteria in the genus ruminococcus are ubiquitous members of the mammalian gastrointestinal tract. in particular, they are important in ruminants where they digest a wide range of plant cell wall polysaccharides. for example, ruminococcus albus 7 is a primary cellulose degrader that produces acetate usable by its bovine host. moreover, it is one of the few organisms that ferments cellulose to form ethanol at mesophilic temperatures in vitro. the mechanism of cellulose degradation by r. albus 7 i ...	2014	25477200
prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks.	metabolic pathways in eubacteria and archaea often are encoded by operons and/or gene clusters (genome neighborhoods) that provide important clues for assignment of both enzyme functions and metabolic pathways. we describe a bioinformatic approach (genome neighborhood network; gnn) that enables large scale prediction of the in vitro enzymatic activities and in vivo physiological functions (metabolic pathways) of uncharacterized enzymes in protein families. we demonstrate the utility of the gnn a ...	2014	24980702
simultaneous detection of major blackleg and soft rot bacterial pathogens in potato by multiplex polymerase chain reaction.	a multiplex polymerase chain reaction (pcr) assay for simultaneous, fast and reliable detection of the main soft rot and blackleg potato pathogens in europe has been developed. it utilises three pairs of primers and enables detection of three groups of pectinolytic bacteria frequently found in potato, namely: pectobacterium atrosepticum, pectobacterium carotovorum subsp. carotovorum together with pectobacterium wasabiae and dickeya spp. in a multiplex pcr assay. in studies with axenic cultures o ...	2014	25506085
comparative genomics of closely related salmonella enterica serovar typhi strains reveals genome dynamics and the acquisition of novel pathogenic elements.	typhoid fever is an infectious disease of global importance that is caused by salmonella enterica subsp. enterica serovar typhi (s. typhi). this disease causes an estimated 200,000 deaths per year and remains a serious global health threat. s. typhi is strictly a human pathogen, and some recovered individuals become long-term carriers who continue to shed the bacteria in their faeces, thus becoming main reservoirs of infection.	2014	25412680
fha interaction with phosphothreonine of tssl activates type vi secretion in agrobacterium tumefaciens.	the type vi secretion system (t6ss) is a widespread protein secretion system found in many gram-negative bacteria. t6sss are highly regulated by various regulatory systems at multiple levels, including post-translational regulation via threonine (thr) phosphorylation. the ser/thr protein kinase ppka is responsible for this thr phosphorylation regulation, and the forkhead-associated (fha) domain-containing fha-family protein is the sole t6ss phosphorylation substrate identified to date. here we d ...	2014	24626341
fermentation technologies for the optimization of marine microbial exopolysaccharide production.	in the last decades, research has focused on the capabilities of microbes to secrete exopolysaccharides (eps), because these polymers differ from the commercial ones derived essentially from plants or algae in their numerous valuable qualities. these biopolymers have emerged as new polymeric materials with novel and unique physical characteristics that have found extensive applications. in marine microorganisms the produced eps provide an instrument to survive in adverse conditions: they are fou ...	2014	24857960
tuning of peroxiredoxin catalysis for various physiological roles.	peroxiredoxins (prxs) make up an ancient family of enzymes that are the predominant peroxidases for nearly all organisms and play essential roles in reducing hydrogen peroxide, organic hydroperoxides, and peroxynitrite. even between distantly related organisms, the core protein fold and key catalytic residues related to its cysteine-based catalytic mechanism have been retained. given that these enzymes appeared early in biology, prxs have experienced more than 1 billion years of optimization for ...	2014	25403613
inactivation of the organic hydroperoxide stress resistance regulator ohrr enhances resistance to oxidative stress and isoniazid in mycobacterium smegmatis.	the organic hydroperoxide stress resistance regulator (ohrr) is a marr type of transcriptional regulator that primarily regulates the expression of organic hydroperoxide reductase (ohr) in bacteria. in mycobacteria, the genes encoding these proteins exist in only a few species, which include the fast-growing organism mycobacterium smegmatis. to delineate the roles of ohr and ohrr in defense against oxidative stress in m. smegmatis, strains lacking the expression of these proteins were constructe ...	2014	25313389
inactivation of the organic hydroperoxide stress resistance regulator ohrr enhances resistance to oxidative stress and isoniazid in mycobacterium smegmatis.	the organic hydroperoxide stress resistance regulator (ohrr) is a marr type of transcriptional regulator that primarily regulates the expression of organic hydroperoxide reductase (ohr) in bacteria. in mycobacteria, the genes encoding these proteins exist in only a few species, which include the fast-growing organism mycobacterium smegmatis. to delineate the roles of ohr and ohrr in defense against oxidative stress in m. smegmatis, strains lacking the expression of these proteins were constructe ...	2014	25313389
1,2-β-oligoglucan phosphorylase from listeria innocua.	we characterized recombinant lin1839 protein (lin1839r) belonging to glycoside hydrolase family 94 from listeria innocua. lin1839r catalyzed the synthesis of a series of 1,2-β-oligoglucans (sopn: n denotes degree of polymerization) using sophorose (sop2) as the acceptor and α-d-glucose 1-phosphate (glc1p) as the donor. lin1839r recognized glucose as a very weak acceptor substrate to form polymeric 1,2-β-glucan. the degree of polymerization of the 1,2-β-glucan gradually decreased with long-term i ...	2014	24647662
from plant infectivity to growth patterns: the role of blue-light sensing in the prokaryotic world.	flavin-based photoreceptor proteins of the lov (light, oxygen, and voltage) and bluf (blue light sensing using flavins) superfamilies are ubiquitous among the three life domains and are essential blue-light sensing systems, not only in plants and algae, but also in prokaryotes. here we review their biological roles in the prokaryotic world and their evolution pathways. an unexpected large number of bacterial species possess flavin-based photosensors, amongst which are important human and plant p ...	2014	27135492
disruption of gene pqqa or pqqb reduces plant growth promotion activity and biocontrol of crown gall disease by rahnella aquatilis hx2.	rahnella aquatilis strain hx2 has the ability to promote maize growth and suppress sunflower crown gall disease caused by agrobacterium vitis, a. tumefaciens, and a. rhizogenes. pyrroloquinoline quinone (pqq), a cofactor of aldose and alcohol dehydrogenases, is required for the synthesis of an antibacterial substance, gluconic acid, by hx2. mutants of hx2 unable to produce pqq were obtained by in-frame deletion of either the pqqa or pqqb gene. in this study, we report the independent functions o ...	2014	25502691
