Publications

unusual entropy-driven affinity of chromobacterium violaceum lectin cv-iil toward fucose and mannose.	the purple pigmented bacterium chromobacterium violaceum is a dominant component of tropical soil microbiota that can cause rare but fatal septicaemia in humans. its sequenced genome provides insight into the abundant potential of this organism for biotechnological and pharmaceutical applications and allowed an orf encoding a protein that is 60% identical to the fucose binding lectin (pa-iil) from pseudomonas aeruginosa and the mannose binding lectin (rs-iil) from ralstonia solanacearum to be id ...	2006	16768446
induction of lateral root structure formation on petunia roots: a novel effect of gmi1000 ralstonia solanacearum infection impaired in hrp mutants.	ralstonia solanacearum is a soilborne plant pathogen that invades its host via roots. as in many gram-negative bacterial plant pathogens, the r. solanacearum hrp type iii secretion system is essential for interactions of the bacterium with plants; however, the related mechanisms involved in disease expression are largely unknown. in this work, we examined the effects of infection by r. solanacearum gmi1000 and hrp mutants on the root system of petunia plants. both the wild-type and mutant strain ...	2006	16776293
activation of the global gene regulator prra (rega) from rhodobacter sphaeroides.	prra is a global transcription regulator activated upon phosphorylation by its cognate kinase prrb in response to low oxygen levels in rhodobacter sphaeroides. here we show by gel filtration, analytical ultracentrifugation, and nmr diffusion measurements that treatment of prra with a phosphate analogue, bef(3)(-), results in dimerization of the protein, producing a protein that binds dna. no dimeric species was observed in the absence of bef(3)(-). upon addition of bef(3)(-), the inhibitory acti ...	2006	16784239
flavin adenine dinucleotide-dependent 4-phospho-d-erythronate dehydrogenase is responsible for the 4-phosphohydroxy-l-threonine pathway in vitamin b6 biosynthesis in sinorhizobium meliloti.	the vitamin b6 biosynthetic pathway in sinorhizobium meliloti is similar to that in escherichia coli k-12; in both organisms this pathway includes condensation of two intermediates, 1-deoxy-d-xylulose 5-phosphate and 4-phosphohydroxy-l-threonine (4pht). here, we report cloning of a gene designated pdxr that functionally corresponds to the pdxb gene of e. coli and encodes a dye-linked flavin adenine dinucleotide-dependent 4-phospho-d-erythronate (4pe) dehydrogenase. this enzyme catalyzes the oxid ...	2006	16788172
popf1 and popf2, two proteins secreted by the type iii protein secretion system of ralstonia solanacearum, are translocators belonging to the hrpf/nopx family.	ralstonia solanacearum gmi1000 is a gram-negative plant pathogen which contains an hrp gene cluster which codes for a type iii protein secretion system (ttss). we identified two novel hrp-secreted proteins, called popf1 and popf2, which display similarity to one another and to putative ttss translocators, hrpf and nopx, from xanthomonas spp. and rhizobia, respectively. they also show similarities with ttss translocators of the yopb family from animal-pathogenic bacteria. both popf1 and popf2 bel ...	2006	16788199
identification of a response regulator gene for catabolite control from a pcb-degrading beta-proteobacteria, acidovorax sp. kks102.	acidovorax sp. (formally pseudomonas sp.) strain kks102 carries a bph operon for the degradation of pcb/biphenyl. transcription from the pe promoter for the bph operon was found to be under catabolite control, i.e. the promoter activity was at a lower level when succinate, fumarate or acetate was added to the culture. some mutations in the immediate upstream region of the pe promoter resulted in catabolite-insensitive and constitutively low promoter activity, suggesting that a transcriptional ac ...	2006	16796688
an mmp liberates the ninjurin a ectodomain to signal a loss of cell adhesion.	matrix metalloproteinases (mmps) are important for developmental tissue remodeling and for the inflammatory response. although the vertebrate mmp family is large and functionally redundant, the fruitfly drosophila melanogaster has only two mmps, both essential genes. our previous work demonstrated that mmp1 is required for growth of the tracheal system, and we suggested that the mutant phenotype resulted from aberrant persistence of cell adhesion to the extracellular matrix. here we report the i ...	2006	16815999
the brucella abortus cyclic beta-1,2-glucan virulence factor is substituted with o-ester-linked succinyl residues.	brucella periplasmic cyclic beta-1,2-glucan plays an important role during bacterium-host interaction. nuclear magnetic resonance spectrometry analysis, thin-layer chromatography, and deae-sephadex chromatography were used to characterize brucella abortus cyclic glucan. in the present study, we report that a fraction of b. abortus cyclic beta-1,2-glucan is substituted with succinyl residues, which confer anionic character on the cyclic beta-1,2-glucan. the oligosaccharide backbone is substituted ...	2006	16816173
ntlrp1, a tobacco leucine-rich repeat gene with a possible role as a modulator of the hypersensitive response.	plant defense responses against pathogens often involve the restriction of the pathogen to its site of penetration achieved through the combined effects of the hypersensitive response (hr) and its tightly connected localized acquired resistance (lar). the tobacco dd9-3 expressed sequence tag was previously isolated from a screen designed to isolate genes induced early during the hr, thus potentially involved in the induction/regulation of the hr or lar. translation of the open reading frame of d ...	2006	16838787
phase variation and genomic architecture changes in azospirillum.	the plant growth-promoting rhizobacterium azospirillum lipoferum 4b generates in vitro at high frequency a stable nonswimming phase variant designated 4v(i), which is distinguishable from the wild type by the differential absorption of dyes. the frequency of variants generated by a reca mutant of a. lipoferum 4b was increased up to 10-fold. the pleiotropic modifications characteristic of the phase variant are well documented, but the molecular processes involved are unknown. here, the objective ...	2006	16855225
gastrodia anti-fungal protein from the orchid gastrodia elata confers disease resistance to root pathogens in transgenic tobacco.	diseases of agricultural crops are caused by pathogens from several higher-order phylogenetic lineages including fungi, straminipila, eubacteria, and metazoa. these pathogens are commonly managed with pesticides due to the lack of broad-spectrum host resistance. gastrodia anti-fungal protein (gafp; gastrodianin) may provide a level of broad-spectrum resistance due to its documented anti-fungal activity in vitro and structural similarity to insecticidal lectins. we transformed tobacco (nicotiana ...	2006	16858580
influence of plant diversity and elevated atmospheric carbon dioxide levels on belowground bacterial diversity.	changes in aboveground plant species diversity as well as variations of environmental conditions such as exposure of ecosystems to elevated concentrations of atmospheric carbon dioxide may lead to changes in metabolic activity, composition and diversity of belowground microbial communities, both bacterial and fungal.	2006	16872510
