Visual proteomics of the human pathogen Leptospira interrogans
Open accessAbstract
Systems biology conceptualizes biological systems as dynamic networks of interacting elements, whereby functionally important properties are thought to emerge from the structure of such networks. Owing to the ubiquitous role of complexes of interacting proteins in biological systems, their subunit composition and temporal and spatial arrangement within the cell are of particular interest. 'Visual proteomics' attempts to localize individual macromolecular complexes inside of intact cells by template matching reference structures into cryo-electron tomograms. Here we combined quantitative mass spectrometry and cryo-electron tomography to detect, count and localize specific protein complexes in the cytoplasm of the human pathogen Leptospira interrogans. We describe a scoring function for visual proteomics and assess its performance and accuracy under realistic conditions. We discuss current and general limitations of the approach, as well as expected improvements in the future.
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The finding is in good agreement with the volume of the relevant cell types, namely approximately 0.2 μm3 in L. interrogans, and about 30 μm3 in S. cerevisiae and 4000 μm3 in U2OS.
“This finding is furthermore in good agreement with the volume of the relevant cell types, namely ∼0.2 μm3 in L. interrogans (Beck et al, 2009), and about ∼30 μm3 in S. cerevisiae and ∼4000 μm3 in U2OS, (assuming spherical shape and 4 and 20 μm diameter for yeast and U2OS, respectively).”
From The quantitative proteome of a human cell line (2011) · cites this paper as Beck et al, 2009
Those proteins make up the majority of the total protein mass and a considerable fraction of the cytoplasmic volume, while proteins functioning in signaling, protein transport, or regulatory pathways, e.g. transcription factors, comprise a minority of the quantitative proteome.
“Those proteins make up the majority of the total protein mass (Malmstrom et al, 2009) and a considerable fraction of the cytoplasmic volume (Beck et al, 2009), while proteins functioning in signaling, protein transport, or regulatory pathways, e.g. transcription factors, comprise a minority of the quantitative proteome.”
From The quantitative proteome of a human cell line (2011) · cites this paper as Beck et al, 2009
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- Authors
- Beck, M., Malmström, J. A., Lange, V., Schmidt, A., Deutsch, E. W., & Aebersold, R.
- Affiliations
- ETH Zurich (CH)
- Institute for Systems Biology (US)
- University of Zurich (CH)
- Corresponding author
- Aebersold, Ruedi
- Venue
- Nature Methods
- Published
- 2009-10-18
- Volume
- 6
- Issue
- 11
- Pages
- 817-823
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- PMC
- PMC2862215
- OpenAlex
- W2061835758
- Cited by
- 156
- References
- 20
- Citations by year
- 2025: 3 · 2024: 7 · 2023: 2 · 2022: 6 · 2021: 5 · 2020: 7 · 2019: 9 · 2018: 10 · 2017: 15 · 2016: 6 · 2015: 7 · 2014: 5 · 2013: 11 · 2012: 25
- FWCI
- 12.08
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Methods (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Lund University Publications (Lund University) (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Funders
- National Institutes of Health (n01hv28179-12-0-0)
- National Heart, Lung, and Blood Institute (N01 HV028179, N01-HV-28179)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Immunology and Microbiology › Parasitology › Leptospirosis research and findings
- Keywords
- Leptospira interrogans, protein complexes, cryo-electron tomography, template matching, protein complex localization, cytoplasm, scoring functions, pathogenic bacteria, systems biology
- MeSH terms
- Bacterial Proteins, Chromatography, Liquid, Ciprofloxacin, Computer Simulation, Leptospira interrogans, Stress, Physiological, Cryoelectron Microscopy, Proteome, Proteomics, Tandem Mass Spectrometry, Electron Microscope Tomography
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