arabidopsis and maize rida proteins preempt reactive enamine/imine damage to branched-chain amino acid biosynthesis in plastids.	rida (for reactive intermediate deaminase a) proteins are ubiquitous, yet their function in eukaryotes is unclear. it is known that deleting salmonella enterica rida causes ser sensitivity and that s. enterica rida and its homologs from other organisms hydrolyze the enamine/imine intermediates that thr dehydratase forms from ser or thr. in s. enterica, the ser-derived enamine/imine inactivates a branched-chain aminotransferase; rida prevents this damage. arabidopsis thaliana and maize (zea mays) ...	2014	25070638
mechanism of escherichia coli resistance to pyrrhocoricin.	due to their lack of toxicity to mammalian cells and good serum stability, proline-rich antimicrobial peptides (pr-amps) have been proposed as promising candidates for the treatment of infections caused by antimicrobial-resistant bacterial pathogens. it has been hypothesized that these peptides act on multiple targets within bacterial cells, and therefore the likelihood of the emergence of resistance was considered to be low. here, we show that spontaneous escherichia coli mutants resistant to p ...	2014	24590485
rapid identification of stenotrophomonas maltophilia by peptide nucleic acid fluorescence in situ hybridization.	the objective of this study was to develop a novel peptide nucleic acid (pna) probe for stenotrophomonas maltophilia identification by fluorescence in situ hybridization (fish). the probe was evaluated using 33 human and veterinary clinical s. maltophilia isolates and 45 reference strains representing common bacterial species in the respiratory tract. the probe displayed 100% sensitivity and 100% specificity on pure cultures and allowed detection in sputum from cystic fibrosis patients. the dete ...	2014	25356348
the diguanylate cyclase sadc is a central player in gac/rsm-mediated biofilm formation in pseudomonas aeruginosa.	pseudomonas aeruginosa is a gram-negative opportunistic human pathogen and a threat for immunocompromised and cystic fibrosis patients. it is responsible for acute and chronic infections and can switch between these lifestyles upon taking an informed decision involving complex regulatory networks. the rets/lads/gac/rsm network and the cyclic-di-gmp (c-di-gmp) signaling pathways are both central to this phenomenon redirecting the p. aeruginosa population toward a biofilm mode of growth, which is ...	2014	25225264
the diguanylate cyclase gcba facilitates pseudomonas aeruginosa biofilm dispersion by activating bdla.	biofilm dispersion is a highly regulated process that allows biofilm bacteria to respond to changing environmental conditions and to disseminate to new locations. the dispersion of biofilms formed by the opportunistic pathogen pseudomonas aeruginosa is known to require a number of cyclic di-gmp (c-di-gmp)-degrading phosphodiesterases (pdes) and the chemosensory protein bdla, with bdla playing a pivotal role in regulating pde activity and enabling dispersion in response to a wide array of cues. b ...	2014	25331436
the diguanylate cyclase gcba facilitates pseudomonas aeruginosa biofilm dispersion by activating bdla.	biofilm dispersion is a highly regulated process that allows biofilm bacteria to respond to changing environmental conditions and to disseminate to new locations. the dispersion of biofilms formed by the opportunistic pathogen pseudomonas aeruginosa is known to require a number of cyclic di-gmp (c-di-gmp)-degrading phosphodiesterases (pdes) and the chemosensory protein bdla, with bdla playing a pivotal role in regulating pde activity and enabling dispersion in response to a wide array of cues. b ...	2014	25331436
exopolysaccharides produced by marine bacteria and their applications as glycosaminoglycan-like molecules.	although polysaccharides are ubiquitous and the most abundant renewable bio-components, their studies, covered by the glycochemistry and glycobiology fields, remain a challenge due to their high molecular diversity and complexity. polysaccharides are industrially used in food products; human therapeutics fall into a more recent research field and pharmaceutical industry is looking for more and more molecules with enhanced activities. glycosaminoglycans (gags) found in animal tissues play a criti ...	2014	25340049
a complex gene locus enables xyloglucan utilization in the model saprophyte cellvibrio japonicus.	the degradation of plant biomass by saprophytes is an ecologically important part of the global carbon cycle, which has also inspired a vast diversity of industrial enzyme applications. the xyloglucans (xygs) constitute a family of ubiquitous and abundant plant cell wall polysaccharides, yet the enzymology of xyg saccharification is poorly studied. here, we present the identification and molecular characterization of a complex genetic locus that is required for xyloglucan utilization by the mode ...	2014	25171165
the plant pathogen xanthomonas campestris pv. campestris exploits n-acetylglucosamine during infection.	n-acetylglucosamine (glcnac), the main component of chitin and a major constituent of bacterial peptidoglycan, is present only in trace amounts in plants, in contrast to the huge amount of various sugars that compose the polysaccharides of the plant cell wall. thus, glcnac has not previously been considered a substrate exploited by phytopathogenic bacteria during plant infection. xanthomonas campestris pv. campestris, the causal agent of black rot disease of brassica plants, expresses a carbohyd ...	2014	25205095
expression of colsr genes increased in the rpf mutants of xanthomonas oryzae pv. oryzae kacc10859.	the rpf genes and cols xoo1207/colr xoo1208 were known to require for virulence of xanthomonas oryzae pv. oryzae (xoo). in xoo kacc10331 genome, two more cols/colr genes, cols xoo3534 (raxh)/colr xoo3535 (raxr) and cols xoo3762/colr xoo3763 were annotated. the cols xoo3534/colr xoo3535 were known to control avrxa21 activity and functions of cols xoo3762/colr xoo3763 were unknown in xoo. to characterize the relationship between rpf and cols/colr genes, expression of cols/colr genes in rpf mutants ...	2014	25289017
insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters.	although biosynthetic gene clusters (bgcs) have been discovered for hundreds of bacterial metabolites, our knowledge of their diversity remains limited. here, we used a novel algorithm to systematically identify bgcs in the extensive extant microbial sequencing data. network analysis of the predicted bgcs revealed large gene cluster families, the vast majority uncharacterized. we experimentally characterized the most prominent family, consisting of two subfamilies of hundreds of bgcs distributed ...	2014	25036635
the interaction pattern between a homology model of 40s ribosomal s9 protein of rhizoctonia solani and 1-hydroxyphenaize by docking study.	1-hydroxyphenazine (1-oh-phz), a natural product from pseudomonas aeruginosa strain sd12, was earlier reported to have potent antifungal activity against rhizoctonia solani. in the present work, the antifungal activity of 1-oh-phz on 40s ribosomal s9 protein was validated by molecular docking approach. 1-oh-phz showed interaction with two polar contacts with residues, arg69 and phe19, which inhibits the synthesis of fungal protein. our study reveals that 1-oh-phz can be a potent inhibitor of 40s ...	2014	24864254
