Proteomic composition of eukaryotic and bacterial RNA decay condensates suggests convergent evolution

Abstract

Bacterial cells have a unique challenge to organize their cytoplasm without the use of membrane-bound organelles. Biomolecular condensates (henceforth BMCs) are a class of nonmembrane-bound organelles, which, through the physical process of phase separation, can form liquid-like droplets with proteins/nucleic acids. BMCs have been broadly characterized in eukaryotic cells, and BMCs have been recently identified in bacteria, with the first and best studied example being bacterial ribonucleoprotein bodies (BR-bodies). BR-bodies contain the RNA decay machinery and show functional parallels to eukaryotic P-bodies (PBs) and stress granules (SGs). Due to the finding that mRNA decay machinery is compartmentalized in BR-bodies and in eukaryotic PBs/SGs, we will explore the functional similarities in the proteins, which are known to enrich in these structures based on recent proteomic studies. Interestingly, despite the use of different mRNA decay and post-transcriptional regulatory machinery, this analysis has revealed evolutionary convergence in the classes of enriched enzymes in these structures.

Figure 1.

(A) Schematic of biomolecular condensate phase separation. Biomolecules that undergo phase separation are called drivers/scaffolds. Molecules that interact with scaffolds and are recruited into condensates are called clients. (B) BR-bodies compose heterogeneous client composition within a single cell. The schematic shows BR-body accessory proteins, RhlE, and Hfq are contained in a subset of cellular BR-bodies within a cell and assemble into RhlE and Hfq only condensates. Each cell contains a heterogeneous mixture of condensates, suggesting RNP condensates are specialized to facilitate mRNA processing/decay. (C) Properties of BR-bodies under different cellular environments. (Left) BR-bodies are dynamic structures under exponential growth conditions and they rapidly exchange RNAs and proteins with the surroundings and organize active mRNA decay in bacteria. (Right) It is unknown whether BR-bodies act as storage condensates under different conditions.

Figure 2.

Key differences in mRNA decay condensates in eukaryotes and bacteria. (A) The eukaryotic decapping complex that remove the 5’ -end 7-methyl guanylate (m7G) cap attached to the 5’-end of mRNA is localized in p-bodies s. (B) Bacterial decapping enzymes RppH and NudC that remove 5’ -end triphosphate (PPP) or nicotinamide adenine dinucleotide (NAD+) modified nucleotides leaving a 5’-end monophosphate (5’P) at the 5’-end are depleted from BR-bodies.