quantitative detection of the nosz gene, encoding nitrous oxide reductase, and comparison of the abundances of 16s rrna, narg, nirk, and nosz genes in soils.	nitrous oxide (n2o) is an important greenhouse gas in the troposphere controlling ozone concentration in the stratosphere through nitric oxide production. in order to quantify bacteria capable of n2o reduction, we developed a sybr green quantitative real-time pcr assay targeting the nosz gene encoding the catalytic subunit of the nitrous oxide reductase. two independent sets of nosz primers flanking the nosz fragment previously used in diversity studies were designed and tested (k. kloos, a. mer ...	2006	16885263
characterization of the mrgrs locus of the opportunistic pathogen burkholderia pseudomallei: temperature regulates the expression of a two-component signal transduction system.	burkholderia pseudomallei is a saprophyte in tropical environments and an opportunistic human pathogen. this versatility requires a sensing mechanism that allows the bacterium to respond rapidly to altered environmental conditions. we characterized a two-component signal transduction locus from b. pseudomallei 204, mrgr and mrgs, encoding products with extensive homology with response regulators and histidine protein kinases of escherichia coli, bordetella pertussis, and vibrio cholerae.	2006	16893462
mutations in the lrpe gene of ralstonia solanacearum affects hrp pili production and virulence.	the ralstonia solanacearum hrpb-regulated gene lrpe (hpx5/brg24) encodes a popc-like leucine-rich repeat (lrr) protein that carries 11 tandem lrr in the central region. defects in the lrpe gene slightly reduced the virulence of r. solanacearum on host plants and changed the bacterial morphology leading to the formation of large aggregates in a minimal medium. the aggregation in the deltalrpe background required the presence of a functional hrp type iii secretion system. in wild-type r. solanacea ...	2006	16903354
pseudomonas syringae hrpj is a type iii secreted protein that is required for plant pathogenesis, injection of effectors, and secretion of the hrpz1 harpin.	the bacterial plant pathogen pseudomonas syringae requires a type iii protein secretion system (ttss) to cause disease. the p. syringae ttss is encoded by the hrp-hrc gene cluster. one of the genes within this cluster, hrpj, encodes a protein with weak similarity to yopn, a type iii secreted protein from the animal pathogenic yersinia species. here, we show that hrpj is secreted in culture and translocated into plant cells by the p. syringae pv. tomato dc3000 ttss. a dc3000 hrpj mutant, unl140, ...	2006	16923873
the structure of mbti from mycobacterium tuberculosis, the first enzyme in the biosynthesis of the siderophore mycobactin, reveals it to be a salicylate synthase.	the ability to acquire iron from the extracellular environment is a key determinant of pathogenicity in mycobacteria. mycobacterium tuberculosis acquires iron exclusively via the siderophore mycobactin t, the biosynthesis of which depends on the production of salicylate from chorismate. salicylate production in other bacteria is either a two-step process involving an isochorismate synthase (chorismate isomerase) and a pyruvate lyase, as observed for pseudomonas aeruginosa, or a single-step conve ...	2006	16923875
evolution of vitamin b2 biosynthesis: 6,7-dimethyl-8-ribityllumazine synthases of brucella.	the penultimate step in the biosynthesis of riboflavin (vitamin b2) involves the condensation of 3,4-dihydroxy-2-butanone 4-phosphate with 5-amino-6-ribitylamino-2,4(1h,3h)-pyrimidinedione, which is catalyzed by 6,7-dimethyl-8-ribityllumazine synthase (lumazine synthase). pathogenic brucella species adapted to an intracellular lifestyle have two genes involved in riboflavin synthesis, ribh1 and ribh2, which are located on different chromosomes. the ribh2 gene was shown previously to specify a lu ...	2006	16923880
residues involved in fecr binding are localized on one side of the feca signaling domain in escherichia coli.	ferric citrate transport in escherichia coli involves proteins encoded by the fec genes, including the transport and signaling protein feca and the signal transducing protein fecr. randomly isolated feca point mutants showed a reduced interaction with fecr and a reduced transcription initiation of the ferric citrate transport genes. the mutations were localized on one side of the feca signaling domain, which might form the interface to fecr. some of the mutants showed strongly reduced iron trans ...	2006	16923915
exopolysaccharide-associated protein sorting in environmental organisms: the pep-cterm/epsh system. application of a novel phylogenetic profiling heuristic.	protein translocation to the proper cellular destination may be guided by various classes of sorting signals recognizable in the primary sequence. detection in some genomes, but not others, may reveal sorting system components by comparison of the phylogenetic profile of the class of sorting signal to that of various protein families.	2006	16930487
integrated regulation of the type iii secretion system and other virulence determinants in ralstonia solanacearum.	in many plant and animal bacterial pathogens, the type iii secretion system (ttss) that directly translocates effector proteins into the eukaryotic host cells is essential for the development of disease. in all species studied, the transcription of the ttss and most of its effector substrates is tightly regulated by a succession of consecutively activated regulators. however, the whole genetic programme driven by these regulatory cascades is still unknown, especially in bacterial plant pathogens ...	2006	16933989
specific binding of the xanthomonas campestris pv. vesicatoria arac-type transcriptional activator hrpx to plant-inducible promoter boxes.	the pathogenicity of the plant-pathogenic bacterium xanthomonas campestris pv. vesicatoria depends on a type iii secretion system which is encoded by the 23-kb hrp (hypersensitive response and pathogenicity) gene cluster. expression of the hrp operons is strongly induced in planta and in a special minimal medium and depends on two regulatory proteins, hrpg and hrpx. in this study, dna affinity enrichment was used to demonstrate that the arac-type transcriptional activator hrpx binds to a conserv ...	2006	16936021
genetic transplantation: salmonella enterica serovar typhimurium as a host to study sigma factor and anti-sigma factor interactions in genetically intractable systems.	in salmonella enterica serovar typhimurium, sigma(28) and anti-sigma factor flgm are regulatory proteins crucial for flagellar biogenesis and motility. in this study, we used s. enterica serovar typhimurium as an in vivo heterologous system to study sigma(28) and anti-sigma(28) interactions in organisms where genetic manipulation poses a significant challenge due to special growth requirements. the chromosomal copy of the s. enterica serovar typhimurium sigma(28) structural gene flia was exchang ...	2006	16352826
