BR-Bodies Provide Selectively Permeable Condensates that Stimulate mRNA Decay and Prevent Release of Decay Intermediates

Biomolecular condensates play a key role in organizing RNAs and proteins into membraneless organelles. Bacterial RNP-bodies (BR-bodies) are a biomolecular condensate containing the RNA degradosome mRNA decay machinery, but the biochemical function of such organization remains poorly defined. Here, we define the RNA substrates of BR-bodies through enrichment of the bodies followed by RNA sequencing (RNA-seq). We find that long, poorly translated mRNAs, small RNAs, and antisense RNAs are the main substrates, while rRNA, tRNA, and other conserved non-coding RNAs (ncRNAs) are excluded from these bodies. BR-bodies stimulate the mRNA decay rate of enriched mRNAs, helping to reshape the cellular mRNA pool. We also observe that BR-body formation promotes complete mRNA decay, avoiding the buildup of toxic endo-cleaved mRNA decay intermediates. The combined selective permeability of BR-bodies for both enzymes and substrates together with the stimulation of the sub-steps of mRNA decay provide an effective organization strategy for bacterial mRNA decay. [Display omitted] •Differential centrifugation enrichment identified RNAs in BR-bodies•BR-bodies are enriched in mRNAs, sRNAs, and antisense RNAs•BR-bodies exclude tRNAs, ribosomes, and the nucleoid•BR-bodies globally stimulate the multi-step bacterial mRNA decay pathway Al-Husini et al. show that BR-bodies are enriched with mRNAs, sRNAs, and antisense RNAs, while they exclude tRNAs, rRNAs, and other highly structured ncRNAs. BR-bodies assemble preferentially with long, poorly translated mRNAs, where RNase E and degradosome-associated exoribonucleases help to stimulate the multi-step mRNA decay pathway.