Global Gene Expression Analysis of the Heat Shock Response in the Phytopathogen
            <i>Xylella fastidiosa</i>

Koide, Tie; Vêncio, Ricardo Z. N.; Gomes, Suely L.

doi:10.1128/jb.00182-06

Cited by 43 publications

(52 citation statements)

References 64 publications

(69 reference statements)

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“…qPCR assays were performed in triplicate with the gene-specific primer pairs shown in Table S1 in the supplemental material from two biological replicas distinct from those performed for microarray analysis. Threshold values were normalized according to the threshold cycle of CDS XF2175 (dnaQ), which is expressed at similar levels under all conditions tested according to our microarray data and was also used previously (15,40). The change in the expression of each gene was calculated using the 2 Ϫ⌬⌬CT method (46).…”

Section: Methodsmentioning

confidence: 99%

The Iron Stimulon of Xylella fastidiosa Includes Genes for Type IV Pilus and Colicin V-Like Bacteriocins

Zaini¹,

Fogaça²,

Lupo³

et al. 2008

J Bacteriol

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Xylella fastidiosa is the etiologic agent of a wide range of plant diseases, including citrus variegated chlorosis (CVC), a major threat to citrus industry. The genomes of several strains of this phytopathogen were completely sequenced, enabling large-scale functional studies. DNA microarrays representing 2,608 (91.6%) coding sequences (CDS) of X. fastidiosa CVC strain 9a5c were used to investigate transcript levels during growth with different iron availabilities. When treated with the iron chelator 2,2-dipyridyl, 193 CDS were considered up-regulated and 216 were considered down-regulated. Upon incubation with 100 M ferric pyrophosphate, 218 and 256 CDS were considered up-and down-regulated, respectively. Differential expression for a subset of 44 CDS was further evaluated by reverse transcription-quantitative PCR. Several CDS involved with regulatory functions, pathogenicity, and cell structure were modulated under both conditions assayed, suggesting that major changes in cell architecture and metabolism occur when X. fastidiosa cells are exposed to extreme variations in iron concentration. Interestingly, the modulated CDS include those related to colicin V-like bacteriocin synthesis and secretion and to functions of pili/fimbriae. We also investigated the contribution of the ferric uptake regulator Fur to the iron stimulon of X. fastidiosa. The promoter regions of the strain 9a5c genome were screened for putative Fur boxes, and candidates were analyzed by electrophoretic mobility shift assays. Taken together, our data support the hypothesis that Fur is not solely responsible for the modulation of the iron stimulon of X. fastidiosa, and they present novel evidence for iron regulation of pathogenicity determinants.When challenged with limiting iron concentrations such as those encountered in host tissues, pathogenic bacteria commonly manage iron homeostasis by releasing iron from intracellular reservoirs and increasing the expression of iron acquisition systems (73). This allows survival in an otherwise prohibiting environment, since iron is an essential cofactor for many proteins mediating electron transfer and redox reactions. Besides functioning as a barrier against pathogens, light control of free iron concentration within host tissues reduces the deleterious effects of iron overload, such as the generation of reactive oxygen species (78,83). Strict control of iron metabolism is also observed for bacteria, and in most cases it is exerted by the ferric uptake regulator, Fur. When bound to Fe 2ϩ , this intracellular iron sensor is capable of binding to Fur boxes at operator sequences, blocking the transcription of genes involved in many cellular processes besides iron uptake (1). The description of the iron regulatory circuitry has recently increased in complexity due to the discovery of other transcriptional repressors and of small noncoding regulatory RNAs (23,51,82).Many pathogenic bacteria have also evolved to couple the iron-limiting response to the expression of other virulence determinants, such as exo...

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Section: Methodsmentioning

confidence: 99%

The Iron Stimulon of Xylella fastidiosa Includes Genes for Type IV Pilus and Colicin V-Like Bacteriocins

Zaini¹,

Fogaça²,

Lupo³

et al. 2008

J Bacteriol

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“…Transcriptome analysis has been used to compare growth in biofilm and planktonic cells (16), freshly isolated bacteria, or axenic culture (15) and in genotyping studies comparing different strains (30,47). Analysis of the response of X. fastidiosa to heat stress was recently carried out (31), determining the genes involved in the heat shock response in the citrus strain 9a5c. A total of 261 genes were induced, and 222 genes were repressed, as determined after different times of exposure to 40°C (31).…”

mentioning

confidence: 99%

“…Analysis of the response of X. fastidiosa to heat stress was recently carried out (31), determining the genes involved in the heat shock response in the citrus strain 9a5c. A total of 261 genes were induced, and 222 genes were repressed, as determined after different times of exposure to 40°C (31).…”