identification of the syr-syp box in the promoter regions of genes dedicated to syringomycin and syringopeptin production by pseudomonas syringae pv. syringae b301d.	the phytotoxins syringopeptin and syringomycin are synthesized by nonribosomal peptide synthetases which are encoded by the syringomycin (syr) and syringopeptin (syp) genomic island of pseudomonas syringae pv. syringae. previous studies demonstrated that expression of the syr-syp genes was controlled by the sala-syrf regulatory pathway, which in turn was induced by plant signal molecules. in this study, the 132-kb syr-syp genomic island was found to be organized into five polycistronic operons a ...	2006	16352832
orthomcl-db: querying a comprehensive multi-species collection of ortholog groups.	the orthomcl database (http://orthomcl.cbil.upenn.edu) houses ortholog group predictions for 55 species, including 16 bacterial and 4 archaeal genomes representing phylogenetically diverse lineages, and most currently available complete eukaryotic genomes: 24 unikonts (12 animals, 9 fungi, microsporidium, dictyostelium, entamoeba), 4 plants/algae and 7 apicomplexan parasites. orthomcl software was used to cluster proteins based on sequence similarity, using an all-against-all blast search of eac ...	2006	16381887
orthomcl-db: querying a comprehensive multi-species collection of ortholog groups.	the orthomcl database (http://orthomcl.cbil.upenn.edu) houses ortholog group predictions for 55 species, including 16 bacterial and 4 archaeal genomes representing phylogenetically diverse lineages, and most currently available complete eukaryotic genomes: 24 unikonts (12 animals, 9 fungi, microsporidium, dictyostelium, entamoeba), 4 plants/algae and 7 apicomplexan parasites. orthomcl software was used to cluster proteins based on sequence similarity, using an all-against-all blast search of eac ...	2006	16381887
the genome sequence of methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and h2 for methane formation and atp synthesis.	methanosphaera stadtmanae has the most restricted energy metabolism of all methanogenic archaea. this human intestinal inhabitant can generate methane only by reduction of methanol with h2 and is dependent on acetate as a carbon source. we report here the genome sequence of m. stadtmanae, which was found to be composed of 1,767,403 bp with an average g+c content of 28% and to harbor only 1,534 protein-encoding sequences (cds). the genome lacks 37 cds present in the genomes of all other methanoge ...	2006	16385054
involvement of quinolinate phosphoribosyl transferase in promotion of potato growth by a burkholderia strain.	burkholderia sp. strain psjn stimulates root growth of potato explants compared to uninoculated controls under gnotobiotic conditions. in order to determine the mechanism by which this growth stimulation occurs, we used tn5 mutagenesis to produce a mutant, h41, which exhibited no growth-promoting activity but was able to colonize potato plants as well as the wild-type strain. the gene associated with the loss of growth promotion in h41 was shown to exhibit 65% identity at the amino acid level to ...	2006	16391116
a tyrosinase with an abnormally high tyrosine hydroxylase/dopa oxidase ratio.	the sequencing of the genome of ralstonia solanacearum[salanoubat m, genin s, artiguenave f, et al. (2002) nature 415, 497-502] revealed several genes that putatively code for polyphenol oxidases (ppos). this soil-borne pathogenic bacterium withers a wide range of plants. we detected the expression of two ppo genes (accession numbers np_518458 and np_519622) with high similarity to tyrosinases, both containing the six conserved histidines required to bind the pair of type-3 copper ions at the ac ...	2006	16403014
identification of open reading frames unique to a select agent: ralstonia solanacearum race 3 biovar 2.	an 8x draft genome was obtained and annotated for ralstonia solanacearum race 3 biovar 2 (r3b2) strain uw551, a united states department of agriculture select agent isolated from geranium. the draft uw551 genome consisted of 80,169 reads resulting in 582 contigs containing 5,925,491 base pairs, with an average 64.5% gc content. annotation revealed a predicted 4,454 protein coding open reading frames (orfs), 43 trnas, and 5 rrnas; 2,793 (or 62%) of the orfs had a functional assignment. the uw551 ...	2006	16404955
antimicrobial activity of glycosidase inhibitory protein isolated from cyphomandra betacea sendt. fruit.	broad-spectrum antimicrobial activity of an invertase inhibitory protein (iip) isolated from cyphomandra betacea ripe fruits is documented. minimal inhibitory concentration (mic) values were determined by agar macrodilution and broth microdilution assays. this iip inhibited the growth of xylophagous and phytopatogenic fungi (ganoderma applanatum, schizophyllum commune, lenzites elegans, pycnoporus sanguineous, penicillium notatum, aspergillus niger, phomopsis sojae and fusarium mango) and phytop ...	2006	16406143
mage: a microbial genome annotation system supported by synteny results.	magnifying genomes (mage) is a microbial genome annotation system based on a relational database containing information on bacterial genomes, as well as a web interface to achieve genome annotation projects. our system allows one to initiate the annotation of a genome at the early stage of the finishing phase. mage's main features are (i) integration of annotation data from bacterial genomes enhanced by a gene coding re-annotation process using accurate gene models, (ii) integration of results o ...	2006	16407324
a selc-associated genomic island of the extraintestinal avian pathogenic escherichia coli strain ben2908 is involved in carbohydrate uptake and virulence.	the complete nucleotide sequence and genetic organization of a new genomic island (agi-3) isolated from the extraintestinal avian pathogenic escherichia coli strain ben2908 is reported. this 49,600-bp island is inserted at the selc locus and contains putative mobile genetic elements such as a phage-related integrase gene, transposase genes, and direct repeats. agi-3 shows a mosaic structure of five modules. some of these modules are present in other e. coli strains and in other pathogenic bacter ...	2006	16428402
production and properties of the native chromobacterium violaceum fucose-binding lectin (cv-iil) compared to homologous lectins of pseudomonas aeruginosa (pa-iil) and ralstonia solanacearum (rs-iil).	chromobacterium violaceum is a versatile, violet pigment (violacein)-producing beta-proteobacterium, confined to tropical and subtropical regions, dwelling in soil and water, like pseudomonas aeruginosa and ralstonia solanacearum. these three bacteria are saprophytes that occasionally become aggressive opportunistic pathogens virulently attacking animals (the first two) and plants (the third). the recent availability of their genome sequences enabled identification in the c. violaceum genome of ...	2006	16436433
positive selection of the hrp pilin hrpe of the plant pathogen xanthomonas.	the plant-pathogenic bacterium xanthomonas campestris pv. vesicatoria possesses a type iii secretion (tts) system which is encoded by the 23-kb hrp (hypersensitive response and pathogenicity) gene cluster. the tts system is necessary for pathogenicity in susceptible hosts and induction of the hypersensitive response in resistant plants. at the cell surface, the tts system is associated with an extracellular filamentous structure, the hrp pilus, which serves as a conduit for the transfer of bacte ...	2006	16452423
the genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium thiobacillus denitrificans.	the complete genome sequence of thiobacillus denitrificans atcc 25259 is the first to become available for an obligately chemolithoautotrophic, sulfur-compound-oxidizing, beta-proteobacterium. analysis of the 2,909,809-bp genome will facilitate our molecular and biochemical understanding of the unusual metabolic repertoire of this bacterium, including its ability to couple denitrification to sulfur-compound oxidation, to catalyze anaerobic, nitrate-dependent oxidation of fe(ii) and u(iv), and to ...	2006	16452431
within-species flagellin polymorphism in xanthomonas campestris pv campestris and its impact on elicitation of arabidopsis flagellin sensing2-dependent defenses.	bacterial flagellins have been portrayed as a relatively invariant pathogen-associated molecular pattern. we have found within-species, within-pathovar variation for defense-eliciting activity of flagellins among xanthomonas campestris pv campestris (xcc) strains. arabidopsis thaliana flagellin sensing2 (fls2), a transmembrane leucine-rich repeat kinase, confers flagellin responsiveness. the flg22 region was the only xcc flagellin region responsible for detectable elicitation of arabidopsis defe ...	2006	16461584
nitrous oxide reductase genes (nosz) of denitrifying microbial populations in soil and the earthworm gut are phylogenetically similar.	earthworms emit nitrous oxide (n2o) and dinitrogen (n2). it has been hypothesized that the in situ conditions of the earthworm gut activates ingested soil denitrifiers during gut passage and leads to these in vivo emissions (m. a. horn, a. schramm, and h. l. drake, appl. environ. microbiol. 69:1662-1669, 2003). this hypothesis implies that the denitrifiers in the earthworm gut are not endemic to the gut but rather are regular members of the soil denitrifier population. to test this hypothesis, t ...	2006	16461644
coexistence of burkholderia, cupriavidus, and rhizobium sp. nodule bacteria on two mimosa spp. in costa rica.	rrna gene sequencing and pcr assays indicated that 215 isolates of root nodule bacteria from two mimosa species at three sites in costa rica belonged to the genera burkholderia, cupriavidus, and rhizobium. this is the first report of cupriavidus sp. nodule symbionts for mimosa populations within their native geographic range in the neotropics. burkholderia spp. predominated among samples from mimosa pigra (86% of isolates), while there was a more even distribution of cupriavidus, burkholderia, a ...	2006	16461667
insights on the evolution of trehalose biosynthesis.	the compatible solute trehalose is a non-reducing disaccharide, which accumulates upon heat, cold or osmotic stress. it was commonly accepted that trehalose is only present in extremophiles or cryptobiotic organisms. however, in recent years it has been shown that although higher plants do not accumulate trehalose at significant levels they have actively transcribed genes encoding the corresponding biosynthetic enzymes.	2006	17178000
plant nbs-lrr proteins in pathogen sensing and host defense.	plant proteins belonging to the nucleotide-binding site-leucine-rich repeat (nbs-lrr) family are used for pathogen detection. like the mammalian nod-lrr protein 'sensors' that detect intracellular conserved pathogen-associated molecular patterns, plant nbs-lrr proteins detect pathogen-associated proteins, most often the effector molecules of pathogens responsible for virulence. many virulence proteins are detected indirectly by plant nbs-lrr proteins from modifications the virulence proteins inf ...	2006	17110940
dissecting the wrky web of plant defense regulators.		2006	17121464
the effect of the chemical, biological, and physical environment on quorum sensing in structured microbial communities.	as researchers attempt to study quorum sensing in relevant clinical or environmental settings, it is apparent that many factors have the potential to affect signaling. these factors span a range of physical, chemical, and biological variables that can impact signal production, stability and distribution. optimizing experimental systems to natural or clinical environments may be crucial for defining when and where quorum sensing occurs. these points are illustrated in our case study of s. aureus ...	2006	17047948
the effect of the chemical, biological, and physical environment on quorum sensing in structured microbial communities.	as researchers attempt to study quorum sensing in relevant clinical or environmental settings, it is apparent that many factors have the potential to affect signaling. these factors span a range of physical, chemical, and biological variables that can impact signal production, stability and distribution. optimizing experimental systems to natural or clinical environments may be crucial for defining when and where quorum sensing occurs. these points are illustrated in our case study of s. aureus ...	2006	17047948
bacterial elicitation and evasion of plant innate immunity.	recent research on plant responses to bacterial attack has identified extracellular and intracellular host receptors that recognize conserved pathogen-associated molecular patterns and more specialized virulence proteins, respectively. these findings have shed light on our understanding of the molecular mechanisms by which bacteria elicit host defences and how pathogens have evolved to evade or suppress these defences.	2006	16936700
tico: a tool for postprocessing the predictions of prokaryotic translation initiation sites.	exact localization of the translation initiation sites (tis) in prokaryotic genomes is difficult to achieve using conventional gene finders. we recently introduced the program tico for postprocessing tis predictions based on a completely unsupervised learning algorithm. the program can be utilized through our web interface at http://tico.gobics.de/ and it is also freely available as a commandline version for linux and windows. the latest version of our program provides a tool for visualization o ...	2006	16845076
potent induction of arabidopsis thaliana flowering by elevated growth temperature.	the transition to flowering is an important event in the plant life cycle and is modulated by several environmental factors including photoperiod, light quality, vernalization, and growth temperature, as well as biotic and abiotic stresses. in contrast to light and vernalization, little is known about the pathways that mediate the responses to other environmental variables. a mild increase in growth temperature, from 23 degrees c to 27 degrees c, is equally efficient in inducing flowering of ara ...	2006	16839183
amplification generates modular diversity at an avirulence locus in the pathogen phytophthora.	the destructive late blight pathogen phytophthora infestans is notorious for its rapid adaptation to circumvent detection mediated by plant resistance (r) genes. we performed comparative genomic hybridization on microarrays (array-cgh) in a near genome-wide survey to identify genome rearrangements related to changes in virulence. six loci with copy number variation were found, one of which involves an amplification colocalizing with a previously identified locus that confers avirulence in combin ...	2006	16818726
