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
8 postdoctoral fellows, 3 graduate student

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 35 components, 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, 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. Ubp6 can be regulated independently of other proteasome subunits, thus altering the nature of the proteasome’s activity. Interestingly, it is under the control of ubiquitin via a transcriptional mechanism that remains to be fully described.

A related problem is how ubiquitin-conjugates and ubiquitin-like proteins 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, such as Rad23, Dsk2, and Ddi1. Rad23-like proteins, which mediate the indirect pathway of recognition, are not only ubiquitin-like proteins also ubiquitin chain binding proteins, thus when they dock onto proteasomes they deliver ubiquitin conjugates. We don’t understand why multiple pathways of conjugate recognition are used or the basis for their selectivity. Two neighboring proteasome subunits serve as receptors for the reversibly-bound factors that assist in proteasome function. Together they form a scaffold that arranges Rad23, Ubp6, and Hul5 in proximity to one another on the proteasome. Interestingly, each of these associated proteins is active on multiubiquitin chains, serving either to bind, disassemble, or extend chains.

References:

• Hanna, J., Hathaway, N.A., Tone, Y., Elsasser, S., Kirkpatrick, D.S., Leggett, D.S., Crosas, B., Gygi, S.P., King, R.W., and Finley, D. (2006) Deubiquitinating enzyme Ubp6 functions noncatalytically to delay proteasomal degradation. Cell 127, 99-111.
• Crosas, B., Hanna, J., Kirkpatrick, D.S., Zhang, D.P., Tone, Y., Hathaway, N.A., Buecker, C., Leggett, D.S., Schmidt, M., King, R.W., Gygi, S.P., and Daniel Finley. (2006) Ubiquitin chain remodeling at the proteasome regulates protein degradation. Cell 127, 1401-1413.
• Hanna, J., Meides, A., Zhang, D.P., , and Finley, D. (2007) A ubiquitin stress response induces altered proteasome composition. Cell 129, 747-760.