Lon and Clp family proteases and chaperones share homologous substrate-recognition domains

Lon protease and members of the Clp family of molecular chaperones and prot ease regulatory subunits contain homologous regions with properties expecte d for substrate-binding domains. Fragments corresponding to these sequences are stably and independently folded for Lon, ClpA, and ClpY. The correspon ding regions from ClpB and ClpX are unstable. All five fragments exhibit di stinct patterns of binding to three proteins that are protease substrates i n vivo: the heat shock transcription factor sigma(32), the SOS mutagenesis protein UmuD, and Are repressor bearing the SsrA degradation tag. Recogniti on of UmuD is mediated through peptide sequences within a 24-residue N term inal region whereas recognition of both sigma(32) and SsrA-tagged Arc requi res sequences at the C terminus. These results indicate that the Lon and Cl p proteases use the same mechanism of substrate discrimination and suggest that these related ATP-dependent bacterial proteases scrutinize accessible or disordered regions of potential substrates for the presence of specific targeting sequences.