Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic characterization of a virulence-deficient phosphatidylcholine-negative Agrobacterium tumefaciens mutant

ABSTRACT: To learn more about the global effects of phosphatidylcholine (PC)-deficiency in A. tumefaciens, we performed transcriptomic studies comparing the wild type and a PC-deficient DpmtA Dpcs mutant. We expanded the number of affected virulence genes and showed that the loss of PC was correlated with altered expression of multiple genes encoding membrane or membrane-associated proteins and proteins which fulfil their function at the membrane. The PC-deficient mutant analyzed in this study is further described in Sonja Klüsener, Stephanie Hacker, Yun-Long Tsai, Julia E. Bandow, Ronald Gust, Erh-Min Lai and Franz Narberhaus. 2010. Proteomic and transcriptomic characterization of a virulence-deficient phosphatidylcholine-negative Agrobacterium tumefaciens mutant.

ORGANISM(S): Agrobacterium fabrum str. C58

PROVIDER: GSE21223 | GEO | 2010/04/07

SECONDARY ACCESSION(S): PRJNA126483

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcriptomic characterization of a virulence-deficient phosphatidylcholine-negative Agrobacterium tumefaciens mutant

Project description:To learn more about the global effects of phosphatidylcholine (PC)-deficiency in A. tumefaciens, we performed transcriptomic studies comparing the wild type and a PC-deficient DpmtA Dpcs mutant. We expanded the number of affected virulence genes and showed that the loss of PC was correlated with altered expression of multiple genes encoding membrane or membrane-associated proteins and proteins which fulfil their function at the membrane. The PC-deficient mutant analyzed in this study is further described in Sonja Klüsener, Stephanie Hacker, Yun-Long Tsai, Julia E. Bandow, Ronald Gust, Erh-Min Lai and Franz Narberhaus. 2010. Proteomic and transcriptomic characterization of a virulence-deficient phosphatidylcholine-negative Agrobacterium tumefaciens mutant. Total RNA was extracted from A. tumefaciens C58 wild-type and PC-deficient mutant cells grown under virulence-induced and non-induced conditions. The 4-plex NimbleGen Gene Expression Array for A. tumefaciens (Design ID 080630) represents 5344 genes and is based on NCBI reference sequences NC_003062, NC_003063, NC_003064 and NC_003065. Each gene is represented by 6 probes (45mer-60mer oligonucleotides), each in two copies on different locations on the array. Three biological replicates for each cultivation condition were analyzed for A. tumefaciens wild-type and PC-deficient mutant strains.

2010-04-07 | E-GEOD-21223 | biostudies-arrayexpress

XB001: Shortening of membrane lipid acyl chains compensates for phosphatidylcholine deficiency in choline‐auxotroph yeast

Project description:Phosphatidylcholine (PC) is an abundant membrane lipid component in most eukaryotes including yeast. PC has been assigned a multitude of functions in addition to that of building block of the lipid bilayer. Here we show that PC is evolvable essential in yeast by isolating suppressor mutants devoid of PC that exhibit robust growth. The requirement for PC is suppressed by monosomy of chromosome XV, or by a point mutation in the ACC1 gene encoding acetyl-CoA carboxylase. Although these two genetic adaptations rewire lipid biosynthesis differently, both decrease Acc1 activity thereby reducing the average acyl chain length. Accordingly, soraphen A, a specific inhibitor of Acc1, rescues a yeast mutant with deficient PC synthesis. In the aneuploid suppressor, up-regulation of lipid synthesis is instrumental to accomplish feed-back inhibition of Acc1 by acyl-CoA produced by the fatty acid synthase (FAS). The results show that yeast regulates acyl chain length by fine-tuning the activities of Acc1 and FAS, and indicate that PC evolved by benefitting the maintenance of membrane fluidity.

2021-08-04 | GSE75725 | GEO

Global consequences of phosphatidylcholine reduction in Bradyrhizobium japonicum

Project description:Analysis of a Bradyrhizobium japonicum pmtA mutant. PmtA catalyzes the first of three consecutive methylation reactions leading to phosphatidylcholine (PC) formation in B. japonicum. Disruption of the pmtA gene results in a significantly reduced PC content causing a defect in symbiosis with the soybean host. This study provides the first insight into global transcriptomic changes of a bacterial phosphatidylcholine biosynthesis mutant. Cells of the pmtA mutant and the wild type were grown to mid-exponential phase in full medium (PSY) under aerobic culture conditions. Keywords: genetic modification

2008-04-17 | GSE11187 | GEO

Global consequences of phosphatidylcholine reduction in Bradyrhizobium japonicum

2008-04-17 | E-GEOD-11187 | biostudies-arrayexpress

Agrobacterium fabrum str. C58

Project description:Transcriptomic characterization of a virulence-deficient phosphatidylcholine-negative Agrobacterium tumefaciens mutant

| PRJNA126483 | ENA

Hepatic Phosphatidylcholine Catabolism Driven by PNPLA7 and PNPLA8 Supplies Endogenous Choline to Replenish the Methionine Cycle with Methyl Groups II

