Publications

diverse mechanisms of post-transcriptional repression by the small rna regulator of glucose-phosphate stress.	the escherichia coli small rna sgrs controls a metabolic stress response that occurs upon accumulation of certain glycolytic intermediates. sgrs base pairs with and represses translation of ptsg and manxyz mrnas, which encode sugar transporters, and activates translation of yigl mrna, encoding a sugar phosphatase. this study defines four new genes as direct targets of e. coli sgrs. these new targets, asd, adiy, fole and purr, encode transcription factors or enzymes of diverse metabolic pathways, ...	2015	26411266
my life with mu.		2015	26442190
diverse mechanisms of post-transcriptional repression by the small rna regulator of glucose-phosphate stress.	the escherichia coli small rna sgrs controls a metabolic stress response that occurs upon accumulation of certain glycolytic intermediates. sgrs base pairs with and represses translation of ptsg and manxyz mrnas, which encode sugar transporters, and activates translation of yigl mrna, encoding a sugar phosphatase. this study defines four new genes as direct targets of e. coli sgrs. these new targets, asd, adiy, fole and purr, encode transcription factors or enzymes of diverse metabolic pathways, ...	2015	26411266
deciphering the regulatory circuitry that controls reversible lysine acetylation in salmonella enterica.	in salmonella enterica, the reversible lysine acetylation (rla) system is comprised of the protein acetyltransferase (pat) and sirtuin deacetylase (cobb). rla controls the activities of many proteins, including the acetyl coenzyme a (acetyl-coa) synthetase (acs), by modulating the degree of acs acetylation. we report that iolr, a myo-inositol catabolism repressor, activates the expression of genes encoding components of the rla system. in vitro evidence shows that the iolr protein directly regul ...	2015	26199328
experimental approaches to identify small rnas and their diverse roles in bacteria--what we have learnt in one decade of mica research.	nowadays the identification of small rnas (srnas) and characterization of their role within regulatory networks takes a prominent place in deciphering complex bacterial phenotypes. compared to the study of other components of bacterial cells, this is a relatively new but fast-growing research field. although reports on new srnas appear regularly, some srnas are already subject of research for a longer time. one of such srnas is mica, a srna best described for its role in outer membrane remodelin ...	2015	25974745
phylum-wide analysis of genes/proteins related to the last steps of assembly and export of extracellular polymeric substances (eps) in cyanobacteria.	many cyanobacteria produce extracellular polymeric substances (eps) with particular characteristics (e.g. anionic nature and presence of sulfate) that make them suitable for industrial processes such as bioremediation of heavy metals or thickening, suspending or emulsifying agents. nevertheless, their biosynthetic pathway(s) are still largely unknown, limiting their utilization. in this work, a phylum-wide analysis of genes/proteins putatively involved in the assembly and export of eps in cyanob ...	2015	26437902
characterization of a cfr-carrying plasmid from porcine escherichia coli that closely resembles plasmid pea3 from the plant pathogen erwinia amylovora.	the multiresistance gene cfr was found in two porcine escherichia coli isolates, one harboring it on the conjugative 33,885-bp plasmid pfsec-01, the other harboring it in the chromosomal dna. sequence analysis of pfsec-01 revealed that a 6,769-bp fragment containing the cfr gene bracketed by two is26 elements was inserted into a plasmid closely related to pea3 from the plant pathogen erwinia amylovora, suggesting that pfsec-01 may be transferred between different bacterial genera of both animal ...	2015	26525796
characterization of a cfr-carrying plasmid from porcine escherichia coli that closely resembles plasmid pea3 from the plant pathogen erwinia amylovora.	the multiresistance gene cfr was found in two porcine escherichia coli isolates, one harboring it on the conjugative 33,885-bp plasmid pfsec-01, the other harboring it in the chromosomal dna. sequence analysis of pfsec-01 revealed that a 6,769-bp fragment containing the cfr gene bracketed by two is26 elements was inserted into a plasmid closely related to pea3 from the plant pathogen erwinia amylovora, suggesting that pfsec-01 may be transferred between different bacterial genera of both animal ...	2015	26525796
foreign dna capture during crispr-cas adaptive immunity.	bacteria and archaea generate adaptive immunity against phages and plasmids by integrating foreign dna of specific 30-40-base-pair lengths into clustered regularly interspaced short palindromic repeat (crispr) loci as spacer segments. the universally conserved cas1-cas2 integrase complex catalyses spacer acquisition using a direct nucleophilic integration mechanism similar to retroviral integrases and transposases. how the cas1-cas2 complex selects foreign dna substrates for integration remains ...	2015	26503043
targeted predation of extrafloral nectaries by insects despite localized chemical defences.	extrafloral (ef) nectaries recruit carnivorous arthropods that protect plants from herbivory, but they can also be exploited by nectar thieves. we studied the opportunistic, targeted predation (and destruction) of ef nectaries by insects, and the localized chemical defences that plants presumably use to minimize this effect. in field and laboratory experiments, we identified insects that were possibly responsible for ef nectary predation in vicia faba (fava bean) and determined the extent and ac ...	2015	26446809
antimicrobial resistance: a global multifaceted phenomenon.	antimicrobial resistance (amr) is one of the most serious global public health threats in this century. the first world health organization (who) global report on surveillance of amr, published in april 2014, collected for the first time data from national and international surveillance networks, showing the extent of this phenomenon in many parts of the world and also the presence of large gaps in the existing surveillance. in this review, we focus on antibacterial resistance (abr), which repre ...	2015	26343252
integrative conjugative elements of the icepan family play a potential role in pantoea ananatis ecological diversification and antibiosis.	pantoea ananatis is a highly versatile enterobacterium isolated from diverse environmental sources. the ecological diversity of this species may be attributed, in part, to the acquisition of mobile genetic elements. one such element is an integrative and conjugative element (ice). by means of in silico analyses the ice elements belonging to a novel family, icepan, were identified in the genome sequences of five p. ananatis strains and characterized. pcr screening showed that icepan is prevalent ...	2015	26106378
