| determination of the crystal structure and active residues of fabv, the enoyl-acp reductase from xanthomonas oryzae. | enoyl-acp reductase (enr) catalyses the last reduction reaction in the fatty acid elongation cycle in bacteria and is a good antimicrobial target candidate. fabv is the most recently discovered class of enr, but we lack information about the atomic structure and the key residues involved in reductase activity except for the known conserved tyrosine and lysine residues in the y-x(8)-k active site motif. | 2011 | 22039545 |
| effect of modified glucose catabolism on xanthan production in xanthomonas oryzae pv. oryzae. | in this study, the glucose 6-phosphate dehydrogenase gene (xoo2314) was inactivated in order to modulate the intracellular glucose 6-phosphate, and its effects on xanthan production in a wild-type strain of xanthomonas oryzae were evaluated. the intracellular glucose 6-phosphate was increased from 17.6 to 99.4 μmol g(-1) (dry cell weight) in the gene-disrupted mutant strain. the concomitant increase in the glucose 6-phosphate was accompanied by an increase in xanthan production of up to 2.23 g l ... | 2011 | 22075924 |
| Screening and Identification of Antimicrobial Compounds from Streptomyces bottropensis Suppressing Rice Bacterial Blight. | Xanthomonas oryzae pv. oryzae (Xoo) is the most devastating pathogen to Oryza sativa and has been shown to cause bacterial blight. Two bioactive compounds showing antimicrobial activities against Xoo strain KACC 10331 were isolated from a Streptomyces bottropensis strain. The ethyl acetate extract was fractionated on a Sephadex LH-20 column, and then purified by preparative HPLC. The purified compounds were identified as bottromycin A2 and dunaimycin D3S by HR/MS and 1H NMR analyses. The MIC val ... | 2011 | 22210608 |
| Antimicrobial Compounds Profile During Cheonggukjang Fermentation Against Xanthomonas oryzae pv. oryzae (Xoo). | Xanthomonas oryzae causes rice bacterial blight, which has been reported as one of the most destructive diseases of rice. Metabolites were identified through cheonggukjang, a traditional Korean fermented soybean product fermented by the Bacillus spp., to control the bacteria. HPLC, MS, and UPLC-Q-TOF-MS analyses were performed to identify metabolites responsible for antimicrobial activity. In this analysis, the m/z values of 253.0498, 283.0600, 269.0455, 992.6287, and 1,006.6436 were identified ... | 2011 | 22127125 |
| Type Three Effector Gene Distribution and Sequence Analysis Provide New Insights into the Pathogenicity of Plant-Pathogenic Xanthomonas arboricola. | Xanthomonas arboricola is a complex bacterial species which mainly attacks fruit trees and is responsible for emerging diseases in Europe. It comprises seven pathovars (X. arboricola pv. pruni, X. arboricola pv. corylina, X. arboricola pv. juglandis, X. arboricola pv. populi, X. arboricola pv. poinsettiicola, X. arboricola pv. celebensis, and X. arboricola pv. fragariae), each exhibiting characteristic disease symptoms and distinct host specificities. To better understand the factors underlying ... | 2012 | 22101042 |
| crystal structure of malonyl coa-acyl carrier protein transacylase from xanthomanous oryzae pv. oryzae and its proposed binding with acp. | xanthomonas oryzae pv. oryzae (xoo) is a plant bacterial pathogen that causes bacterial blight (bb) disease, resulting in serious production losses of rice. the crystal structure of malonyl coa-acyl carrier protein transacylase (xomcat), encoded by the gene fabd (xoo0880) from xoo, was determined at 2.3 å resolution in complex with ncyclohexyl-2-aminoethansulfonic acid. malonyl coa-acyl carrier protein transacylase transfers malonyl group from malonyl coa to acyl carrier protein (acp). the trans ... | 2011 | 22134719 |
| crystal structure of malonyl coa-acyl carrier protein transacylase from xanthomanous oryzae pv. oryzae and its proposed binding with acp. | xanthomonas oryzae pv. oryzae (xoo) is a plant bacterial pathogen that causes bacterial blight (bb) disease, resulting in serious production losses of rice. the crystal structure of malonyl coa-acyl carrier protein transacylase (xomcat), encoded by the gene fabd (xoo0880) from xoo, was determined at 2.3 å resolution in complex with ncyclohexyl-2-aminoethansulfonic acid. malonyl coa-acyl carrier protein transacylase transfers malonyl group from malonyl coa to acyl carrier protein (acp). the trans ... | 2011 | 22134719 |
| soybean homologs of mpk4 negatively regulate defense responses and positively regulate growth and development. | mitogen-activated protein kinase (mapk) cascades play important roles in disease resistance in model plant species such as arabidopsis (arabidopsis thaliana) and tobacco (nicotiana tabacum). however, the importance of mapk signaling pathways in the disease resistance of crops is still largely uninvestigated. to better understand the role of mapk signaling pathways in disease resistance in soybean (glycine max), 13, nine, and 10 genes encoding distinct mapks, mapkks, and mapkkks, respectively, we ... | 2011 | 21878550 |
| Computational and Biochemical Analysis of the Xanthomonas Effector AvrBs2 and Its Role in the Modulation of Xanthomonas Type Three Effector Delivery. | Effectors of the bacterial type III secretion system provide invaluable molecular probes to elucidate the molecular mechanisms of plant immunity and pathogen virulence. In this report, we focus on the AvrBs2 effector protein from the bacterial pathogen Xanthomonas euvesicatoria (Xe), the causal agent of bacterial spot disease of tomato and pepper. Employing homology-based structural analysis, we generate a three-dimensional structural model for the AvrBs2 protein and identify catalytic sites in ... | 2011 | 22144898 |
| characteristic expression of rice pathogenesis-related proteins in rice leaves during interactions with xanthomonas oryzae pv. oryzae. | pathogenesis-related (pr) proteins play an important role in the disease resistance response. to better understand the function of rice pr proteins, we examined the expressions of ten pr proteins in rice leaves at different developmental stages with or without the interaction between rice and xanthomonas oryzae pv. oryzae (xoo). the results showed that most of the pr proteins were expressed in rice leaves in normal growth conditions, suggesting that they play a role in rice growth. six out of te ... | 2011 | 22187088 |
| The Ax21 protein is a cell-cell signal that regulates virulence in the nosocomial pathogen Stenotrophomonas maltophilia. | Stenotrophomonas maltophilia encodes proteins related to the Rax proteins of Xanthomonas oryzae, which are required for the synthesis and secretion of the Ax21 protein. Here we show that Ax21 acts as a cell-cell signal to regulate a diverse range of functions, including virulence, in this nosocomial pathogen. | 2011 | 21908663 |
