Many reagents have been emerged to study the function of specific enzymes in 17 vitro. On the other hand, target specific reagents are scarce or need improvement allowing 18 investigations of the function of individual enzymes in a cellular context. We here report the 19 development of a target-selective fluorescent small-molecule activity-based DUB probe that is 20 active in live cells and whole animals. The probe labels active Ubiquitin Carboxy-terminal 21Hydrolase L1 (UCHL1), also known as neuron-specific protein PGP9.5 (PGP9.5) and 22 parkinson disease 5 (PARK5), a DUB active in neurons that constitutes 1-2% of total brain 23 protein. UCHL1 variants have been linked with the neurodegenerative disorders Parkinson's 24 and Alzheimer's disease. In addition, high levels of UCHL1 also correlate often with cancer 25 and especially metastasis. The function of UCHL1 or its role in cancer and neurodegenerative 26 disease is poorly understood and few UCHL1 specific research tools exist. We show that the 27 reagents reported here are specific for UCHL1 over all other DUBs detectable by competitive 28 activity-based protein profiling and by mass spectrometry. Our probe, which contains a 29 cyanimide reactive moiety, binds to the active-site cysteine residue of UCHL1 irreversibly in 30 an activity-dependent manner. Its use is demonstrated by labelling of UCHL1 both in vitro and 31 in cells. We furthermore show that this probe can report UCHL1 activity during the 32 development of zebrafish embryos. 33 1The Ubiquitin system relies to a great extent on cysteine catalysis. Ubiquitin is a small protein 2 that consists of 76 amino acids that can modify target proteins through lysine residues although 3 it is also occasionally found to modify N-termini as well as cysteine and threonine residues. 1-3 4 Addition of ubiquitin is catalyzed by E1 (2), E2 (~40) and E3 (>600) enzymes in an ATP-5 dependent conjugation reaction by specific combinations of E1, E2 and E3 enzymes and it is 6 reversed by any of ~100 deubiquitylating enzymes (DUBs) in humans. 4, 5 The enzyme 7 Ubiquitin Carboxy-terminal Hydrolase L1 (UCHL1), also known as neuron-specific protein 8 PGP9.5 (PGP9.5) and parkinson disease 5 (PARK5), is a small protease that is thought to 9 remove ubiquitin from small substrates and it belongs to the small family of Ubiquitin C-10 terminal Hydrolases (UCHs). 6
11It is clear that UCHL1 can cleave ubiquitin and that mutation and reduced activity of this 12 enzyme have been associated with neurodegenerative diseases, including Parkinson's and 13 Alzheimer's disease. 7-12 High UCHL1 levels correlate with malignancy and metastasis in many 14 cancers 13, 14 and have also been attributed to cellular stress, although the molecular mechanism 15 of all these processes is unclear. 16 We earlier observed extreme levels of UCHL1 activity in lysates from prostate and lung cancer 17 cells using a ubiquitin-derived activity-based probe that targets all cysteine DUBs. 15 We 18 reasoned that a good cell-permeable activity-based probe that targ...