Biological and Biomedical Science
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Daniel Finley

Department of Cell Biology
Harvard Medical School
Building C1, Room 404
240 Longwood Ave.
Boston, MA 02115
Tel: (617) 432-3492
Fax: (617) 432-1144
Email: daniel_finley@hms.harvard.edu

Web Page: The Finley Web Page
9 postdoctoral fellows, 1 graduate student, 1 research assistant

The lab’s main interest is the ubiquitin-proteasome pathway. Currently, we are focusing on the proteasome, the most intricate enzyme of the 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.

 

We recently found 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. 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. 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 highly 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 biquitin 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 more remain to be identified. We are trying to 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.


 

References:

  • Crosas B, Hanna J, Kirkpatrick DS, Zhang DP, Tone Y, Hathaway NA, Buecker C, Leggett DS, Schmidt M, King RW, Gygi SP, and Finley D. (2006) Ubiquitin chain remodeling at the proteasome regulates protein degradation. Cell 127, 1401-1413.

  • Hanna J, Meides A, Zhang DP, and Finley D. (2007) A ubiquitin stress response is distinct from the proteasome stress response and alters proteasome composition. Cell 129,747-760.

  • Park S, Roelofs J, Kim W, Robert J, Schmidt S, Gygi SP, and Finley D. (2009) Hexameric assembly of the proteasomal ATPases is templated through their C-termini. Nature 459, 866-871.

  • 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.