crystallization and preliminary x-ray diffraction analysis of an anti-h(o) lectin from lotus tetragonolobus seeds.	the seed lectin from lotus tetragonolobus (lta) has been crystallized. the best crystals grew over several days and were obtained using the vapour-diffusion method at a constant temperature of 293 k. a complete structural data set was collected at 2.00 angstroms resolution using a synchrotron-radiation source. lta crystals were found to be monoclinic, belonging to space group p2(1), with unit-cell parameters a = 68.89, b = 65.83, c = 102.53 angstroms, alpha = gamma = 90, beta = 92 degrees. molec ...	2006	16820693
plant nbs-lrr proteins: adaptable guards.	the majority of disease resistance genes in plants encode nucleotide-binding site leucine-rich repeat (nbs-lrr) proteins. this large family is encoded by hundreds of diverse genes per genome and can be subdivided into the functionally distinct tir-domain-containing (tnl) and cc-domain-containing (cnl) subfamilies. their precise role in recognition is unknown; however, they are thought to monitor the status of plant proteins that are targeted by pathogen effectors.	2006	16677430
oligonucleotide array for identification and detection of pythium species.	a dna array containing 172 oligonucleotides complementary to specific diagnostic regions of internal transcribed spacers (its) of more than 100 species was developed for identification and detection of pythium species. all of the species studied, with the exception of pythium ostracodes, exhibited a positive hybridization reaction with at least one corresponding species-specific oligonucleotide. hybridization patterns were distinct for each species. the array hybridization patterns included clus ...	2006	16597974
an unsupervised classification scheme for improving predictions of prokaryotic tis.	although it is not difficult for state-of-the-art gene finders to identify coding regions in prokaryotic genomes, exact prediction of the corresponding translation initiation sites (tis) is still a challenging problem. recently a number of post-processing tools have been proposed for improving the annotation of prokaryotic tis. however, inherent difficulties of these approaches arise from the considerable variation of tis characteristics across different species. therefore prior assumptions abou ...	2006	16526950
stimulus perception in bacterial signal-transducing histidine kinases.	two-component signal-transducing systems are ubiquitously distributed communication interfaces in bacteria. they consist of a histidine kinase that senses a specific environmental stimulus and a cognate response regulator that mediates the cellular response, mostly through differential expression of target genes. histidine kinases are typically transmembrane proteins harboring at least two domains: an input (or sensor) domain and a cytoplasmic transmitter (or kinase) domain. they can be identifi ...	2006	17158704
the evolution of two-component systems in bacteria reveals different strategies for niche adaptation.	two-component systems including histidine protein kinases represent the primary signal transduction paradigm in prokaryotic organisms. to understand how these systems adapt to allow organisms to detect niche-specific signals, we analyzed the phylogenetic distribution of nearly 5,000 histidine protein kinases from 207 sequenced prokaryotic genomes. we found that many genomes carry a large repertoire of recently evolved signaling genes, which may reflect selective pressure to adapt to new environm ...	2006	17083272
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-translocating trimeric autotransporters of gram-negative bacteria.		2006	16885434
construction of phylogenetic trees by kernel-based comparative analysis of metabolic networks.	to infer the tree of life requires knowledge of the common characteristics of each species descended from a common ancestor as the measuring criteria and a method to calculate the distance between the resulting values of each measure. conventional phylogenetic analysis based on genomic sequences provides information about the genetic relationships between different organisms. in contrast, comparative analysis of metabolic pathways in different organisms can yield insights into their functional r ...	2006	16753070
structural classification of bacterial response regulators: diversity of output domains and domain combinations.	chey-like phosphoacceptor (or receiver [rec]) domain is a common module in a variety of response regulators of the bacterial signal transduction systems. in this work, 4,610 response regulators, encoded in complete genomes of 200 bacterial and archaeal species, were identified and classified by their domain architectures. previously uncharacterized output domains were analyzed and, in some cases, assigned to known domain families. transcriptional regulators of the ompr, narl, and ntrc families w ...	2006	16740923
the prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains.	ubiquitin (ub)-mediated signaling is one of the hallmarks of all eukaryotes. prokaryotic homologs of ub (this and moad) and e1 ligases have been studied in relation to sulfur incorporation reactions in thiamine and molybdenum/tungsten cofactor biosynthesis. however, there is no evidence for entire protein modification systems with ub-like proteins and deconjugation by deubiquitinating enzymes in prokaryotes. hence, the evolutionary assembly of the eukaryotic ub-signaling apparatus remains unclea ...	2006	16859499
coverage of whole proteome by structural genomics observed through protein homology modeling database.	we have been developing famsbase, a protein homology-modeling database of whole orfs predicted from genome sequences. the latest update of famsbase ( http://daisy.nagahama-i-bio.ac.jp/famsbase/ ), which is based on the protein three-dimensional (3d) structures released by november 2003, contains modeled 3d structures for 368,724 open reading frames (orfs) derived from genomes of 276 species, namely 17 archaebacterial, 130 eubacterial, 18 eukaryotic and 111 phage genomes. those 276 genomes are pr ...	2006	17146617
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
diverse bacterial genomes encode an operon of two genes, one of which is an unusual class-i release factor that potentially recognizes atypical mrna signals other than normal stop codons.	while all codons that specify amino acids are universally recognized by trna molecules, codons signaling termination of translation are recognized by proteins known as class-i release factors (rf). in most eukaryotes and archaea a single rf accomplishes termination at all three stop codons. in most bacteria, there are two rfs with overlapping specificity, rf1 recognizes ua(a/g) and rf2 recognizes u(a/g)a.	2006	16970810
insertion sequence diversity in archaea.	insertion sequences (iss) can constitute an important component of prokaryotic (bacterial and archaeal) genomes. over 1,500 individual iss are included at present in the isfinder database (www-is.biotoul.fr), and these represent only a small portion of those in the available prokaryotic genome sequences and those that are being discovered in ongoing sequencing projects. in spite of this diversity, the transposition mechanisms of only a few of these ubiquitous mobile genetic elements are known, a ...	2007	17347521
