# Mechanisms of Cell Regulation and Manipulation by the Ubiquitin System

> **NIH NIH R35** · YALE UNIVERSITY · 2022 · $933,136

## Abstract

Eukaryotic cells have highly conserved enzymatic systems for ligating ubiquitin (Ub) and related
proteins such as SUMO to proteins. The modifications may lead to degradation of the targeted
protein, usually by the proteasome but sometimes also by the lysosome. Ub and SUMO
modifications are highly dynamic due to specialized proteases that remove them. Both modifiers
have many crucial roles, including important contributions to human biology. Substrates include
naturally short-lived regulators and aberrant “protein quality control” (PQC) substrates. Many
human disorders, including neurodegenerative diseases, diabetes, and different cancers, are
associated with abnormalities in the Ub system. The system presents many potential targets for
drug development against a range of diseases.
In this application, the PI proposes to undertake studies on several newly discovered regulatory
mechanisms, which either alter protein modification by Ub or react to changes in the dynamics of
SUMO modification in striking ways. One focus is on the response of Saccharomyces cerevisiae
cells to loss of a key SUMO protease called Ulp2. The cells very quickly generate a specific two-
chromosome aneuploidy, but this is eventually resolved through in vitro evolution over hundreds
of generations. The evolutionary trajectories are related but distinct, and deep sequencing
technologies turn this into a powerful way to study the physiological mechanisms that allow cells
to adapt and flourish even without a seemingly crucial enzyme.
Another new research direction addresses the regulated proteolysis of an essential yeast protein
that controls both proteasome translocation into the nucleus and PQC at the ribosome. Its
degradation is tightly linked to its functional state. Subcellular movements of proteasomes and
their degradation under starvation conditions will also be examined. A final, also new area
addresses Ub system enzymes from endosymbiotic bacteria that infect humans and other
species. One focus is on a deubiquitylating enzyme (DUB) from Orientia, the causative agent of
scrub typhus, a highly lethal disease. Surprisingly, the DUB protein not only cleaves Ub but also
binds tightly to it as well as to clathrin adaptor proteins, small GTPases, and a specific
phospholipid. The many activities in this single polypeptide are proposed to be coordinated in a
way that favors pathogen infection and propagation. Another DUB of great interest is from
Wolbachia, bacteria that infect millions of arthropod species and exploit this unusual DUB to alter
host reproduction and promote their own inheritance. Wolbachia are being deployed as agents
for fighting disease vectors such as the mosquitoes that transmit dengue fever or malaria.

## Key facts

- **NIH application ID:** 10417189
- **Project number:** 5R35GM136325-03
- **Recipient organization:** YALE UNIVERSITY
- **Principal Investigator:** Mark W Hochstrasser
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $933,136
- **Award type:** 5
- **Project period:** 2020-06-01 → 2025-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10417189

## Citation

> US National Institutes of Health, RePORTER application 10417189, Mechanisms of Cell Regulation and Manipulation by the Ubiquitin System (5R35GM136325-03). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10417189. Licensed CC0.

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