Bacterial protease Lon is a site-specific DNA-binding protein

The product of the Escherichia coli lon gene is the ATP-dependent Lon protease. Lon contributes to the regulation of several important cellular functions, including radiation resistance, cell division, filamentation, capsular polysaccharide production, lysogeny of certain bacteriophages, and proteolytic degradation of certain regulatory and abnormal proteins. Lon homologues are also found in several widely divergent bacteria, as well as in the mitochondria of yeast and humans. E. coli Lon has long been known to bind to DNA, but this interaction has not been further characterized and has generally been assumed to be nonspecific. We now demonstrate that E. coli Lon can bind to a TG-rich DNA promoter element in a sequence-specific manner. This finding is based on the results of experiments employing SouthWestern blotting, protein purification, "shift-shift" electrophoretic mobility shift assays, electrophoretic mobility shift assays using in vitro transcribed and translated Lon, and DNase footprinting. Site-specific DNA binding is likely to be an additional important biochemical characteristic of the multifaceted Lon protease.