genome analysis of minibacterium massiliensis highlights the convergent evolution of water-living bacteria.	filtration usually eliminates water-living bacteria. here, we report on the complete genome sequence of minibacterium massiliensis, a beta-proteobacteria that was recovered from 0.22-mum filtered water used for patients in the hospital. the unexpectedly large 4,110,251-nucleotide genome sequence of m. massiliensis was determined using the traditional shotgun sequencing approach. bioinformatic analyses shows that the m. massiliensis genome sequence illustrates characteristic features of water-liv ...	2007	17722982
assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data.	comparison of completely sequenced microbial genomes has revealed how fluid these genomes are. detecting synteny blocks requires reliable methods to determining the orthologs among the whole set of homologs detected by exhaustive comparisons between each pair of completely sequenced genomes. this is a complex and difficult problem in the field of comparative genomics but will help to better understand the way prokaryotic genomes are evolving.	2007	18047665
separating the effects of mutation and selection in producing dna skew in bacterial chromosomes.	many bacterial chromosomes display nucleotide asymmetry, or skew, between the leading and lagging strands of replication. mutational differences between these strands result in an overall pattern of skew that is centered about the origin of replication. such a pattern could also arise from selection coupled with a bias for genes coded on the leading strand. the relative contributions of selection and mutation in producing compositional skew are largely unknown.	2007	17935620
selection against spurious promoter motifs correlates with translational efficiency across bacteria.	because binding of rnap to misplaced sites could compromise the efficiency of transcription, natural selection for the optimization of gene expression should regulate the distribution of dna motifs capable of rnap-binding across the genome. here we analyze the distribution of the -10 promoter motifs that bind the sigma(70) subunit of rnap in 42 bacterial genomes. we show that selection on these motifs operates across the genome, maintaining an over-representation of -10 motifs in regulatory sequ ...	2007	17710145
real-time pcr: revolutionizing detection and expression analysis of genes.	invention of polymerase chain reaction (pcr) technology by kary mullis in 1984 gave birth to real-time pcr. real-time pcr - detection and expression analysis of gene(s) in real-time - has revolutionized the 21(st) century biological science due to its tremendous application in quantitative genotyping, genetic variation of inter and intra organisms, early diagnosis of disease, forensic, to name a few. we comprehensively review various aspects of real-time pcr, including technological refinement a ...	2007	18645596
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
ancient intron insertion sites and palindromic genomic duplication evolutionally shapes an elementally functioning membrane protein family.	in spite of the recent accumulation of genomic data, the evolutionary pathway in the individual genes of present-day living taxa is still elusive for most genes. among ion channels, inward k+ rectifier (irk) channels are the fundamental and well-defined protein group. we analyzed the genomic structures of this group and compared them among a phylogenetically wide range with our sequenced halocynthia roretzi, a tunicate, irk genomic genes.	2007	17708769
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
the [fefe] hydrogenase of nyctotherus ovalis has a chimeric origin.	the hydrogenosomes of the anaerobic ciliate nyctotherus ovalis show how mitochondria can evolve into hydrogenosomes because they possess a mitochondrial genome and parts of an electron-transport chain on the one hand, and a hydrogenase on the other hand. the hydrogenase permits direct reoxidation of nadh because it consists of a [fefe] hydrogenase module that is fused to two modules, which are homologous to the 24 kda and the 51 kda subunits of a mitochondrial complex i.	2007	18021395
phylogenetic signal and functional categories in proteobacteria genomes.	a comprehensive evolutionary analysis of bacterial genomes implies to identify the hallmark of vertical and non-vertical signals and to discriminate them from the presence of mere phylogenetic noise. in this report we have addressed the impact of factors like the universal distribution of the genes, their essentiality or their functional role in the cell on the inference of vertical signal through phylogenomic methods.	2007	17288580
global expression analysis of nucleotide binding site-leucine rich repeat-encoding and related genes in arabidopsis.	nucleotide binding site-leucine rich repeat (nbs-lrr)-encoding genes comprise the largest class of plant disease resistance genes. the 149 nbs-lrr-encoding genes and the 58 related genes that do not encode lrrs represent approximately 0.8% of all orfs so far annotated in arabidopsis ecotype col-0. despite their prevalence in the genome and functional importance, there was little information regarding expression of these genes.	2007	17956627
multiple mechanisms modulate brassinosteroid signaling.	brassinosteroids are essential hormones for plant growth and development. genetic studies have identified key components of the br signaling pathway, including the cell-surface receptor kinases that perceive br, an intracellular kinase and a phosphatase, and nuclear transcription factors. subsequent biochemical studies have revealed many details about signaling events from br perception at the cell surface to gene expression in the nucleus. recent studies have identified the 14-3-3 proteins as b ...	2007	17904409
the role and regulation of receptor-like kinases in plant defense.	receptor-like kinases (rlks) in plants are a large superfamily of proteins that are structurally similar. rlks are involved in a diverse array of plant responses including development, growth, hormone perception and the response to pathogens. current studies have focused attention on plant receptor-like kinases as an important class of sentinels acting in plant defense responses. rlks have been identified that act in both broad-spectrum, elicitor-initiated defense responses and as dominant resis ...	2007	19936086
pathogen virulence factors as molecular probes of basic plant cellular functions.	to successfully colonize plants, pathogens have evolved a myriad of virulence factors that allow them to manipulate host cellular pathways in order to gain entry into, multiply and move within, and eventually exit the host for a new infection cycle. in the past few years, substantial progress has been made in characterizing the host targets of viral and bacterial virulence factors, providing unique insights into basic plant cellular processes such as gene silencing, vesicle trafficking, hormone ...	2007	17884715
