SILAC analysis of <i>Escherichia coli</i> proteome during progression of growth from exponential to prolonged stationary phase

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ABSTRACT

The expression level of individual proteins varies markedly during the progression of the growth phase in bacteria. A set of proteins was quantified in Escherichia coli total proteome during 14 days of batch cultivation using pulse stable isotope labeled amino acids in cell culture (SILAC)-based quantitative mass spectrometry.

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Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips.

Juri Rappsilber, Matthias Mann, Yasushi Ishihama (2007)

Mass spectrometry (MS)-based proteomics measures peptides derived from proteins by proteolytic cleavage. Before performing the analysis by matrix-assisted laser desorption/ionization-tandem mass spectrometry (MALDI-MS/MS), nanoelectrospray-MS/MS (NanoES-MS/MS) or liquid chromatography-MS/MS (LC-MS/MS), the peptide mixtures need to be cleaned, concentrated and often selectively enriched or pre-fractionated, for which we employ simple, self-made and extremely economical stop-and-go-extraction tips (StageTips). StageTips are ordinary pipette tips containing very small disks made of beads with reversed phase, cation-exchange or anion-exchange surfaces embedded in a Teflon mesh. The fixed nature of the beads allows flexible combination of disks with different surfaces to obtain multi-functional tips. Disks containing different surface functionalities and loose beads such as titania and zirconia for phosphopeptide enrichment can be combined. Incorporation into an automated workflow has also been demonstrated. Desalting and concentration takes approximately 5 min while fractionation or enrichment takes approximately 30 min.

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Culture medium for enterobacteria.

F C Neidhardt, P L Bloch, D F Smith (1974)

A new minimal medium for enterobacteria has been developed. It supports growth of Escherichia coli and Salmonella typhimurium at rates comparable to those of any of the traditional media that have high phosphate concentrations, but each of the macronutrients (phosphate, sulfate, and nitrogen) is present at a sufficiently low level to permit isotopic labeling. Buffering capacity is provided by an organic dipolar ion, morpholinopropane sulfonate, which has a desirable pK (7.2) and no apparent inhibitory effect on growth. The medium has been developed with the objectives of (i) providing reproducibility of chemical composition, (ii) meeting the experimentally determined nutritional needs of the cell, (iii) avoiding an unnecessary excess of the major ionic species, (iv) facilitating the adjustment of the levels of individual ionic species, both for isotopic labeling and for nutritional studies, (v) supplying a complete array of micronutrients, (vi) setting a particular ion as the crop-limiting factor when the carbon and energy source is in excess, and (vii) providing maximal convenience in the manufacture and storage of the medium.

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The quantitative and condition-dependent Escherichia coli proteome

Alexander R. Schmidt, Karl Kochanowski, Silke R Vedelaar … (2015)

Measuring precise concentrations of proteins can provide insights into biological processes. Here, we use efficient protein extraction and sample fractionation and state-of-the-art quantitative mass spectrometry techniques to generate a comprehensive, condition-dependent protein abundance map of Escherichia coli. We measure cellular protein concentrations for 55% of predicted E. coli genes (>2300 proteins) under 22 different experimental conditions and identify methylation and N-terminal protein acetylations previously not known to be prevalent in bacteria. We uncover system-wide proteome allocation, expression regulation, and post-translational adaptations. These data provide a valuable resource for the systems biology and broader E. coli research communities.

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Author and article information

Contributors

Kaspar Reier:

ORCID: https://orcid.org/0000-0001-5484-3909

Jaanus Remme:

ORCID: https://orcid.org/0000-0002-4011-6580

Jennifer Geddes-McAlister: Role: Editor

Journal

Journal ID (nlm-ta): Microbiol Resour Announc

Journal ID (iso-abbrev): Microbiol Resour Announc

Journal ID (publisher-id): mra

Title: Microbiology Resource Announcements

Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )

ISSN (Electronic): 2576-098X

Publication date (Electronic, collection): June 2024

Publication date (Electronic, pub): 23 April 2024

Publication date PMC-release: 23 April 2024

Volume: 13

Issue: 6

Electronic Location Identifier: e00042-24

Affiliations

[1 ]Institute of Molecular and Cell Biology, University of Tartu; , Tartu, Estonia

University of Guelph; , Guelph, Ontario, Canada

Author notes

Address correspondence to Kaspar Reier, Kaspar.Reier@ 123456ut.ee

Address correspondence to Jaanus Remme, jremme@ 123456ut.ee

The authors declare no conflict of interest.

Author information

Kaspar Reier https://orcid.org/0000-0001-5484-3909

Jaanus Remme https://orcid.org/0000-0002-4011-6580

Article

Publisher ID: 00042-24 Publisher ID: mra.00042-24

DOI: 10.1128/mra.00042-24

PMC ID: 11237494

PubMed ID: 38651856

SO-VID: 86d6b5ed-4b80-41d5-b9ad-1686077d95f4

License:

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

History

Date received : 15 January 2024

Date accepted : 05 April 2024

Page count

supplementary-material: 0, authors: 3, Figures: 1, References: 6, Pages: 3, Words: 1170

Funding

Funded by: Eesti Teadusagentuur (ETAg);

Award ID: PUT PRG 1179

Award Recipient : Jaanus Remme

Custom metadata

cover-date June 2024

Keywords: escherichia coli,stationary phase,proteome,silac

Data availability:

Keywords: escherichia coli, stationary phase, proteome, silac

SILAC analysis of Escherichia coli proteome during progression of growth from exponential to prolonged stationary phase

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ABSTRACT

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Most cited references 6

Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips.

Culture medium for enterobacteria.

The quantitative and condition-dependent Escherichia coli proteome

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