identification of bacteriophages for biocontrol of the kiwifruit canker phytopathogen pseudomonas syringae pv. actinidiae.	pseudomonas syringae pv. actinidiae is a reemerging pathogen which causes bacterial canker of kiwifruit (actinidia sp.). since 2008, a global outbreak of p. syringae pv. actinidiae has occurred, and in 2010 this pathogen was detected in new zealand. the economic impact and the development of resistance in p. syringae pv. actinidiae and other pathovars against antibiotics and copper sprays have led to a search for alternative management strategies. we isolated 275 phages, 258 of which were active ...	2014	24487530
commonalities and differences of t3sss in rhizobia and plant pathogenic bacteria.	plant pathogenic bacteria and rhizobia infect higher plants albeit the interactions with their hosts are principally distinct and lead to completely different phenotypic outcomes, either pathogenic or mutualistic, respectively. bacterial protein delivery to plant host plays an essential role in determining the phenotypic outcome of plant-bacteria interactions. the involvement of type iii secretion systems (t3sss) in mediating animal- and plant-pathogen interactions was discovered in the mid-80's ...	2014	24723933
a new and improved host-independent plasmid system for rk2-based conjugal transfer.	bacterial conjugation is a process that is mediated either by a direct cell-to-cell junction or by formation of a bridge between the cells. it is often used to transfer dna constructs designed in escherichia coli to recipient bacteria, yeast, plants and mammalian cells. plasmids bearing the rk2/rp4 origin of transfer (orit) are mostly mobilized using the e. coli s17-1/sm10 donor strains, in which transfer helper functions are provided from a chromosomally integrated rp4::mu. we have observed tha ...	2014	24595202
lectin-like bacteriocins from pseudomonas spp. utilise d-rhamnose containing lipopolysaccharide as a cellular receptor.	lectin-like bacteriocins consist of tandem monocot mannose-binding domains and display a genus-specific killing activity. here we show that pyocin l1, a novel member of this family from pseudomonas aeruginosa, targets susceptible strains of this species through recognition of the common polysaccharide antigen (cpa) of p. aeruginosa lipopolysaccharide that is predominantly a homopolymer of d-rhamnose. structural and biophysical analyses show that recognition of cpa occurs through the c-terminal c ...	2014	24516380
bacterial ice crystal controlling proteins.	across the world, many ice active bacteria utilize ice crystal controlling proteins for aid in freezing tolerance at subzero temperatures. ice crystal controlling proteins include both antifreeze and ice nucleation proteins. antifreeze proteins minimize freezing damage by inhibiting growth of large ice crystals, while ice nucleation proteins induce formation of embryonic ice crystals. although both protein classes have differing functions, these proteins use the same ice binding mechanisms. rath ...	2014	24579057
a linkage between smeijk efflux pump, cell envelope integrity, and σe-mediated envelope stress response in stenotrophomonas maltophilia.	resistance nodulation division (rnd) efflux pumps, such as the smeijk pump of stenotrophomonas maltophilia, are known to contribute to the multidrug resistance in gram-negative bacteria. however, some rnd pumps are constitutively expressed even though no antimicrobial stresses occur, implying that there should be some physical implications for these rnd pumps. in this study, the role of smeijk in antimicrobials resistance, envelope integrity, and σe-mediated envelope stress response (esr) of s. ...	2014	25390933
transcriptional regulation of bacterial virulence gene expression by molecular oxygen and nitric oxide.	molecular oxygen (o2) and nitric oxide (no) are diatomic gases that play major roles in infection. the host innate immune system generates reactive oxygen species and no as bacteriocidal agents and both require o2 for their production. furthermore, the ability to adapt to changes in o2 availability is crucial for many bacterial pathogens, as many niches within a host are hypoxic. pathogenic bacteria have evolved transcriptional regulatory systems that perceive these gases and respond by reprogra ...	2014	25603427
defining the metabolic requirements for the growth and colonization capacity of campylobacter jejuni.	during the last decade campylobacter jejuni has been recognized as the leading cause of bacterial gastroenteritis worldwide. this facultative intracellular pathogen is a member of the epsilonproteobacteria and requires microaerobic atmosphere and nutrient rich media for efficient proliferation in vitro. its catabolic capacity is highly restricted in contrast to salmonella typhimurium and other enteropathogenic bacteria because several common pathways for carbohydrate utilization are either missi ...	2014	25325018
the interaction of human enteric pathogens with plants.	there are an increasing number of outbreaks of human pathogens related to fresh produce. thus, the growth of human pathogens on plants should be explored. human pathogens can survive under the harsh environments in plants, and can adhere and actively invade plants. plant-associated microbiota or insects contribute to the survival and transmission of enteric pathogens in plants. human enteric pathogens also trigger plant innate immunity, but some pathogens-such as salmonella-can overcome this def ...	2014	25288993
tssar: tss annotation regime for drna-seq data.	differential rna sequencing (drna-seq) is a high-throughput screening technique designed to examine the architecture of bacterial operons in general and the precise position of transcription start sites (tss) in particular. hitherto, drna-seq data were analyzed by visualizing the sequencing reads mapped to the reference genome and manually annotating reliable positions. this is very labor intensive and, due to the subjectivity, biased.	2014	24674136
mechanisms of post-transcriptional gene regulation in bacterial biofilms.	biofilms are characterized by a dense multicellular community of microorganisms that can be formed by the attachment of bacteria to an inert surface and to each other. the development of biofilm involves the initial attachment of planktonic bacteria to a surface, followed by replication, cell-to-cell adhesion to form microcolonies, maturation, and detachment. mature biofilms are embedded in a self-produced extracellular polymeric matrix composed primarily of bacterial-derived exopolysaccharides, ...	2014	24724055
the arable ecosystem as battleground for emergence of new human pathogens.	disease incidences related to escherichia coli and salmonella enterica infections by consumption of (fresh) vegetables, sprouts, and occasionally fruits made clear that these pathogens are not only transmitted to humans via the "classical" routes of meat, eggs, and dairy products, but also can be transmitted to humans via plants or products derived from plants. nowadays, it is of major concern that these human pathogens, especially the ones belonging to the taxonomical family of enterobacteriace ...	2014	24688484
