Regulation of protein function by ubiquitination
Aiming to understand how ubiquitinated proteins are selected for degradation and the control of such pathways in physiological contexts.
Why is studying the ubiquitin proteasome system important?
All mammalian cells have to control their protein content to remove damaged proteins and regulate cell growth, function and survival. The major mechanism for controlling intracellular protein levels is through ubiquitination. Key questions forming the basis of our studies are (i) how ubiquitinated proteins are differentially selected for proteasomal degradation, and (ii) how cellular pathways that require ubiquitination are themselves regulated in cells.
How different polyubiquitin chains are decoded
Specificity in the ubiquitin system is generated by the ability of ubiquitin to form eight different polyubiquitin chain linkages. Each type of ubiquitin linkage must be correctly interpreted to facilitate the desired outcome, and ubiquitin binding proteins (UBPs) provide this critical link between chain recognition and cellular fate. We showed that ubiquitin linkage-selective UBPs can distinguish between the two most abundant ubiquitin chains (lysine-48 and lysine-63) and control the degradation of ubiquitinated substrates. We have also recently shown that the proteasome itself can distinguish between different types of lysine-11 linked polyubiquitin chains, dependent on whether they are pure (homotypic) or mixed with other linkages (heterotypic). We are currently using biochemical and genetic approaches to examine the function and physiological importance of other chain-specific UBPs.
How ubiquitin binding proteins regulate protein turnover
We are using forward genetic screens to identify genes required to regulate the degradation of proteins by the proteasome. By the insertion of random mutations into cells expressing proteasome reporters, we can identify genes required for the efficient degradation of these ubiquitinated substrates.
Physiological pathways regulated by ubiquitination
To understand how physiological pathways critically regulated by ubiquitination are themselves controlled, we have focused on the hypoxia response. Using forward genetic screens in human cells we have identified several new regulators of HIF (hypoxia inducible transcription factor) stability. Understanding the mechanisms involved is a current focus of our studies.
Scholz CC, Rodriguez J, Pickel C, Burr S, Fabrizio J, Nolan KA, Spielmann P, Cavadas MAS, Crifo B, Halligan DN, Nathan JA, von Kriegsheim A, Wenger RH, Peet DJ, Cummins EP & Taylor CT. FIH regulates cellular metabolism through hydroxylation of the deubiquitinase OTUB1. Plos Biol. Jan 11; 14 (2016).
Grice GL, Lobb IT, Weekes MP, Gygi SP, Antrobus R & Nathan JA. The Proteasome Distinguishes between Heterotypic and Homotypic Lysine-11-Linked Polyubiquitin Chains. Cell Rep. 12, 545-553 (2015).
Boname JM, Bloor S, Wandel MP, Nathan JA, Antrobus R, Dingwell KS, Thurston TL, Smith DL, Smith JC, Randow F & Lehner PJ. Cleavage by signal peptide peptidase is required for the degradation of selected tail-anchored proteins. J. Cell Biol. 205, 847-862 (2014).
Van den Boomen DJH, Timms RT, Grice GL, Stagg HR, Skødt K, Nathan JA & Lehner PJ. TMEM129 is a Derlin-1 associated ERAD E3 ligase essential for virus-induced degradation of MHC-I. Proc. Natl Acad. Sci USA 111, 11425-1130 (2014).
Nathan JA, Spinnenhirn V, Schmidtke G, Basler M, Groettrup M & Goldberg AL. Immuno- and constitutive proteasomes do not differ in ability to degrade ubiquitinated proteins. Cell 152, 1184–1194 (2013).
Nathan JA, Kim HT, Ting L, Gygi S & Goldberg AL. Why do cell proteins linked to K63-polyubiquitin chains not associate with proteasomes? EMBO J. 32, 552–565 (2013).
Peth A, Nathan JA & Goldberg AL. The ATP costs and time required to degrade ubiquitinated proteins by the 26S proteasome. J. Biol. Chem. 288, 29215–29222 (2013).
Deriziotis P, Andre R, Smith DM, Goold R, Kinghorn KJ, Kristiansen M, Nathan JA, Rosenzweig R, Krutauz D, Glickman MH, Collinge J, Goldberg AL & Tabrizi SJ. Misfolded PrP impairs the UPS by interaction with the 20S proteasome and inhibition of substrate entry. EMBO J. 30, 3065–3077 (2011).