Genome-wide identification of Hfq-regulated small RNAs in the bacterial pathogen Erwinia amylovora
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ABSTRACT:
ORGANISM(S): Erwinia amylovora
PROVIDER: GSE53763 | GEO | 2014/01/15
SECONDARY ACCESSION(S): PRJNA232821
REPOSITORIES: GEO
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Project description:RNA-seq analysis was performed to examine the sRNA transcripts in wild type E. amylovora 1189 and in the deletion mutant of hfq, at 6 and 12 hours of culture in hrp-inducing minimal medium. Total RNA was isolated from wild type Ea1189, and the hfq mutant of Ea1189, at 6 and 12 hours post inoculation in hrp-inducing minimal medium. RNA transcripts that are between 50-350 nucleotides were analyzed by RNA-seq. Intergenic transcripts whose expression was greatly reduced in the hfq mutant than the wild type at both 6 and 12 hours post inoculation in hrp-inducing minimal medium were selected as potential small RNAs.
2014-01-15 | E-GEOD-53763 | biostudies-arrayexpress
Project description:The bacterial pathogen Erwinia amylovora is the causal agent of fire blight, an economically significant disease of apple and pear. Disease initiation by E. amylovora requires the translocation of effector proteins into host cells by the hypersensitive response and pathogenicity (hrp) type III secretion system (T3SS). The alternate sigma factor HrpL positively regulates the transcription of structural and translocated components of the T3SS via hrp promoter elements. To characterize genome-wide hrpL-dependent gene expression in E. amylovora Ea1189, wild-type and Ea1189hrpL strains were cultured in hrp-inducing minimal medium, and total RNA was compared using a custom microarray designed to represent the annotated genes of E. amylovora ATCC 49946. Results revealed 24 genes differentially-regulated in Ea1189hrpL compared to Ea1189 with fold-change expression ratios greater than 1.5; of these, the expression of 19 genes was up-regulated while five genes exhibited negative regulation. To expand our understanding of the HrpL regulon and to elucidate direct versus indirect hrpL-mediated effects on gene expression, the genome of E. amylovora ATCC 49946 was examined in silico using a hidden Markov model assembled from known Erwinia spp. hrp promoters. This technique identified 21 putative type III novel hrp promoters; of these, 8+ were validated with quantitative polymerase chain reaction based on expression analyses. In total, hrpL-regulated genes encode all known components of the hrp T3SS and 5 putative type III effectors. Eight genes displayed apparent indirect hrpL regulation suggesting that the hrpL regulon is connected to downstream signaling networks. Construction of deletion mutants of three novel hrpL-regulated genes has resulted in the identification of additional virulence factors in E. amylovora as well as mutants displaying abnormal motility and biofilm phenotypes.
2012-03-28 | E-TABM-1137 | biostudies-arrayexpress
Project description:Genome-wide identification of Hfq-regulated small RNAs in the bacterial pathogen Erwinia amylovora
| PRJNA232821 | ENA
Project description:Microarray analysis was used to identify genes that were controlled by AmyR in minimal and on immature pear fruits. Consistent with amylovoran production, an inverse correlation was observed between amyR expression and the expression level of amylovoran biosynthetic genes in liquid media. Interestingly, over-expression of AmyR suppressed the expression of type III secretion system genes including hrpA, hrpN and dspEF after pear fruit infection. Consistent with levan production and swarming motility, levasucrase and flagellar genes were both down-regulated both in the amyR mutant and over-expression strains in liquid media. Together, our results suggest that AmyR plays an important role in regulating bacterial exopolysaccharide production and virulence in E. amylovora. A total of 14 samples were analyzed in two conditions: For the in vitro condition (MBMA medium + 1% sorbitol), Erwinia amylovora wild type strain (2 replicates); E. amylovora amyR mutant strain (3 replicates); E. amylovora amyR over-expression strain (3 replicates); For the in vivo condition (on wounded immature pear fruits), Erwinia amylovora wild type strain (2 replicates); E. amylovora amyR mutant strain (2 replicates); E. amylovora amyR over-expression strain (2 replicates).