emra1 membrane fusion protein of francisella tularensis lvs is required for resistance to oxidative stress, intramacrophage survival and virulence in mice.	francisella tularensis is a category a biodefence agent that causes a fatal human disease known as tularaemia. the pathogenicity of f. tularensis depends on its ability to persist inside host immune cells primarily by resisting an attack from host-generated reactive oxygen and nitrogen species (ros/rns). based on the ability of f. tularensis to resist high ros/rns levels, we have hypothesized that additional unknown factors act in conjunction with known antioxidant defences to render ros resista ...	2014	24397487
exopolysaccharide biosynthesis enables mature biofilm formation on abiotic surfaces by herbaspirillum seropedicae.	h. seropedicae associates endophytically and epiphytically with important poaceous crops and is capable of promoting their growth. the molecular mechanisms involved in plant colonization by this microrganism are not fully understood. exopolysaccharides (eps) are usually necessary for bacterial attachment to solid surfaces, to other bacteria, and to form biofilms. the role of h. seropedicae smr1 exopolysaccharide in biofilm formation on both inert and plant substrates was assessed by characteriza ...	2014	25310013
roles of a solo luxr in the biological control agent lysobacter enzymogenes strain oh11.	lysobacter enzymogenes is a ubiquitous plant-associated and environmentally friendly bacterium emerging as a novel biological control agent of plant disease. this bacterium produces diverse antifungal factors, such as lytic enzymes and a secondary metabolite (heat-stable antifungal factor [hsaf]) having antifungal activity with a novel structure and mode of action. the regulatory mechanisms for biosynthesis of antifungal factors is largely unknown in l. enzymogenes. the solo luxr proteins have b ...	2014	24111575
characterization of bacteriophages cp1 and cp2, the strain-typing agents for xanthomonas axonopodis pv. citri.	the strains of xanthomonas axonopodis pv. citri, the causative agent of citrus canker, are historically classified based on bacteriophage (phage) sensitivity. nearly all x. axonopodis pv. citri strains isolated from different regions in japan are lysed by either phage cp1 or cp2; cp1-sensitive (cp1(s)) strains have been observed to be resistant to cp2 (cp2(r)) and vice versa. in this study, genomic and molecular characterization was performed for the typing agents cp1 and cp2. morphologically, c ...	2014	24123743
luxr solos in photorhabdus species.	bacteria communicate via small diffusible molecules to mediate group-coordinated behavior, a process designated as quorum sensing. the basic molecular quorum sensing system of gram-negative bacteria consists of a luxi-type autoinducer synthase producing acyl-homoserine lactones (ahls) as signaling molecules, and a luxr-type receptor detecting the ahls to control expression of specific genes. however, many proteobacteria possess one or more unpaired luxr-type receptors that lack a cognate luxi-li ...	2014	25478328
carbohydrate metabolism in archaea: current insights into unusual enzymes and pathways and their regulation.	the metabolism of archaea, the third domain of life, resembles in its complexity those of bacteria and lower eukarya. however, this metabolic complexity in archaea is accompanied by the absence of many "classical" pathways, particularly in central carbohydrate metabolism. instead, archaea are characterized by the presence of unique, modified variants of classical pathways such as the embden-meyerhof-parnas (emp) pathway and the entner-doudoroff (ed) pathway. the pentose phosphate pathway is only ...	2014	24600042
substrate specificity of cytoplasmic n-glycosyltransferase.	n-linked protein glycosylation is a very common post-translational modification that can be found in all kingdoms of life. the classical, highly conserved pathway entails the assembly of a lipid-linked oligosaccharide and its transfer to an asparagine residue in the sequon nx(s/t) of a secreted protein by the integral membrane protein oligosaccharyltransferase. a few species in the class of γ-proteobacteria encode a cytoplasmic n-glycosylation system mediated by a soluble n-glycosyltransferase ( ...	2014	24962585
melanin-templated rapid synthesis of silver nanostructures.	as a potent antimicrobial agent, silver nanostructures have been used in nanosensors and nanomaterial-based assays for the detection of food relevant analytes such as organic molecules, aroma, chemical contaminants, gases and food borne pathogens. in addition silver based nanocomposites act as an antimicrobial for food packaging materials. in this prospective, the food grade melanin pigment extracted from sponge associated actinobacterium nocardiopsis alba msa10 and melanin mediated synthesis of ...	2014	24885756
biological roles of the o-methyl phosphoramidate capsule modification in campylobacter jejuni.	campylobacter jejuni is a major cause of bacterial gastroenteritis worldwide, and the capsular polysaccharide (cps) of this organism is required for persistence and disease. c. jejuni produces over 47 different capsular structures, including a unique o-methyl phosphoramidate (meopn) modification present on most c. jejuni isolates. although the meopn structure is rare in nature it has structural similarity to some synthetic pesticides. in this study, we have demonstrated, by whole genome comparis ...	2014	24498018
metabolic engineering of microorganisms for the production of l-arginine and its derivatives.	l-arginine (arg) is an important amino acid for both medicinal and industrial applications. for almost six decades, the research has been going on for its improved industrial level production using different microorganisms. while the initial approaches involved random mutagenesis for increased tolerance to arg and consequently higher arg titer, it is laborious and often leads to unwanted phenotypes, such as retarded growth. discovery of l-glutamate (glu) overproducing strains and using them as b ...	2014	25467280
tryptophan-catabolizing enzymes - party of three.	indoleamine 2,3-dioxygenase (ido) and tryptophan 2,3-dioxygenase (tdo) are tryptophan-degrading enzymes that have independently evolved to catalyze the first step in tryptophan catabolism via the kynurenine pathway (kp). the depletion of tryptophan and formation of kp metabolites modulates the activity of the mammalian immune, reproductive, and central nervous systems. ido and tdo enzymes can have overlapping or distinct functions depending on their expression patterns. the expression of tdo and ...	2014	25346733
the role of bacterial protein tyrosine phosphatases in the regulation of the biosynthesis of secreted polysaccharides.	tyrosine phosphorylation and associated protein tyrosine phosphatases are gaining prominence as critical mechanisms in the regulation of fundamental processes in a wide variety of bacteria. in particular, these phosphatases have been associated with the control of the biosynthesis of capsular polysaccharides and extracellular polysaccharides, critically important virulence factors for bacteria.	2014	24295407