rumble in the nuclear jungle: compartmentalization, trafficking, and nuclear action of plant immune receptors.	plants and animals have evolved structurally related innate immune sensors inside cells to detect the presence of microbial molecules. an evolutionary ancient folding machinery becomes engaged for the synthesis of autorepressed receptor forms in both kingdoms. the receptors act as regulatory signal transduction switches and are activated upon direct or indirect perception of non-self structures. recent findings indicate that nucleo-cytoplasmic partitioning and nuclear activity is critical for th ...	2007	17853890
domestication, genomics and the future for banana.	cultivated bananas and plantains are giant herbaceous plants within the genus musa. they are both sterile and parthenocarpic so the fruit develops without seed. the cultivated hybrids and species are mostly triploid (2n = 3x = 33; a few are diploid or tetraploid), and most have been propagated from mutants found in the wild. with a production of 100 million tons annually, banana is a staple food across the asian, african and american tropics, with the 15 % that is exported being important to man ...	2007	17766312
putative prophages related to lytic tailless marine dsdna phage pm2 are widespread in the genomes of aquatic bacteria.	the origin and evolution of viruses is currently a heavily discussed issue. one element in this discussion is the innate viral "self" concept, which suggests that viral structures and functions can be divided into two categories. the first category consists of genetic determinants that are inherited from a viral ancestor and encode the viral "self". the second group consists of another set of structures and functions, the "nonself", which is interchangeable between different viruses and can be o ...	2007	17634101
the barley erf-type transcription factor hvraf confers enhanced pathogen resistance and salt tolerance in arabidopsis.	we isolated hvraf (hordeum vulgare root abundant factor), a cdna encoding a novel ethylene response factor (erf)-type transcription factor, from young seedlings of barley. in addition to the most highly conserved apetala2/erf dna-binding domain, the encoded protein contained an n-terminal mcggail signature sequence, a putative nuclear localization sequence, and a c-terminal acidic transcription activation domain containing a novel mammalian hemopexin domain signature-like sequence. their homolog ...	2007	16937017
functional analysis of burkholderia cepacia genes bced and bcef, encoding a phosphotyrosine phosphatase and a tyrosine autokinase, respectively: role in exopolysaccharide biosynthesis and biofilm formation.	the biosynthesis of the exopolysaccharide (eps) cepacian by burkholderia cepacia complex strains requires the 16.2-kb bce cluster of genes. two of the clustered genes, bced and bcef, code for two proteins homologous to phosphotyrosine phosphatases and tyrosine kinases, respectively. we show experimental evidence indicating that bcef is phosphorylated on tyrosine and that the conserved lysine residue present at position 563 in the walker a atp-binding motif is required for this autophosphorylatio ...	2007	17114319
functional analysis of burkholderia cepacia genes bced and bcef, encoding a phosphotyrosine phosphatase and a tyrosine autokinase, respectively: role in exopolysaccharide biosynthesis and biofilm formation.	the biosynthesis of the exopolysaccharide (eps) cepacian by burkholderia cepacia complex strains requires the 16.2-kb bce cluster of genes. two of the clustered genes, bced and bcef, code for two proteins homologous to phosphotyrosine phosphatases and tyrosine kinases, respectively. we show experimental evidence indicating that bcef is phosphorylated on tyrosine and that the conserved lysine residue present at position 563 in the walker a atp-binding motif is required for this autophosphorylatio ...	2007	17114319
genomic structure and phylogeny of the plant pathogen ralstonia solanacearum inferred from gene distribution analysis.	in the present study, we investigated the gene distribution among strains of the highly polymorphic plant pathogenic beta-proteobacterium ralstonia solanacearum, paying particular attention to the status of known or candidate pathogenicity genes. based on the use of comparative genomic hybridization on a pangenomic microarray for the gmi1000 reference strain, we have defined the conditions that allowed comparison of the repertoires of genes among a collection of 18 strains that are representativ ...	2007	17085551
genomic structure and phylogeny of the plant pathogen ralstonia solanacearum inferred from gene distribution analysis.	in the present study, we investigated the gene distribution among strains of the highly polymorphic plant pathogenic beta-proteobacterium ralstonia solanacearum, paying particular attention to the status of known or candidate pathogenicity genes. based on the use of comparative genomic hybridization on a pangenomic microarray for the gmi1000 reference strain, we have defined the conditions that allowed comparison of the repertoires of genes among a collection of 18 strains that are representativ ...	2007	17085551
glycosylation of pseudomonas aeruginosa strain pa5196 type iv pilins with mycobacterium-like alpha-1,5-linked d-araf oligosaccharides.	pseudomonas aeruginosa is a gram-negative bacterium that uses polar type iv pili for adherence to various materials and for rapid colonization of surfaces via twitching motility. within the p. aeruginosa species, five distinct alleles encoding variants of the structural subunit pila varying in amino acid sequence, length, and presence of posttranslational modifications have been identified. in this work, a combination of mass spectrometry and nuclear magnetic resonance spectroscopy was used to i ...	2007	17085575
glycosylation of pseudomonas aeruginosa strain pa5196 type iv pilins with mycobacterium-like alpha-1,5-linked d-araf oligosaccharides.	pseudomonas aeruginosa is a gram-negative bacterium that uses polar type iv pili for adherence to various materials and for rapid colonization of surfaces via twitching motility. within the p. aeruginosa species, five distinct alleles encoding variants of the structural subunit pila varying in amino acid sequence, length, and presence of posttranslational modifications have been identified. in this work, a combination of mass spectrometry and nuclear magnetic resonance spectroscopy was used to i ...	2007	17085575
the rpot regulon of pseudomonas putida dot-t1e and its role in stress endurance against solvents.	pseudomonas putida encodes 20 extracytoplasmic sigma factors (ecfs). in this study, we show that one of these ecfs, known as ecf-pp12 (pp3006), plays a role in tolerance of toluene and other organic solvents. based on this finding, we have called the gene that encodes this new ecf rpot. the rpot gene forms an operon with the preceding gene and with the gene located downstream. the translated gene product of the open reading frame pp3005 is an inner membrane protein, whereas the pp3007 protein is ...	2007	17071759
