GEO DataSets

(Submitter supplied) Genome sequence analysis of the bacterium Xylella fastidiosa revealed the presence of two genes, named rpoE and rseA, predicted to encode an 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 σE regulon, global gene expression profiles were obtained by DNA microarray analysis of bacterial cells under heat shock identifying 23 sigmaE-dependent genes. more...

Organism:

Xylella fastidiosa

Type:

Expression profiling by array

Platform:

GPL2708

18 Samples

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(Submitter supplied) The phytopathogen Xylella fastidiosa produces two classes of pili, long type IV pili and short type I pili, which are involved in motility and adhesion. In this work, we have investigated the role of σ54 factor and its involvement in the regulation of fimbrial biogenesis in X. fastidiosa. An rpoN null mutant was constructed from citrus strain J1a12, and analyses of global gene expression profile by microarrays comparing the wild type and rpoN mutant strains showed that few genes exhibited differential expression. more...

Organism:

Xylella fastidiosa

Type:

Expression profiling by array

Platform:

GPL2708

6 Samples

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(Submitter supplied) Xylella fastidiosa is a phytopathogenic bacterium responsible for diseases in many economically important crops. Although different strains have been studied, little is known about X. fastidiosa stress responses. One of the best characterized stresses in bacteria is the heat shock response, which induces the expression of specific genes to prevent protein misfolding and aggregation, and to promote degradation of the irreversibly denatured polypeptides. more...

Organism:

Xylella fastidiosa

Type:

Expression profiling by array

Platforms:

GPL3409 GPL2708

52 Samples

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(Submitter supplied) A 4608-spot DNA microarray was printed containing unique internal fragments of 2692 CDS representing 94.5% of all of the 2848 CDS annotated by Simpson et al. (2000, Nature) (http://aeg.lbi.ic.unicamp.br/xf). PCR primers were designed to amplify unique internal fragments of 200-1000 bp of each predicted CDS described in the annotated genome sequence of X. fastidiosa strain 9a5c (http://aeg.lbi.ic.unicamp.br/xf). more...

Organism:

Xylella fastidiosa

8 Series

178 Samples

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(Submitter supplied) Background: Xylella fastidiosa, a Gram-negative fastidious bacterium, grows exclusively 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. Results: In this work, we performed a whole-genome microarray analysis of the X. more...

Organism:

Xylella fastidiosa

Type:

Expression profiling by array

Platform:

GPL2708

24 Samples

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(Submitter supplied) Like other bacterial species, Mycobacterium tuberculosis has multiple sigma (s) factors encoded in its genome. In previously published work, we and others have shown that mutations in some of these transcriptional activators render M. tuberculosis sensitive to various environmental stresses and, in some cases, cause attenuated virulence phenotypes. In this paper, we characterize a M. tuberculosis mutant lacking the ECF s factor sigma-H. more...

Organism:

Mycobacterium tuberculosis

Type:

Expression profiling by array

Platform:

GPL2787

15 Samples

Download data: TXT

(Submitter supplied) In previously published work, we identified three Mycobacterium tuberculosis sigma (s) factor genes responding to heat shock (sigB, sigE and sigH ). Two of them (sigB and sigE ) also responded to SDS exposure. As these responses to stress suggested that the s factors encoded by these genes could be involved in pathogenicity, we are studying their role in physiology and virulence. In this work, we characterize a sigE mutant of M. more...

Organism:

Mycobacterium tuberculosis

Type:

Expression profiling by array

Platform:

GPL2787

15 Samples

Download data: TXT

(Submitter supplied) The alternative sigma factor sigmaB has an important role in the acquisition of stress-resistance in many gram-positive bacteria. In the foodborne pathogen Bacillus cereus sigmaB is activated strongly upon a heat shock and other stress conditions. Here we describe the identification of the set of sigmaB-regulated genes in B. cereus by DNA microarray analysis of the transcriptome upon a mild heat shock. more...

Organism:

Bacillus cereus ATCC 14579

Type:

Expression profiling by array

Platform:

GPL4406

7 Samples

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(Submitter supplied) Vibrio cholerae, the cause of cholera, can grow in a variety of environments outside of human hosts. During infection, the pathogen must adapt to significant environmental alterations, including the elevated temperature of the human gastrointestinal tract. σ32, an alternative sigma factor encoded by rpoH, activates transcription of genes involved in the heat-shock response in several bacterial species. more...

Organism:

Vibrio cholerae; Vibrio cholerae O1 biovar El Tor str. N16961

Type:

Expression profiling by array

Platform:

GPL3651

6 Samples

Download data: TXT

(Submitter supplied) Abstract of associated manuscript: The Bacillus subtilis extracytoplasmic function (ECF) sigma(M) factor is activated by cell envelope stress elicited by antibiotics, and by acid, heat, ethanol and superoxide stresses. Here, we have used several complementary approaches to identify genes controlled by sigma(M). In many cases, expression is only partially dependent on sigma(M) because of both overlapping promoter recognition with other ECF sigma factors and the presence of additional promoter elements. more...

Organism:

Bacillus subtilis

Type:

Expression profiling by array

Platform:

GPL7420

14 Samples

Download data: GPR

(Submitter supplied) Xylella fastidiosa regulates traits important to both virulence of grape as well as colonization of sharpshooter vectors via its production of a fatty acid signal molecule known as DSF whose production is dependent on rpfF. While X. fastidiosa rpfF mutants exhibit increased virulence to plants they are unable to be spread from plant to plant by insect vectors. To gain more insight into the traits that contribute to these processes, a DNA microarray for this species was designed and utilized to determine the RpfF-dependent regulon by transcriptional profiling. more...