| Functional analysis of the aroC gene encoding chorismate synthase from Xanthomonas oryzae pathovar oryzae. | Xanthomonas oryzae pv. oryzae causes bacterial blight in rice, and this bacterial blight has been widely found in the major rice-growing areas. We constructed a transposon mutagenesis library of X. oryzae pv. oryzae and identified a mutant strain (KXOM9) that is deficient for pigment production and virulence. Furthermore, the KXOM9 mutant was unable to grow in minimal medium lacking aromatic amino acids. Thermal asymmetric interlaced-PCR and sequence analysis of KXOM9 revealed that the transposo ... | 2011 | 22169355 |
| horizontal gene transfer in histophilus somni and its role in the evolution of pathogenic strain 2336, as determined by comparative genomic analyses. | abstract: background: pneumonia and myocarditis are the most commonly reported diseases due to histophilus somni, an opportunistic pathogen of the reproductive and respiratory tracts of cattle. thus far only a few genes involved in metabolic and virulence functions have been identified and characterized in h. somni using traditional methods. analyses of the genome sequences of several pasteurellaceae species have provided insights into their biology and evolution. in view of the economic and ec ... | 2011 | 22111657 |
| Pseudomonas syringae pv. actinidiae Draft Genomes Comparison Reveal Strain-Specific Features Involved in Adaptation and Virulence to Actinidia Species. | A recent re-emerging bacterial canker disease incited by Pseudomonas syringae pv. actinidiae (Psa) is causing severe economic losses to Actinidia chinensis and A. deliciosa cultivations in southern Europe, New Zealand, Chile and South Korea. Little is known about the genetic features of this pathovar. We generated genome-wide Illumina sequence data from two Psa strains causing outbreaks of bacterial canker on the A. deliciosa cv. Hayward in Japan (J-Psa, type-strain of the pathovar) and in Italy ... | 2011 | 22132095 |
| Characterization of Streptomyces padanus JAU4234, a Producer of Actinomycin X2, Fungichromin, and a New Polyene Macrolide Antibiotic. | Strain JAU4234, identified as Streptomyces padanus, was isolated from soil collected in Jiangxi Province, China. It produced actinomycin X2, fungichromin, and a new polyene macrolide compound with antifungal activity, antifungalmycin 702. Antifungalmycin 702 had good general antifungal activity and may have potential future agricultural and/or clinical applications. | 2012 | 22057866 |
| inheritance of bacterial blight resistance in the rice cultivar ajaya and high-resolution mapping of a major qtl associated with resistance. | summarythe cultivar ajaya (iet 8585) exhibits durable broad-spectrum resistance to bacterial blight (bb) disease of rice and is widely used as a resistance donor. the present study was carried out to decipher the genetics of bb resistance in ajaya and map the gene(s) conferring resistance. genetic analysis in the f2 indicated a quantitative/additive nature of resistance governed by two loci with equal effects. linked marker analysis and allelic tests revealed that one of the resistance genes is ... | 2011 | 22189605 |
| genetic dissection of the biotic stress response using a genome-scale gene network for rice. | rice is a staple food for one-half the world's population and a model for other monocotyledonous species. thus, efficient approaches for identifying key genes controlling simple or complex traits in rice have important biological, agricultural, and economic consequences. here, we report on the construction of ricenet, an experimentally tested genome-scale gene network for a monocotyledonous species. many different datasets, derived from five different organisms including plants, animals, yeast, ... | 2011 | 22042862 |
| small protein-mediated quorum sensing in a gram-negative bacterium: novel targets for control of infectious disease. | control of gram-negative bacterial infections of plants and animals remains a major challenge because conventional approaches are often not sufficient to eradicate these infections. one major reason for their persistence seems to be the capability of the bacteria to grow within biofilms that protect them from adverse environmental factors. quorum sensing (qs) plays an important role in the formation of biofilms. in qs, small molecules serve as signals to recognize bacterial cell population size, ... | 2011 | 22204763 |
| kdgr, an iclr family transcriptional regulator, inhibits virulence mainly by repression of hrp genes in xanthomonas oryzae pv. oryzae. | kdgr has been reported to negatively regulate the genes involved in degradation and metabolization of pectic acid and other extracellular enzymes in soft-rotting erwinia spp. through direct binding to their promoters. the possible involvement of a kdgr orthologue in virulence by affecting the expression of extracellular enzymes in xanthomonas oryzae pv. oryzae, the causal agent of rice blight disease, was examined by comparing virulence and regulation of extracellular enzymes between the wild ty ... | 2011 | 21984784 |
| Small protein-mediated quorum sensing in a gram-negative bacterium. | The rice XA21 pattern recognition receptor binds a type I secreted sulfated peptide, called axY(S)22, derived from the Ax21 (activator of XA21-mediated immunity) protein. The conservation of Ax21 in all sequenced Xanthomonas spp. and closely related genera suggests that Ax21 serves a key biological function. Here we show that the predicted N-terminal sequence of Ax21 is cleaved prior to secretion outside the cell and that mature Ax21 serves as a quorum sensing (QS) factor in Xanthomonas oryzae p ... | 2011 | 22174954 |
| one-step expression and tyrosine o-sulfonation of ax21 in escherichia coli. | ax21 (activator of xa21-mediated immunity), a pathogen-associated molecular pattern secreted by xanthomonas oryzae pv. oryzae, can be perceived by a membrane-located pattern recognition receptor xa21 and triggered immune responses in rice. an ax21-derived peptide (17-amino acid) containing a sulfated tyrosine-22 (axy(s)22) is sufficient for ax21 activity. here, we expressed ax21 and o-sulfated its tyrosine-22 through coexpressing a putative tyrosine sulfotransferase, raxst, and two other genes i ... | 2012 | 22249854 |
| [identification of extracellular polysaccharide-associated genes in xanthomonas oryzae pv. oryzicola]. | previously, seventeen extracellular polysaccharide-associated mutants of xanthomonas oryzae pv. oryzicola (xoc) were acquired from our randomly tn5-inserted mutant library. to know the tn5-inserted genes of these mutants and their contribution to eps production and virulence in rice, | 2011 | 22233054 |
| environmental factors affecting the expression of pilab as well as the proteome and transcriptome of the grass endophyte azoarcus sp. strain bh72. | bacterial communication is involved in regulation of cellular mechanisms such as metabolic processes, microbe-host interactions or biofilm formation. in the nitrogen-fixing model endophyte of grasses azoarcus sp. strain bh72, known cell-cell signaling systems have not been identified; however, the pila gene encoding the structural protein of type iv pili that are essential for plant colonization appears to be regulated in a population density-dependent manner. | 2012 | 22276194 |
