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Cited by 65RNA and protein synthesis mechanismsAdvanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and Applications

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Measuring the dynamics of E. coli ribosome biogenesis using pulse-labeling and quantitative mass spectrometry

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Chen, Stephen S, Sperling, Edit, Silverman, Josh M, Davis, Joseph H, Williamson, James R·2012·Molecular BioSystems
DOI 10.1039/c2mb25310kPMC PMC3501348
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Abstract

The ribosome is an essential organelle responsible for cellular protein synthesis. Until recently, the study of ribosome assembly has been largely limited to in vitro assays, with few attempts to reconcile these results with the more complex ribosome biogenesis process inside the living cell. Here, we characterize the ribosome synthesis and assembly pathway for each of the E. coli ribosomal protein (r-protein) in vivo using a stable isotope pulse-labeling timecourse. Isotope incorporation into assembled ribosomes was measured by quantitative mass spectrometry (qMS) and fit using steady-state flux models. Most r-proteins exhibit precursor pools ranging in size from 0% to 7% of completed ribosomes, and the sizes of these individual r-protein pools correlate well with the order of r-protein binding in vitro. Additionally, we observe anomalously large precursor pools for specific r-proteins with known extra-ribosomal functions, as well as three r-proteins that apparently turnover during steady-state growth. Taken together, this highly precise, time-dependent proteomic qMS approach should prove useful in future studies of ribosome biogenesis and could be easily extended to explore other complex biological processes in a cellular context.

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  • Roughly 5% of ribosomal proteins are not ribosome-associated per ribosomal protein.

    “We chose 25 proteins because it has been reported that roughly 5% of ribosomal proteins are not ribosome-associated per ribosomal protein.73”

    From Bringing the genetically minimal cell to life on a computer in 4D (2026) · cites this paper as [73]

    The Discussion (page unavailable) reports precursor pools of up to 7% for many E. coli ribosomal proteins, so the paper supports the existence of proteins outside completed ribosomes. It does not establish that roughly 5% of each ribosomal protein is not ribosome-associated: pool sizes vary, and the measured pools include proteins bound to ribosome assembly intermediates as well as free proteins. (LLM, conf=0.85)

    Experimental — accuracy not yet measured

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Metadata

Authors
Chen, S. S., Sperling, E., Silverman, J. M., Davis, J. H., & Williamson, J. R.
Affiliations
Scripps Research Institute (US)
Corresponding author
Williamson, James R
ORCID
Venue
Molecular BioSystems
Publisher
Oxford University Press (OUP)
Published
2012-10-09
Volume
8
Issue
12
Pages
3325-3334
ISSN
  • 1742-2051 (ISSN-L)
  • 1742-206X
DOI
10.1039/c2mb25310k
PMC
PMC3501348
OpenAlex
W2115336799
Cited by
65
References
0
Citations by year
2026: 3 · 2025: 8 · 2024: 6 · 2023: 7 · 2022: 4 · 2021: 7 · 2020: 4 · 2019: 3 · 2018: 3 · 2017: 1 · 2016: 5 · 2015: 6 · 2014: 5 · 2013: 2 · 2012: 1
FWCI
1.80
Type
journal article
Language
en
Open access
Licence
academic.oup.com/pages/standard-publication-reuse-rights (vor)
Locations
  • Molecular BioSystems (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
Funders
National Institute of General Medical Sciences (R37GM053757)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
  • Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
Keywords
ribosome biogenesis, ribosomal proteins, Escherichia coli, ribosome assembly, precursor pool, quantitative mass spectrometry
MeSH terms
Escherichia coli, Nitrogen Isotopes, Ribosomal Proteins, Ribosomes, RNA, Ribosomal, Mass Spectrometry, Escherichia coli Proteins, Proteomics, Ribosome Subunits, Small, Bacterial, Ribosome Subunits, Large, Bacterial

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