Dataset Information

Adaptation response to carbon starvation

ABSTRACT: full nutrition control

INSTRUMENT(S): LTQ-Orbitrap

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

SUBMITTER: Waltraud Schulze

LAB HEAD: Waltraud Schulze

PROVIDER: PRD000722 | Pride | 2013-06-19

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	PRIDE_Exp_Complete_Ac_26499.pride.mgf.gz	Mgf
	PRIDE_Exp_Complete_Ac_26499.pride.mztab.gz	Mztab
	PRIDE_Exp_Complete_Ac_26499.xml.gz	Xml
	PRIDE_Exp_Complete_Ac_26500.pride.mgf.gz	Mgf
	PRIDE_Exp_Complete_Ac_26500.pride.mztab.gz	Mztab

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Publications

Proteomics wants cRacker: automated standardized data analysis of LC-MS derived proteomic data.

Zauber Henrik H Schulze Waltraud X WX

Journal of proteome research 20120928 11

The large-scale analysis of thousands of proteins under various experimental conditions or in mutant lines has gained more and more importance in hypothesis-driven scientific research and systems biology in the past years. Quantitative analysis by large scale proteomics using modern mass spectrometry usually results in long lists of peptide ion intensities. The main interest for most researchers, however, is to draw conclusions on the protein level. Postprocessing and combining peptide intensiti ...[more]

PMID: 22978295

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Project description:Mycobacterium tuberculosis was grown in Middlebrook 7H9 medium supplemented with 0.4% glycerol, 0.085% NaCL, 0.5% BSA and 0.05% Tyloxapol in roller bottle culture (2 rpm at 37°C). To induce starvation, exponentially growing bacteria were washed and resuspended in PBS supplemented with 0.025% Tyloxapol. Cultures were harvested at 0h, 12h and 24h after starvation induction. After harvesting and lysis, proteins were extracted, reduced, alkylated, and digested using trypsin. The peptides were analysed in DDA mode on a Thermo LTQ Orbitrap XL. Data analysis: Thermo raw files were converted into mzXML format using ProteoWizard. The acquired MS2 spectra were searched with OMSSA (2.1.9), X!Tandem (CYCLONE, 2010.12.01.1), and MyriMatch (2.1.114) against an Mtb H37Rv protein database (TubercuList v2.3, April 2011) additionally containing reversed sequences of all proteins in the database. Search parameters were as follows: semi-tryptic peptides (proteolytic cleavage after lysine and arginine unless followed by proline) and up to two missed cleavages were allowed, mass tolerance of the precursor ions was set to 20 ppm. Carbamidomethylation at cysteines was set as a fixed modification and oxidation at methionines as a variable modification. The output of the search engine was processed using PeptideProphet and iProphet. Only peptides at a false discovery rate of less than 1% were taken into consideration for further analysis. For MS1 based label-free quantification the openMS v1.8 framework was used as described by (Weisser et al., 2013). Signals were normalised on peptide feature level such that the median signal in each sample is the same. Abundances of the three most intense peptides were averaged to get a protein abundance value. The same peptides were used for protein quantification across all samples and proteins with less than three peptides were included. Associated RNA-seq data have been deposited to EBI ArrayExpress with accession number E-MTAB-1616.

Project description:Filamentous fungi are confronted with changes and limitations of their carbon source during growth in their natural habitats and during industrial applications. To survive life-threatening starvation conditions, carbon from extra- and intracellular resources becomes mobilized to fuel fungal self-propagation. Key to understand the underlying cellular processes is the system-wide analysis of fungal starvation responses in a temporal and spatial resolution. The knowledge deduced is important for the development of optimized industrial production processes. This study describes the physiological, morphological and genome-wide transcriptional changes caused by prolonged carbon starvation during submerged batch cultivation of the filamentous fungus Aspergillus niger. Bioreactor cultivation supported highly reproducible growth conditions and monitoring of physiological parameters. Changes in hyphal growth and morphology were analyzed at distinct cultivation phases using automated image analysis. The Affymetrix GeneChip platform was used to establish genome-wide transcriptional profiles for three selected time points during prolonged carbon starvation. Compared to the exponential growth transcriptome, about 50% (7,292) of all genes displayed differential genes expression during at least one of the starvation time points. Enrichment analysis of Gene Ontology, Pfam domain and KEGG pathway annotations uncovered autophagy and asexual reproduction as major global transcriptional trends. Induced transcription of genes encoding hydrolytic enzymes was accompanied by increased secretion of hydrolases including chitinases, glucanases, proteases and phospholipases as identified by mass spectrometry. This study is the first system-wide analysis of the carbon starvation response in a filamentous fungus. Morphological, transcriptomic and secretomic analyses identified key events important for fungal survival and their chronology. The dataset obtained forms a comprehensive framework for further elucidation of the interrelation and interplay of the individual cellular events involved.