Dataset Information

Protein synthesis rate is the predominant regulator of protein expression during differentiation

ABSTRACT: The protein expression changes was measured at five time points (Exp1: 0, 12, 24 h; Exp2: 6, 12, 48 h) in differentiating THP-1 cell (human) cells and at three time points(0, 12, 24 h) in differentiating C2C12 cells(mouse), using two triple, or one triple Stable isotope labeling by amino acids in cell culture (SILAC) experiment, respectively. These measurements were compared to the relative synthesis and degradation rates in both proliferating and differentiating cells. All measurements were performed in biological triplicates. Sample processing: The lysate was boiled in 1 % deoxycholate, before being separated by SDS-PAGE and/or in-solution digested to peptides and separated by isoelectric focusing (IEF). Finally we measured the synthesis and degradation rates of macromolecular sub-complexes as they eluted from a size exclusion chromatography (SEC) column. Here the cells were lysed by douncing, macromolecular complexes concentrated on a 100 kDa molecular weight cut-off filter, before being fractionated by HPLC-SEC into 48 fractions. The fractions were subsequently individually in solution-digested and analyzed by LC-MS/MS. As a general rule it seems that protein expression is largely controlled by changes in the relative synthesis rate, whereas the relative degradation rate of the majority of proteins stays constant. In these data, we also observe that the proteins in defined sub-structures of larger protein complexes tend to have highly correlated synthesis and degradation rates but that this does not necessarily extend to the holo-complex. Data analysis: Raw MS files from an LTQ-Orbitrap or LTQ-Orbitrap-Velos were analyzed by MaxQuant, MS/MS spectra were searched against Uniprot (proteomes) human 21/6/2011 or mouse 20/4/2012 by the Andromeda search engine. For identification, the false discovery rate (FDR) was set to 0.01 on the protein and on the peptide levels.

INSTRUMENT(S): LTQ Orbitrap, LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (human) Mus Musculus (mouse)

SUBMITTER: Anders Kristensen

LAB HEAD: Anders Kristensen

PROVIDER: PXD000328 | Pride | 2013-09-10

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	AK_C2C12_Diff_Exp3_01.raw	Raw
	AK_C2C12_Diff_Exp3_02.raw	Raw
	AK_C2C12_Diff_Exp3_03.raw	Raw
	AK_C2C12_Diff_Exp3_04.raw	Raw
	AK_C2C12_Diff_Exp3_05_repeat.raw	Raw

Items per page:

1 - 5 of 446

Publications

Protein synthesis rate is the predominant regulator of protein expression during differentiation.

Kristensen Anders R AR Gsponer Joerg J Foster Leonard J LJ

Molecular systems biology 20130101

External perturbations, by forcing cells to adapt to a new environment, often elicit large-scale changes in gene expression resulting in an altered proteome that improves the cell's fitness in the new conditions. Steady-state levels of a proteome depend on transcription, the levels of transcripts, translation and protein degradation but system-level contribution that each of these processes make to the final protein expression change has yet to be explored. We therefore applied a systems biology ...[more]

PMID: 24045637

Similar Datasets

Project description:Bacterial adaptation involves extensive cellular reorganization. In particular, growth rate adjustments are associated with substantial modifications of gene expression and mRNA abundance. In this work we aimed to assess the role of mRNA degradation during such variations. A genome-wide transcriptomic-based method was used to determine mRNA half-lives. The model bacterium Lactococcus lactis was used and five growth rates were studied in continuous cultures under isoleucine-limitation and in batch cultures during the adaptation to the isoleucine starvation. During continuous isoleucine-limited growth, the mRNAs of different genes had different half-lives. The stability of most of the transcripts was not constant, and increased as the growth rate decreased. This half-life diversity was analyzed to investigate determinants of mRNA stability. The concentration, length, codon adaptation index and secondary structures of mRNAs were found to contribute to the regulation of mRNA stability in these conditions. However, the growth rate was, by far, the most influential determinant. The respective influences of mRNA degradation and transcription on the regulation of intra-cellular transcript concentration were estimated. The role of degradation on mRNA homeostasis was clearly evidenced: for more than 90 % of the mRNAs studied during continuous isoleucine-limited growth of L. lactis, degradation was antagonistic to transcription. Although both transcription and degradation had, opposite effects,, the mRNA changes in response to growth rate were driven by transcription. Interestingly, degradation control increased during the dynamic adaptation of bacteria as the growth rate reduced due to progressive isoleucine starvation in batch cultures. This work shows that mRNA decay differs between gene transcripts and according to the growth rate. It demonstrates that mRNA degradation is an important regulatory process involved in bacterial adaptation. However, its impact on the regulation of mRNA levels is smaller than that of transcription in the conditions studied. In the study presented here mRNA stabilities were analyzed at 5 growth rates. For each growth rate mRNA levels were measured in a time course experiment following rifampicin addition. At least 12 time points per growth rate are available, including 3 replicates of the zero.