Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Escherichia coli proteome upon sudden carbon starvation

ABSTRACT: We studied the proteome changes in Escherichia coli growing in rich media, and compared the changes between exponential phase cells and those underwent sudden carbon starvations.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Escherichia Coli

SUBMITTER: Handuo Shi

LAB HEAD: Kerwyn Casey Huang

PROVIDER: PXD024151 | Pride | 2021-03-09

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	e033784.raw	Raw
	e033784_Proteins.xlsx	Xlsx
	e033788.raw	Raw
	e033792.raw	Raw
	e033796.raw	Raw

Items per page:

1 - 5 of 6

Similar Datasets

Escherichia coli proteome during outgrowth from stationary phase

Project description:We studied the proteomic dynamics of Escherichia coli cells exiting stationary phase and identified unique dynamics for the proteins.

2021-01-22 | PXD023729 | Pride

METTL21C methylates Alanine tRNA synthetase at lysine 943 in muscle tissue

Project description:Protein lysine methylation is a common post-translational modification (PTM) detected throughout the human proteome that plays important roles in diverse biological processes. In the human genome, there are greater than one hundred known and candidate protein lysine methyltransferases (PKMTs), many with important links to human disease. METTL21C (methyltransferase-like protein 21C) is a PKMT implicated in muscle biology and reported to methylate VCP (valosin-containing protein/p97) and HSPA8 (heat shock 70kDa protein 8). However, a clear in vitro methyltransferase activity for METTL21C is yet to be demonstrated. Thus, whether METTL21C is indeed an active enzyme that directly methylates substrate/s is unclear. Here, we use an unbiased biochemical-based screening assay coupled to mass spectrometry to identify Alanine-tRNA-Synthetase 1 (AARS1) as a direct substrate of METTL21C. METTL21C catalyzes mono-, di- and tri-methylation of lysine 943 of AARS1 (AARS1-K943me) in vitro and in vivo. In vitro methylation of AARS1 by METTL21C is independent of ATP or tRNA molecules. In contrast to AARS1, and in conflict with previous reports, we do not detect METTL21C methylation activity on VCP and HSPA8. Depletion of METTL21C in METTL21C-expressing cells leads to depletion of AARS1-K943 methylation. Finally, METTL2C is almost exclusively expressed in muscle tissue, and accordingly we detect the METTL21C-catalyzed methylation event of AARS1 in mouse skeletal muscle tissue. Together, our work identifies AARS1 as a bona fide substrate of METTL21C and suggests a role for the METTL21C-AARS1 axis in the regulation of protein synthesis in muscle tissue. In addition, our study describes a straightforward protocol for elucidating physiologic substrates of little characterized or uncharacterized PKMTs

2020-07-02 | PXD019886 | Pride

Phosphoproteomics of Arabidopsis flg22 treated nuclear samples

Project description:To study the effect of microbe-associated molecular pattern (MAMP) treatment (flg22) on the phosphorylation of nuclear proteins, we treated Arabidopsis plants with flg22 and after isolation of nuclear proteins, we enriched for phosphopeptides and then carried out LC-MS/MS analyses. We used statistical analysis tools to identify differentially phosphorylated proteins in response to MAMP treatment in the mock and treated samples.

2022-02-28 | PXD008403 | Pride

BIGenomics_Agilent_15k_templates

Project description:Hybridization of ligation probes to a zipcode (tag) microarray. The purpose of the experiment was to establish functionality and target specificity of the ligation probes by using pools of synthetic templates with all of the probes. The templates are 80-mer synthetic dsDNA molecules, each specific for a single probe. Each probe is a ssDNA molecule containing target recognition sequences, PCR primer binding sequences and a unique tag sequence. If a matching target sequence is present in the mixture, the probes is ligated into a circular molecule, which can be PCR amplified and hybrized on a microarray harbouring complementary tag sequences.