| the burkholderia cenocepacia bdsf quorum sensing fatty acid is synthesized by a bifunctional crotonase homologue having both dehydratase and thioesterase activities. | signal molecules of the diffusible signal factor (dsf) family have been shown recently to be involved in regulation of pathogenesis and biofilm formation in diverse gram-negative bacteria. dsf signals are reported to be active not only on their cognate bacteria, but also on unrelated bacteria and the pathogenic yeast, candida albicans. dsfs are monounsaturated fatty acids of medium chain length containing an unusual cis-2 double bond. although genetic analyses had identified genes involved in ds ... | 2012 | 22221091 |
| the colrs system of xanthomonas oryzae pv. oryzae is required for virulence and growth in iron-limiting conditions. | xanthomonas oryzae pv. oryzae, the causal agent of bacterial blight of rice, produces siderophores only under iron-limiting conditions. we screened 15 400 mtn5-induced mutants of x. oryzae pv. oryzae and isolated 27 mutants that produced siderophores even under iron-replete conditions. we found that the mtn5 insertions in 25 of these mutants were in or close to six genes. mutants with insertions in five of these genes [cols, xoo1806 (a conserved hypothetical protein), acnb, prpr and prpb] exhibi ... | 2012 | 22257308 |
| overexpression of the pathogen-inducible wheat tawrky45 gene confers disease resistance to multiple fungi in transgenic wheat plants. | recently we cloned and characterized the gene for the wheat transcription factor tawrky45 and showed that tawrky45 was upregulated in response to benzothiadiazole (bth) and fusarium head blight (fhb) and that its overexpression conferred enhanced resistance against f. graminearum. to characterize the functional role of tawrky45 in the disease resistance of wheat, in the present study we conducted expression analyses of tawrky45 with inoculations of powdery mildew and leaf rust and evaluated tawr ... | 2011 | 23136468 |
| isolation and partial characterization of antibacterial lipopeptide produced by paenibacillus polymyxa hka-15 against phytopathogen xanthomonas campestris pv. phaseoli m-5. | an antibacterial metabolite was isolated from paenibacillus polymyxa hka-15, a soybean bacterial endophyte. the purification of the crude metabolite from paenibacillus polymyxa hka-15 was done by column chromatography. in tlc, a spot with an r ( f ) value of 0.86 (±0.02) from the purified fraction showed bioactivity against xanthomonas campestris pv. phaseoli m-5. in sds-page, the purified antibiotic was separated in the molecular weight range of 3.5 kda. the exact molecular weight of the active ... | 2011 | 22805811 |
| adaptive evolution of xa21 homologs in gramineae. | the xa21 protein has broad spectrum resistance against xanthomonas oryzae pv. oryzae. although xa21-mediated immunity is well characterized, little is known about the origin and evolutionary history of this gene in grasses. therefore, we analyzed all xa21 gene homologs in eight whole-genome sequenced rice lines, as well as in four gramineous genomes, rice, brachypodium, sorghum and maize; using arabidopsis xa21 homologs as outgroups, 17, 7, 7 and 3 xa21 homologs were detected in these four grass ... | 2011 | 22451352 |
| [expression and functional analysis of osrboh gene family in rice immune response]. | the preliminary role of respiratory burst oxidase homolog (rboh) in plant immune response is defined, but the exact function of osrboh gene in rice immune response and its expression pattern is yet unclear. in order to clarify the role of osrboh in rice immune response, we screened seven osrboh genes from the latest rice genome annotation database. the result of tissue specific expression analysis demonstrated that osrbohd was expressed only in spike and calli, and osrbohe and osrbohf were only ... | 2011 | 22393712 |
| common motifs in the response of cereal primary metabolism to fungal pathogens are not based on similar transcriptional reprogramming. | during compatible interactions with their host plants, biotrophic plant-pathogens subvert host metabolism to ensure the sustained provision of nutrient assimilates by the colonized host cells. to investigate, whether common motifs can be revealed in the response of primary carbon and nitrogen metabolism toward colonization with biotrophic fungi in cereal leaves, we have conducted a combined metabolome and transcriptome study of three quite divergent pathosystems, the barley powdery mildew fungus ... | 2011 | 22645534 |
| allele mining in barley genetic resources reveals genes of race-non-specific powdery mildew resistance. | race-non-specific, or quantitative, pathogen resistance is of high importance to plant breeders due to its expected durability. however, it is usually controlled by multiple quantitative trait loci (qtl) and therefore difficult to handle in practice. knowing the genes that underlie race-non-specific resistance (nr) would allow its exploitation in a more targeted manner. here, we performed an association-genetic study in a customized worldwide collection of spring barley accessions for candidate ... | 2011 | 22629270 |
| allele mining in barley genetic resources reveals genes of race-non-specific powdery mildew resistance. | race-non-specific, or quantitative, pathogen resistance is of high importance to plant breeders due to its expected durability. however, it is usually controlled by multiple quantitative trait loci (qtl) and therefore difficult to handle in practice. knowing the genes that underlie race-non-specific resistance (nr) would allow its exploitation in a more targeted manner. here, we performed an association-genetic study in a customized worldwide collection of spring barley accessions for candidate ... | 2011 | 22629270 |
| cloning of a conserved receptor-like protein kinase gene and its use as a functional marker for homoeologous group-2 chromosomes of the triticeae species. | receptor-like kinases (rlks) play broad biological roles in plants. we report on a conserved receptor-like protein kinase (rpk) gene from wheat and other triticeae species. the tarpk1 was isolated from the triticum aestivum cv. prins - triticum timopheevii introgression line igvi-465 carrying the powdery mildew resistance gene pm6. the tarpk1 was mapped to homoeologous chromosomes 2a (tarpk1-2a), 2d (tarpk1-2d) and the pm6-carrier chromosome 2g (tarpk1-2g) of igvi-465. under the tested condition ... | 2012 | 23272050 |
| molecular and pathogenic characterization of new xanthomonas oryzae pv. oryzae strains from the coastline region of fangchenggang city in china. | virulence assays and dna polymorphism analyses were used to characterize 33 xanthomonas oryzae pv. oryzae (xoo) strains collected from the coastline region of fangchenggang city in china. two new pathogenic races (fxp1 and fxp2), were determined by leaf-clipping inoculation of 12 near-isogenic international rice-bacterial blight (irbb) rice lines, each containing a single resistance gene. race fxp1 consisted of twenty-eight strains that were incompatible on irbb5 and irbb7, while race fxp2 inclu ... | 2012 | 23264131 |
