Dataset Information

Proteomics and constraint-based modelling reveal enzyme kinetic properties of C. reinhardtii on a genome-scale

ABSTRACT: Here we generated protein abundance data, covering between 2337 and 3708 proteins, from Chlamydomonas reinhardtii cells grown in various experiments and employed them with constraint-based metabolic models to estimate in vivo maximum apparent turnover numbers for this model organism.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Escherichia Coli

TISSUE(S): Photosynthetic Cell

SUBMITTER: David Zimmer

LAB HEAD: Zoran Nikoloski

PROVIDER: PXD037599 | Pride | 2023-08-01

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	20211216MS231TMqcond001.mzML_25.qpsm	Mzml
	20211216MS231TMqcond001.wiff	Wiff
	20211216MS231TMqcond001.wiff.scan	Wiff
	20211216MS231TMqcond002.mzML_24.qpsm	Mzml
	20211216MS231TMqcond002.wiff	Wiff

Items per page:

1 - 5 of 100

Similar Datasets

Project description:Alga-derived lipids represent an attractive potential source of biofuels. However, lipid accumulation in algae is a stress response tightly coupled to growth arrest, thereby imposing a major limitation on productivity. To identify master regulators of lipid accumulation and decipher the regulation of lipid biosynthetic pathway, we performed an integrative chromatin signature and transcriptomic analysis in the alga Chlamydomonas reinhardtii. Genome-wide histone modification profiling revealed remarkable differences in functional chromatin states between algae and higher eukaryotes and uncovered regulatory components at the core of lipid accumulation pathways. We identified the transcription factor PSR1 as a pivotal master switch that triggers cytosolic lipid hyper-accumulation an order of magnitude higher than stress regimens have achieved. Dissection of the PSR1 target network corroborates its central role in coordinating multiple stress responses. The comprehensive maps of functional chromatin signatures in a major clade of eukaryotic life and the discovery of a central regulator of algal lipid metabolism will facilitate targeted engineering strategies in microalgae. 1. Genome-wide H3K4me3 time series profiling (at 0 hr, 10 min, 30 min, 1 hr, 2hr, 6 hr, 8 hr, 24 hr and 48 hr after nitrogen starvation) was performed to determine time point to capture maximal chromatin changes. 2. Genome-wide H3K4me3, H3K27ac, H3K9me3, H3K27me3, H3K36me3 and Pol II profiling were performed at 0 hr, 1 hr after nitrogen starvation and 1 hr after sulfur starvation to determine chromatin signatures. Genome-wide H3K4me2 profiling was performed at 0 hr before starvation. 3. Transcriptome time series profiling (at 0 hr, 10 min, 30 min, 1 hr, 2hr, 6 hr, 8 hr, 24 hr and 48 hr after nitrogen and sulfur starvation separately) for chromatin signature characterization and integrative analysis. 4. Genome-wide PSR1 binding profiling was performed with polyclonal antibody against PSR1 peptide A region and PSR1 peptide B region individually. (At 30 min and 1 hr after nitrogen starvation, and 1 hr, 2 hr and 6 hr after sulfur starvation.) Please note that the following reference genome and gene models used in these experiments are linked below; C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz reference_gene_model.gtf.gz These are based off Phytozome (http://www.phytozome.net/) which does not provide access to earlier version data.

Dataset Information

Proteomics and constraint-based modelling reveal enzyme kinetic properties of C. reinhardtii on a genome-scale

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets