BBS Faculty Member - Daniel Finley

Daniel Finley

Department of Cell Biology

Harvard Medical School
Building C1, Room 404
240 Longwood Avenue
Boston, MA 02115
Tel: 617-432-3492
Fax: 617-432-1144
Lab Members: 7 postdoctoral fellows, 3 graduate students
Visit my lab page here.

The lab’s main interest is the proteasome, the most intricate enzyme of the ubiquitin pathway and a key regulator of cellular function. Although it has over 33 subunits, the proteasome is very amenable to biochemistry—it is abundant, stable, and easy to purify and assay. Using yeast genetics we can manipulate its structure with relative freedom. Some of the questions we are interested in are, how does the proteasome recognize its substrates, how does it coordinate deubiquitination with degradation, how does it assemble, and how does unfold and translocate the substrate.

An important finding from the lab was that the proteasome as it had been studied in different labs for several decades is missing a variety of key factors, since routine purifications strip them off. One is a deubiquitinating enzyme, Ubp6 (known in mammals as Usp14). This is a powerful inhibitor of the proteasome. Ubp6 functions noncatalytically to delay the degradation of ubiquitinated substrate proteins. While it inhibits degradation, Ubp6 gradually deubiquitinates the target protein. With time, deubiquitination proceeds towards completion, and the substrate loses its chain and degradation is irreversibly inhibited. With Randy King, we identified small-molecule inhibitors of Usp14 from humans, which penetrate cells and allow for enhanced degradation of many proteins, including toxic proteins involved in various diseases. Another proteasome-associated factor is Hul5, a ubiquitin ligase. Progressive deubiquitination of the substrate by Ubp6 is antagonized by Hul5. Thus, ubiquitin chains are in a dynamic state on the proteasome, and these chain dynamics regulate substrate selection by the proteasome.

A related problem is how ubiquitin-conjugates are recognized by the proteasome. We find that ubiquitin conjugates are recognized both by specific integral subunits of the proteasome and by other proteins that associate reversibly with the proteasome via ubiquitin-like domains. So far five distinct ubiquitin receptors are known, but genetic analysis indicates that this is not the complete complement. We are trying to identify new receptors and better understand why substrate recognition by the proteasome involves so many factors.

The proteasome is divided into a 19-subunit regulatory particle (RP) and a 28-subunit core particle (CP). Six distinct ATPases (the Rpt proteins) form a ring complex within the RP and link it to the CP. We recently showed that the C-termini of several of the Rpts play a critical role in assembly of the RP. We also identified three new chaperone proteins that assist in RP assembly by binding near to the Rpt C-termini. The chaperones appear to prevent the RP-CP interaction at specific sites until the proper time has come for each specific assembly event.

Last Update: 8/5/2015


For a complete listing of publications click here.



Roelofs J, Park S, Haas W, Tian G, McAllister FE, Huo Y, Lee , Zhang F, Shi Y, Gygy SP and Finley D. (2009) Chaperone-mediated pathway of proteasome regulatory particle assembly. Nature 459, 861-865 (2009).

Lee, B.H., Lee M.J., Park, S., Oh, D.C., Elsasser, S., Chen, P.C., Gartner, C., Dimova, N., Hanna, J., Gygi, S.P., Wilson, S.M., King, R.W., Finley, D. Enhancement of proteasome activity by a small-molecule inhibitor of Usp14.
Nature 467, 179-184 (2010).

Park, S., Li, X., Kim, H. K., Singh, C. R., Tian, G., Hoyt, M. A., Lovell, S., Battaile, K. P., Zolkiewski, M., Coffino, P., Roelofs, J., Cheng, Y., and Finley, D. (2013) Reconfiguration of the proteasome during chaperone-mediated assembly.
Nature 497, 512-516 (2013).

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