Phosphoarginine modulates oligomerization and repressor activity of mycobacterial ClpC2

Phosphoarginine (pArg) modifications direct proteins for proteolytic destruction by ClpC1P1P2, an essential mycobacterial protease that has emerged as a promising antibacterial drug target against Mycobacterium tuberculosis . The broader regulatory landscape surrounding pArg is poorly understood. Here, we establish a mechanistic connection between pArg binding and the activity of ClpC2, a non-proteolytic transcriptional repressor with homology to the ClpC1 N-terminal domain. Biophysical studies reveal that ClpC2 forms concentration-dependent higher-order oligomers that bind cooperatively to operator sequences in the clpC2 promoter. A high-resolution crystal structure of the Streptomyces thermoviolaceus ClpC2 C-terminal domain reveals a conserved dimerization interface mediated by a C-terminal helix, which is sterically disrupted by pArg binding. Consequently, we find that binding of pArg, as well as some ClpC1-targeting antibiotics, disrupts ClpC2 oligomerization, dissociates ClpC2 from its operator DNA, and relieves transcriptional repression in vitro . Moreover, comparative analysis of clpC2 promoters with single versus dual operator sites predicts differences in regulatory sensitivity across mycobacterial species. Together, these findings establish ClpC2 as a pArg-responsive sensor capable of mechanistically linking elevated pArg levels to downstream transcriptional regulation.