Identification of proteins interacting with the N-terminal half of endoribonuclease RNase E in Escherichia coli

In E. coli endoribonuclease RNase E (Rne) plays a central role in RNA processing and decay. Rne consists of an N-terminal catalytic domain (NTD) and a C-terminal scaffolding domain, separated by a membrane targeting sequence (MTS). While the scaffolding domain represents a hub for interaction, only few proteins are known to bind the Rne-NTD. One example is protein RapZ, which forms a transient complex with the Rne-NTD to target a small RNA to decay. Here, we screened a genomic bacterial two-hybrid library for proteins binding to the Rne N-terminal half including the MTS. We retrieved fragments of 43 proteins, of which 15 were validated to bind Rne as full-length proteins. We distinguished three groups: Group I likely uses a membrane domain to bind a segment in Rne that comprises the MTS. Group II proteins are cytoplasmic and bind the Rne-NTD. Group III proteins bind the Rne-NTD and additionally the MTS region, indicating two distinct interaction surfaces. RNA-seq revealed that overproduction of three group II proteins including YegJ generates similar effects on the transcriptome. Genes carrying Rne cleavage sites were enriched among downregulated genes but depleted from upregulated genes, suggesting increased Rne activity. Interestingly, strong overexpression of yegJ destabilizes rRNA and arrests growth. Apparently, YegJ damages the membrane, granting periplasmic RNase I and presumably also Rne access to cytoplasmic rRNA. We present a catalogue of proteins binding the Rne N-terminal half, which may provide a valuable resource for further investigation of these interactions and their roles.