Understanding the mechanism of protein processing by the proteasomePublic Deposited
The ubiquitin-proteasome system degrades regulatory proteins and thereby controls a broad range of cellular processes such as the cell cycle, DNA-repair, gene transcription and signal transduction. The proteasome typically degrades its substrates completely into small peptides. However, biological exceptions do occur. For example, the activity of a handful of transcriptional factors, such as mammalian NF-?B, Drosophila melanogaster Cubitus interruptus and its vertebrate homolog Gli3, and yeast Spt23 and Mga2, are regulated through partial protein degradation by the proteasome. Here I have identified and characterized a novel signal in the substrate proteins that causes this processing. The minimum signal consists of a simple sequence stretch preceding a tightly folded domain in the direction of proteasome movement. The strength of the processing signal depends on the complexity of the simple sequence regardless of identity of amino acid, the resistance of the folded domain to unraveling by the proteasome, and an appropriate spacing between the simple sequence and folded domain. We show that two unrelated transcription factors, Cubitus interruptus and NF- ?B, utilize this mechanism to undergo partial degradation by the proteasome in vivo. In the Gli family of proteins, the processing signal was only identified in Gli3, but not in Gli1 and Gli2, which may explain the distinct processing events in the Gli protein family. Therefore, these findings suggest that the mechanism is conserved evolutionarily and that processing signals may be widespread in regulatory proteins. To further assess how widely processing is utilized as a regulatory method for the proteasome in signal transduction in the cell, I have carried out a large-scale screen of protein databases using bioinformatics as an approach. Among the newly identified examples of processing, we further analyzed the processing of transcription factor Smad1. We found, in a similar manner, the processing signal in Smad1 leads to the formation of a N-terminally truncated Smad1 fragment including the MH2 domain and part of the linker region. The processing depends on the ubiqutin-proteasome system. The processed Smad1 fragment represses the BMP signaling in Xenopus embryo and human cells. I am currently investigating the mechanism by which the Smad1 processing antagonizes the BMP signaling. Protein processing greatly expands the functional roles of the proteasome in cell signaling. Whether the processing is only restricted to transcription factors or it's a more general regulatory method for the proteasome than currently appreciated is worth exploring in the future.