Substrate Targeting in the Ubiquitin System

e-amino group of lysine residues in substrate proteins. In many cases, this ubiquitination complex catalyzes the formation of a polyubiquitin chain on the substrate. Jeffrey D. Laney and Mark Hochstrasser* University of Chicago Department of Biochemistry and Despite this fairly well-characterized enzymatic pathMolecular Biology way for ubiquitin conjugation, how proteins are selected Chicago, Illinois 60637 for their ultimate demise is only beginning to be clarified. This process must be highly specific, since short-lived proteins have to be identified and differentiated from Ubiquitin, named for its expression in a wide variety of the numerous stable polypeptides that coexist in the tissues and organisms, is extraordinarily well conserved cell and sometimes even in the same protein complex. in creatures as diverse as yeast and man. Perhaps it is Degradation of substrates by the ubiquitin system apnot surprising then that the proteolytic system involving pears to be mediated by specific degradation signals, ubiquitin plays a central role in the control of many basic which are sequence or structural features of the subcellular processes. In addition to degrading damaged, strate that are required for rapid proteolysis. In addition misfolded, or misassembled proteins, the ubiquitin systo providing a ubiquitinatable lysine residue(s), these tem targets many naturally short-lived proteins, includsignals contain elements that are targeted directly by ing transcription factors, cell growth modulators, signal the ubiquitination apparatus, which in most cases is transducers, and cell cycle proteins. A requisite step expected to be a specific E2/E3 complex. In this minirefor the degradation of these substrates is the covalent view, we highlight recent findings on the specific recogattachment of ubiquitin. Targeted proteins are often nition of several physiological substrates of the ubiquitin modified by polymers of ubiquitin, which triggers their system, emphasizing and contrasting the substrate rapid destruction by a large, complex protease, the 26S characteristics that are recognized by the ubiquitin-conproteasome (Hershko and Ciechanover, 1998). jugating machinery. We also consider how the associaThe 76–amino acid ubiquitin polypeptide is conjution of these degradation signals with their respective gated to proteins via a reversible isopeptide linkage ubiquitination complexes might be regulated. Ubiquibetween the carboxy-terminus of ubiquitin and lysine tination of cell cycle regulators is discussed in the acside chains in the target protein. Attachment of ubiquitin companying minireview (Koepp et al., 1999). to its substrates is mediated by a conserved cascade Phosphorylation-Dependent Degradation Signals of enzymatic reactions. The pathway is initiated by the The transcription factor NF-kB, a central player in imATP-dependent activation of ubiquitin’s C terminus by mune and inflammatory responses, is activated by the ubiquitin-activating enzyme (E1). A concerted, two-step ubiquitin-proteasome pathway. In quiescent cells, NFreaction results in a high-energy thioester linkage bekB is held in a latent state in the cytoplasm in a complex tween ubiquitin and E1. Through a thioester transfer with a member of the IkB family of inhibitors, such that reaction, the ubiquitin is then passed to a ubiquitinthe NF-kB nuclear localization signal (NLS) is occluded. conjugating enzyme (E2). These enzymes function with In response to external stimuli, IkB is degraded in a the E3 ubiquitin–protein ligases to attach ubiquitin to the ubiquitin-dependent manner, allowing nuclear translocation of NF-kB, which leads to a variety of transcriptional responses (reviewed by Ghosh et al., 1998). * To whom correspondence should be addressed (e-mail: hoc1@ midway.uchicago.edu). The following model has emerged for the signal-