the dnd operon for dna phosphorothioation modification system in escherichia coli is located in diverse genomic islands.	strains of escherichia coli that are non-typeable by pulsed-field gel electrophoresis (pfge) due to in-gel degradation can influence their molecular epidemiological data. the dna degradation phenotype (dnd(+)) is mediated by the dnd operon that encode enzymes catalyzing the phosphorothioation of dna, rendering the modified dna susceptible to oxidative cleavage during a pfge run. in this study, a pcr assay was developed to detect the presence of the dnd operon in dnd(+) e. coli strains and to imp ...	2015	25879448
enzymatic synthesis of nucleobase-modified udp-sugars: scope and limitations.	glucose-1-phosphate uridylyltransferase in conjunction with udp-glucose pyrophosphorylase was found to catalyse the conversion of a range of 5-substituted utp derivatives into the corresponding udp-galactose derivatives in poor yield. notably the 5-iodo derivative was not converted to udp-sugar. in contrast, udp-glucose pyrophosphorylase in conjunction with inorganic pyrophosphatase was particularly effective at converting 5-substituted utp derivatives, including the iodo compound, into a range ...	2015	25662737
the crystal structure of erwinia amylovora levansucrase provides a snapshot of the products of sucrose hydrolysis trapped into the active site.	levansucrases are members of the glycoside hydrolase family and catalyse both the hydrolysis of the substrate sucrose and the transfer of fructosyl units to acceptor molecules. in the presence of sufficient sucrose, this may either lead to the production of fructooligosaccharides or fructose polymers. aim of this study is to rationalise the differences in the polymerisation properties of bacterial levansucrases and in particular to identify structural features that determine different product sp ...	2015	26208466
actin as deathly switch? how auxin can suppress cell-death related defence.	plant innate immunity is composed of two layers--a basal immunity, and a specific effector-triggered immunity, which is often accompanied by hypersensitive cell death. initiation of cell death depends on a complex network of signalling pathways. the phytohormone auxin as central regulator of plant growth and development represents an important component for the modulation of plant defence. in our previous work, we showed that cell death is heralded by detachment of actin from the membrane. both, ...	2015	25933033
natural phenolic metabolites from endophytic aspergillus sp. ifb-yxs with antimicrobial activity.	prompted by the pressing necessity to conquer phytopathogenic infections, the antimicrobial compounds were characterized with bioassay-guided method from the ethanol extract derived from the solid-substrate fermentation of aspergillus sp. ifb-yxs, an endophytic fungus residing in the apparently healthy leave of ginkgo biloba l. the aim of this work was to evaluate the antimicrobial activity and mechanism(s) of these bioactive compounds against phytopathogens. among the compounds, xanthoascin (1) ...	2015	26004581
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
pathogen surveillance in wild bottlenose dolphins tursiops truncatus.	the number and prevalence of diseases is rapidly increasing in the marine ecosystem. although there is an increase in the number of marine diseases observed world-wide, current understanding of the pathogens associated with marine mammals is limited. an important need exists to develop and apply platforms for rapid detection and characterization of pathogenic agents to assess, prevent and respond to disease outbreaks. in this study, a broad-spectrum molecular detection technology capable of dete ...	2015	26480911
secg is required for antibiotic activities of pseudomonas sp. yl23 against erwinia amylovora and dickeya chrysanthemi.	strain yl23 was isolated from soybean root tips and identified to be pseudomonas sp. this strain showed broad-spectrum antibacterial activity against bacterial pathogens that are economically important in agriculture. to characterize the genes dedicated to antibacterial activities against microbial phytopathogens, a tn5-mutation library of yl23 was constructed. plate bioassays revealed that the mutant yl23-93 lost its antibacterial activities against erwinia amylovora and dickeya chrysanthemi as ...	2015	25708938
droplet digital pcr for absolute quantification of pathogens.	the recent advent of different digital pcr (dpcr) platforms is enabling the expansion of this technology for research and diagnostic applications worldwide. the main principle of dpcr, as in other pcr-based methods including quantitative pcr (qpcr), is the specific amplification of a nucleic acid target. the distinctive feature of dpcr is the separation of the reaction mixture into thousands to millions of partitions which is followed by a real time or end point detection of the amplification. t ...	2015	25981265
examining reaction specificity in pvcb, a source of diversity in isonitrile-containing natural products.	many bacteria produce isonitrile-containing natural products that are derived from aromatic amino acids. the synthetic clusters that control biosynthesis most commonly encode two enzymes, designated pvca and pvcb, as well as additional enzymes that direct synthesis of the natural product. the pvca enzyme installs the isonitrile moiety at the amino group of either tyrosine or tryptophan, as dictated by the particular pathway. the common pathway intermediate produced by pvca is directed toward dif ...	2015	25866990
deciphering the conserved genetic loci implicated in plant disease control through comparative genomics of bacillus amyloliquefaciens subsp. plantarum.	to understand the growth-promoting and disease-inhibiting activities of plant growth-promoting rhizobacteria (pgpr) strains, the genomes of 12 bacillus subtilis group strains with pgpr activity were sequenced and analyzed. these b. subtilis strains exhibited high genomic diversity, whereas the genomes of b. amyloliquefaciens strains (a member of the b. subtilis group) are highly conserved. a pairwise blastp matrix revealed that gene family similarity among bacillus genomes ranges from 32 to 90%, ...	2015	26347755
the contribution of genetic recombination to crispr array evolution.	crispr (clustered regularly interspaced short palindromic repeats) is a microbial immune system against foreign dna. recognition sequences (spacers) encoded within the crispr array mediate the immune reaction in a sequence-specific manner. the known mechanisms for the evolution of crispr arrays include spacer acquisition from foreign dna elements at the time of invasion and array erosion through spacer deletion. here, we consider the contribution of genetic recombination between homologous crisp ...	2015	26085541