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confidence: 99%

The Single Extracytoplasmic-Function Sigma Factor of Xylella fastidiosa Is Involved in the Heat Shock Response and Presents an Unusual Regulatory Mechanism

et al. 2007

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Genome sequence analysis of the bacterium Xylella fastidiosa revealed the presence of two genes, named rpoE and rseA, predicted to encode an extracytoplasmic function (ECF) sigma factor and an anti-sigma factor, respectively. In this work, an rpoE null mutant was constructed in the citrus strain J1a12 and shown to be sensitive to exposure to heat shock and ethanol. To identify the X. fastidiosa E regulon, global gene expression profiles were obtained by DNA microarray analysis of bacterial cells under heat shock, identifying 21 Edependent genes. These genes encode proteins belonging to different functional categories, such as enzymes involved in protein folding and degradation, signal transduction, and DNA restriction modification and hypothetical proteins. Several putative E -dependent promoters were mapped by primer extension, and alignment of the mapped promoters revealed a consensus sequence similar to those of ECF sigma factor promoters of other bacteria. Like other ECF sigma factors, rpoE and rseA were shown to comprise an operon in X. fastidiosa, together with a third open reading frame (XF2241). However, upon heat shock, rpoE expression was not induced, while rseA and XF2241 were highly induced at a newly identified E -dependent promoter internal to the operon. Therefore, unlike many other ECF sigma factors, rpoE is not autoregulated but instead positively regulates the gene encoding its putative anti-sigma factor.Regulation of gene expression is required for adaptive response of bacteria to distinct environmental stimuli. Bacterial sigma factors regulate gene expression by conferring different promoter specificities on RNA polymerase during transcription initiation. Bacterial genomes usually encode one principal sigma factor for transcription of housekeeping genes, of which sigma 70 of Escherichia coli is the prototype, and a variable number of alternative sigma factors that coordinate specific regulons (61). The extracytoplasmic function (ECF) sigma factors were initially described as a distinct group of the sigma 70 family based on sequence similarity. This group initially included the presently well-characterized ECF sigma factors In the traditional model for regulation of ECF sigma factors, an extracytoplasmic signal releases the sigma ECF from antisigma factor inhibition and thereby leads to the transcription of the target genes, usually including its own operon, a mechanism of positive autoregulation that allows amplification and turn-off of the signal (26). Genome sequencing revealed that ECF sigma factors are widespread in several bacterial species, and characterization of multiple members of this group has shown that they share some common features. They recognize preferentially a promoter element with an "AAC" motif in the Ϫ35 region, are cotranscribed with an anti-sigma factor in an auto-regulated operon, and regulate functions associated with the cell envelope (26).A combination of genetic strategies with genomewide expression experiments and bioinformatics analysis has provided a powerful w...

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“…6,10 Gene expression profiling by cDNA microarray analysis has become a powerful tool for simultaneously determining the presence of a wide diversity of genes within given E. coli strain conditions. This method has been used in various studies involving taxonomy, 11 heat shock, 12 biofilm formation, 13,14 genotyping of microbial strains 15 and detection of environmentally important genes. 16,17 Recently, cDNA microarray analysis was used to detect antimicrobial resistance genes 18 and virulence genes [19][20][21] of E. coli and other strains.…”

Section: Introductionmentioning

confidence: 99%

Genome‐wide transcriptome analysis of fluoroquinolone resistance in clinical isolates of Escherichia coli

et al. 2011

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Abbreviations & AcronymsObjectives: Coincident with their worldwide use, resistance to fluoroquinolones in Escherichia coli has increased. To identify the gene expression profiles underlying fluoroquinolone resistance, we carried out genome-wide transcriptome analysis of fluoroquinolone-sensitive E. coli. Methods: Four fluoroquinolone-sensitive E. coli and five fluoroquinolone-resistant E. coli clinical isolates were subjected to complementary deoxyribonucleic acid microarray analysis. Some upregulated genes' expression was verified by real-time polymerase chain reaction using 104 E. coli clinical isolates, and minimum inhibitory concentration tests were carried out by using their transformants. Results: A total of 40 genes were significantly upregulated in fluoroquinoloneresistant E. coli isolates (P < 0.05). The expression of phage shock protein operons, which are involved in biofilm formation, was markedly upregulated in our profile of fluoroquinolone-resistant E. coli. One of the phage shock protein operons, pspC, was significantly upregulated in 50 fluoroquinolone-resistant E. coli isolates (P < 0.0001). The expression of type I fimbriae genes, which are pilus operons involved in biofilm formation, were markedly downregulated in fluoroquinolone-resistant E. coli. Deoxyribonucleic acid adenine methyltransferase (dam), which represses type I fimbriae genes, was significantly upregulated in the clinical fluoroquinolone-resistant E. coli isolates (P = 0.007). We established pspC-and dam-expressing E. coli transformants from fluoroquinolone-sensitive E. coli, and the minimum inhibitory concentration tests showed that the transformants acquired fluoroquinolone resistance, suggesting that upregulation of these genes contributes to acquiring fluoroquinolone resistance. Conclusions: Upregulation of psp operones and dam underlying pilus operons downregulation might be associated with fluoroquinolone resistance in E. coli.

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Global Gene Expression Analysis of the Heat Shock Response in the Phytopathogen Xylella fastidiosa

Cited by 43 publications

References 64 publications

The Iron Stimulon of Xylella fastidiosa Includes Genes for Type IV Pilus and Colicin V-Like Bacteriocins

The Iron Stimulon of Xylella fastidiosa Includes Genes for Type IV Pilus and Colicin V-Like Bacteriocins

The Single Extracytoplasmic-Function Sigma Factor of Xylella fastidiosa Is Involved in the Heat Shock Response and Presents an Unusual Regulatory Mechanism

Genome‐wide transcriptome analysis of fluoroquinolone resistance in clinical isolates of Escherichia coli

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