| a structure-based classification of class a β-lactamases, a broadly diverse family of enzymes. | for medical biologists, sequencing has become a commonplace technique to support diagnosis. rapid changes in this field have led to the generation of large amounts of data, which are not always correctly listed in databases. this is particularly true for data concerning class a β-lactamases, a group of key antibiotic resistance enzymes produced by bacteria. many genomes have been reported to contain putative β-lactamase genes, which can be compared with representative types. we analyzed several ... | 2016 | 26511485 |
| a structure-based classification of class a β-lactamases, a broadly diverse family of enzymes. | for medical biologists, sequencing has become a commonplace technique to support diagnosis. rapid changes in this field have led to the generation of large amounts of data, which are not always correctly listed in databases. this is particularly true for data concerning class a β-lactamases, a group of key antibiotic resistance enzymes produced by bacteria. many genomes have been reported to contain putative β-lactamase genes, which can be compared with representative types. we analyzed several ... | 2016 | 26511485 |
| abc transporters involved in export of cell surface glycoconjugates. | complex glycoconjugates play critical roles in the biology of microorganisms. despite the remarkable diversity in glycan structures and the bacteria that produce them, conserved themes are evident in the biosynthesis-export pathways. one of the primary pathways involves representatives of the atp-binding cassette (abc) transporter superfamily. these proteins are responsible for the export of a wide variety of cell surface oligo- and polysaccharides in both gram-positive and gram-negative bacteri ... | 2010 | 20805402 |
| annotation of protein domains reveals remarkable conservation in the functional make up of proteomes across superkingdoms. | the functional repertoire of a cell is largely embodied in its proteome, the collection of proteins encoded in the genome of an organism. the molecular functions of proteins are the direct consequence of their structure and structure can be inferred from sequence using hidden markov models of structural recognition. here we analyze the functional annotation of protein domain structures in almost a thousand sequenced genomes, exploring the functional and structural diversity of proteomes. we find ... | 2011 | 24710297 |
| genome-wide gene order distances support clustering the gram-positive bacteria. | initially using 143 genomes, we developed a method for calculating the pair-wise distance between prokaryotic genomes using a monte carlo method to estimate the conservation of gene order. the method was based on repeatedly selecting five or six non-adjacent random orthologs from each of two genomes and determining if the chosen orthologs were in the same order. the raw distances were then corrected for gene order convergence using an adaptation of the jukes-cantor model, as well as using the co ... | 2015 | 25653643 |
| genome-wide gene order distances support clustering the gram-positive bacteria. | initially using 143 genomes, we developed a method for calculating the pair-wise distance between prokaryotic genomes using a monte carlo method to estimate the conservation of gene order. the method was based on repeatedly selecting five or six non-adjacent random orthologs from each of two genomes and determining if the chosen orthologs were in the same order. the raw distances were then corrected for gene order convergence using an adaptation of the jukes-cantor model, as well as using the co ... | 2015 | 25653643 |
| in silico characterization of pectate lyase protein sequences from different source organisms. | a total of 121 protein sequences of pectate lyases were subjected to homology search, multiple sequence alignment, phylogenetic tree construction, and motif analysis. the phylogenetic tree constructed revealed different clusters based on different source organisms representing bacterial, fungal, plant, and nematode pectate lyases. the multiple accessions of bacterial, fungal, nematode, and plant pectate lyase protein sequences were placed closely revealing a sequence level similarity. the multip ... | 2010 | 21048874 |
| evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems. | the deaminase-like fold includes, in addition to nucleic acid/nucleotide deaminases, several catalytic domains such as the jab domain, and others involved in nucleotide and adp-ribose metabolism. using sensitive sequence and structural comparison methods, we develop a comprehensive natural classification of the deaminase-like fold and show that its ancestral version was likely to operate on nucleotides or nucleic acids. consequently, we present evidence that a specific group of jab domains are l ... | 2011 | 21890906 |
| micheck: a web tool for fast checking of syntactic annotations of bacterial genomes. | the annotation of newly sequenced bacterial genomes begins with running several automatic analysis methods, with major emphasis on the identification of protein-coding genes. dna sequences are heterogeneous in local nucleotide composition and this leads sometimes to sequences being annotated as authentic genes when they are not protein-coding genes or are true but uncharacterized protein-coding genes. this first annotation step is generally followed by an expert manual annotation of the predicte ... | 2005 | 15980515 |
| a database of bacterial lipoproteins (dolop) with functional assignments to predicted lipoproteins. | lipid modification of the n-terminal cys residue (n-acyl-s-diacylglyceryl-cys) has been found to be an essential, ubiquitous, and unique bacterial posttranslational modification. such a modification allows anchoring of even highly hydrophilic proteins to the membrane which carry out a variety of functions important for bacteria, including pathogenesis. hence, being able to identify such proteins is of great value. to this end, we have created a comprehensive database of bacterial lipoproteins, c ... | 2006 | 16585737 |
| transcriptional regulatory network discovery via multiple method integration: application to e. coli k12. | transcriptional regulatory network (trn) discovery from one method (e.g. microarray analysis, gene ontology, phylogenic similarity) does not seem feasible due to lack of sufficient information, resulting in the construction of spurious or incomplete trns. we develop a methodology, trnd, that integrates a preliminary trn, microarray data, gene ontology and phylogenic similarity to accurately discover trns and apply the method to e. coli k12. the approach can easily be extended to include other me ... | 2007 | 17397539 |
