Distribution of the ribosome associated endonuclease Rae1 and the potential role of conserved amino acids in codon recognition

Abstract

We recently identified a novel ribonuclease in Bacillus subtilis called Rae1 that cleaves mRNAs in a translation-dependent manner. Rae1 is a member of the NYN/PIN family of ribonucleases and is highly conserved in the Firmicutes, the Cyanobacteria and the chloroplasts of photosynthetic algae and plants. We have proposed a model in which Rae1 enters the A-site of ribosomes that are paused following translation of certain sequences that are still ill-defined. In the only case identified thus far, Rae1 cleaves between a conserved glutamate and lysine codon during translation of a short peptide called S1025. Certain other codons are also tolerated on either side of the cleavage site, but these are recognized less efficiently. The model of Rae1 docked in the A-site allows us to make predictions about which conserved residues may be important for recognition of mRNA, the tRNA in the adjacent P-site and binding to the 50S ribosome subunit.

Organellar and Secretory Ribonucleases: Major Players in Plant RNA Homeostasis

“…Although seventeen chloroplastic RNases were predicted by mining the Arabidopsis genome for RNase annotations , this figure certainly needs to be revised. Some predicted RNases were indeed shown to carry other functions (see, for example, the L-PSP/RidA enzyme; Niehaus et al, 2014), and new RNases keep being discovered in bacteria, some of them with a chloroplast homolog awaiting characterization (see, for example, the Rae1/YacP endoribonuclease; Condon et al, 2018). Indeed, as direct evidence of its cyanobacterial origin, nearly all chloroplast RNase homologs are present in bacteria Germain et al, 2013;dos Santos et al, 2018).…”

Systematic sequencing of chloroplast transcript termini fromArabidopsis thalianareveals >200 transcription initiation sites and the extensive imprints of RNA-binding proteins and secondary structures

“…Concerning 5' termini, this might include the roles of the sigma factors that specify PEP initiation sites (112) and other PEP-associated proteins (PAPs; 113), a closer view at RNase J specificity, or a better understanding of some of the numerous factors that have been implicated in rRNA maturation (6). Terminome-Seq would be an excellent choice to gain additional insight into poorly-characterized RNases whose targets have only begun to be described (114)(115)(116).…”

The torpedo effect inBacillus subtilis:RNase J1 resolves stalled transcription complexes

“…Until relatively recently, 5 0 -to-3 0 exoribonucleases were believed to be exclusively eukaryotic. However, a bacterial 5 0 -to-3 0 exoribonuclease, RNase J1, was discovered in the model soil-dwelling organism Bacillus subtilis (Mathy et al, 2007) and shown to be widespread in bacteria and archaea (Phung et al, 2013;Condon et al, 2018). RNase J1 is a member of the b-lactamase family of ribonucleases that also possesses endoribonucleolytic activity, at least in vitro (Even et al, 2005).…”