DNA microarray-based genome comparison of a pathogenic and a nonpathogenic strain of Xylella fastidiosa delineates genes important for bacterial virulence.
ABSTRACT Xylella fastidiosa is a phytopathogenic bacterium that causes serious diseases in a wide range of economically important crops. Despite extensive comparative analyses of genome sequences of Xylella pathogenic strains from different plant hosts, nonpathogenic strains have not been studied. In this report, we show that X. fastidiosa strain J1a12, associated with citrus variegated chlorosis (CVC), is nonpathogenic when injected into citrus and tobacco plants. Furthermore, a DNA microarray-based comparison of J1a12 with 9a5c, a CVC strain that is highly pathogenic and had its genome completely sequenced, revealed that 14 coding sequences of strain 9a5c are absent or highly divergent in strain J1a12. Among them, we found an arginase and a fimbrial adhesin precursor of type III pilus, which were confirmed to be absent in the nonpathogenic strain by PCR and DNA sequencing. The absence of arginase can be correlated to the inability of J1a12 to multiply in host plants. This enzyme has been recently shown to act as a bacterial survival mechanism by down-regulating host nitric oxide production. The lack of the adhesin precursor gene is in accordance with the less aggregated phenotype observed for J1a12 cells growing in vitro. Thus, the absence of both genes can be associated with the failure of the J1a12 strain to establish and spread in citrus and tobacco plants. These results provide the first detailed comparison between a nonpathogenic strain and a pathogenic strain of X. fastidiosa, constituting an important step towards understanding the molecular basis of the disease.
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ABSTRACT: A diverse set of phage lineages is associated with the bacterial plant-pathogen genomes sequenced to date. Analysis of 37 genomes revealed 5,169 potential genes (approximately 4.3 Mbp) of phage origin, and at least 50% had no function assigned or are nonessential to phage biology. Some phytopathogens have transcriptionally active prophage genes under conditions that mimic plant infection, suggesting an association between plant disease and prophage transcriptional modulation. The role of prophages within genomes for cell biology varies. For pathogens such as Pectobacter, Pseudomonas, Ralstonia, and Streptomyces, involvement of prophage in disease symptoms has been demonstrated. In Xylella and Xanthomonas, prophage activity is associated with genome rearrangements and strain differentiation. For other pathogens, prophage roles are yet to be established. This review integrates available information in a unique interface ( http://propnav.esalq.usp.br ) that may be assessed to improve research in prophage biology and its association with genome evolution and pathogenicity. Expected final online publication date for the Annual Review of Phytopathology Volume 51 is August 04, 2013. Please see http://www.annualreviews.org/catalog/pubdates.aspx for revised estimates.Annual Review of Phytopathology 05/2013; DOI:10.1146/annurev-phyto-081211-173010 · 11.00 Impact Factor
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ABSTRACT: One of the possible applications of the DNA Microarray technique is the detention of levels of genic expression or the genome comparison by CGH (Comparative Genome Hybridization) . The traditional methods of analysis in molecular biology are limited to the study of one gene, or group of genes, for experiment. The technology known as DNA Microarray has shown great impact in the field of the genic expression, once it allows monitor a whole genome and simultaneously verifies the interactions among thousand of genes . A form to select genic fragments to be printed on the slides is through the sequencing of the whole genome. This way, after an annotation, we can discover which the genes that are found in the genome. Of ownership of the sequences, primers are synthesized to amplify each gene . Another way is through the creation of genomic library of shotgun, and a DNA array (DNA chip). In a DNA array, clones where the RNA transcripts hybridize are selected, and the DNA fragment of each clone is sequenced later for the identification of the genes . This work presents an approach to find genes in clones of library of shotgun, from partially sequenced genomes, to be used in projects of analyses of transcriptions. Comparative analyses of genomes, biological database, tools of bioinformatics and process algebra in database identify clones having one or more genes in its sequences. Clones having unique genes are an alternative to the necessity of synthesis of primers that can be used as marking molecular of genes in the genomes. Identifying clones that contain genes and knowing which are their functions; a DNA array for the analyses of transcriptions and genome comparative can be created. The objective of this approach is to allow that sequenced clones of shotgun during the genome project can be used concomitantly for analyses using CGH, analyses of genic expression and assembly of genomes. This approach allows analyses of clones during the sequencing, what makes possible the selection of interest genes to be placed on the slides for the construction of a DNA array. When this DNA array is complete, the sequencing of clones of the libraries of shotgun is interrupts, so results in lower cost for the analyses of the genomes. Besides, making use of clones with genes that compose such arrangement, it is always possible to remake the DNA array without the necessity to command the synthesis of primers as it happens currently. The version of this approach in relational database was used to select clones of a genomic library of Bradyrhizobium elkanii SEMIA 587. Clones produced and sequenced had been used in the assembly of the genome of B. elkanii and in the production of a DNA array of known genes. This partial DNA array was used for studies of genic expression of B. elkanii during the symbiosis with soy plants (Glycine Max), involving aspects of the nodulation of the plant and biological fixation of the N 2 . Additionally, this DNA array was applied for comparative studies between B. elkanii, Bradyrhizobium japonicum and Rhizobium etli, using CGH . Once that satisfactory resulted have been gotten, the extended version using process algebra in relational database will allow to greater flexibility in the searches of excellent clones containing genes. This approach will be used for phylogenetic analyses of Rhizobiaceae using CGH and in the production of a DNA array containing 90% of the genes of the B. elkanii for analyses of transcriptions.
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ABSTRACT: Xylella fastidiosa is responsible for a wide range of economically important plant diseases. We report here the crystal structure and kinetic data of Xylellain, the first cysteine protease characterized from the genome of the pathogenic X. fastidiosa strain 9a5c. Xylellain has a papain-family fold, and part of the N-terminal sequence blocks the enzyme active site, thereby mediating protein activity. One novel feature identified in the structure is the presence of a ribonucleotide bound outside the active site. We show that this ribonucleotide plays an important regulatory role in Xylellain enzyme kinetics, possibly functioning as a physiological mediator.FEBS letters 01/2013; 587(4). DOI:10.1016/j.febslet.2013.01.009 · 3.34 Impact Factor