| gene duplications in prokaryotes can be associated with environmental adaptation. | gene duplication is a normal evolutionary process. if there is no selective advantage in keeping the duplicated gene, it is usually reduced to a pseudogene and disappears from the genome. however, some paralogs are retained. these gene products are likely to be beneficial to the organism, e.g. in adaptation to new environmental conditions. the aim of our analysis is to investigate the properties of paralog-forming genes in prokaryotes, and to analyse the role of these retained paralogs by relati ... | 2010 | 20961426 |
| nutritional immunity: transition metals at the pathogen-host interface. | transition metals occupy an essential niche in biological systems. their electrostatic properties stabilize substrates or reaction intermediates in the active sites of enzymes, and their heightened reactivity is harnessed for catalysis. however, this heightened activity also renders transition metals toxic at high concentrations. bacteria, like all living organisms, must regulate their intracellular levels of these elements to satisfy their physiological needs while avoiding harm. it is therefor ... | 2012 | 22796883 |
| structural and functional characterization of an orphan atp-binding cassette atpase involved in manganese utilization and tolerance in leptospira spp. | pathogenic leptospira species are the etiological agents of the widespread zoonotic disease leptospirosis. most organisms, including leptospira, require divalent cations for proper growth, but because of their high reactivity, these metals are toxic at high concentrations. therefore, bacteria have acquired strategies to maintain metal homeostasis, such as metal import and efflux. by screening leptospira biflexa transposon mutants for their ability to use mn(2+), we have identified a gene encodin ... | 2013 | 24123817 |
| the hd-gyp domain protein rpfg of xanthomonas oryzae pv. oryzicola regulates synthesis of extracellular polysaccharides that contribute to biofilm formation and virulence on rice. | bacterial leaf streak caused by xanthomonas oryzae pv. oryzicola (xoc) is one of the most important diseases in rice. however, little is known about the pathogenicity mechanisms of xoc. here we have investigated the function of three hd-gyp domain regulatory proteins in biofilm formation, the synthesis of virulence factors and virulence of xoc. deletion of rpfg resulted in altered production of extracellular polysaccharides (eps), abolished virulence on rice and enhanced biofilm formation, but h ... | 2013 | 23544067 |
| a novel pyrroloquinoline quinone-dependent 2-keto-d-glucose dehydrogenase from pseudomonas aureofaciens. | a gene encoding an enzyme similar to a pyrroloquinoline quinone (pqq)-dependent sugar dehydrogenase from filamentous fungi, which belongs to new auxiliary activities (aa) family 12 in the cazy database, was cloned from pseudomonas aureofaciens. the deduced amino acid sequence of the cloned enzyme showed only low homology to previously characterized pqq-dependent enzymes, and multiple-sequence alignment analysis showed that the enzyme lacks one of the three conserved arginine residues that functi ... | 2015 | 25645559 |
| 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 |
| methods of combinatorial optimization to reveal factors affecting gene length. | in this paper we present a novel method for genome ranking according to gene lengths. the main outcomes described in this paper are the following: the formulation of the genome ranking problem, presentation of relevant approaches to solve it, and the demonstration of preliminary results from prokaryotic genomes ordering. using a subset of prokaryotic genomes, we attempted to uncover factors affecting gene length. we have demonstrated that hyperthermophilic species have shorter genes as compared ... | 2012 | 23300345 |
| 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 |
| new feel for new phyla. | | 2008 | 18665943 |
| a computational method to predict genetically encoded rare amino acids in proteins. | in several natural settings, the standard genetic code is expanded to incorporate two additional amino acids with distinct functionality, selenocysteine and pyrrolysine. these rare amino acids can be overlooked inadvertently, however, as they arise by recoding at certain stop codons. we report a method for such recoding prediction from genomic data, using read-through similarity evaluation. a survey across a set of microbial genomes identifies almost all the known cases as well as a number of no ... | 2005 | 16168086 |
| self-targeting by crispr: gene regulation or autoimmunity? | the recently discovered prokaryotic immune system known as crispr (clustered regularly interspaced short palindromic repeats) is based on small rnas ('spacers') that restrict phage and plasmid infection. it has been hypothesized that crisprs can also regulate self gene expression by utilizing spacers that target self genes. by analyzing crisprs from 330 organisms we found that one in every 250 spacers is self-targeting, and that such self-targeting occurs in 18% of all crispr-bearing organisms. ... | 2010 | 20598393 |
| protein-translocating trimeric autotransporters of gram-negative bacteria. | | 2006 | 16885434 |
| stretches of alternating pyrimidine/purines and purines are respectively linked with pathogenicity and growth temperature in prokaryotes. | the genomic fractions of purine (rr) and alternating pyrimidine/purine (yr) stretches of 10 base pairs or more, have been linked to genomic at content, the formation of different dna helices, strand-biased gene distribution, dna structure, and more. although some of these factors are a consequence of the chemical properties of purines and pyrimidines, a thorough statistical examination of the distributions of yr/rr stretches in sequenced prokaryotic chromosomes has to the best of our knowledge, ... | 2009 | 19646265 |
| mosaic: an online database dedicated to the comparative genomics of bacterial strains at the intra-species level. | the recent availability of complete sequences for numerous closely related bacterial genomes opens up new challenges in comparative genomics. several methods have been developed to align complete genomes at the nucleotide level but their use and the biological interpretation of results are not straightforward. it is therefore necessary to develop new resources to access, analyze, and visualize genome comparisons. | 2008 | 19038022 |
| insertion sequences. | insertion sequences (iss) constitute an important component of most bacterial genomes. over 500 individual iss have been described in the literature to date, and many more are being discovered in the ongoing prokaryotic and eukaryotic genome-sequencing projects. the last 10 years have also seen some striking advances in our understanding of the transposition process itself. not least of these has been the development of various in vitro transposition systems for both prokaryotic and eukaryotic e ... | 1998 | 9729608 |