genomic basis of the differences between cider and dessert apple varieties.	unraveling the genomic processes at play during variety diversification is of fundamental interest for understanding evolution, but also of applied interest in crop science. it can indeed provide knowledge on the genetic bases of traits for crop improvement and germplasm diversity management. apple is one of the most important fruit crops in temperate regions, having both great economic and cultural values. sweet dessert apples are used for direct consumption, while bitter cider apples are used ...	2015	26240603
a useful methoxyvinyl cation equivalent: α-t-butyldimethylsilyl-α-methoxyacetaldehyde.	described are the synthesis and application of α-t-butyldimethylsilyl-α-methoxyacetaldehyde as a formal methoxyvinyl cation equivalent. addition of grignard reagents to the title aldehyde, followed by treatment of the intermediate β-hydroxysilanes with kh, gives good yields of large z-methoxyvinylated products. assuming a peterson-like elimination mechanism, one can infer that the grignard addition proceeds with high syn selectivity. these results are consistent with a chelation control model in ...	2015	26028786
whole-genome comparative analysis of virulence genes unveils similarities and differences between endophytes and other symbiotic bacteria.	plant pathogens and endophytes co-exist and often interact with the host plant and within its microbial community. the outcome of these interactions may lead to healthy plants through beneficial interactions, or to disease through the inducible production of molecules known as virulence factors. unravelling the role of virulence in endophytes may crucially improve our understanding of host-associated microbial communities and their correlation with host health. virulence is the outcome of a comp ...	2015	26074885
interaction of the rcsb response regulator with auxiliary transcription regulators in escherichia coli.	the rcs phosphorelay is a two-component signal transduction system that is induced by cell envelope stress. rcsb, the response regulator of this signaling system, is a pleiotropic transcription regulator, which is involved in the control of various stress responses, cell division, motility, and biofilm formation. rcsb regulates transcription either as a homodimer or together with auxiliary regulators, such as rcsa, bglj, and gade in escherichia coli. in this study, we show that rcsb in addition ...	2015	26635367
variation in phenolic compounds and antioxidant activity in apple seeds of seven cultivars.	polyphenols are the predominant ingredients in apple seeds. however, few data are available on the phenolic profile or antioxidant activity in apple seeds in previous researches. in this study, low-molecular-weight phenolic compounds and antioxidant activity in seeds, peels, and flesh of seven apple cultivars grown in northwest china were measured and analyzed using hplc and frap, dpph, abts assays, respectively. hplc analysis revealed phloridzin as the dominant phenolic compound in the seeds wi ...	2015	27081364
variation in phenolic compounds and antioxidant activity in apple seeds of seven cultivars.	polyphenols are the predominant ingredients in apple seeds. however, few data are available on the phenolic profile or antioxidant activity in apple seeds in previous researches. in this study, low-molecular-weight phenolic compounds and antioxidant activity in seeds, peels, and flesh of seven apple cultivars grown in northwest china were measured and analyzed using hplc and frap, dpph, abts assays, respectively. hplc analysis revealed phloridzin as the dominant phenolic compound in the seeds wi ...	2015	27081364
some biological activities of epaltes divaricata l. - an in vitro study.	novel chemical molecules recovered from endangered medicinal plants have wide applications and have the potential to cure different diseases caused by microorganisms. the aim of this study was to investigate in vitro antimicrobial, α-glucosidase inhibition and antioxidant activity of different solvent extracts of epaltes divaricata l.	2015	25879935
genome mining: prediction of lipopeptides and polyketides from bacillus and related firmicutes.	bacillus and related genera in the bacillales within the firmicutes harbor a variety of secondary metabolite gene clusters encoding polyketide synthases and non-ribosomal peptide synthetases responsible for remarkable diverse number of polyketides (pks) and lipopeptides (lps). these compounds may be utilized for medical and agricultural applications. here, we summarize the knowledge on structural diversity and underlying gene clusters of lps and pks in the bacillales. moreover, we evaluate by us ...	2015	25893081
interaction of the rcsb response regulator with auxiliary transcription regulators in escherichia coli.	the rcs phosphorelay is a two-component signal transduction system that is induced by cell envelope stress. rcsb, the response regulator of this signaling system, is a pleiotropic transcription regulator, which is involved in the control of various stress responses, cell division, motility, and biofilm formation. rcsb regulates transcription either as a homodimer or together with auxiliary regulators, such as rcsa, bglj, and gade in escherichia coli. in this study, we show that rcsb in addition ...	2015	26635367
development of the first cisgenic apple with increased resistance to fire blight.	the generation and selection of novel fire blight resistant apple genotypes would greatly improve the management of this devastating disease, caused by erwinia amylovora. such resistant genotypes are currently developed by conventional breeding, but novel breeding technologies including cisgenesis could be an alternative approach. a cisgenic apple line c44.4.146 was regenerated using the cisgene fb_mr5 from wild apple malus ×robusta 5 (mr5), and the previously established method involving a. tum ...	2015	26624292
role of the pre-neck appendage protein (dpo7) from phage vb_sepis-phiipla7 as an anti-biofilm agent in staphylococcal species.	staphylococcus epidermidis and staphylococcus aureus are important causative agents of hospital-acquired infections and bacteremia, likely due to their ability to form biofilms. the production of a dense exopolysaccharide (eps) matrix enclosing the cells slows the penetration of antibiotic down, resulting in therapy failure. the eps depolymerase (dpo7) derived from bacteriophage vb_sepis-phiipla7, was overexpressed in escherichia coli and characterized. a dose dependent but time independent resp ...	2015	26635776
complete genomic and lysis-cassette characterization of the novel phage, kbnp1315, which infects avian pathogenic escherichia coli (apec).	avian pathogenic escherichia coli (apec) is a major pathogen that causes avian colibacillosis and is associated with severe economic losses in the chicken-farming industry. here, bacteriophage kbnp1315, infecting apec strain kbp1315, was genomically and functionally characterized. the evolutionary relationships of kbnp1315 were analyzed at the genomic level using gene (protein)-sharing networks, the markov clustering (mcl) algorithm, and comparative genomics. our network analysis showed that kbn ...	2015	26555076
