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The expression profiles of PSPTO_2222 and PSPTO_2222-2223 mutants in MM or KB

ABSTRACT: PSPTO_2222 and PSPTO_2222-2223 deletions mutants were grown in MM or KB, and their expression profiles were analyzed.

ORGANISM(S): Pseudomonas syringae pv. tomato str. DC3000

PROVIDER: GSE15032 | GEO | 2010/12/31

SECONDARY ACCESSION(S): PRJNA114757

REPOSITORIES: GEO

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The expression profiles of PSPTO_2222 and PSPTO_2222-2223 mutants in MM or KB

Project description:PSPTO_2222 and PSPTO_2222-2223 deletions mutants were grown in MM or KB, and their expression profiles were analyzed. 2222MM: PSPTO_2222 mutants cultured in MM. 3/2 MM: PSPTO_2222-2223 deletion mutants cultured in MM. 3-2 kb: PSPTO_2222-2223 deletion mutants cultured in KB. P2KB: PSPTO_2222 mutants cultured in KB.

2010-12-31 | E-GEOD-15032 | biostudies-arrayexpress

Pseudomonas syringae pv. tomato str. DC3000

Project description:The expression profiles of PSPTO_2222 and PSPTO_2222-2223 mutants in MM or KB

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ChIP-seq and RNA-seq for RhpR in KB and MM medium

Project description:Pseudomonas syringae, the leading cause of crop diseases world-wide, uses type III secretion system (T3SS) to invade host plants. Our previous studies demonstrate that two-component system RhpRS enable P. syringae to coordinate T3SS gene expression, which is dependent on the phosphorylation state of RhpR in different environmental conditions. Homologs of RhpRS are distributed in a wide range of bacterial species, indicating a general regulatory mechanism. However, it remains elusive that how RhpRS relies on external signals and phosphorylation state to exercise its regulatory functions. To this end, we performed ChIP-seq assays to identify specific binding sites of RhpR and RhpRD70A in either King’s B (KB, T3SS-inhibiting medium) or minimal medium (MM, T3SS-inducing medium). Through data analysis, we identified 125 KB-dependent binding sites and 188 phosphorylation-dependent binding sites of RhpR. In KB, RhpR directly positively regulated cytochrome c550 production (via ccmA) and alcohol dehydrogenase activity (via adhB), but negatively regulated anthranilate synthase activity (via trpG) and protease activity (via hemB). Besides, phosphorylated RhpR (RhpR-P) directly negatively regulated T3SS (via hrpR and hopR1), swimming motility (via flhA), c-di-GMP level (via PSPPH_2590) and biofilm formation (via algD), while positively regulated twitching motility (via fimA) and lipopolysaccharide production (via PSPPH_2653). Our RNA-seq analyses newly identified 474 and 840 genes that regulated by RhpR in KB and MM respectively. Collectively, the present study revealed that rich nutrient condition allows RhpR to directly regulate the multiple metabolic pathways of P. syringae, while phosphorylation enables RhpR to specifically control virulence and cell envelope. RhpRS governs both virulence and multiple metabolic pathways by tuning its phosphorylation and sensing environmental signals in KB, respectively.

2019-03-01 | GSE122629 | GEO

ChIP-seq and RNA-seq for RhpR in KB and MM medium

Project description:ChIP-seq and RNA-seq for RhpR in KB and MM medium

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NF-kB activation confers a prolonged event-free-survival in newly diagnosed myeloma patients harboring t(4;14) treated with bortezomib.

Project description:NF-kB pathway activation is the hallmark of hematological malignancies. In multiple myeloma (MM), a large variety of genomic alterations leading to either inactivation of repressor such as TRAF3, CYLD or cIAP1/2 or amplification of activators such as CD40 or NIK collectively contribute to frequently deregulate NF-kB signaling. In order to evaluate the prognostic impact of NF-kB mutations in MM, we performed a comprehensive analysis of a panel of newly diagnosed patients with cIAP1/2 biallelic deletion. We found that all patients have dysregulated NF-kB pathway and the majority of them presented t(4;14). Then we analyzed clinical outcome of 37 MM at presentation with t(4;14) and treated with bortezomib according to their NF-kB status. We showed that increase of NF-kB activity confers prolonged event-free survival. Altogether, our data suggest that NF-kB activation resulting from NF-kB mutations (ie cIAP1/2 deletion) or other mechanisms improves outcome of t(4;14)-positive MM treated with bortezomib.

2015-09-15 | GSE31272 | GEO

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Project description:Cellulosimicrobium sp. MM strain:MM Genome sequencing and assembly

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Emticicia sp. MM strain:MM

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RNA expression in KATOIII cells harboring biallelic deletions of the +22.6-kb site, epithelial-specific enchancer of ABO gene

Project description:Wild-type KATOIII cells and their derived mutant clones B3 and B4 harboring biallelic deletions of the +22.6-kb site, located 22.6 kb downstream from the ABO translation start site

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Streptococcus pneumoniae D39 wild-type grown in CDM+10 mM arginine compared to D39 wild type grown in CDM + 0.05 mM arginine

Project description:Comparison of Streptococcus pneumoniae D39 wild-type grown in CDM+10 mM arginine compared to D39 wild type grown in CDM + 0.05 mM arginine to define the genome-wide transcriptional response to arginine. Details described in Kloosterman TG and Kuipers OP. ArgR1 and AhrC Mediate Arginine-Dependent Regulation of Arginine Acquisition- and Virulence Genes in the Human Pathogen Streptococcus pneumoniae. JBC 2011

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mCMV m06 deletion mutants

Project description:mCMV m06 deletion mutants were sequenced and compared for additional deletions.

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