Koide T, Zaini PA, Moreira LM, Vencio RZN, Matsukuma AY, Durham AM et al.. DNA microarray-based genome comparison of a pathogenic and a nonpathogenic strain of Xylella fastidiosa delineates genes important for bacterial virulence. J Bacteriol 186: 5442-5449

Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, SP, Brazil.
Journal of Bacteriology (Impact Factor: 2.81). 09/2004; 186(16):5442-9. DOI: 10.1128/JB.186.16.5442-5449.2004
Source: PubMed


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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    • "DNA microarray-based genome composition analysis is a good alternative to full genome sequencing and has been used in comparative studies to analyze various bacterial pathogens including Mycobacterium tuberculosis (Behr et al., 1999), Helicobacter pylori (Salama et al., 2000), Pseudomonas aeruginosa (Wolfgang et al., 2003), Yersinia pestis, and Y. pseudotuberculosis (Hinchliffe et al., 2003). A nonpathogenic strain J1a12 of Xylella fastidiosa associated with citrus could easily be differentiated from the pathogenic strain 9a5c causing variegated chlorosis, through DNA microarray-based comparison (Koide et al., 2004). It was revealed that 14 coding sequences of strain 9a5c are absent or highly divergent in strain J1a12. "

    04/2013; 8(1):1-11. DOI:10.5897/BMBR12.007
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    • "Arginase regulates the production of nitric oxide (NO), which is induced in a jasmonate-dependent manner in response to wounding and is strongly implicated in the activation of disease resistance genes [60,31]. In microorganisms, arginase activity has been correlated with pathogenicity [61] and was shown to act as a bacterial survival mechanism by downregulating host nitric oxide production [62]. Other transcripts expressed by FOM in planta, specifically or otherwise, are involved in ubiquitinylation and protein degradation, both of which are necessary for pathogenicity in F. oxysporum f. sp. "
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    ABSTRACT: Fusarium oxysporum f. sp. melonis Snyd. & Hans. (FOM) causes Fusarium wilt, the most important infectious disease of melon (Cucumis melo L.). The four known races of this pathogen can be distinguished only by infection on appropriate cultivars. No molecular tools are available that can discriminate among the races, and the molecular basis of compatibility and disease progression are poorly understood. Resistance to races 1 and 2 is controlled by a single dominant gene, whereas only partial polygenic resistance to race 1,2 has been described. We carried out a large-scale cDNA-AFLP analysis to identify host genes potentially related to resistance and susceptibility as well as fungal genes associated with the infection process. At the same time, a systematic reisolation procedure on infected stems allowed us to monitor fungal colonization in compatible and incompatible host-pathogen combinations. Melon plants (cv. Charentais Fom-2), which are susceptible to race 1,2 and resistant to race 1, were artificially infected with a race 1 strain of FOM or one of two race 1,2 w strains. Host colonization of stems was assessed at 1, 2, 4, 8, 14, 16, 18 and 21 days post inoculation (dpi), and the fungus was reisolated from infected plants. Markedly different colonization patterns were observed in compatible and incompatible host-pathogen combinations. Five time points from the symptomless early stage (2 dpi) to obvious wilting symptoms (21 dpi) were considered for cDNA-AFLP analysis. After successful sequencing of 627 transcript-derived fragments (TDFs) differentially expressed in infected plants, homology searching retrieved 305 melon transcripts, 195 FOM transcripts expressed in planta and 127 orphan TDFs. RNA samples from FOM colonies of the three strains grown in vitro were also included in the analysis to facilitate the detection of in planta-specific transcripts and to identify TDFs differentially expressed among races/strains. Our data suggest that resistance against FOM in melon involves only limited transcriptional changes, and that wilting symptoms could derive, at least partially, from an active plant response.We discuss the pathogen-derived transcripts expressed in planta during the infection process and potentially related to virulence functions, as well as transcripts that are differentially expressed between the two FOM races grown in vitro. These transcripts provide candidate sequences that can be further tested for their ability to distinguish between races.Sequence data from this article have been deposited in GenBank, Accession Numbers: HO867279-HO867981.
    BMC Genomics 02/2011; 12(1):122. DOI:10.1186/1471-2164-12-122 · 3.99 Impact Factor
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    • "RNA samples were evaluated by electrophoresis on formaldehyde-agarose gels and stored at -80°C. Microarray slides covering more than 94% of all X. fastidiosa genes, spotted at least in duplicate, were prepared as previously described [29]. Fluorescent-labeled cDNA preparation, microarray hybridization, washing and scanning were performed as previously described [25]. "
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    ABSTRACT: Xylella fastidiosa, a Gram-negative fastidious bacterium, grows in the xylem of several plants causing diseases such as citrus variegated chlorosis. As the xylem sap contains low concentrations of amino acids and other compounds, X. fastidiosa needs to cope with nitrogen limitation in its natural habitat. In this work, we performed a whole-genome microarray analysis of the X. fastidiosa nitrogen starvation response. A time course experiment (2, 8 and 12 hours) of cultures grown in defined medium under nitrogen starvation revealed many differentially expressed genes, such as those related to transport, nitrogen assimilation, amino acid biosynthesis, transcriptional regulation, and many genes encoding hypothetical proteins. In addition, a decrease in the expression levels of many genes involved in carbon metabolism and energy generation pathways was also observed. Comparison of gene expression profiles between the wild type strain and the rpoN null mutant allowed the identification of genes directly or indirectly induced by nitrogen starvation in a σ54-dependent manner. A more complete picture of the σ54 regulon was achieved by combining the transcriptome data with an in silico search for potential σ54-dependent promoters, using a position weight matrix approach. One of these σ54-predicted binding sites, located upstream of the glnA gene (encoding glutamine synthetase), was validated by primer extension assays, confirming that this gene has a σ54-dependent promoter. Together, these results show that nitrogen starvation causes intense changes in the X. fastidiosa transcriptome and some of these differentially expressed genes belong to the σ54 regulon.
    BMC Microbiology 08/2010; 10(1):231. DOI:10.1186/1471-2180-10-231 · 2.73 Impact Factor
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