2012-02-24 | E-MEXP-3538 | biostudies-arrayexpress

Using Shewanella baltica ecotypes as a model for transcriptional variation

Project description:Assessment of individual whole cell transcriptional variation among closely related bacterial ecotypes Here we used 4 replicates each containing 3 independent biological replicates as well as dye swaps per each replicate. We hybridized in a two color format but analyzed in a one color format.

2012-04-30 | E-GEOD-37672 | biostudies-arrayexpress

PglL enzymes of Burkholderia species are serine preferring oligosaccharidetransferases which targets conserved proteins and sites across the genus -DsbA1 analysis

Project description:Glycosylation analysis of DsbA1 proteins expressed in Burkholderia cenocepacia strains

2021-07-21 | PXD023955 | Pride

Effect of the IRE1a-XBP1 pathway inhibition during T helper 2 differentiation

Project description:The purpose of the study was to examine the role of the IRE1a-XBP1 pathway during Th2 lymphocyte activation and differentiation. In vitro Th2 cells were treated with 4μ8c, a drug that specifically inhibits IRE1a endonuclease activity, and transcriptomes were compared.

2018-07-20 | E-MTAB-6894 | biostudies-arrayexpress

Genome-wide consequences of compromised NMD and their relavence for variable clinical phenotype of patients with UPF3B mutations [CNV]

Project description:Nonsense-mediated mRNA decay (NMD) surveillance pathways are best known to be involved in the degradation of mRNA with premature termination codons (PTCs). More recent studies demonstrate that the role of NMD pathways goes well beyond the degradation of PTC containing mRNA, into the regulation of cell function and thus normal development. We have taken advantage of the availability of naturally occurring loss of function mutations in the UPF3B gene, a major component of the exon junction complex (EJC), to inquire about genome-wide consequences of compromised NMD. We identify that about 5% of the lymphoblastoid cell transcriptome is directly or indirectly impacted upon in patients with UPF3B mutations with minimal effect on alternative splicing. We identify UPF3A-NMD as a likely, major modifier of the UPF3B patient phenotype through variable UPF3A protein stabilisation. Among the most consistently deregulated direct targets of UPF3B-NMD we identify the ARHGAP24 as the most likely gene implicated in the neuronal phenotype of UPF3B patients. To assess the impact of UPF3B-NMD deficiency on human transcriptome, we sequenced polyA RNA extracted from lymphoblastoid cell lines of patients (n=4) and controls (n=2). We complemented the analysis using Affymetrix Human Exon 1.0 St array using total RNA of the same cell line from patients (n=5, 3 of whom were also sequenced) and controls (n=5). Moreover, we overlapped identified differently expressed genes with copy number variation data of the patients, obtained using Illumina Human Omniexpress chip, to exclude possible false positive.

2011-11-01 | E-GEOD-27412 | biostudies-arrayexpress

5'-RACE-Seq analysis of Salmonella hilD and leuO promoters' response to adjacent transcription

Project description:Gene silencing by nucleoid-associated protein H-NS is sensitive to neighbouring transcription. This effect does not require neighbouring transcription to elongate into the silenced region. Here we measured how activating transcription of a tetRA cassette positioned upstream of either hilD or leuO promoters of Salmonella affected the activity of these promoters. The tetRA cassette included a strong Rho-independent transcription terminator at the 3' end of tetA. Transcription of the cassette was activated with anhydrotetracycline (AHTc). The activities of hilD and leuO promoters were measured upon performing template-switching reverse transcription follwed by semi-quantitative PCR and Illumina high-throughput sequencing.

2024-10-19 | E-MTAB-13482 | biostudies-arrayexpress

PglL enzymes of Burkholderia species are serine preferring oligosaccharidetransferases which targets conserved proteins and sites across the genus -DsbA1 analysis of Burkholderia humptydooensis MSMB43 and Burkholderia ubonensis MSMB22

Project description:Glycosylation analysis of DsbA1 proteins expressed in Burkholderia humptydooensis MSMB43 and Burkholderia ubonensis MSMB22

2021-07-21 | PXD024056 | Pride