Project description:Choline supplies methyl groups for regeneration of methionine and the methyl donor S-adenosylmethionine in the liver. Here we demonstrate that the catabolism of membrane phosphatidylcholine (PC) into water-soluble glycerophosphocholine (GPC) by the phospholipase/lysophospholipase PNPLA8-PNPLA7 axis enables endogenous choline stored in hepatic PC to be utilized in methyl metabolism. PNPLA7-deficient mice show marked decreases in hepatic GPC, choline, and several metabolites related to the methionine cycle, accompanied by various signs of methionine insufficiency including growth retardation, hypoglycemia, hypolipidemia, increased energy consumption, reduced adiposity, increased FGF21, and an altered epigenetic methylation landscape. Moreover, PNPLA8-deficient mice recapitulate most of these phenotypes. In contrast to wild-type mice fed a methionine/choline-deficient diet, both knockout strains display a decreased hepatic triglyceride likely via reductions of lipogenesis and GPC-derived glycerol flux. Collectively, our findings highlight the biological importance of phospholipid catabolism driven by PNPLA8/PNPLA7 in methyl group flux and triglyceride synthesis in the liver.

2022-11-30 | GSE217136 | GEO

Hepatic Phosphatidylcholine Catabolism Driven by PNPLA7 and PNPLA8 Supplies Endogenous Choline to Replenish the Methionine Cycle with Methyl Groups III

2022-11-30 | GSE217137 | GEO

Hepatic Phosphatidylcholine Catabolism Driven by PNPLA7 and PNPLA8 Supplies Endogenous Choline to Replenish the Methionine Cycle with Methyl Groups I

2022-11-30 | GSE217135 | GEO

Phosphatidylcholine editing is critical to lipid homeostasis in Arabidopsis trigalactosyldiacylglycerol1 mutants

Project description:Lipid remodeling is crucial for plant responses to abiotic stress and metabolic disturbances. A key aspect of this process involves the modification of phosphatidylcholine (PC) acyl chains by lysophosphatidylcholine: acyl-CoA acyltransferases (LPCATs). To understand their role in lipid homeostasis, we studied the trigalactosyldiacylglycerol1 (tgd1) mutant, which exhibits significant increases in fatty acid synthesis and flux through PC due to disrupted inter-organelle lipid trafficking. We discovered that the elevated fatty acid synthesis in tgd1 is due to the posttranslational activation of plastidic acetyl-coenzyme A carboxylase (ACCase). Global transcriptomic profiling revealed 62 significantly upregulated genes in tgd1, with 27 (44%) involved in RNA and DNA modifications, suggesting a role for posttranscriptional mechanisms in adapting to lipid trafficking disruptions. Additionally, transcript levels of LPCATs and several genes regulating ACCase were moderately increased in tgd1. Genetic analysis showed that knocking out LPCAT1 and LPCAT2 was lethal in the tgd1 background. Furthermore, plants homozygous for lpcat2 and heterozygous for lpcat1 in the tgd1 background displayed reduced levels of PC and TAG, along with altered fatty acid compositions. Our findings provide mechanistic insights into fatty acid synthesis regulation and highlight the critical role of LPCATs in maintaining cellular lipid homeostasis when fatty acid production exceeds the cellular demand for membrane lipid synthesis.

2024-09-16 | PXD054661 | Pride

Activation of phosphatidylcholine-cycle enzymes in human epithelial ovarian cancer cells

Project description:Altered phosphatidylcholine (PC) metabolism in epithelial ovarian cancer (EOC) can provide choline-based imaging approaches as powerful tools to improve diagnosis and identify new therapeutic targets. Biochemical, protein and mRNA expression analyses demonstrated that the increase in the major choline-containing metabolite phosphocholine (PCho) in EOC compared with normal and non-tumoral immortalized counterparts (EONT) mainly rely upon: 1) ChoK activation, consistent with higher protein content and increased ChoK? mRNA expression levels; 2) PC-plc activation, consistent with higher, previously reported, protein expression. More limited and variable sources of PCho could derive, in some EOC cells, from activation of Phospholipase D or GPC-pd. Phospholipase A2 activity and isoforms’ expression levels were lower or unchanged in EOC compared with EONT cells. Increased ChoK? mRNA, as well as ChoK and PC-plc protein expression, were also detected in surgical specimens isolated from EOC patients. Overall, we demonstrated that the elevated PCho pool detected in EOC cells primarily resulted from the upregulation/activation of ChoK and PC-plc involved in the biosynthetic and in a degradative pathway of the PC-cycle, respectively. 20 EOC frozen surgical specimens, 8 EOC cell lines and Ovarian Surface Epithelial (OSE) cells (4 different preparations, 3 of them pooled in one sample).

2009-12-07 | E-GEOD-19352 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data