type iv pilus biogenesis, twitching motility, and dna uptake in thermus thermophilus: discrete roles of antagonistic atpases pilf, pilt1, and pilt2.	natural transformation has a large impact on lateral gene flow and has contributed significantly to the ecological diversification and adaptation of bacterial species. thermus thermophilus hb27 has emerged as the leading model organism for studies of dna transporters in thermophilic bacteria. recently, we identified a zinc-binding polymerization nucleoside triphosphatase (ntpase), pilf, which is essential for the transport of dna through the outer membrane. here, we present genetic evidence that ...	2014	24212586
structural and biochemical analysis of a unique phosphatase from bdellovibrio bacteriovorus reveals its structural and functional relationship with the protein tyrosine phosphatase class of phytase.	bdellovibrio bacteriovorus is an unusual δ-proteobacterium that invades and preys on other gram-negative bacteria and is of potential interest as a whole cell therapeutic against pathogens of man, animals and crops. ptps (protein tyrosine phosphatases) are an important class of enzyme involved in desphosphorylating a variety of substrates, often with implications in cell signaling. the b. bacteriovorus open reading frame bd1204 is predicted to encode a ptp of unknown function. bd1204 is both str ...	2014	24718691
homogalacturonan-modifying enzymes: structure, expression, and roles in plants.	understanding the changes affecting the plant cell wall is a key element in addressing its functional role in plant growth and in the response to stress. pectins, which are the main constituents of the primary cell wall in dicot species, play a central role in the control of cellular adhesion and thereby of the rheological properties of the wall. this is likely to be a major determinant of plant growth. how the discrete changes in pectin structure are mediated is thus a key issue in our understa ...	2014	25056773
transcriptomic analysis reveals new regulatory roles of clp signaling in secondary metabolite biosynthesis and surface motility in lysobacter enzymogenes oh11.	lysobacter enzymogenes is a bacterial biological control agent emerging as a new source of antibiotic metabolites, such as heat-stable antifungal factor (hsaf) and the antibacterial factor wap-8294a2. the regulatory mechanism(s) for antibiotic metabolite biosynthesis remains largely unknown in l. enzymogenes. clp, a cyclic adenosine monophosphate (camp)-receptor-like protein, is shown to function as a global regulator in modulating biocontrol-associated traits in l. enzymogenes. however, the gen ...	2014	25236801
identification and biosynthesis of a novel xanthomonadin-dialkylresorcinol-hybrid from azoarcus sp. bh72.	a novel xanthomonadin-dialkylresorcinol hybrid named arcuflavin was identified in azoarcus sp. bh72 by a combination of feeding experiments, hplc-ms and maldi-ms and gene clusters encoding the biosynthesis of this non-isoprenoid aryl-polyene containing pigment are reported. a chorismate-utilizing enzyme from the xanb2-type producing 3- and 4-hydroxybenzoic acid and an amp-ligase encoded by these gene clusters were characterized, that might perform the first two steps of the polyene biosynthesis. ...	2014	24618669
identification of the catalytic triad of family s46 exopeptidases, closely related to clan pa endopeptidases.	the exopeptidases of family s46 are exceptional, as the closest homologs of these enzymes are the endopeptidases of clan pa. the three-dimensional structure of s46 enzymes is unknown and only one of the catalytic residues, the serine, has been identified. the catalytic histidine and aspartate residues are not experimentally identified. here we present phylogenetic and experimental data that identify all residues of the catalytic triad of s46 peptidase, dipeptidyl aminopeptidase bii (dap bii) fro ...	2014	24598890
a system to automatically classify and name any individual genome-sequenced organism independently of current biological classification and nomenclature.	a broadly accepted and stable biological classification system is a prerequisite for biological sciences. it provides the means to describe and communicate about life without ambiguity. current biological classification and nomenclature use the species as the basic unit and require lengthy and laborious species descriptions before newly discovered organisms can be assigned to a species and be named. the current system is thus inadequate to classify and name the immense genetic diversity within s ...	2014	24586551
phenotypic heterogeneity, a phenomenon that may explain why quorum sensing does not always result in truly homogenous cell behavior.	phenotypic heterogeneity describes the occurrence of "nonconformist" cells within an isogenic population. the nonconformists show an expression profile partially different from that of the remainder of the population. phenotypic heterogeneity affects many aspects of the different bacterial lifestyles, and it is assumed that it increases bacterial fitness and the chances for survival of the whole population or smaller subpopulations in unfavorable environments. well-known examples for phenotypic ...	2015	26025903
comparative genomics and metabolic profiling of the genus lysobacter.	lysobacter species are gram-negative bacteria widely distributed in soil, plant and freshwater habitats. lysobacter owes its name to the lytic effects on other microorganisms. to better understand their ecology and interactions with other (micro)organisms, five lysobacter strains representing the four species l. enzymogenes, l. capsici, l. gummosus and l. antibioticus were subjected to genomics and metabolomics analyses.	2015	26597042
diversity and activity of lysobacter species from disease suppressive soils.	the genus lysobacter includes several species that produce a range of extracellular enzymes and other metabolites with activity against bacteria, fungi, oomycetes, and nematodes. lysobacter species were found to be more abundant in soil suppressive against the fungal root pathogen rhizoctonia solani, but their actual role in disease suppression is still unclear. here, the antifungal and plant growth-promoting activities of 18 lysobacter strains, including 11 strains from rhizoctonia-suppressive ...	2015	26635735
the multiple dsf-family qs signals are synthesized from carbohydrate and branched-chain amino acids via the fas elongation cycle.	members of the diffusible signal factor (dsf) family are a novel class of quorum sensing (qs) signals in diverse gram-negative bacteria. although previous studies have identified rpff as a key enzyme for the biosynthesis of dsf family signals, many questions in their biosynthesis remain to be addressed. in this study with the phytopathogen xanthomonas campestris pv. campestris (xcc), we show that xcc produces four dsf-family signals (dsf, bdsf, cdsf and idsf) during cell culture, and that idsf i ...	2015	26289160
