Cell cycle-controlled clearance of the CcrM DNA methyltransferase by Lon is dependent on DNA-facilitated proteolysis and substrate polar sequestration

Abstract

N6-adenine methylation catalyzed by the DNA methyltransferase CcrM is an essential epigenetic event of the Caulobacter cell cycle. Limiting CcrM to a specific time period during the cell cycle relies on temporal control of ccrM transcription and CcrM proteolysis. We investigated how Lon, a protease from AAA+ superfamily conserved from bacteria to humans, temporally degrades CcrM to maintain differential chromosomal methylation state, thereby regulating transcription factor synthesis and enabling cell cycle progression. We demonstrate that CcrM degradation by Lon requires DNA as an adaptor for robust proteolysis. Lon, a DNA-bound protein, is constitutively active throughout the cell cycle, but allows CcrM mediated DNA methylation only when CcrM is transcribed and translated upon completion of DNA replication. An additional mechanism to limit CcrM activity to a narrow window of the cell cycle is its sequestration to the pole of the progeny stalked cell, which prevents physical contact with DNA-bound Lon. Thus, we have provided evidence for a novel mechanism for substrate selection by the Lon protease, providing robust cell cycle control mediated by DNA methylation.