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

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

PROVIDER: PRJNA505809 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8200060.fastq.gz	Fastqsanger.gz
	SRR8200070.fastq.gz	Fastqsanger.gz
	SRR8200080_1.fastq.gz	Fastqsanger.gz
	SRR8200080_2.fastq.gz	Fastqsanger.gz
	SRR8200061.fastq.gz	Fastqsanger.gz

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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.

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Chidamide used in MM cell line [ChIP-seq]

Project description:Chidamide used in MM cell line [ChIP-seq]

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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.

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C. perfringens 13 strain: growth with 1 mM homocysteine vs growth with 0.5 mM cystine

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ChIP-seq and RNA-seq analyses in human multiple myeloma cell line MM.1S

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