RNase E is the most common RNA decay nuclease in bacteria, setting the global mRNA decay rate and scaffolding formation of the RNA degradosome complex and BR-bodies. To properly set the global mRNA decay rate, RNase E from Escherichia coli and neighboring gamma-proteobacteria were found to autoregulate RNase E levels via the decay of its mRNA9s 59 UTR.  While the 59 UTR is absent from other groups of bacteria in the Rfam database, we identified that the alpha-proteobacterium Caulobacter crescentus RNase E contains a similar 59 UTR structure that promotes RNase E autoregulation. In both bacteria, the C-terminal IDR of RNase E is required for proper autoregulation to occur, and this IDR is also necessary and sufficient for RNase E to phase-separate, generating BR-bodies. Using in vitro purified RNase E, we find that the IDR9s ability to promote phase-separation correlates with enhanced 59 UTR cleavage, suggesting that phase-separation of RNase E with the 59 UTR enhances autoregulation. Finally, using growth competition experiments we find that a strain capable of autoregulation rapidly outcompetes a strain with a 59 UTR mutation that cannot autoregulate, suggesting autoregulation promotes optimal cellular fitness.

Caulobacter crescentus RNase E condensation contributes to autoregulation and fitness