A retropepsin-like bacterial protease regulates ribosome modification and polypeptide production

Adaptations to fluctuating environmental conditions require bacteria to make large-scale proteomic shifts on short timescales. We previously characterised the tri-partite RimABK protein complex responsible for the post-translational modification of the ribosome in response to environmental cues. Regulated control of RpsF polyglutamylation by RimK rapidly influenced the proteome of Pseudomonas fluorescens cells to facilitate colonisation of the plant rhizosphere. Here, we conduct a detailed investigation of the RimB protease. We show RimB to be a bifunctional retropepsin-like aspartic endopeptidase that uniquely recognises and removes glutamate residues from polyglutamated RpsF and stimulates poly-α-L-glutamate synthesis by RimK. We determine the minimal recognition requirements for RimB proteolysis and identify the catalytic aspartate residue required for function. Further, we identify a novel hybrid enzyme composed of RimB and RimK domains that also possesses protease activity. Phylogenetic analysis of accessions encoding either the hybrid or individual RimB and RimK proteins reveals a pattern of rim gene evolution that is distinct from that of the host organisms and reveals potential alternative targets of RimB.