| unifying themes in microbial associations with animal and plant hosts described using the gene ontology. | microbes form intimate relationships with hosts (symbioses) that range from mutualism to parasitism. common microbial mechanisms involved in a successful host association include adhesion, entry of the microbe or its effector proteins into the host cell, mitigation of host defenses, and nutrient acquisition. genes associated with these microbial mechanisms are known for a broad range of symbioses, revealing both divergent and convergent strategies. effective comparisons among these symbioses, ho ... | 2010 | 21119014 |
| intergenic transposable elements are not randomly distributed in bacteria. | insertion sequences (iss) are mobile genetic elements in bacterial genomes. in general, intergenic is elements are probably less deleterious for their hosts than intragenic iss, simply because they have a lower likelihood of disrupting native genes. however, since promoters, shine-dalgarno sequences, and transcription factor binding sites are intergenic and upstream of genes, i hypothesized that not all neighboring gene orientations (ngos) are selectively equivalent for is insertion. to test thi ... | 2010 | 20697140 |
| production of the cannibalism toxin sdp is a multistep process that requires sdpa and sdpb. | during the early stages of sporulation, a subpopulation of bacillus subtilis cells secrete toxins that kill their genetically identical siblings in a process termed cannibalism. one of these toxins is encoded by the sdpc gene of the sdpabc operon. the active form of the sdp toxin is a 42-amino-acid peptide with a disulfide bond which is processed from an internal fragment of pro-sdpc. the factors required for the processing of pro-sdpc into mature sdp are not known. we provide evidence that pro- ... | 2013 | 23687264 |
| 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 |
| metagenomic profiling: microarray analysis of an environmental genomic library. | genomic libraries derived from environmental dna (metagenomic libraries) are useful for characterizing uncultured microorganisms. however, conventional library-screening techniques permit characterization of relatively few environmental clones. here we describe a novel approach for characterization of a metagenomic library by hybridizing the library with dna from a set of groundwater isolates, reference strains, and communities. a cosmid library derived from a microcosm of groundwater microorgan ... | 2003 | 12902288 |
| metaproteomic analysis of ratoon sugarcane rhizospheric soil. | the current study was undertaken to elucidate the mechanism of yield decline in ratoon sugarcane using soil metaproteomics combined with community level physiological profiles (clpp) analysis. | 2013 | 23773576 |
| evolution of the chaperone/usher assembly pathway: fimbrial classification goes greek. | many proteobacteria use the chaperone/usher pathway to assemble proteinaceous filaments on the bacterial surface. these filaments can curl into fimbrial or nonfimbrial surface structures (e.g., a capsule or spore coat). this article reviews the phylogeny of operons belonging to the chaperone/usher assembly class to explore the utility of establishing a scheme for subdividing them into clades of phylogenetically related gene clusters. based on usher amino acid sequence comparisons, our analysis s ... | 2007 | 18063717 |
| coevolution of the atpase clpv, the sheath proteins tssb and tssc, and the accessory protein tagj/hsie1 distinguishes type vi secretion classes. | the type vi secretion system (t6ss) is a bacterial nanomachine for the transport of effector molecules into prokaryotic and eukaryotic cells. it involves the assembly of a tubular structure composed of tssb and tssc that is similar to the tail sheath of bacteriophages. the sheath contracts to provide the energy needed for effector delivery. the aaa(+) atpase clpv disassembles the contracted sheath, which resets the systems for reassembly of an extended sheath that is ready to fire again. this me ... | 2014 | 25305017 |
| bacterial genome instability. | bacterial genomes are remarkably stable from one generation to the next but are plastic on an evolutionary time scale, substantially shaped by horizontal gene transfer, genome rearrangement, and the activities of mobile dna elements. this implies the existence of a delicate balance between the maintenance of genome stability and the tolerance of genome instability. in this review, we describe the specialized genetic elements and the endogenous processes that contribute to genome instability. we ... | 2014 | 24600039 |
| the recx protein interacts with the reca protein and modulates its activity in herbaspirillum seropedicae. | dna repair is crucial to the survival of all organisms. the bacterial reca protein is a central component in the sos response and in recombinational and sos dna repairs. the recx protein has been characterized as a negative modulator of reca activity in many bacteria. the reca and recx genes of herbaspirillum seropedicae constitute a single operon, and evidence suggests that recx participates in sos repair. in the present study, we show that the h. seropedicae recx protein (recx hs) can interact ... | 2012 | 23044625 |
| impact of azospirillum sp. b510 inoculation on rice-associated bacterial communities in a paddy field. | rice seedlings were inoculated with azospirillum sp. b510 and transplanted into a paddy field. growth in terms of tiller numbers and shoot length was significantly increased by inoculation. principal-coordinates analysis of rice bacterial communities using the 16s rrna gene showed no overall change from b510 inoculation. however, the abundance of veillonellaceae and aurantimonas significantly increased in the base and shoots, respectively, of b510-inoculated plants. the abundance of azospirillum ... | 2013 | 24256970 |
| the role of bacterial biofilms and surface components in plant-bacterial associations. | the role of bacterial surface components in combination with bacterial functional signals in the process of biofilm formation has been increasingly studied in recent years. plants support a diverse array of bacteria on or in their roots, transport vessels, stems, and leaves. these plant-associated bacteria have important effects on plant health and productivity. biofilm formation on plants is associated with symbiotic and pathogenic responses, but how plants regulate such associations is unclear ... | 2013 | 23903045 |
| biological nitrogen fixation in non-legume plants. | nitrogen is an essential nutrient in plant growth. the ability of a plant to supply all or part of its requirements from biological nitrogen fixation (bnf) thanks to interactions with endosymbiotic, associative and endophytic symbionts, confers a great competitive advantage over non-nitrogen-fixing plants. | 2013 | 23478942 |
| a genomic survey of reb homologs suggests widespread occurrence of r-bodies in proteobacteria. | bacteria and eukaryotes are involved in many types of interaction in nature, with important ecological consequences. however, the diversity, occurrence, and mechanisms of these interactions often are not fully known. the obligate bacterial endosymbionts of paramecium provide their hosts with the ability to kill sensitive paramecium strains through the production of r-bodies, highly insoluble coiled protein ribbons. r-bodies have been observed in a number of free-living bacteria, where their func ... | 2013 | 23450193 |