exploring the microbiota dynamics related to vegetable biomasses degradation and study of lignocellulose-degrading bacteria for industrial biotechnological application.	the aims of this study were to evaluate the microbial diversity of different lignocellulosic biomasses during degradation under natural conditions and to isolate, select, characterise new well-adapted bacterial strains to detect potentially improved enzyme-producing bacteria. the microbiota of biomass piles of arundo donax, eucalyptus camaldulensis and populus nigra were evaluated by high-throughput sequencing. a highly complex bacterial community was found, composed of ubiquitous bacteria, with ...	2015	25641069
identification of a small molecule signaling factor that regulates the biosynthesis of the antifungal polycyclic tetramate macrolactam hsaf in lysobacter enzymogenes.	lysobacter species are emerging as new sources of antibiotics. the regulation of these antibiotics is not well understood. here, we identified a small molecule metabolite (ledsf3) that regulates the biosynthesis of the antifungal antibiotic heat-stable antifungal factor (hsaf), a polycyclic tetramate macrolactam with a structure and mode of action distinct from the existing antifungal drugs. ledsf3 was isolated from the culture broth of lysobacter enzymogenes, and its chemical structure was esta ...	2015	25301587
identification of a small molecule signaling factor that regulates the biosynthesis of the antifungal polycyclic tetramate macrolactam hsaf in lysobacter enzymogenes.	lysobacter species are emerging as new sources of antibiotics. the regulation of these antibiotics is not well understood. here, we identified a small molecule metabolite (ledsf3) that regulates the biosynthesis of the antifungal antibiotic heat-stable antifungal factor (hsaf), a polycyclic tetramate macrolactam with a structure and mode of action distinct from the existing antifungal drugs. ledsf3 was isolated from the culture broth of lysobacter enzymogenes, and its chemical structure was esta ...	2015	25301587
contribution of physical interactions to signaling specificity between a diguanylate cyclase and its effector.	cyclic diguanylate (c-di-gmp) is a bacterial second messenger that controls multiple cellular processes. c-di-gmp networks have up to dozens of diguanylate cyclases (dgcs) that synthesize c-di-gmp along with many c-di-gmp-responsive target proteins that can bind and respond to this signal. for such networks to have order, a mechanism(s) likely exists that allow dgcs to specifically signal their targets, and it has been suggested that physical interactions might provide such specificity. our resu ...	2015	26670387
bacterial signal transduction by cyclic di-gmp and other nucleotide second messengers.	the first international symposium on c-di-gmp signaling in bacteria (22 to 25 march 2015, harnack-haus, berlin, germany)brought together 131 molecular microbiologists from 17 countries to discuss recent progress in our knowledge of bacterial nucleotide second messenger signaling. while the focus was on signal input, synthesis, degradation, and the striking diversity of the modes of action of the current second messenger paradigm, i.e., cyclic di-gmp (c-di-gmp), “classics” like camp and (p)ppgpp ...	2015	26055111
bacterial signal transduction by cyclic di-gmp and other nucleotide second messengers.	the first international symposium on c-di-gmp signaling in bacteria (22 to 25 march 2015, harnack-haus, berlin, germany)brought together 131 molecular microbiologists from 17 countries to discuss recent progress in our knowledge of bacterial nucleotide second messenger signaling. while the focus was on signal input, synthesis, degradation, and the striking diversity of the modes of action of the current second messenger paradigm, i.e., cyclic di-gmp (c-di-gmp), “classics” like camp and (p)ppgpp ...	2015	26055111
genome sequence of lysobacter dokdonensis ds-58(t), a gliding bacterium isolated from soil in dokdo, korea.	lysobacter dokdonensis ds-58, belonging to the family xanthomonadaceae, was isolated from a soil sample in dokdo, korea in 2011. strain ds-58 is the type strain of l. dokdonensis. in this study, we determined the genome sequence to describe the genomic features including annotation information and cog functional categorization. the draft genome sequence consists of 25 contigs totaling 3,274,406 bp (67.24 % g + c) and contains 3,155 protein coding genes, 2 copies of ribosomal rna operons, and 48 ...	2015	26664701
type iii secretion systems: the bacterial flagellum and the injectisome.	the flagellum and the injectisome are two of the most complex and fascinating bacterial nanomachines. at their core, they share a type iii secretion system (t3ss), a transmembrane export complex that forms the extracellular appendages, the flagellar filament and the injectisome needle. recent advances, combining structural biology, cryo-electron tomography, molecular genetics, in vivo imaging, bioinformatics and biophysics, have greatly increased our understanding of the t3ss, especially the str ...	2015	26370933
nodulation characterization and proteomic profiling of bradyrhizobium liaoningense ccbau05525 in response to water-soluble humic materials.	the lignite biodegradation procedure to produce water-soluble humic materials (wshm) with a penicillium stain was established by previous studies in our laboratory. this study researched the effects of wshm on the growth of bradyrhizobium liaoningense ccbau05525 and its nodulation on soybean. results showed that wshm enhanced the cell density of ccbau05525 in culture, and increased the nodule number, nodule fresh weight and nitrogenase activity of the inoculated soybean plants. then the chemical ...	2015	26054030
a bioinformatic survey of distribution, conservation, and probable functions of luxr solo regulators in bacteria.	luxr solo transcriptional regulators contain both an autoinducer binding domain (abd; n-terminal) and a dna binding helix-turn-helix domain (hth; c-terminal), but are not associated with a cognate n-acyl homoserine lactone (ahl) synthase coding gene in the same genome. although a few luxr solos have been characterized, their distributions as well as their role in bacterial signal perception and other processes are poorly understood. in this study we have carried out a systematic survey of distri ...	2015	25759807
dna-binding properties of a cgmp-binding crp homologue that controls development of metabolically dormant cysts of rhodospirillum centenum.	rhodospirillum centenum utilizes 3',5'-cyclic guanosine monophosphate (cgmp) as a messenger to regulate development of desiccation-resistant cysts. in this study, we demonstrated that gcya, gcyb and gcyc, coding for putative subunits of a guanylyl cyclase, increase expression from 8- to 500-fold when cells transition from vegetative to cyst phases of growth. this induction did not occur in a strain that is defective in cgmp synthesis or in a strain that contains a deletion of cgra that codes for ...	2015	26362215
genome wide transcriptional profiling of herbaspirillum seropedicae smr1 grown in the presence of naringenin.	herbaspirillum seropedicae is a diazotrophic bacterium which associates endophytically with economically important gramineae. flavonoids such as naringenin have been shown to have an effect on the interaction between h. seropedicae and its host plants. we used a high-throughput sequencing based method (rna-seq) to access the influence of naringenin on the whole transcriptome profile of h. seropedicae. three hundred and four genes were downregulated and seventy seven were upregulated by naringeni ...	2015	26052319