functional characterization of abed, an rnd-type membrane transporter in antimicrobial resistance in acinetobacter baumannii.	acinetobacter baumannii is becoming an increasing menace in health care settings especially in the intensive care units due to its ability to withstand adverse environmental conditions and exhibit innate resistance to different classes of antibiotics. here we describe the biological contributions of abed, a novel membrane transporter in bacterial stress response and antimicrobial resistance in a. baumannii.	2015	26496475
fire blight control: the struggle goes on. a comparison of different fire blight control methods in switzerland with respect to biosafety, efficacy and durability.	fire blight (fb), caused by erwinia amylovora, is one of the most important pome fruit pathogens worldwide. to control this devastating disease, various chemical and biological treatments are commonly applied in switzerland, but they fail to keep the infection at an acceptable level in years of heavy disease pressure. the swiss authorities therefore currently allow the controlled use of the antibiotic streptomycin against fb in years that are predicted to have heavy infection periods, but only o ...	2015	26378562
the escherichia coli narl receiver domain regulates transcription through promoter specific functions.	the escherichia coli response regulator narl controls transcription of genes involved in nitrate respiration during anaerobiosis. narl consists of two domains joined by a linker that wraps around the interdomain interface. phosphorylation of the narl n-terminal receiver domain (rd) releases the, otherwise sequestered, c-terminal output domain (od) that subsequently binds specific dna promoter sites to repress or activate gene expression. the aim of this study is to investigate the extent to whic ...	2015	26307095
medfly ceratitis capitata as potential vector for fire blight pathogen erwinia amylovora: survival and transmission.	monitoring the ability of bacterial plant pathogens to survive in insects is required for elucidating unknown aspects of their epidemiology and for designing appropriate control strategies. erwinia amylovora is a plant pathogenic bacterium that causes fire blight, a devastating disease in apple and pear commercial orchards. studies on fire blight spread by insects have mainly focused on pollinating agents, such as honeybees. however, the mediterranean fruit fly (medfly) ceratitis capitata (dipte ...	2015	25978369
identification of dfra14 in two distinct plasmids conferring trimethoprim resistance in actinobacillus pleuropneumoniae.	the objective of this study was to determine the distribution and genetic basis of trimethoprim resistance in actinobacillus pleuropneumoniae isolates from pigs in england.	2015	25957382
genome-wide survey of two-component signal transduction systems in the plant growth-promoting bacterium azospirillum.	two-component systems (tcs) play critical roles in sensing and responding to environmental cues. azospirillum is a plant growth-promoting rhizobacterium living in the rhizosphere of many important crops. despite numerous studies about its plant beneficial properties, little is known about how the bacterium senses and responds to its rhizospheric environment. the availability of complete genome sequenced from four azospirillum strains (a. brasilense sp245 and cbg 497, a. lipoferum 4b and azospiri ...	2015	26489830
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
the waal gene mutation compromised the inhabitation of enterobacter sp. ag1 in the mosquito gut environment.	the mosquito gut harbors a variety of bacteria that are dynamically associated with mosquitoes in various contexts. however, little is known about bacterial factors that affect bacterial inhabitation in the gut microbial community. enterobacter sp. ag1 is a predominant gram negative bacterium in the mosquito midgut.	2015	26306887
biocontrol mechanism by root-associated bacillus amyloliquefaciens fzb42 - a review.	bacillus amyloliquefaciens subsp. plantarum fzb42 is a gram-positive model bacterium for unraveling plant-microbe interactions in bacilli. in addition, fzb42 is used commercially as biofertilizer and biocontrol agent in agriculture. genome analysis of fzb42 revealed that nearly 10% of the fzb42 genome is devoted to synthesizing antimicrobial metabolites and their corresponding immunity genes. however, recent investigations in planta demonstrated that - except surfactin - the amount of such compo ...	2015	26284057
bacterial extracellular polysaccharides in biofilm formation and function.	microbes produce a biofilm matrix consisting of proteins, extracellular dna, and polysaccharides that is integral in the formation of bacterial communities. historical studies of polysaccharides revealed that their overproduction often alters the colony morphology and can be diagnostic in identifying certain species. the polysaccharide component of the matrix can provide many diverse benefits to the cells in the biofilm, including adhesion, protection, and structure. aggregative polysaccharides ...	2015	26185074
the stringent response regulator dksa is required for salmonella enterica serovar typhimurium growth in minimal medium, motility, biofilm formation, and intestinal colonization.	salmonella enterica serovar typhimurium is a facultative intracellular human and animal bacterial pathogen posing a major threat to public health worldwide. salmonella pathogenicity requires complex coordination of multiple physiological and virulence pathways. dksa is a conserved gram-negative regulator that belongs to a distinct group of transcription factors that bind directly to the rna polymerase secondary channel, potentiating the effect of the signaling molecule ppgpp during a stringent r ...	2015	26553464
the stringent response regulator dksa is required for salmonella enterica serovar typhimurium growth in minimal medium, motility, biofilm formation, and intestinal colonization.	salmonella enterica serovar typhimurium is a facultative intracellular human and animal bacterial pathogen posing a major threat to public health worldwide. salmonella pathogenicity requires complex coordination of multiple physiological and virulence pathways. dksa is a conserved gram-negative regulator that belongs to a distinct group of transcription factors that bind directly to the rna polymerase secondary channel, potentiating the effect of the signaling molecule ppgpp during a stringent r ...	2015	26553464
clustered regularly interspaced short palindromic repeats are emm type-specific in highly prevalent group a streptococci.	clustered regularly interspaced short palindromic repeats (crispr) are the bacterial adaptive immune system against foreign nucleic acids. given the variable nature of crispr, it could be a good marker for molecular epidemiology. group a streptococcus is one of the major human pathogens. it has two crispr loci, including crispr01 and crispr02. the aim of this study was to analyze the distribution of crispr-associated gene cassettes (cas) and crispr arrays in highly prevalent emm types. the cas c ...	2015	26710228
