Yaowen Wu: Chemical Biology of Membrane Trafficking and Autophagy

Concept

The foundation of living systems is based on chemical reactions. They are spatiotemporally regulated in response to extra- or intracellular stimuli. Of importance to understand the mechanism of life is the ability to visualize and to perturb these reactions. Chemical tools provide unique means to emulate or modulate biological systems to either investigate the underlying biology or create new function.

In my laboratory, we run both biology-driven and chemistry-driven projects. In the former, we have defined biological questions, which are not readily solved by traditional biological methods. We tackle these problems using novel chemical approaches in combination with biochemical and cell biological methods. In the later, we develop novel chemical tools that can be widely used to investigate biology. These approaches make it possible to reveal new mechanism of biology.


Autophagy

Autophagy is an evolutionarily conserved self-eating process in eukaryotes, mainly involved in elimination of organelles and aggregated proteins. Malfunction of autophagy has been associated with diverse human diseases, including cancer, neurodegeneration, cardiac hypertrophy, and pathogen infection. Formation of double-membrane autophagosome is the key process in autophagy. The regulatory pathways of autophagy and the formation of autophagosome remain the most important questions for understanding autophagy.

Using a combination of cell biology, structural biology and chemical genetic approaches, we have elucidated fundamental mechanisms underlying autophagy. Our laboratory has elaborated a novel mode of action for virulent bacteria (Legionella) against host autophagy. We have identified novel chemotypes for autophagy modulation and new cellular targets involved in new mechanism of autophagy regulation.


Membrane trafficking and small GPTases (G-proteins)

Due to the spatial segregation of intracellular organelles of eukaryotic cells a sophisticated system of vesicular transport is required to ensure the communication between different compartments. Rab GTPases function as key regulators of intracellular vesicular transport. With the help a complex network of Rab regulators and effectors, Rab GTPases regulate these processes through tightly controlled enzymatic GTPase cycle and spatial distribution in cells. We are interested in answering the question of how these complex biological reactions are coordinated and how the malfunction of these processes link to diseases. These questions have been assessed at both the molecular and the cellular level in a quantitative manner.


Protein chemical modification

Labeling proteins with synthetic probes, such as fluorophores, affinity tags, and other functional labels is enormously useful for characterizing protein function in vitro, in live cells, or in whole organisms. Chemical methods have substantially expanded the tools that are can be used to modify proteins. Our work has been focused on preparation of post-translationally modified proteins. These semi-synthetic protein probes have been very useful in the investigation of protein functions in membrane trafficking and autophagy. We are interested in developing new methods for protein modification/labeling. These methodologies have been valuable for visualizing biochemical reactions in living systems and proteomic studies. Such developments not only facilitate the study of the system we are interested but contribute new tools to the larger biological field.


Chemical and chemo-optogenetics

Genetic perturbations by gain or loss of gene function through overexpression, knock-out or knock-down approaches is powerful for biological studies. However, traditional genetic approaches are chronic (hours to days). Consequently, the phenotype may not be detected due to adaptation and the dynamics of phenotypic change cannot be followed. Chemical genetic approaches using small molecules are acute, reversible, conditional and tunable and have been very useful to dissect the complexity of biological regulatory networks. However, many of these compounds have additional off-target effects that may confound elucidation of biological systems in certain contexts. Our laboratory has developed the first bioorthogonal and reversible chemically induced dimerization (CID) system (SLF’-TMP system) for controlling protein function by small molecules in live cells. A photoactivatable CID (pCID) system using photo-caged dimerizer, NovcTMP-Cl, has been established in the lab, which allows superior spatiotemporal control of protein function in live cells. We have developed novel “Molecular Activity Painting (MAP)” strategy by combining pCID with immobilized artificial receptors to enable “painting” of signaling molecules and their activity at micrometer-scale at the plasma membrane. Using photoactivatable dual-chemically induced dimerization (pdCID) system, we developed a Multi-directional Activity Control (MAC) approach to spatiotemporally control cellular signaling and intracellular cargo transport.


Selected recent publications:

Yang A, Pantoom S, Wu YW. (2017) Elucidation of anti-autophagy mechanism of the Legionella effector RavZ using semisynthetic LC3 proteins. eLife pii: e23905.
Chen X, Venkatachalapathy M, Kamps D, Weigel S, Kumar R, Orlich M, Garrecht R, Hirtz M, Niemeyer CM, Wu YW*, Dehmelt L*. (2017) “Molecular Activity Painting”: Switch-like, light-controlled perturbations inside living cells. Angew. Chem. Int. Ed. 56 (21): 5916-5920.
Voss S, Krüger DM, Koch O, Wu YW. (2016) Spatiotemporal imaging of small GTPases activity in live cells. Proc. Natl. Acad. Sci. U. S. A. 113(50):14348-14353.
Liu W, Li F, Chen X, Yi L, Wu YW. (2014) A rapid and fluorogenic TMP-AcBOPDIPY probe for covalent labeling of proteins in live cells. J. Am. Chem. Soc. 136 (12): 4468-71.
Liu P, Calderon A, Konstantinidis G, Hou J, Voss S, Chen X, Li F, Banerjee S, Hoffmann JE, Theiss C, Dehmelt L, Wu YW. (2014) A bioorthogonal small-molecule switch system for controlling protein function in live cells. Angew. Chem. Int. Ed. 53 (38):10049-55.

Full list of publications Group website


Open positions
We are looking for highly motivated postdoctoral or doctoral fellows who have a background of cell biology, biochemistry, chemical biology and synthetic chemistry.
Students are welcome to carry out their bachelor, master thesis in our lab.

Publications

Author

Title

Year sorteringsordning

Fulltext

Chen, Xi
Venkatachalapathy, Muthukumaran
Dehmelt, Leif; et al.

Multidirectional Activity Control of Cellular Processes by a Versatile Chemo-optogenetic Approach
Angewandte Chemie International Edition, 57(37): 11993-11997

2018

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Chen, Xi
Wu, Yao-Wen

Tunable and Photoswitchable Chemically Induced Dimerization for Chemo-optogenetic Control of Protein and Organelle Positioning
Angewandte Chemie International Edition, 57(23): 6796-6799

2018

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