Ph.D., 1991, University of Gdansk, Poland
Research Interests
We are broadly interested in the role, function and regulation of the ubiquitin-proteasome system. Our former projects focused on the mechanism by which proteins are recruited for degradation by the 26S proteasome in yeast. We have recently initiated three new research directions that focus on the role of proteasomal proteolysis in 1) autoimmune diseases (type 1 diabetes); 2) protein misfolding diseases (liver disease associated with alpha 1 antitrypsin deficiency); and early antiviral responses (ectromelia virus/primary mouse macrophages). Biochemical and cellular approaches are our primary research tools.
Recent Publications
  • PiZ mouse liver accumulates polyubiquitin conjugates that associate with catalytically active 26S proteasomes.
    Haddock CJ, Blomenkamp K, Gautam M, James J, Mielcarska J, Gogol E, Teckman J, Skowyra D. PLoS One. (2014) 9(9):e106371.
  • Broad utility of an affinity-enrichment strategy for unanchored polyubiquitin chains.
    Strachan J, Shaw B, Tooth D, Krishna VG, de Pozo JC, Hill K, Bennett M, Gautam M, Skowyra D, Jacobson AD, Liu CW, Oldham N, Layfield R. J Proteomics Bioinform. (2013) S7:1-7.
  • Immunoproteasome activation during early antiviral response in mouse pancreatic β-cells by IFNβ: New insights into auto-antigen generation in Type I diabetes?
    Freudenburg W, Gautam M, Chakraborty P, James J, Richards J, et al. J Clin Cell Immunol. (2013) 4(2).
  • Reduction in ATP levels triggers immunoproteasome activation by the 11S (PA28) regulator during early antiviral response mediated by IFNbeta in mouse pancreatic beta-cells.
    Freudenburg W, Gautam M, Chakraborty P, Richards J, Salvatori A, Baldwin A, Schriewer J, Buller M, Corbett J, Skowyra D. PLOS One. (2013) 8(2):e52408.

Full list of publications in PubMed: Skowyra D
Significant Publications as an Independent Investigator

Release of ubiquitin-charged Cdc34-S~Ub from the RING domain is essential for ubiquitination of the SCFCdc4-bound substrate Sic1.

Andrew E Deffenbaugh, K. Matthew Scaglione, Lingxiao Zhang, Johnnie M. Moore, Tione Buranda, Larry A. Sklar, and Dorota Skowyra.

Cell. 114(5):611-622, 2003. (PMID 13678584)

The mechanism of polyubiquitination was initially thought to involve stable interaction between the E2, the E3 and a substrate. Our "hit and run" hypothesis (Figure below) published in Deffenbaugh et al. was the first to propose that, in contrast to stability of the E3-substrate interaction, the process of polyubiquitination involves repeated cycles of interaction between the E2 and the E3. In the same study, we also provided evidence suggesting that a release of ubiquitin-charged Cdc34 E2 from its primary recruitment site on the RING domain of SCFCdc4 could play a role in the process of polyubiquitination.

The "Hit and Run" model for Cdc34 function with SCFCdc4.

ATP hydrolysis-dependent disassembly of the 26S proteasome is part of the catalytic cycle.

Shalon E. Babbitt, Alexi Kiss, Andrew E. Deffenbaugh, Yie-Hwa Chang, Eric Bailly, Hediye Erdjument-Bromage, Paul Tempst, Tione Buranda, Larry A. Sklar, Jennifer Baumler, Edward Gogol, and Dorota Skowyra.

Cell. 121(4):553-565, 2005 (PMID 15907469)

Using the yeast 26S proteasomes co-purified with proteasome-interacting proteins (PIPs), such as polyubiquitinated substrates and the SCF E3 ubiquitin ligase complexes, we showed that the end of substrate proteolysis is linked to an ATP hydrolysis-dependent dissociation and disassembly of the 19S activator, and that this step co-incides with a burst-like release of product peptides. Based on these findings, we proposed the "chew and spew" model for coupling ATP hydrolysis with diassembly of the 26S proteasome (Figure below). This study was the first demonstration that disassembly of the 26S proteasome could be linked to the catalytic cycle.

The "Chew and Spew" model for coupling ATP hydrolysis to disassembly of the 26S proteasome.

Destabilization of binding to cofactors and SCFMet30 is a rate-limiting regulatory step in degradation of polyubiquitinated Met4 by the 26S proteasome.

Srikripa Chandrasekaran, Andrew E. Deffenbaugh, David A. Ford, Eric Bailly, Neal Mathias, and Dorota Skowyra.

Mol. Cell. 24(5):689-699, 2006. (PMID 17157252)

In Chandrasekaran et al., we reported a novel regulatory mechanism in which a substrate polyubiquitinated with the cannonical K48-type of polyubiquitin chain can collaborate with other proteins to temporarily stall its own degradation until receiving a further regulatory signal, This paradigm was established by reconstruction of the SCFMet30-mediated polyubiquitination and proteolysis of Met4, the transcriptional master regulator of genes involved in methionine biosynthesis in yeast (Figure below).

Roadmap highlighting the relationship between the SCFMet30-Met4 interplay and the regulatory schemes involved in sulfur assimilation, oxidative stress and cell division (Chandrasekaran and Skowyra, 2008.