the rpot regulon of pseudomonas putida dot-t1e and its role in stress endurance against solvents.	pseudomonas putida encodes 20 extracytoplasmic sigma factors (ecfs). in this study, we show that one of these ecfs, known as ecf-pp12 (pp3006), plays a role in tolerance of toluene and other organic solvents. based on this finding, we have called the gene that encodes this new ecf rpot. the rpot gene forms an operon with the preceding gene and with the gene located downstream. the translated gene product of the open reading frame pp3005 is an inner membrane protein, whereas the pp3007 protein is ...	2007	17071759
pirin regulates pyruvate catabolism by interacting with the pyruvate dehydrogenase e1 subunit and modulating pyruvate dehydrogenase activity.	the protein pirin, which is involved in a variety of biological processes, is conserved from prokaryotic microorganisms, fungi, and plants to mammals. it acts as a transcriptional cofactor or an apoptosis-related protein in mammals and is involved in seed germination and seedling development in plants. in prokaryotes, while pirin is stress induced in cyanobacteria and may act as a quercetinase in escherichia coli, the functions of pirin orthologs remain mostly uncharacterized. we show that the s ...	2007	16980458
pirin regulates pyruvate catabolism by interacting with the pyruvate dehydrogenase e1 subunit and modulating pyruvate dehydrogenase activity.	the protein pirin, which is involved in a variety of biological processes, is conserved from prokaryotic microorganisms, fungi, and plants to mammals. it acts as a transcriptional cofactor or an apoptosis-related protein in mammals and is involved in seed germination and seedling development in plants. in prokaryotes, while pirin is stress induced in cyanobacteria and may act as a quercetinase in escherichia coli, the functions of pirin orthologs remain mostly uncharacterized. we show that the s ...	2007	16980458
the mi-9 gene from solanum arcanum conferring heat-stable resistance to root-knot nematodes is a homolog of mi-1.	resistance conferred by the mi-1 gene from solanum peruvianum is effective and widely used for limiting root-knot nematode (meloidogyne spp.) yield loss in tomato (solanum lycopersicum), but the resistance is ineffective at soil temperatures above 28 degrees c. previously, we mapped the heat-stable resistance gene mi-9 in solanum arcanum accession la2157 to the short arm of chromosome 6, in a genetic interval as mi-1 and the cladosporium fulvum resistance gene cf2. we developed a fine map of the ...	2007	17172289
capa, an autotransporter protein of campylobacter jejuni, mediates association with human epithelial cells and colonization of the chicken gut.	two putative autotransporter proteins, capa and capb, were identified in silico from the genome sequence of campylobacter jejuni nctc11168. the genes encoding each protein contain homopolymeric tracts, suggestive of phase variation mediated by a slipped-strand mispairing mechanism; in each case the gene sequence contained frameshifts at these positions. the c-terminal two-thirds of the two genes, as well as a portion of the predicted signal peptides, were identical; the remaining n-terminal port ...	2007	17172331
capa, an autotransporter protein of campylobacter jejuni, mediates association with human epithelial cells and colonization of the chicken gut.	two putative autotransporter proteins, capa and capb, were identified in silico from the genome sequence of campylobacter jejuni nctc11168. the genes encoding each protein contain homopolymeric tracts, suggestive of phase variation mediated by a slipped-strand mispairing mechanism; in each case the gene sequence contained frameshifts at these positions. the c-terminal two-thirds of the two genes, as well as a portion of the predicted signal peptides, were identical; the remaining n-terminal port ...	2007	17172331
the sphingomonas plasmid pcar3 is involved in complete mineralization of carbazole.	we determined the complete 254,797-bp nucleotide sequence of the plasmid pcar3, a carbazole-degradative plasmid from sphingomonas sp. strain ka1. a region of about 65 kb involved in replication and conjugative transfer showed similarity to a region of plasmid pnl1 isolated from the aromatic-degrading novosphingobium aromaticivorans strain f199. the presence of many insertion sequences, transposons, repeat sequences, and their remnants suggest plasticity of this plasmid in genetic structure. alth ...	2007	17172338
the sphingomonas plasmid pcar3 is involved in complete mineralization of carbazole.	we determined the complete 254,797-bp nucleotide sequence of the plasmid pcar3, a carbazole-degradative plasmid from sphingomonas sp. strain ka1. a region of about 65 kb involved in replication and conjugative transfer showed similarity to a region of plasmid pnl1 isolated from the aromatic-degrading novosphingobium aromaticivorans strain f199. the presence of many insertion sequences, transposons, repeat sequences, and their remnants suggest plasticity of this plasmid in genetic structure. alth ...	2007	17172338
development of signature-tagged mutagenesis in burkholderia pseudomallei to identify genes important in survival and pathogenesis.	burkholderia pseudomallei, the causative agent of melioidosis, is an important human pathogen in southeast asia and northern australia for which a vaccine is unavailable. a panel of 892 double signature-tagged mutants was screened for virulence using an intranasal balb/c mouse model of infection. a novel dna tag microarray identified 33 mutants as being attenuated in spleens, while 6 were attenuated in both lungs and spleens. the transposon insertion sites in spleen-attenuated mutants revealed g ...	2007	17189432
development of signature-tagged mutagenesis in burkholderia pseudomallei to identify genes important in survival and pathogenesis.	burkholderia pseudomallei, the causative agent of melioidosis, is an important human pathogen in southeast asia and northern australia for which a vaccine is unavailable. a panel of 892 double signature-tagged mutants was screened for virulence using an intranasal balb/c mouse model of infection. a novel dna tag microarray identified 33 mutants as being attenuated in spleens, while 6 were attenuated in both lungs and spleens. the transposon insertion sites in spleen-attenuated mutants revealed g ...	2007	17189432
evolutionary dynamics of ralstonia solanacearum.	we investigated the genetic diversity, extent of recombination, natural selection, and population divergence of ralstonia solanacearum samples obtained from sources worldwide. this plant pathogen causes bacterial wilt in many crops and constitutes a serious threat to agricultural production due to its very wide host range and aggressiveness. five housekeeping genes, dispersed around the chromosome, and three virulence-related genes, located on the megaplasmid, were sequenced from 58 strains belo ...	2007	17189443
evolutionary dynamics of ralstonia solanacearum.	we investigated the genetic diversity, extent of recombination, natural selection, and population divergence of ralstonia solanacearum samples obtained from sources worldwide. this plant pathogen causes bacterial wilt in many crops and constitutes a serious threat to agricultural production due to its very wide host range and aggressiveness. five housekeeping genes, dispersed around the chromosome, and three virulence-related genes, located on the megaplasmid, were sequenced from 58 strains belo ...	2007	17189443