| 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 |
| the emergence of 2-oxoglutarate as a master regulator metabolite. | the metabolite 2-oxoglutarate (also known as α-ketoglutarate, 2-ketoglutaric acid, or oxoglutaric acid) lies at the intersection between the carbon and nitrogen metabolic pathways. this compound is a key intermediate of one of the most fundamental biochemical pathways in carbon metabolism, the tricarboxylic acid (tca) cycle. in addition, 2-oxoglutarate also acts as the major carbon skeleton for nitrogen-assimilatory reactions. experimental data support the conclusion that intracellular levels of ... | 2015 | 26424716 |
| rtx proteins: a highly diverse family secreted by a common mechanism. | repeats-in-toxin (rtx) exoproteins of gram-negative bacteria form a steadily growing family of proteins with diverse biological functions. their common feature is the unique mode of export across the bacterial envelope via the type i secretion system and the characteristic, typically nonapeptide, glycine- and aspartate-rich repeats binding ca(2+) ions. in this review, we summarize the current state of knowledge on the organization of rtx loci and on the biological and biochemical activities of t ... | 2010 | 20528947 |
| the elusive object of desire--interactions of bacteriophages and their hosts. | bacteria and their viruses (phages) are locked in an evolutionary contest, with each side producing constantly changing mechanisms of attack and defense that are aimed to increase the odds of survival. as a result, phages play central roles in a great variety of genetic processes and increase the rate of evolutionary change of the bacterial host, which could ultimately work to the benefit of the host in a long run. | 2008 | 18400552 |
| a score of the ability of a three-dimensional protein model to retrieve its own sequence as a quantitative measure of its quality and appropriateness. | despite the remarkable progress of bioinformatics, how the primary structure of a protein leads to a three-dimensional fold, and in turn determines its function remains an elusive question. alignments of sequences with known function can be used to identify proteins with the same or similar function with high success. however, identification of function-related and structure-related amino acid positions is only possible after a detailed study of every protein. folding pattern diversity seems to ... | 2010 | 20830209 |
| plants versus pathogens: an evolutionary arms race. | the analysis of plant-pathogen interactions is a rapidly moving research field and one that is very important for productive agricultural systems. the focus of this review is on the evolution of plant defence responses and the coevolution of their pathogens, primarily from a molecular-genetic perspective. it explores the evolution of the major types of plant defence responses including pathogen associated molecular patterns and effector triggered immunity as well as the forces driving pathogen e ... | 2010 | 21743794 |
| genome comparison and context analysis reveals putative mobile forms of restriction-modification systems and related rearrangements. | the mobility of restriction-modification (rm) gene complexes and their association with genome rearrangements is a subject of active investigation. here we conducted systematic genome comparisons and genome context analysis on fully sequenced prokaryotic genomes to detect rm-linked genome rearrangements. rm genes were frequently found to be linked to mobility-related genes such as integrase and transposase homologs. they were flanked by direct and inverted repeats at a significantly high frequen ... | 2010 | 20071371 |
| nuclease activity of legionella pneumophila cas2 promotes intracellular infection of amoebal host cells. | legionella pneumophila, the primary agent of legionnaires' disease, flourishes in both natural and man-made environments by growing in a wide variety of aquatic amoebae. recently, we determined that the cas2 protein of l. pneumophila promotes intracellular infection of acanthamoeba castellanii and hartmannella vermiformis, the two amoebae most commonly linked to cases of disease. the cas2 family of proteins is best known for its role in the bacterial and archeal clustered regularly interspaced s ... | 2014 | 25547789 |
| nuclease activity of legionella pneumophila cas2 promotes intracellular infection of amoebal host cells. | legionella pneumophila, the primary agent of legionnaires' disease, flourishes in both natural and man-made environments by growing in a wide variety of aquatic amoebae. recently, we determined that the cas2 protein of l. pneumophila promotes intracellular infection of acanthamoeba castellanii and hartmannella vermiformis, the two amoebae most commonly linked to cases of disease. the cas2 family of proteins is best known for its role in the bacterial and archeal clustered regularly interspaced s ... | 2014 | 25547789 |
| siderophore-mediated iron acquisition influences motility and is required for full virulence of the xylem-dwelling bacterial phytopathogen pantoea stewartii subsp. stewartii. | iron is a key micronutrient for microbial growth but is often present in low concentrations or in biologically unavailable forms. many microorganisms overcome this challenge by producing siderophores, which are ferric-iron chelating compounds that enable the solubilization and acquisition of iron in a bioactive form. pantoea stewartii subsp. stewartii, the causal agent of stewart's wilt of sweet corn, produces a siderophore under iron-limiting conditions. the proteins involved in the biosynthesi ... | 2014 | 25326304 |
| siderophore-mediated iron acquisition influences motility and is required for full virulence of the xylem-dwelling bacterial phytopathogen pantoea stewartii subsp. stewartii. | iron is a key micronutrient for microbial growth but is often present in low concentrations or in biologically unavailable forms. many microorganisms overcome this challenge by producing siderophores, which are ferric-iron chelating compounds that enable the solubilization and acquisition of iron in a bioactive form. pantoea stewartii subsp. stewartii, the causal agent of stewart's wilt of sweet corn, produces a siderophore under iron-limiting conditions. the proteins involved in the biosynthesi ... | 2014 | 25326304 |
| motif depletion in bacteriophages infecting hosts with crispr systems. | crispr is a microbial immune system likely to be involved in host-parasite coevolution. it functions using target sequences encoded by the bacterial genome, which interfere with invading nucleic acids using a homology-dependent system. the system also requires protospacer associated motifs (pams), short motifs close to the target sequence that are required for interference in crispr types i and ii. here, we investigate whether pams are depleted in phage genomes due to selection pressure to escap ... | 2014 | 25103210 |
| metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. | | 2014 | 24758379 |
| 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 |
| a new computational method for the detection of horizontal gene transfer events. | in recent years, the increase in the amounts of available genomic data has made it easier to appreciate the extent by which organisms increase their genetic diversity through horizontally transferred genetic material. such transfers have the potential to give rise to extremely dynamic genomes where a significant proportion of their coding dna has been contributed by external sources. because of the impact of these horizontal transfers on the ecological and pathogenic character of the recipient o ... | 2005 | 15716310 |
| crystal structure of rlmm, the 2'o-ribose methyltransferase for c2498 of escherichia coli 23s rrna. | rlmm (ygde) catalyzes the s-adenosyl methionine (adomet)-dependent 2'o methylation of c2498 in 23s ribosomal rna (rrna) of escherichia coli. previous experiments have shown that rlmm is active on 23s rrna from an rlmm knockout strain but not on mature 50s subunits from the same strain. here, we demonstrate rlmm methyltransferase (mtase) activity on in vitro transcribed 23s rrna and its domain v. we have solved crystal structures of e. coli rlmm at 1.9 å resolution and of an rlmm-adomet complex a ... | 2012 | 22923526 |
| the tyrosine aminomutase tam1 is required for β-tyrosine biosynthesis in rice. | non-protein amino acids, often isomers of the standard 20 protein amino acids, have defense-related functions in many plant species. a targeted search for jasmonate-induced metabolites in cultivated rice (oryza sativa) identified (r)-β-tyrosine, an isomer of the common amino acid (s)-α-tyrosine in the seeds, leaves, roots, and root exudates of the nipponbare cultivar. assays with 119 diverse cultivars showed a distinct presence/absence polymorphism, with β-tyrosine being most prevalent in temper ... | 2015 | 25901084 |
| dispersal and regulation of an adaptive mutagenesis cassette in the bacteria domain. | recently, a multiple gene cassette with mutagenic translation synthesis activity was identified and shown to be under lexa regulation in several proteobacteria species. in this work, we have traced down instances of this multiple gene cassette across the bacteria domain. phylogenetic analyses show that this cassette has undergone several reorganizations since its inception in the actinobacteria, and that it has dispersed across the bacterial domain through a combination of vertical inheritance, ... | 2006 | 16407325 |
| protein secretion systems in bacterial-host associations, and their description in the gene ontology. | protein secretion plays a central role in modulating the interactions of bacteria with their environments. this is particularly the case when symbiotic bacteria (whether pathogenic, commensal or mutualistic) are interacting with larger host organisms. in the case of gram-negative bacteria, secretion requires translocation across the outer as well as the inner membrane, and a diversity of molecular machines have been elaborated for this purpose. a number of secreted proteins are destined to enter ... | 2009 | 19278550 |
| the genetic organisation of prokaryotic two-component system signalling pathways. | two-component systems (tcss) are modular and diverse signalling pathways, involving a stimulus-responsive transfer of phosphoryl groups from transmitter to partner receiver domains. tcs gene and domain organisation are both potentially informative regarding biological function, interaction partnerships and molecular mechanisms. however, there is currently little understanding of the relationships between domain architecture, gene organisation and tcs pathway structure. | 2010 | 21172000 |
| crispr interference: rna-directed adaptive immunity in bacteria and archaea. | sequence-directed genetic interference pathways control gene expression and preserve genome integrity in all kingdoms of life. the importance of such pathways is highlighted by the extensive study of rna interference (rnai) and related processes in eukaryotes. in many bacteria and most archaea, clustered, regularly interspaced short palindromic repeats (crisprs) are involved in a more recently discovered interference pathway that protects cells from bacteriophages and conjugative plasmids. crisp ... | 2010 | 20125085 |
| protein export according to schedule: architecture, assembly, and regulation of type iii secretion systems from plant- and animal-pathogenic bacteria. | flagellar and translocation-associated type iii secretion (t3s) systems are present in most gram-negative plant- and animal-pathogenic bacteria and are often essential for bacterial motility or pathogenicity. the architectures of the complex membrane-spanning secretion apparatuses of both systems are similar, but they are associated with different extracellular appendages, including the flagellar hook and filament or the needle/pilus structures of translocation-associated t3s systems. the needle ... | 2012 | 22688814 |
| a type iv translocated legionella cysteine phytase counteracts intracellular growth restriction by phytate. | the causative agent of legionnaires' pneumonia, legionella pneumophila, colonizes diverse environmental niches, including biofilms, plant material, and protozoa. in these habitats, myo-inositol hexakisphosphate (phytate) is prevalent and used as a phosphate storage compound or as a siderophore. l. pneumophila replicates in protozoa and mammalian phagocytes within a unique "legionella-containing vacuole." the bacteria govern host cell interactions through the icm/dot type iv secretion system (t4s ... | 2014 | 25339170 |
| a subset of the diverse cog0523 family of putative metal chaperones is linked to zinc homeostasis in all kingdoms of life. | cog0523 proteins are, like the nickel chaperones of the ureg family, part of the g3e family of gtpases linking them to metallocenter biosynthesis. even though the first cog0523-encoding gene, cobw, was identified almost 20 years ago, little is known concerning the function of other members belonging to this ubiquitous family. | 2009 | 19822009 |
| lysobacter enzymogenes uses two distinct cell-cell signaling systems for differential regulation of secondary-metabolite biosynthesis and colony morphology. | lysobacter enzymogenes is a ubiquitous environmental bacterium that is emerging as a potentially novel biological control agent and a new source of bioactive secondary metabolites, such as the heat-stable antifungal factor (hsaf) and photoprotective polyene pigments. thus far, the regulatory mechanism(s) for biosynthesis of these bioactive secondary metabolites remains largely unknown in l. enzymogenes. in the present study, the diffusible signal factor (dsf) and diffusible factor (df)-mediated ... | 2013 | 23974132 |
| 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 |