nonmedical uses of antibiotics: time to restrict their use?	the global crisis of antibiotic resistance has reached a point where, if action is not taken, human medicine will enter a postantibiotic world and simple injuries could once again be life threatening. new antibiotics are needed urgently, but better use of existing agents is just as important. more appropriate use of antibiotics in medicine is vital, but the extensive use of antibiotics outside medical settings is often overlooked. antibiotics are commonly used in animal husbandry, bee-keeping, f ...	2015	26444324
mechanisms of resistance to aminoglycoside antibiotics: overview and perspectives.	aminoglycoside (ag) antibiotics are used to treat many gram-negative and some gram-positive infections and, importantly, multidrug-resistant tuberculosis. among various bacterial species, resistance to ags arises through a variety of intrinsic and acquired mechanisms. the bacterial cell wall serves as a natural barrier for small molecules such as ags and may be further fortified via acquired mutations. efflux pumps work to expel ags from bacterial cells, and modifications here too may cause furt ...	2015	26877861
mechanisms of resistance to aminoglycoside antibiotics: overview and perspectives.	aminoglycoside (ag) antibiotics are used to treat many gram-negative and some gram-positive infections and, importantly, multidrug-resistant tuberculosis. among various bacterial species, resistance to ags arises through a variety of intrinsic and acquired mechanisms. the bacterial cell wall serves as a natural barrier for small molecules such as ags and may be further fortified via acquired mutations. efflux pumps work to expel ags from bacterial cells, and modifications here too may cause furt ...	2015	26877861
polymorphism of crispr shows separated natural groupings of shigella subtypes and evidence of horizontal transfer of crispr.	clustered, regularly interspaced, short palindromic repeats (crispr) act as an adaptive rna-mediated immune mechanism in bacteria. they can also be used for identification and evolutionary studies based on polymorphisms within the crispr locus. we amplified and analyzed 6 crispr loci from 237 shigella strains belonging to the 4 species groups, as well as 13 escherichia coli strains. the crispr-associated (cas) gene sequence arrays of these strains were screened and compared. the crispr sequences ...	2015	26327282
the bacterial pangenome as a new tool for analysing pathogenic bacteria.	the bacterial pangenome was introduced in 2005 and, in recent years, has been the subject of many studies. thanks to progress in next-generation sequencing methods, the pangenome can be divided into two parts, the core (common to the studied strains) and the accessory genome, offering a large panel of uses. in this review, we have presented the analysis methods, the pangenome composition and its application as a study of lifestyle. we have also shown that the pangenome may be used as a new tool ...	2015	26442149
a vaccine approach for the prevention of infections by multidrug-resistant enterococcus faecium.	the incidence of multidrug-resistant enterococcus faecium hospital infections has been steadily increasing. with the goal of discovering new vaccine antigens, we systematically fractionated and purified four distinct surface carbohydrates from e. faecium endocarditis isolate tx16, shown previously to be resistant to phagocytosis in the presence of human serum. the two most abundant polysaccharides consist of novel branched heteroglycan repeating units that include signature sugars altruronic aci ...	2015	26109072
genomic, proteomic and morphological characterization of two novel broad host lytic bacteriophages φpd10.3 and φpd23.1 infecting pectinolytic pectobacterium spp. and dickeya spp.	pectinolytic pectobacterium spp. and dickeya spp. are necrotrophic bacterial pathogens of many important crops, including potato, worldwide. this study reports on the isolation and characterization of broad host lytic bacteriophages able to infect the dominant pectobacterium spp. and dickeya spp. affecting potato in europe viz. pectobacterium carotovorum subsp. carotovorum (pcc), p. wasabiae (pwa) and dickeya solani (dso) with the objective to assess their potential as biological disease control ...	2015	25803051
analysis of the link between the redox state and enzymatic activity of the htra (degp) protein from escherichia coli.	bacterial htras are proteases engaged in extracytoplasmic activities during stressful conditions and pathogenesis. a model prokaryotic htra (htra/degp from escherichia coli) requires activation to cleave its substrates efficiently. in the inactive state of the enzyme, one of the regulatory loops, termed la, forms inhibitory contacts in the area of the active center. reduction of the disulfide bond located in the middle of la stimulates htra activity in vivo suggesting that this s-s bond may play ...	2015	25710793
antimicrobial cyclic peptides for plant disease control.	antimicrobial cyclic peptides derived from microbes bind stably with target sites, have a tolerance to hydrolysis by proteases, and a favorable degradability under field conditions, which make them an attractive proposition for use as agricultural fungicides. antimicrobial cyclic peptides are classified according to the types of bonds within the ring structure; homodetic, heterodetic, and complex cyclic peptides, which in turn reflect diverse physicochemical features. most antimicrobial cyclic p ...	2015	25774105
identification and regulation of a novel citrobacter rodentium gut colonization fimbria (gcf).	the gram-negative enteric bacterium citrobacter rodentium is a natural mouse pathogen that has been extensively used as a surrogate model for studying the human pathogens enteropathogenic and enterohemorrhagic escherichia coli. all three pathogens produce similar attaching and effacing (a/e) lesions in the intestinal epithelium. during infection, these bacteria employ surface structures called fimbriae to adhere and colonize the host intestinal epithelium. for c. rodentium, the roles of only a s ...	2015	25666139
suppression of capsule expression in δlon strains of escherichia coli by two novel rpob mutations in concert with hns: possible role for dna bending at rcsa promoter.	analyses of mutations in genes coding for subunits of rna polymerase always throw more light on the intricate events that regulate the expression of gene(s). lon protease of escherichia coli is implicated in the turnover of rcsa (positive regulator of genes involved in capsular polysaccharide synthesis) and sula (cell division inhibitor induced upon dna damage). failure to degrade rcsa and sula makes lon mutant cells to overproduce capsular polysaccharides and to become sensitive to dna damaging ...	2015	26403574