2013-01-01 | E-GEOD-37064 | biostudies-arrayexpress
Project description:We conducted genome-wide microarray analyses to determine the regulons of RcsB and RcsC in liquid medium and, for the first time, on immature pear fruit. Our array analyses identified a total of 648 genes differentially regulated by the RcsCB in vitro and in vivo. Consistent with our previous findings, RcsB acts as a positive regulator in both conditions, while RcsC positively controls amylovoran biosynthetic gene expression in vivo, but negatively in vitro. Besides amylovoran biosynthesis and regulatory genes, cell wall and cell envelope (membrane) as well as regulatory genes were the major components of the RcsBC regulon, including many novel genes. In addition, we have also demonstrated that transcripts of rcsA, rcsC and rcsD genes, but not rcsB gene, were up-regulated when grown in minimal medium or after infection of pear fruits compared to LB medium. Furthermore, a hidden Markov model (HMM) has predicted 60 genes with candidate RcsB binding site in the intergenic regions of the E. amylovora ATCC 49946 genome and 18 (28) of them were identified in the microarray assay. Based on our findings, a working model has been proposed to illustrate how the Rcs phosphorelay system regulates virulence gene expression in E. amylovora. A total of 12 samples were analyzed in two conditions: For in vitro condition (MBMA medium + 1% sorbitol), Erwinia amylovora wild type strain (2 replicates); E. amylovora rcsB mutant strain (2 replicates); E. amylovora rcsC mutant strain (2 replicates): For in vivo condition (on wounded immature pear fruits), Erwinia amylovora wild type strain (2 replicates); E. amylovora rcsB mutant strain (2 replicates); E. amylovora rcsC mutant strain (2 replicates).
2012-02-18 | E-GEOD-30751 | biostudies-arrayexpress
Project description:ra05-02_erwinia - erwinia - Identification of Arabidopsis genes regulataed by Erwinia amylovora and of a subset of Arabiddopsis genes regulated by the type three secretion system of Erwinia amylovora. Keywords: normal vs disease comparison
2007-08-09 | GSE8701 | GEO
Project description:We conducted genome-wide microarray analyses to determine the regulons of RcsB and RcsC in liquid medium and, for the first time, on immature pear fruit. Our array analyses identified a total of 648 genes differentially regulated by the RcsCB in vitro and in vivo. Consistent with our previous findings, RcsB acts as a positive regulator in both conditions, while RcsC positively controls amylovoran biosynthetic gene expression in vivo, but negatively in vitro. Besides amylovoran biosynthesis and regulatory genes, cell wall and cell envelope (membrane) as well as regulatory genes were the major components of the RcsBC regulon, including many novel genes. In addition, we have also demonstrated that transcripts of rcsA, rcsC and rcsD genes, but not rcsB gene, were up-regulated when grown in minimal medium or after infection of pear fruits compared to LB medium. Furthermore, a hidden Markov model (HMM) has predicted 60 genes with candidate RcsB binding site in the intergenic regions of the E. amylovora ATCC 49946 genome and 18 (28) of them were identified in the microarray assay. Based on our findings, a working model has been proposed to illustrate how the Rcs phosphorelay system regulates virulence gene expression in E. amylovora.
2012-02-18 | GSE30751 | GEO
Project description:This RNA-seq analysis examined the global effect of RpoN in E. amylovora under the T3SS-inducing condition. The rpoN mutant showed differential expression of 8% genes in the genome, which include significant down-regulation of T3SS genes.
2021-12-02 | GSE162090 | GEO
Project description:Arabidopsis seedling were exposed in co-culture to E. amylovora mVOC and data show that mVOCs promote plant growth and early responses
2023-04-04 | GSE223760 | GEO