Dataset Information

The response of the Escherichia coli proteome to deuteration and minimal media

ABSTRACT: Substitution of hydrogen for deuterium strongly affects biological systems. While higher eukaryotes, such as plants and mammals, hardly survive >30% deuterium content of water and nutrients, many microorganisms can grow on fully deuterated media albeit at reduced rates. Due to the large relative mass change, H/D replacement leads to pronounced changes in chemical reaction rates and equilibria. Very little is known how these physico-chemical effects influence cellular life at the systems level. Here we have followed the adaptation of a large part of the E. coli proteome from growth on a protonated full medium, over a protonated minimal to a completely deuterated minimal medium. More than 1800 proteins could be quantified under all conditions and several hundreds show strong regulation in both adaptation processes. As expected, the adaption to minimal medium mostly upregulates amino acid synthesis and sugar metabolism. In contrast, deuteration causes a very wide response over many cell function categories. No morphological effects are apparent under light and electron microscopy. Most of the regulated proteins have enzymatic functions involving hydrogen transfer reactions. This indicates that kinetic isotope effects and not changes in biomolecular stability are the dominant mechanisms that affect cellular function under deuteration.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Escherichia Coli

TISSUE(S): Permanent Cell Line Cell, Cell Culture

SUBMITTER: Alexander Schmidt

LAB HEAD: Alexander Schmidt

PROVIDER: PXD009736 | Pride | 2020-05-26

REPOSITORIES: Pride

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Publications

Deuterium induces a distinctive <i>Escherichia coli</i> proteome that correlates with the reduction in growth rate.

Opitz Christian C Ahrné Erik E Goldie Kenneth N KN Schmidt Alexander A Grzesiek Stephan S

The Journal of biological chemistry 20181213 7

Substitution of protium (H) for deuterium (D) strongly affects biological systems. Whereas higher eukaryotes such as plants and mammals hardly survive a deuterium content of >30%, many microorganisms can grow on fully deuterated media, albeit at reduced rates. Very little is known about how the H/D replacement influences life at the systems level. Here, we used MS-based analysis to follow the adaptation of a large part of the <i>Escherichia coli</i> proteome from growth on a protonated full medi ...[more]

PMID: 30545941

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Project description:Collagen deposition is a key process during idiopathic pulmonary fibrosis (IPF); however, little is known about the dynamics of collagen formation during disease development. Tissue samples of early stages of human disease are not readily available and it is difficult to identify changes in collagen content, since standard collagen analysis does not distinguish between 'old' and 'new' collagen. Therefore, the current study aimed to (i) investigate the dynamics of new collagen formation in mice using bleomycin-induced lung fibrosis in which newly synthesized collagen was labelled with deuterated water and (ii) use this information to identify genes and processes correlated to new collagen formation from gene expression analysis. Lung fibrosis was induced in female C57BL/6 mice by bleomycin instillation and sacrificed. Animals were sacrificed at 1 to 5 weeks after fibrosis induction. Collagen synthesized during the week before sacrifice was labelled with deuterium by providing mice with deuterated drinking water. After sacrifice, lung tissue was collected for microarray analysis, determination of new collagen formation, and histology. Deuterated water labelling showed a strong increase in new collagen formation already during the first week after fibrosis induction and a complete return to baseline at five weeks. Correlation of new collagen formation data with gene expression data revealed fibrosis specific processes, of which proliferation was an unexpected one. This was confirmed by measuring cell proliferation and collagen synthesis simultaneously using deuterated water incorporation. Furthermore, new collagen formation strongly correlated with gene expression of e.g. elastin, tenascin C, MMP-14, lysyl oxidase, and type V collagen. These data demonstrate, using a novel combination of technologies, that proliferation and extracellular matrix production are correlated to the core process of fibrosis, i.e. the formation of new collagen. In addition, it identified genes directly correlated to fibrosis, thus providing more insight into the aetiology of IPF. Total RNA was obtained from mouse lungs at timepoint 0 as a control (n = 7) or timepoints 1 (n = 7), 2 (n = 6), 3 (n = 6), 4 (n = 6) or 5 (n = 6) weeks after bleomycin-instillation to induce lung fibrosis.

Dataset Information

The response of the Escherichia coli proteome to deuteration and minimal media

Publications

Deuterium induces a distinctive <i>Escherichia coli</i> proteome that correlates with the reduction in growth rate.

Similar Datasets

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