fine-scale analysis of 16s rrna sequences reveals a high level of taxonomic diversity among vaginal atopobium spp.	although vaginal microbial communities of some healthy women have high proportions of atopobium vaginae, the genus atopobium is more commonly associated with bacterial vaginosis, a syndrome associated with an increased risk of adverse pregnancy outcomes and the transmission of sexually transmitted diseases. genetic differences within atopobium species may explain why single species can be associated with both health and disease. we used 16s rrna gene sequences from previously published studies t ...	2015	25778779
recent trends in control methods for bacterial wilt diseases caused by ralstonia solanacearum.	previous studies have described the development of control methods against bacterial wilt diseases caused by ralstonia solanacearum. this review focused on recent advances in control measures, such as biological, physical, chemical, cultural, and integral measures, as well as biocontrol efficacy and suppression mechanisms. biological control agents (bcas) have been dominated by bacteria (90%) and fungi (10%). avirulent strains of r. solanacearum, pseudomonas spp., bacillus spp., and streptomyces ...	2015	25762345
draft genomes, phylogenetic reconstruction, and comparative genomics of two novel cohabiting bacterial symbionts isolated from frankliniella occidentalis.	obligate bacterial symbionts are widespread in many invertebrates, where they are often confined to specialized host cells and are transmitted directly from mother to progeny. increasing numbers of these bacteria are being characterized but questions remain about their population structure and evolution. here we take a comparative genomics approach to investigate two prominent bacterial symbionts (bfo1 and bfo2) isolated from geographically separated populations of western flower thrips, frankli ...	2015	26185096
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
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
draft genome sequence of erwinia billingiae osu19-1, isolated from a pear tree canker.	plant-associated erwinia include pathogenic and nonpathogenic species. we report the 5.6-mb genome sequence of erwinia billingiae osu19-1, isolated from a canker on a pear tree inoculated with erwinia amylovora. osu19-1 and a closely related european isolate, e. billingiae eb661(t), share many similarities including 40 kb of plasmid sequence.	2015	26430039
genetic islands in pome fruit pathogenic and non-pathogenic erwinia species and related plasmids.	new pathogenic bacteria belonging to the genus erwinia associated with pome fruit trees (erwinia, e. piriflorinigrans, e. uzenensis) have been increasingly described in the last years, and comparative analyses have found that all these species share several genetic characteristics. studies at different level (whole genome comparison, virulence genes, plasmid content, etc.) show a high intraspecies homogeneity (i.e., among e. amylovora strains) and also abundant similarities appear between the di ...	2015	26379649
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
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
antimicrobial bacteriophage-derived proteins and therapeutic applications.	antibiotics have the remarkable power to control bacterial infections. unfortunately, widespread use, whether regarded as prudent or not, has favored the emergence and persistence of antibiotic resistant strains of human pathogenic bacteria, resulting in a global health threat. bacteriophages (phages) are parasites that invade the cells of virtually all known bacteria. phages reproduce by utilizing the host cell's machinery to replicate viral proteins and genomic material, generally damaging and ...	2015	26442196
the olive knot disease as a model to study the role of interspecies bacterial communities in plant disease.	there is an increasing interest in studying interspecies bacterial interactions in diseases of animals and plants as it is believed that the great majority of bacteria found in nature live in complex communities. plant pathologists have thus far mainly focused on studies involving single species or on their interactions with antagonistic competitors. a bacterial disease used as model to study multispecies interactions is the olive knot disease, caused by pseudomonas savastanoi pv. savastanoi (ps ...	2015	26113855
tritagonist as a new term for uncharacterised microorganisms in environmental systems.		2015	26035056
tritagonist as a new term for uncharacterised microorganisms in environmental systems.		2015	26035056
hydroxycinnamic acid degradation, a broadly conserved trait, protects ralstonia solanacearum from chemical plant defenses and contributes to root colonization and virulence.	plants produce hydroxycinnamic acid (hca) defense compounds to combat pathogens, such as the bacterium ralstonia solanacearum. we showed that an hca degradation pathway is genetically and functionally conserved across diverse r. solanacearum strains. further, a feruloyl-coa synthetase (δfcs) mutant that cannot degrade hca was less virulent on tomato plants. to understand the role of hca degradation in bacterial wilt disease, we tested the following hypotheses: hca degradation helps the pathogen ...	2015	25423265
the bacterial alarmone (p)ppgpp activates the type iii secretion system in erwinia amylovora.	the hypersensitive response and pathogenicity (hrp) type iii secretion system (t3ss) is a key pathogenicity factor in erwinia amylovora. previous studies have demonstrated that the t3ss in e. amylovora is transcriptionally regulated by a sigma factor cascade. in this study, the role of the bacterial alarmone ppgpp in activating the t3ss and virulence of e. amylovora was investigated using ppgpp mutants generated by red recombinase cloning. the virulence of a ppgpp-deficient mutant (ppgpp(0)) as ...	2015	25666138
oleanolic acid induces the type iii secretion system of ralstonia solanacearum.	ralstonia solanacearum, the causal agent of bacterial wilt, can naturally infect a wide range of host plants. the type iii secretion system (t3ss) is a major virulence determinant in this bacterium. studies have shown that plant-derived compounds are able to inhibit or induce the t3ss in some plant pathogenic bacteria, though no specific t3ss inhibitor or inducer has yet been identified in r. solanacearum. in this study, a total of 50 different compounds were screened and almost half of them (22 ...	2015	26732647
phytopath: an integrative resource for plant pathogen genomics.	phytopath (www.phytopathdb.org) is a resource for genomic and phenotypic data from plant pathogen species, that integrates phenotypic data for genes from phi-base, an expertly curated catalog of genes with experimentally verified pathogenicity, with the ensembl tools for data visualization and analysis. the resource is focused on fungi, protists (oomycetes) and bacterial plant pathogens that have genomes that have been sequenced and annotated. genes with associated phi-base data can be easily id ...	2015	26476449
