Evidence map›Paper›PMID 26147956›Full record

ArticleJournal of proteome research2015

Identification of Salmonella Typhimurium Deubiquitinase SseL Substrates by Immunoaffinity Enrichment and Quantitative Proteomic Analysis.

Ernesto S Nakayasu, Michael A Sydor, Roslyn N Brown, Ryan L Sontag, Tiago J P Sobreira, Gordon W Slysz, Daniel R Humphrys, Tatiana Skarina, Olena Onoprienko, Rosa Di Leo and 7 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of proteome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

7 citing papers in PubMed.

  1. Article
  2. Article
  3. Targeting E3 Ubiquitin Ligases and Deubiquitinases in Ciliopathy and Cancer.International journal of molecular sciences · 2020
    Review
  4. Review
  5. Resolving the Complexity of Ubiquitin Networks.Frontiers in molecular biosciences · 2020
    Review
  6. Infection and immunity · 2019
    Article
  7. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

17 authors.

Ernesto S NakayasuBiological Science Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States.
Michael A SydorBiological Science Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States.
Roslyn N BrownBiological Science Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States.
Ryan L SontagBiological Science Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States.
Tiago J P SobreiraNational Center for Research in Energy and Materials, National Laboratory for Biosciences (LNBio) , Campinas, Sao Paulo 13083-970, Brazil.
Gordon W SlyszBiological Science Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States.
Daniel R HumphrysBiological Science Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States.
Tatiana SkarinaDepartment of Chemical Engineering and Applied Chemistry, Banting and Best Department of Medical Research, Midwest Centre for Structural Genomics, University of Toronto , Toronto, Ontario M5G 1L6, Canada.
Olena OnoprienkoDepartment of Chemical Engineering and Applied Chemistry, Banting and Best Department of Medical Research, Midwest Centre for Structural Genomics, University of Toronto , Toronto, Ontario M5G 1L6, Canada.
Rosa Di LeoDepartment of Chemical Engineering and Applied Chemistry, Banting and Best Department of Medical Research, Midwest Centre for Structural Genomics, University of Toronto , Toronto, Ontario M5G 1L6, Canada.
Brooke L Deatherage KaiserBiological Science Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States.
Jie LiDepartment of Molecular Microbiology & Immunology, Oregon Health & Science University , Portland, Oregon 97239, United States.
Charles AnsongBiological Science Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States.
Eric D CambronneDepartment of Molecular Microbiology & Immunology, Oregon Health & Science University , Portland, Oregon 97239, United States.
Richard D SmithBiological Science Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States.
Alexei SavchenkoDepartment of Chemical Engineering and Applied Chemistry, Banting and Best Department of Medical Research, Midwest Centre for Structural Genomics, University of Toronto , Toronto, Ontario M5G 1L6, Canada.
Joshua N AdkinsBiological Science Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States.

Funding

Midwest Center for Structural GenomicsU54GM094585 · NIGMS · UNIVERSITY OF CHICAGO · PI MINOR, WLADEK · 2010 to 2014
$33.7M
Equipment Supplement Request for a Research Resource for Ultra-sensitive High Throughput ProteomicsP41GM103493 · NIGMS · BATTELLE PACIFIC NORTHWEST LABORATORIES · PI SMITH, RICHARD D · 2012 to 2022
$22.6M
Consortia for High-Throughput-Enabled Structural Biology Partnerships (U01)U01GM094623 · NIGMS · BATTELLE PACIFIC NORTHWEST LABORATORIES · PI ADKINS, JOSHUA N. · 2010 to 2014
$5.2M
Type IV Secretion Determinants in Effector Proteins of Coxiella burnetiiR21AI088275 · NIAID · OREGON HEALTH & SCIENCE UNIVERSITY · PI CAMBRONNE, ERIC D · 2010 to 2011
$422k
NIAID NIH HHS R21 AI088275NIGMS NIH HHS GM094585NIGMS NIH HHS GM094623NIGMS NIH HHS P41 GM103493NIGMS NIH HHS P41 GM103493-10NIGMS NIH HHS U01 GM094623NIGMS NIH HHS U54 GM094585
6 · The paper itself

Abstract

Ubiquitination is a key protein post-translational modification that regulates many important cellular pathways and whose levels are regulated by equilibrium between the activities of ubiquitin ligases and deubiquitinases. Here, we present a method to identify specific deubiquitinase substrates based on treatment of cell lysates with recombinant enzymes, immunoaffinity purification, and global quantitative proteomic analysis. As a model system to identify substrates, we used a virulence-related deubiquitinase, SseL, secreted by Salmonella enterica serovar Typhimurium into host cells. Using this approach, two SseL substrates were identified in the RAW 264.7 murine macrophage-like cell line, S100A6 and heterogeneous nuclear ribonuclear protein K, in addition to the previously reported K63-linked ubiquitin chains. These substrates were further validated by a combination of enzymatic and binding assays. This method can be used for the systematic identification of substrates of deubiquitinases from other organisms and applied to study their functions in physiology and disease.

Indexed as

AnimalsBacterial ProteinsCell LineImmunoassayMass SpectrometryMiceProtein Interaction MappingProtein Processing, Post-TranslationalProteomicsSalmonella typhimuriumUbiquitinationUbiquitin-Specific ProteasesBacterial ProteinsUbiquitin-Specific Proteasesdeubiquitinasemass spectrometrypost-translational modificationsubstrate identificationUbiquitination

Identifiers

PMID26147956
PMCPMC4561012

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.