PSI Structural Biology Knowledgebase

PSI | Structural Biology Knowledgebase
Header Icons
E-Collection

Related Articles
Families in Gene Neighborhoods
June 2015
Signaling: A Platform for Opposing Functions
May 2015
Nuclear Pore Complex: A Flexible Transporter
February 2015
Nuclear Pore Complex: Higher Resolution of Macromolecules
February 2015
Nuclear Pore Complex: Integrative Approach to Probe Nup133
February 2015
Piecing Together the Nuclear Pore Complex
February 2015
iTRAQing the Ubiquitinome
July 2014
CAAX Endoproteases
August 2013
The Immune System: A Strong Competitor
June 2013
The Immune System: Strand Swapping for T-Cell Inhibition
June 2013
PDZ Domains
April 2013
Protein Interaction Networks: Adding Structure to Protein Networks
April 2013
Protein Interaction Networks: Morph to Assemble
April 2013
Protein Interaction Networks: Reading Between the Lines
April 2013
Protein Interaction Networks: When the Sum Is Greater than the Parts
April 2013
Alpha-Catenin Connections
March 2013
Cytochrome Oxidase
November 2012
Bacterial Phosphotransferase System
October 2012
Solute Channels
September 2012
Budding ensemble
August 2012
The machines behind the spindle assembly checkpoint
June 2012
G Protein-Coupled Receptors
May 2012
Revealing the Nuclear Pore Complex
March 2012
Topping off the proteasome
March 2012
Anchoring's the way
February 2012
Reading out regioselectivity
December 2011
An effective and cooperative dimer
November 2011
PDZ domains: sometimes it takes two
November 2011
Raising a glass to GLIC
August 2011
A2A Adenosine Receptor
May 2011
A growing family
February 2011
FERM-ly bound
February 2011
CXCR4
January 2011
Guard cells pick up the SLAC
December 2010
Zinc Transporter ZntB
July 2010
Zinc Transporter ZntB
July 2010
Importance of extension for integrin
June 2010
Spot protein-protein interactions… fast
March 2010
Alg13 Subunit of N-Acetylglucosamine Transferase
February 2010
Urea transporter
February 2010
Two-component signaling
December 2009
ABA receptor...this time for real?
November 2009
Network coverage
November 2009
Get3 into the groove
October 2009
Guanine Nucleotide Exchange Factor Vav1 and Rho GTPase Rac1
October 2009
GPCR subunits: Separate but not equal
September 2009
Proofreading RNA
July 2009
Ribonuclease and Ribonuclease Inhibitor
April 2009
The elusive helicase
April 2009
Click for cancer-protein interactions
December 2008

Research Themes Protein-protein interactions

iTRAQing the Ubiquitinome

SBKB [doi:10.1038/sbkb.2014.211]
Technical Highlight - July 2014
Short description: An inflammatory signal triggers broad changes to protein ubiquitination and chromatin regulation in immune cells.

Immunofluorescence reveals DBC1 protein degradation in immune cells after inflammatory stimulus, (left) DBC1 in green in the control and (right) following LPS stimulation. Figure courtesy of Joshua Adkins.

Immune cells must respond quickly to invading pathogens. One strategy for rapid regulatory change is to alter post-translational modifications such as ubiquitination across the proteome. Adkins and colleagues (PSI MCSG in partnership with PCSEP) have taken a quantitative proteomics approach to study ubiquitination dynamics in macrophage-like murine cells upon stimulation by bacterial lipopolysaccharide (LPS), a pro-inflammatory elicitor of innate immunity.

The authors used the ubiquitin-binding domain Dsk2-UBA to enrich for modified proteins at four time points within four hours of LPS treatment, corresponding to a window of dynamic regulation assessed by western blot. Proteins were labeled using 8-plex isobaric tags for relative and absolute quantitation (iTRAQ), followed by fractionation and liquid chromatography–tandem mass spectrometry.

They detected 1,057 proteins enriched for pathways in which ubiquitinated proteins are overrepresented. Seventy-eight of those were differentially abundant between time points, among which was the deubiquitinase ataxin-3. Since ataxin-3 activity is known to be regulated by ubiquitination, the authors examined whether its ubiquitination affected the overall deubiquitinase activity of the cell: ataxin-3 activity increased slightly at four hours, linked to an increase in its own ubiquitination level and a decrease in global protein ubiquitination levels. Treating cells with proteasome inhibitor confirmed that deubiquitinases play an important role alongside protein degradation in regulating ubiquitination levels.

Leveraging prior proteomic and microarray time course data from LPS-treated cells, the researchers found proteins that appeared to be degraded after treatment, identified by a drop in protein but not in gene expression levels. An interesting member of this set is deleted in breast cancer 1 (DBC1), a histone deacetylase inhibitor that has been implicated in inflammation response in mice. Immunofluorescence and western blotting revealed that levels of a nuclear form of DBC1 are reduced after LPS treatment, while a truncated cytoplasm version stays constant. Based on proteasome and caspase inhibitor experiments, the researchers suggest a model linking inflammation to chromatin remodeling: LPS causes caspase processing and ubiquitin-mediated degradation of DBC1, which allows for the deacetylation of an acetylated form of histone 4 (H4K12ac).

This work shows that integrating data from large-scale approaches enables the study of both global regulatory patterns and the specific mechanisms of response to an inflammatory signal.

Tal Nawy

References

  1. E.S. Nakayasu et al. Multi-omic data integration links Deleted in Breast Cancer 1 (DBC1) degradation to chromatin remodeling in inflammatory response.
    Mol. Cell. Proteomics. 12, 2136-47 (2013). doi:10.1074/mcp.M112.026138

Structural Biology Knowledgebase ISSN: 1758-1338
Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of Health