phytopath: an integrative resource for plant pathogen genomics.	phytopath (www.phytopathdb.org) is a resource for genomic and phenotypic data from plant pathogen species, that integrates phenotypic data for genes from phi-base, an expertly curated catalog of genes with experimentally verified pathogenicity, with the ensembl tools for data visualization and analysis. the resource is focused on fungi, protists (oomycetes) and bacterial plant pathogens that have genomes that have been sequenced and annotated. genes with associated phi-base data can be easily id ...	2015	26476449
water extract from spent mushroom substrate of hericium erinaceus suppresses bacterial wilt disease of tomato.	culture filtrates of six different edible mushroom species were screened for antimicrobial activity against tomato wilt bacteria ralstonia solanacearum b3. hericium erinaceus, lentinula edodes (sanjo 701), grifola frondosa, and hypsizygus marmoreus showed antibacterial activity against the bacteria. water, n-butanol, and ethyl acetate extracts of spent mushroom substrate (sms) of h. erinaceus exhibited high antibacterial activity against different phytopathogenic bacteria: pectobacterium carotov ...	2015	26539048
the complete genome, structural proteome, comparative genomics and phylogenetic analysis of a broad host lytic bacteriophage ϕd3 infecting pectinolytic dickeya spp.	plant necrotrophic dickeya spp. are among the top ten most devastating bacterial plant pathogens able to infect a number of different plant species worldwide including economically important crops. little is known of the lytic bacteriophages infecting dickeya spp. a broad host lytic bacteriophage ϕd3 belonging to the family myoviridae and order caudovirales has been isolated in our previous study. this report provides detailed information of its annotated genome, structural proteome and phylogen ...	2015	26405503
plant and pathogen nutrient acquisition strategies.	nutrients are indispensable elements required for the growth of all living organisms including plants and pathogens. phyllosphere, rhizosphere, apoplast, phloem, xylem, and cell organelles are the nutrient niches in plants that are the target of bacterial pathogens. depending upon nutrients availability, the pathogen adapts various acquisition strategies and inhabits the specific niche. in this review, we discuss the nutrient composition of different niches in plants, the mechanisms involved in ...	2015	26442063
origin of the outbreak in france of pseudomonas syringae pv. actinidiae biovar 3, the causal agent of bacterial canker of kiwifruit, revealed by a multilocus variable-number tandem-repeat analysis.	the first outbreaks of bacterial canker of kiwifruit caused by pseudomonas syringae pv. actinidiae biovar 3 were detected in france in 2010. p. syringae pv. actinidiae causes leaf spots, dieback, and canker that sometimes lead to the death of the vine. p. syringae pv. actinidifoliorum, which is pathogenic on kiwi as well, causes only leaf spots. in order to conduct an epidemiological study to track the spread of the epidemics of these two pathogens in france, we developed a multilocus variable-n ...	2015	26209667
development of a multiple loci variable number of tandem repeats analysis (mlva) to unravel the intra-pathovar structure of pseudomonas syringae pv. actinidiae populations worldwide.	the bacterial canker of kiwifruit by pseudomonas syringae pv. actinidiae is an emblematic example of a catastrophic disease of fruit crops. in 2008 a new, extremely virulent form of the pathogen emerged and rapidly devastated many actinidia spp. orchards all over the world. in order to understand differences in populations within this pathovar and to elucidate their diffusion and movements on world scale, it is necessary to be able to quickly and on a routine basis compare new isolates with prev ...	2015	26262683
plant myb transcription factors: their role in drought response mechanisms.	water scarcity is one of the major causes of poor plant performance and limited crop yields worldwide and it is the single most common cause of severe food shortage in developing countries. several molecular networks involved in stress perception, signal transduction and stress responses in plants have been elucidated so far. transcription factors are major players in water stress signaling. in recent years, different myb transcription factors, mainly in arabidopsis thaliana (l.) heynh. but also ...	2015	26184177
application of zinc chloride precipitation method for rapid isolation and concentration of infectious pectobacterium spp. and dickeya spp. lytic bacteriophages from surface water and plant and soil extracts.	this is the first report describing precipitation of bacteriophage particles with zinc chloride as a method of choice to isolate infectious lytic bacteriophages against pectobacterium spp. and dickeya spp. from environmental samples. the isolated bacteriophages are ready to use to study various (ecological) aspects of bacteria-bacteriophage interactions. the method comprises the well-known precipitation of phages from aqueous extracts of the test material by addition of zncl2, resuscitation of b ...	2015	26099750
application of zinc chloride precipitation method for rapid isolation and concentration of infectious pectobacterium spp. and dickeya spp. lytic bacteriophages from surface water and plant and soil extracts.	this is the first report describing precipitation of bacteriophage particles with zinc chloride as a method of choice to isolate infectious lytic bacteriophages against pectobacterium spp. and dickeya spp. from environmental samples. the isolated bacteriophages are ready to use to study various (ecological) aspects of bacteria-bacteriophage interactions. the method comprises the well-known precipitation of phages from aqueous extracts of the test material by addition of zncl2, resuscitation of b ...	2015	26099750
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
lengths of orthologous prokaryotic proteins are affected by evolutionary factors.	proteins of the same functional family (for example, kinases) may have significantly different lengths. it is an open question whether such variation in length is random or it appears as a response to some unknown evolutionary driving factors. the main purpose of this paper is to demonstrate existence of factors affecting prokaryotic gene lengths. we believe that the ranking of genomes according to lengths of their genes, followed by the calculation of coefficients of association between genome ...	2015	26114113
long-term survival of borrelia burgdorferi lacking the hibernation promotion factor homolog in the unfed tick vector.	borrelia burgdorferi, a causative agent of lyme borreliosis, is a zoonotic pathogen that survives in nutrient-limited environments within a tick, prior to transmission to its mammalian host. survival under these prolonged nutrient-limited conditions is thought to be similar to survival during stationary phase, which is characterized by growth cessation and decreased protein production. multiple ribosome-associated proteins are implicated in stationary-phase survival of escherichia coli. these pr ...	2015	26438790