exploiting quorum sensing interfering strategies in gram-negative bacteria for the enhancement of environmental applications.	quorum sensing (qs) is a widespread intercellular form of communication to coordinate physiological processes and cooperative activities of bacteria at the population level, and it depends on the production, secretion, and detection of small diffusible autoinducers, such as acyl-homoserine lactones (ahls), auto-inducing oligo-peptides (aips) and autoinducer 2. in this review, the function of qs autoinducers of gram-negative bacteria in different aspects of wastewater treatment systems is examine ...	2015	26779175
exploiting quorum sensing interfering strategies in gram-negative bacteria for the enhancement of environmental applications.	quorum sensing (qs) is a widespread intercellular form of communication to coordinate physiological processes and cooperative activities of bacteria at the population level, and it depends on the production, secretion, and detection of small diffusible autoinducers, such as acyl-homoserine lactones (ahls), auto-inducing oligo-peptides (aips) and autoinducer 2. in this review, the function of qs autoinducers of gram-negative bacteria in different aspects of wastewater treatment systems is examine ...	2015	26779175
vapd in xylella fastidiosa is a thermostable protein with ribonuclease activity.	xylella fastidiosa strain 9a5c is a gram-negative phytopathogen that is the causal agent of citrus variegated chlorosis (cvc), a disease that is responsible for economic losses in brazilian agriculture. the most well-known mechanism of pathogenicity for this bacterial pathogen is xylem vessel occlusion, which results from bacterial movement and the formation of biofilms. the molecular mechanisms underlying the virulence caused by biofilm formation are unknown. here, we provide evidence showing t ...	2015	26694028
new insights into the biological role of the osmoregulated periplasmic glucans in pathogenic and symbiotic bacteria.	this review emphasizes the biological roles of the osmoregulated periplasmic glucans (opgs). osmoregulated periplasmic glucans occur in almost all α-, β- and γ-proteobacteria. this polymer of glucose is required for full virulence. the roles of the opgs are complex and vary depending on the species. here, we outline the four major roles of the opgs through four different pathogenic and one symbiotic bacterial models (dickeya dadantii, salmonella enterica, pseudomonas aeruginosa, brucella abortus ...	2015	26265506
fleq coordinates flagellum-dependent and -independent motilities in pseudomonas syringae pv. tomato dc3000.	motility plays an essential role in bacterial fitness and colonization in the plant environment, since it favors nutrient acquisition and avoidance of toxic substances, successful competition with other microorganisms, the ability to locate the preferred hosts, access to optimal sites within them, and dispersal in the environment during the course of transmission. in this work, we have observed that the mutation of the flagellar master regulatory gene, fleq, alters bacterial surface motility and ...	2015	26296726
tonb energy transduction systems of riemerella anatipestifer are required for iron and hemin utilization.	riemerella anatipestifer (r. anatipestifer) is one of the most important pathogens in ducks. the bacteria causes acute or chronic septicemia characterized by fibrinous pericarditis and meningitis. the r. anatipestifer genome encodes multiple iron/hemin-uptake systems that facilitate adaptation to iron-limited host environments. these systems include several tonb-dependent transporters and three tonb proteins responsible for energy transduction. these three tonb genes are present in all the r. an ...	2015	26017672
how do base-pairing small rnas evolve?	the increasing numbers of characterized base-pairing small rnas (srnas) and the identification of these regulators in a broad range of bacteria are allowing comparisons between species and explorations of srna evolution. in this review, we describe some examples of trans-encoded base-pairing srnas that are species-specific and others that are more broadly distributed. we also describe examples of srna orthologs where different features are conserved. these examples provide the background for a d ...	2015	25934120
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
genome-wide identification of genes necessary for biofilm formation by nosocomial pathogen stenotrophomonas maltophilia reveals that orphan response regulator fsnr is a critical modulator.	stenotrophomonas maltophilia is a gram-negative bacterial pathogen of increasing concern to human health. most clinical isolates of s. maltophilia efficiently form biofilms on biotic and abiotic surfaces, making this bacterium resistant to a number of antibiotic treatments and therefore difficult to eliminate. to date, very few studies have investigated the molecular and regulatory mechanisms responsible for s. maltophilia biofilm formation. here we constructed a random transposon insertion muta ...	2015	25480754
selenite protection of tellurite toxicity toward escherichia coli.	in this work the influence of selenite on metal resistance in escherichia coli was examined. both synergistic and antagonistic resistance and toxicities were found upon co exposure with selenite. in wild type cells co-exposure to selenite had little effect on arsenic resistance, decreased resistance to cadmium and mercury but led to a dramatically increased resistance to tellurite of 32-fold. due to the potential importance of thiol chemistry in metal biochemistry, deletion strains in γ-glutamyl ...	2015	26732755
fleq dna binding consensus sequence revealed by studies of fleq-dependent regulation of biofilm gene expression in pseudomonas aeruginosa.	the transcription factor fleq from pseudomonas aeruginosa derepresses expression of genes involved in biofilm formation when intracellular levels of the second messenger cyclic diguanosine monophosphate (c-di-gmp) are high. fleq also activates transcription of flagellar genes, and the expression of these genes is highest at low intracellular c-di-gmp. fleq thus plays a central role in mediating the transition between planktonic and biofilm lifestyles of p. aeruginosa. previous work showed that f ...	2015	26483521
fleq dna binding consensus sequence revealed by studies of fleq-dependent regulation of biofilm gene expression in pseudomonas aeruginosa.	the transcription factor fleq from pseudomonas aeruginosa derepresses expression of genes involved in biofilm formation when intracellular levels of the second messenger cyclic diguanosine monophosphate (c-di-gmp) are high. fleq also activates transcription of flagellar genes, and the expression of these genes is highest at low intracellular c-di-gmp. fleq thus plays a central role in mediating the transition between planktonic and biofilm lifestyles of p. aeruginosa. previous work showed that f ...	2015	26483521
