Senior Research Scientist/Joint Faculty, ProfessorOffice: MRB 273Phone: 970-492-4117Education: Ph.D., University of California at BerkeleyEmail: Bob.Cohen@Colostate.eduResearch Title: Recognition and metabolism of polyubiquitin protein modifications
Molecular recognition and protein-protein interactions as applied to ubiquitin biochemistry and ubiquitin-proteasome mediated protein degradation.
The ubiquitin system is the major route of regulated intracellular proteolysis in all eukaryotes, and it is responsible for the control of numerous key regulatory proteins. In this pathway, proteins are modified by covalent attachment of ubiquitin, a 76-amino acid protein. Typically, multiple ubiquitins in the form of a polyubiquitin chain are elaborated from one or more lysine sidechains of the target protein. Classically, polyubiquitinated proteins are known to be recognized and degraded by the 26S proteasome, a 2.5 MDa ATP-dependent protease complex. However, depending upon the types of ubiquitin-ubiquitin linkages in the polyubiquitin chain, ubiquitination also can lead to other fates. Thus, mono- or polyubiquitin signals are used in endocytosis and protein trafficking, transcription activation, kinase activation cascades, and chromatin remodeling. Ubiquitin can be removed from conjugates through the action of various deubiquitinating enzymes (DUBs); consequently, many DUBs serve important regulatory functions.
Our research is focused on two areas of ubiquitin biochemistry: (1) assembly and recognition of linkage-specific polyubiquitin conjugates, and (2) the structures, mechanisms, and functions of deubiquitinating enzymes. Our experimental approaches range from protein biochemistry and biophysical studies to cell biology and yeast genetics.
Ndoja, A., Cohen, R.E., and Yao, T. (2014) Ubiquitin signals proteolysis-independent stripping of transcription factors. Molecular Cell, in press.
Nakasone, M.A., Livnat-Levanon, N., Glickman, M.H., Cohen, R.E., Fushman, D. (2013) Mixed-linkage ubiquitin chains send mixed messages. Structure 21:727-740.
Sims, J.J., Scavone, F., Cooper, E.M., Kane, L.A., Youle, R.J., Boeke, J.D., and Cohen R.E. (2012) Polyubiquitin-sensor proteins reveal localization and linkage-type dependence of cellular ubiquitin signaling. Nature Methods 9:303-309.
Samara, N.L., Datta, A.B., Berndsen, C.E., Zhang, X., Yao, T., Cohen, R.E., and Wolberger, C. (2010) Structural insights into the assembly and function of the SAGA deubiquitinating module. Science 328:1025-1029.
Carlile, C.M., Pickart, C.M., Matunis, M.J., and Cohen, R.E. (2009) Synthesis of free and proliferating nuclear antigen-bound polyubiquitin chains by the RING E3 ubiquitin ligase Rad5. J. Biol. Chem. 284:29326-29334.
Cooper, E.M., Boeke, J.D., Cohen, R.E. (2010) Specificity of the BRISC deubiquitinating enzyme is not due to selective binding to K63-linked polyubiquitin. J. Biol. Chem. 285: 10344-10352
Sims, J.J., Haririnia, H., Dickinson, B., Fushman, D., and Cohen, R.E. (2009) Avid interactions underlie the K63-linked polyubiquitin binding specificities observed for UBA domains. Nat. Struct. Mol. Biol., 16:883-889.
Sims, J.J., and Cohen, R.E. (2009) Linkage-specific avidity defines the lysine 63-linked polyubiquitin binding preference of Rap80. Molec. Cell, 33:775-783.
Cooper, E.M., Cutcliffe, C., Kristiansen, T.Z., Pandey, A., Pickart, C.M., and Cohen, R.E. (2009) K63-specific deubiquitination by two JAMM/MPN+ complexes: BRISC-associated Brcc36 and proteasomal Poh1. EMBO J, 28:621-631.
Wang, T., Yin, L., Cooper, E.M., Lai, M.Y., Dickey, S., Pickart, C.M., Fushman, D., Wilkinson, K.D., Cohen, R.E.*, and Wolberger, C.* (2009) Evidence for bidentate substrate binding as the basis for the K48 linkage specificity of Otubain 1. J. Molec. Biol., 386:1011-1023. *co-corresponding authors.
Yao, T., Song, L., Jin, J., Cai, Y., Takahashi, H., Swanson, S.K., Washburn, M.P., Florens, L., Conaway, R.C., Cohen, R.E., and Conaway, J.W. (2008) Distinct modes of regulation of the Uch37 deubiquitinating enzyme in the proteasome and the INO80 chromatin remodeling complex. Molec. Cell 31: 909-917.
Winborn, B.J., Travis, S.M., Todi, S.V., Scaglione, K.M., Xu, P., Williams, A.J., Cohen, R.E., Peng, J., and Paulson, H.L. (2008) The deubiquitinating enzyme ataxin-3, a polyglutamine disease protein, edits K63-linkages in mixed linkage ubiquitin chains. J. Biol. Chem. 283: 26436-26443.
Yao, T., Song, L., Xu, W., DeMartino, G.N., Florens, L., Swanson, S.K., Washburn, M.P., Conaway, R.C., Conaway, J.W.*, and Cohen, R.E.* (2006) Proteasome recruitment and activation of the Uch37 deubiquitinating enzyme by Adrm1. Nature Cell Biol. 8:994-1002. *co-corresponding authors.
Hu, M., Li, P., Song, L., Jeffrey, P.D., Chenova, T., Wilkinson, K.D., Cohen, R.E., and Shi, Y. (2005) Structure and mechanisms of the proteasome-associated deubiquitinating enzyme USP14. EMBO J. 24: 3747-3756.
Wicks, S..J., Haros, K., Maillard, M., Song, L., Cohen, R.E., Dijke, P.T., and Chantry, A. (2005) The deubiquitinating enzyme UCH37 interacts with Smads and regulates TGF-beta signalling. Oncogene 24:8080-8084.
Chai, Y., Shoesmith Berke, S., Cohen, R.E., and Paulson, H.L. (2004) Poly-ubiquitin binding by the polyglutamine disease protein ataxin-3 links its normal function to protein surveillance pathways. J. Biol. Chem. 279: 3605-3611.
Hu, M., Li, P., Li, M., Li, W., Yao, T., Wu, J.-W., Gu, W., Cohen, R.E., and Shi, Y. (2002) Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde. Cell 111:1141-1154.
Yao, T., and Cohen, R.E. (2005) Ubiquitin-ovomucoid fusion proteins as model substrates for monitoring degradation and deubiquitination by proteasomes. Methods Enzymol. 398:522-540.
You, J., Cohen, R.E., and Pickart, C.M. (1999) Construct for high level eukaryotic gene expression and low misincorporation of lysine for arginine during expression of pET-encoded proteins in Escherichia coli. BioTechniques 26: 950-954.
Yao, T., and Cohen, R.E. (2000) Cyclization of polyubiquitin by the E2-25K ubiquitin conjugating enzyme. J. Biol. Chem. 275: 36862-36868.
Pickart, C.M., and Cohen, R.E. (2004) Proteasomes and their kin: proteases in the machine age. Nature Reviews Molecular Cell Biology 5:177-187.
Yao, T., and Cohen, R.E. (2002) A cryptic protease couples deubiquitination and degradation by the proteasome. Nature 419: 403-407.
Johnston, S.C., Riddle, S.M., Cohen, R.E.*, and Hill, C.P.* (1999) Structural basis for the specificity of ubiquitin C-terminal hydrolases. EMBO J. 18: 3877-3887. *co-corresponding authors.