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Faculty Alexander Amerik
Assistant Professor of Genetics and Developmental Biology
amerik@uchc.edu
Areas of Interest:
Our research focuses on the role of the ubiquitin system in protein
degradation and sorting. Conjugation to ubiquitin is an obligatory step
for protein degradation in eukaryotes. Precise control of protein
breakdown by the ubiquitin system is crucial for numerous cellular
processes including cell cycle progression, cell growth and
proliferation, signal transduction, and transcription. This system has
been implicated in several forms of malignancy, in the pathogenesis of
several genetic diseases, in immune surveillance/viral pathogenesis, and
in chronic degenerative disorders of the nervous system.
Ubiquitination is a reversible process. Ubiquitin is a stable protein
and, therefore, it has to be recycled by the action of DUBs prior to the
degradation of ubiquitin-protein conjugates. Many DUBs have been
recently identified in eukaryotic organisms. However, relatively little
is known about their physiological functions or natural substrates.
Potentially, DUBs may act as negative and positive regulators of the
ubiquitin system. In addition to ubiquitin recylcing, they are involved
in processing of ubiquitin precursors, in proofreading of protein
ubiquitination and in disassembly of inhibitory ubiquitin chains.
We use a simple eukaryote Saccharomyces cerevisiae as a model system
because it provides the possibility, at a level not yet available in any
other eukaryotic organism, of both genetic manipulation and detailed
biochemical analysis. Given the high degree of conservation of
fundamental metabolic systems between yeast and higher eukaryotes in
general, the results of our research will provide important insights
into selective protein degradation in other eukaryotes as well. Our
long-term goal is to identify and to characterize particular members of
the yeast DUB family that are responsible for each step of ubiquitin
homeostasis in the eukaryotic cell.
Lab Rotation Projects:
Analysis of the yeast deubiquitinating enzymes*
#1 - Affinity purification of the yeast protein complexes
containing deubiquitinating enzyme Doa4.
Doa4 is a critical player in ubiquitin homeostasis in the yeast
Saccharomyces cerevisiae. We have found that Doa4 is involved in
ubiquitin recycling at the 26S proteasome and at the cytoplasmic face of
the late endosome. We believe that the enzymatic activity of Doa4 must
be thoroughly regulated. Otherwise, uncontrolled deubiquitination may
have critical consequences for eukaryotic cell. Conceivably, regulation
of Doa4 occurs at the levels of interaction with protein cofactors. The
major goal of this project is to identify Doa4 partners in yeast. The
results will be important for understanding the mechanistic details of
how Doa4 functions in vivo.
#2 – Analysis of the molecular basis for genetic interaction
between mutations in deubiquitinating enzyme Doa4and class E vacuolar
protein sorting factors.
Inactivation of the class E vacuolar protein factors leads to
efficient suppression of doa4 mutant phenotypes. To determine the
mechanisms of this suppression, we plan to conduct a mutant screen based
on the mini-Tn3 transposon-mutagenized library. We expect that this
approach will identify deubiquitinating enzymes that are involved, along
with Doa4, in membrane protein trafficking in yeast.
*Deubiquitinating enzymes are highly specific proteases that remove
ubiquitin (a small protein that modifies substrate proteins) from
ubiquitin-protein conjugates and are responsible for processing of
ubiquitin precursors.
Amerik
Lab Page
Selected Publications:
Amerik, AY, Hochstrasser, M. Mechanism and function of
deubiquitinating enzymes. Biochem. et Biophys. Atca., (in press).
Amerik, AY, Akhtar, N., Hochstrasser, M. Two conserved motifs are
essential for interaction of the Doa4 deubiquitinating enzyme with the
late endosome. (manuscript in preparation).
Amerik, AY, Hochstrasser, M. 2004. The Saccharomyces cerevisiae
deubiquitinating enzyme Doa4. In handbook of proteolytic enzymes, 2nd
edition (Barrett, AJ, Rawlings, ND, Woessner, JF eds) London: Academic
Press.
Amerik, AY, Li, SJ, Hochstrasser, M. 2000. Analysis of the
deubiquitinating enzymes of the yeast Saccharomyces cerevisiae. Biol
Chem. Sep-Oct;381(9-10):981-92.
Amerik AY, Nowak J, Swaminathan S, Hochstrasser M. 2000. The Doa4
deubiquitinating enzyme is functionally linked to the vacuolar
protein-sorting and endocytic pathways. Mol Biol Cell.
Oct;11(10):3365-80. |
