Modification of proteins by ubiquitin (Ub)-like proteins (UBLs) plays an important role in many cellular processes, including cell cycle progression, nuclear transport, and autophagy. Protein modification occurs via UBL-conjugating and -deconjugating enzymes, which presumably exert a regulatory function by determining the conjugation status of the substrate proteins. To target and identify UBL-modifying enzymes, we produced Nedd8, ISG15, and SUMO-1 in Escherichia coli and equipped them with a C-terminal electrophilic trap (vinyl sulfone [VS]) via an intein-based method. These C-terminally modified UBL probes reacted with purified UBL-activating (E1), -conjugating (E2), and -deconjugating enzymes in a covalent fashion. Modified UBLs were radioiodinated and incubated with cell lysates prepared from mouse cell lines and tissues to allow visualization of polypeptides reactive with individual UBL probes. The cell type-and tissue-specific labeling patterns observed for the UBL probes reflect distinct expression profiles of active enzymes, indicating tissuespecific functions of UBLs. We identify Ub C-terminal hydrolase L1 (UCH-L1) and DEN1/NEDP1/SENP8, in addition to UCH-L3, as proteases with specificity for Nedd8. The Ub-specific protease isopeptidase T/USP5 is shown to react with ISG15-VS. Furthermore, we demonstrate that the desumoylation enzyme SuPr-1 can be modified by SUMO-1-VS, a modification that is dependent on the SuPr-1 active-site cysteine. The UBL probes described here will be valuable tools for the further characterization of the enzymatic pathways that govern modification by UBLs.Ubiquitin (Ub) is a conserved 76-amino-acid protein attached posttranslationally to substrate proteins. This conjugation occurs through an isopeptide bond between the C-terminal carboxylate of Ub and the ε-NH 2 of a lysine side chain in the target protein. Conjugation is achieved by the sequential action of an E1 activating enzyme, E2 conjugating enzymes, and E3 ligases (22). The removal of Ub from substrates is carried out by deubiquitinating enzymes. The long-known Ubspecific cysteine protease families of Ub C-terminal hydrolases (UCHs) and Ub-specific processing proteases (UBPs/USPs) were recently joined by a Ub-specific JAMM motif containing metalloprotease and cysteine proteases containing an OTU domain (2,8,13,63,67).Ub-like proteins (UBLs) are a set of small proteins that share with Ub the ability to be conjugated to a lysine residue in a substrate protein (26). Many UBLs are related in sequence to Ub, and a three-dimensional fold similar to that in Ub has been reported for Nedd8 and SUMO (3, 66). The UBLs ISG15 (also called UCRP) and FAT10 resemble two Ub moieties fused in tandem (19, 54). UBLs do not generally appear to be assembled into multimeric chains upon conjugation to substrates, with the possible exception of SUMO-2 and SUMO-3 (62). Like Ub, most UBLs are expressed as inactive precursors, with extensions at the C terminus, which prevent direct conjugation (26) ( Table 1). These precursors must be processed by sp...

Cyclin dependent kinase 5 (cdk5) activity is critical for development and function of the nervous system. Cdk5 activity is dependent on association with the regulators p35 and p39 whose expression is highly regulated in the developing nervous system. We have identified a small 200bp fragment of the p39 promoter that is sufficient for cell type-specific expression in neuronal cells. Mutational analysis revealed that a cluster of predicted binding sites for Sp1, AP-1/CREB/ATF and E box-binding transcription factors is essential for full activity of the p39 promoter. Electrophoretic mobility shift assays revealed that Sp1 and Sp3 bound to sequences required for p39 promoter function and chromatin immunoprecipitation assays confirmed binding of these proteins to the endogenous p39 promoter. Furthermore, depletion of either Sp1 or Sp3 by siRNA reduced expression from the p39 promoter. Our data suggest that the ubiquitously expressed transcription factors Sp1 and Sp3 regulate transcription of the cdk5 regulator p39 in neuronal cells, possibly in cooperation with tissue-specific transcription factors.