diversity of cyclic di-gmp-binding proteins and mechanisms.	cyclic di-gmp (c-di-gmp) synthetases and hydrolases (ggdef, eal, and hd-gyp domains) can be readily identified in bacterial genome sequences by using standard bioinformatic tools. in contrast, identification of c-di-gmp receptors remains a difficult task, and the current list of experimentally characterized c-di-gmp-binding proteins is likely incomplete. several classes of c-di-gmp-binding proteins have been structurally characterized; for some others, the binding sites have been identified; and ...	2015	26055114
diversity of cyclic di-gmp-binding proteins and mechanisms.	cyclic di-gmp (c-di-gmp) synthetases and hydrolases (ggdef, eal, and hd-gyp domains) can be readily identified in bacterial genome sequences by using standard bioinformatic tools. in contrast, identification of c-di-gmp receptors remains a difficult task, and the current list of experimentally characterized c-di-gmp-binding proteins is likely incomplete. several classes of c-di-gmp-binding proteins have been structurally characterized; for some others, the binding sites have been identified; and ...	2015	26055114
classification and taxonomy of vegetable macergens.	macergens are bacteria capable of releasing pectic enzymes (pectolytic bacteria). these enzymatic actions result in the separation of plant tissues leading to total plant destruction. this can be attributed to soft rot diseases in vegetables. these macergens primarily belong to the genus erwinia and to a range of opportunistic pathogens namely: the xanthomonas spp., pseudomonas spp., clostridium spp., cytophaga spp., and bacillus spp. they consist of taxa that displayed considerable heterogeneit ...	2015	26640465
complete sequence and detailed analysis of the first indigenous plasmid from xanthomonas oryzae pv. oryzicola.	bacterial plasmids have a major impact on metabolic function and adaptation of their hosts. an indigenous plasmid was identified in a chinese isolate (gx01) of the invasive phytopathogen xanthomonas oryzae pv. oryzicola (xoc), the causal agent of rice bacterial leaf streak (bls). to elucidate the biological functions of the plasmid, we have sequenced and comprehensively annotated the plasmid.	2015	26498126
ethylene: traffic controller on hormonal crossroads to defense.	ethylene (et) is an important hormone in plant responses to microbial pathogens and herbivorous insects, and in the interaction of plants with beneficial microbes and insects. early et signaling events during these biotic interactions involve activities of mitogen-activated protein kinases and ethylene response factor transcription factors. rather than being the principal regulator, et often modulates defense signaling pathways, including those regulated by jasmonic acid and salicylic acid. horm ...	2015	26482888
systemic responses in a tolerant olive (olea europaea l.) cultivar upon root colonization by the vascular pathogen verticillium dahliae.	verticillium wilt of olive (vwo) is caused by the vascular pathogen verticillium dahliae. one of the best vwo management measures is the use of tolerant cultivars; however, our knowledge on vwo tolerance/resistance genetics is very limited. a transcriptomic analysis was conducted to (i) identify systemic defense responses induced/repressed in aerial tissues of the tolerant cultivar frantoio upon root colonization by v. dahliae, and (ii) determine the expression pattern of selected defense genes ...	2015	26441865
identification of bradyrhizobium elkanii genes involved in incompatibility with soybean plants carrying the rj4 allele.	symbioses between leguminous plants and soil bacteria known as rhizobia are of great importance to agricultural production and nitrogen cycling. while these mutualistic symbioses can involve a wide range of rhizobia, some legumes exhibit incompatibility with specific strains, resulting in ineffective nodulation. the formation of nodules in soybean plants (glycine max) is controlled by several host genes, which are referred to as rj genes. the soybean cultivar barc2 carries the rj4 gene, which re ...	2015	26187957
controlling weeds with fungi, bacteria and viruses: a review.	weeds are a nuisance in a variety of land uses. the increasing prevalence of both herbicide resistant weeds and bans on cosmetic pesticide use has created a strong impetus to develop novel strategies for controlling weeds. the application of bacteria, fungi and viruses to achieving this goal has received increasingly great attention over the last three decades. proposed benefits to this strategy include reduced environmental impact, increased target specificity, reduced development costs compare ...	2015	26379687
metabolomics reveals differences of metal toxicity in cultures of pseudomonas pseudoalcaligenes kf707 grown on different carbon sources.	co-contamination of metals and organic pollutants is a global problem as metals interfere with the metabolism of complex organics by bacteria. based on a prior observation that metal tolerance was altered by the sole carbon source being used for growth, we sought to understand how metal toxicity specifically affects bacteria using an organic pollutant as their sole carbon source. to this end metabolomics was used to compare cultures of pseudomonas pseudoalcaligenes kf707 grown on either biphenyl ...	2015	26347721
is the efficacy of biological control against plant diseases likely to be more durable than that of chemical pesticides?	the durability of a control method for plant protection is defined as the persistence of its efficacy in space and time. it depends on (i) the selection pressure exerted by it on populations of plant pathogens and (ii) on the capacity of these pathogens to adapt to the control method. erosion of effectiveness of conventional plant protection methods has been widely studied in the past. for example, apparition of resistance to chemical pesticides in plant pathogens or pests has been extensively d ...	2015	26284088
the xanthomonas oryzae pv. oryzae pilz domain proteins function differentially in cyclic di-gmp binding and regulation of virulence and motility.	the pilz domain proteins have been demonstrated to be one of the major types of receptors mediating cyclic di-gmp (c-di-gmp) signaling pathways in several pathogenic bacteria. however, little is known about the function of pilz domain proteins in c-di-gmp regulation of virulence in the bacterial blight pathogen of rice xanthomonas oryzae pv. oryzae. here, the roles of pilz domain proteins pxo_00049 and pxo_02374 in c-di-gmp binding, regulation of virulence and motility, and subcellular localizat ...	2015	25911481
tryptophan-kynurenine pathway is dysregulated in inflammation, and immune activation.	the kynurenine (kyn) pathway is the major route for tryptophan (trp) metabolism, and it contributes to several fundamental biological processes. trp is constitutively oxidized by tryptophan 2, 3-dioxygenase in liver cells. in other cell types, it is catalyzed by an alternative inducible indoleamine-pyrrole 2, 3-dioxygenase (ido) under certain pathophysiological conditions, which consequently increases the formation of kyn metabolites. ido is up-regulated in response to inflammatory conditions as ...	2015	25961549
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