Organism:

Xylella fastidiosa; Xylella fastidiosa 9a5c; Xylella fastidiosa Temecula1

Type:

Expression profiling by array

Platform:

GPL15652

1 Sample

Download data: TXT

(Submitter supplied) Xylella fastidiosa is the etiologic agent of a wide range of plant diseases including citrus variegated chlorosis (CVC), a major threat to the Brazilian citrus industry. Genome sequences of several strains of this phytopathogen are accessible, enabling large-scale functional studies. Transcript levels in different iron availabilities were assessed with DNA microarrays representing 2608 (91.6%) coding sequences (CDS) of X. more...

Organism:

Xylella fastidiosa

Type:

Expression profiling by array

Platform:

GPL2708

22 Samples

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(Submitter supplied) Xylella fastidiosa is the etiologic agent of a wide range of plant diseases including citrus variegated chlorosis (CVC), a major threat to the Brazilian citrus industry. Genome sequences of several strains of this phytopathogen are accessible, enabling large-scale functional studies. Transcript levels in different iron availabilities were assessed with DNA microarrays representing 2608 (91.6%) coding sequences (CDS) of X. more...

Organism:

Xylella fastidiosa

Type:

Expression profiling by array

Platform:

GPL2708

22 Samples

Download data

(Submitter supplied) The foodborne pathogen Listeria monocytogenes uses a number of transcriptional regulators, including the negative regulator CtsR, to control gene expression under different environmental conditions and in response to stress. Gene expression patterns of DctsR log phase cells were compared to both wt and ictsR-mcsA log phase cells grown with 0.5mM IPTG to identify CtsR-dependent genes.We identified 62 CtsR-dependent genes that showed significant expression ratios (adj. more...

Organism:

Listeria monocytogenes; Listeria innocua

Type:

Expression profiling by array

Platform:

GPL5029

2 Samples

Download data: GPR

(Submitter supplied) A 4608-spot DNA microarray was printed containing unique internal fragments of 2572 CDS representing 90.3% of all of the 2848 CDS annotated by Simpson et al. (2000, Nature) (http://aeg.lbi.ic.unicamp.br/xf). PCR primers were designed to amplify unique internal fragments of 200-1000 bp of each predicted CDS described in the annotated genome sequence of X. fastidiosa strain 9a5c (http://aeg.lbi.ic.unicamp.br/xf). more...

Organism:

Xylella fastidiosa

1 Series

8 Samples

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(Submitter supplied) Nostoc punctiforme is a filamentous cyanobacterium capable if differentiating normal vegetative cells into nitrogen fixing heterocysts and spore-like akinetes. Here the effects of a sigma factor (sigG) mutation on the transcriptome was analyzed under 1) normal vegetative growth, and 2) following akinete induction. A zwf strain grown with fructose differentiates into akinetes following transfer to darkness. more...

Organism:

Nostoc punctiforme

Type:

Expression profiling by array

Platform:

GPL19195

2 Samples

Download data: TXT

(Submitter supplied) The foodborne pathogen Listeria monocytogenes uses a number of transcriptional regulators, including the negative regulator HrcA, to control gene expression under different environmental conditions and in response to stress. Gene expression patterns of DhrcA stationary phase cells were compared to wt to identify hrcA-dependent genes. We identified 61 HrcA-dependent genes that showed significant expression ratios (adj. more...

Organism:

Listeria monocytogenes; Listeria innocua

Type:

Expression profiling by array

Platform:

GPL5029

1 Sample

Download data: GPR

(Submitter supplied) Extracytoplasmic function (ECF) sigma factors are known to play an important role in the bacterial response to various environmental stresses. Porphyromonas gingivalis, a prominent etiological agent in human periodontitis, possesses six putative ECF sigma factors. So far, information is limited on an ECF sigma factor, PGN_0319. It has been recently reported that the expression of genes encoding some of the ECF sigma factors including PGN_0319 was affected by hemin availability. more...

Organism:

Porphyromonas gingivalis ATCC 33277; Porphyromonas gingivalis

Type:

Expression profiling by array

Platform:

GPL21477

4 Samples

Download data: TXT

(Submitter supplied) Comprison of the transcriptome of wild type Bacillus subtilis to the mutants sigW, rasP and prsW to select all candidate sigW regulated genes. We identified 89 genes as being sigW regulated, including several non-coding RNA's. The effects of rasP and prsW mutations on sigW regulated genes were relatively mild, implying that RasP or PrsW are not strictly required for sigW activation. The rasP mutant has a peliotropic phenotype, affecting competence development, protein secretion and membrane protein production. more...

Organism:

Bacillus subtilis subsp. subtilis str. 168

Type:

Expression profiling by genome tiling array

Platform:

GPL15150

11 Samples

Download data: PAIR

(Submitter supplied) This study addresses the key role of the extracytoplasmic function (ECF) sigma factor DdvS in the Gram-negative bacterium Myxococcus xanthus. It allows us to determine its regulon and it shows that the expression of ddvS and its regulón depends on the global regulatory complex CarD-CarG.

Organism:

Myxococcus xanthus

Type:

Expression profiling by array

Platform:

GPL24768

8 Samples

Download data: TXT