acylation of biomolecules in prokaryotes: a widespread strategy for the control of biological function and metabolic stress.	acylation of biomolecules (e.g., proteins and small molecules) is a process that occurs in cells of all domains of life and has emerged as a critical mechanism for the control of many aspects of cellular physiology, including chromatin maintenance, transcriptional regulation, primary metabolism, cell structure, and likely other cellular processes. although this review focuses on the use of acetyl moieties to modify a protein or small molecule, it is clear that cells can use many weak organic aci ...	2015	26179745
evolutionary switches between two serine codon sets are driven by selection.	serine is the only amino acid that is encoded by two disjoint codon sets so that a tandem substitution of two nucleotides is required to switch between the two sets. previously published evidence suggests that, for the most evolutionarily conserved serines, the codon set switch occurs by simultaneous substitution of two nucleotides. here we report a genome-wide reconstruction of the evolution of serine codons in triplets of closely related species from diverse prokaryotes and eukaryotes. the res ...	2016	27799560
novel conopeptides of largely unexplored indo pacific conus sp.	cone snails are predatory creatures using venom as a weapon for prey capture and defense. since this venom is neurotoxic, the venom gland is considered as an enormous collection of pharmacologically interesting compounds having a broad spectrum of targets. as such, cone snail peptides represent an interesting treasure for drug development. here, we report five novel peptides isolated from the venom of conus longurionis, conus asiaticus and conus australis. lo6/7a and lo6/7b were retrieved from c ...	2016	27801785
plant resistance inducers against pathogens in solanaceae species-from molecular mechanisms to field application.	this review provides a current summary of plant resistance inducers (pris) that have been successfully used in the solanaceae plant family to protect against pathogens by activating the plant's own defence. solanaceous species include many important crops such as potato and tomato. we also present findings regarding the molecular processes after application of pris, even if the number of such studies still remains limited in this plant family. in general, there is a lack of patterns regarding th ...	2016	27706100
directed evolution of fls2 towards novel flagellin peptide recognition.	microbe-associated molecular patterns (mamps) are molecules, or domains within molecules, that are conserved across microbial taxa and can be recognized by a plant or animal immune system. although mamp receptors have evolved to recognize conserved epitopes, the mamps in some microbial species or strains have diverged sufficiently to render them unrecognizable by some host immune systems. in this study, we carried out in vitro evolution of the arabidopsis thaliana flagellin receptor flagellin-se ...	2016	27270917
the effector awr5 from the plant pathogen ralstonia solanacearum is an inhibitor of the tor signalling pathway.	bacterial pathogens possess complex type iii effector (t3e) repertoires that are translocated inside the host cells to cause disease. however, only a minor proportion of these effectors have been assigned a function. here, we show that the t3e awr5 from the phytopathogen ralstonia solanacearum is an inhibitor of tor, a central regulator in eukaryotes that controls the switch between cell growth and stress responses in response to nutrient availability. heterologous expression of awr5 in yeast ca ...	2016	27257085
bacterial avrrpt2-like cysteine proteases block activation of the arabidopsis mitogen-activated protein kinases, mpk4 and mpk11.	to establish infection, pathogens deliver effectors into host cells to target immune signaling components, including elements of mitogen-activated protein kinase (mpk) cascades. the virulence function of avrrpt2, one of the first identified pseudomonas syringae effectors, involves cleavage of the plant defense regulator, rpm1-interacting protein4 (rin4), and interference with plant auxin signaling. we show now that avrrpt2 specifically suppresses the flagellin-induced phosphorylation of arabidop ...	2016	27208280
hrcu and hrpp are pathogenicity factors in the fire blight pathogen erwinia amylovora required for the type iii secretion of dspa/e.	many gram-negative bacterial pathogens mediate host-microbe interactions via utilization of the type iii secretion (t3s) system. the t3s system is a complex molecular machine consisting of more than 20 proteins. collectively, these proteins translocate effectors across extracellular space and into the host cytoplasm. successful translocation requires timely synthesis and allocation of both structural and secreted t3s proteins. based on amino acid conservation in animal pathogenic bacteria, hrcu ...	2016	27206522
direct and indirect targeting of pp2a by conserved bacterial type-iii effector proteins.	bacterial avre-family type-iii effector proteins (t3es) contribute significantly to the virulence of plant-pathogenic species of pseudomonas, pantoea, ralstonia, erwinia, dickeya and pectobacterium, with hosts ranging from monocots to dicots. however, the mode of action of avre-family t3es remains enigmatic, due in large part to their toxicity when expressed in plant or yeast cells. to search for targets of wtse, an avre-family t3e from the maize pathogen pantoea stewartii subsp. stewartii, we e ...	2016	27191168
a novel multilocus variable number tandem repeat analysis typing scheme for african phylotype iii strains of the ralstonia solanacearum species complex.	background. reliable genotyping that provides an accurate description of diversity in the context of pathogen emergence is required for the establishment of strategies to improve disease management. multilocus variable number tandem repeat analysis (mlva) is a valuable genotyping method. it can be performed at small evolutionary scales where high discriminatory power is needed. strains of the ralstonia solanacearum species complex (rssc) are highly genetically diverse. these destructive pathogen ...	2016	27168969
whole-genome sequence of pseudomonas graminis strain uasws1507, a potential biological control agent and biofertilizer isolated in switzerland.	we report here the whole-genome shotgun sequence of the strain uasws1507 of the species pseudomonas graminis, isolated in switzerland from an apple tree. this is the first genome registered for this species, which is considered as a potential and valuable resource of biological control agents and biofertilizers for agriculture.	2016	27795260