RNA editing in bacteria recodes multiple proteins and regulates an evolutionarily conserved toxin-antitoxin system

Abstract

Adenosine (A) to inosine (I) RNA editing is widespread in eukaryotes. In prokaryotes, however, A-to-I RNA editing was only reported to occur in tRNAs but not in protein-coding genes. By comparing DNA and RNA sequences of , we show for the first time that A-to-I editing occurs also in prokaryotic mRNAs and has the potential to affect the translated proteins and cell physiology. We found 15 novel A-to-I editing events, of which 12 occurred within known protein-coding genes where they always recode a tyrosine (TAC) into a cysteine (TGC) codon. Furthermore, we identified the tRNA-specific adenosine deaminase (tadA) as the editing enzyme of all these editing sites, thus making it the first identified RNA editing enzyme that modifies both tRNAs and mRNAs. Interestingly, several of the editing targets are self-killing toxins that belong to evolutionarily conserved toxin-antitoxin pairs. We focused on hokB, a toxin that confers antibiotic tolerance by growth inhibition, as it demonstrated the highest level of such mRNA editing. We identified a correlated mutation pattern between the edited and a DNA hard-coded Cys residue positions in the toxin and demonstrated that RNA editing occurs in in two additional bacterial species. Thus, not only the toxin is evolutionarily conserved but also the editing itself within the toxin is. Finally, we found that RNA editing in increases as a function of cell density and enhances its toxicity. Our work thus demonstrates the occurrence, regulation, and functional consequences of RNA editing in bacteria.

A-to-I RNA editing in bacteria increases pathogenicity and tolerance to oxidative stress

“…In E . coli , the tadA gene encoding tRNA-specific adenosine deaminase was responsible for bacterial tRNA and mRNA editing [ 18 ]. To investigate this possibility in Xoc , we constructed the tadA deletion and overexpressing strains, ΔtadA and tadA OE , respectively (see Methods).…”

“…Recently, Bar-Yaacov and colleagues demonstrated that nonsynonymous A-to-I editing can occur in bacterial mRNA [ 18 ]. The authors found that A-to-I editing in hokB , which encodes a toxin that confers antibiotic tolerance, increases as a function of cell density and enhances toxicity of the protein [ 18 ]. Furthermore, tRNA-specific adenosine deaminase (TadA) was identified as the A-to-I editing enzyme in Escherichia coli , which expands the role of tadA as both a tRNA- and mRNA-editing enzyme in bacteria [ 19 ].…”

Upgraded adenine base editor (uABE) with minimized RNA off-targeting activity

“…1b). To facilitate this test, we generated a robust reporter by cloning the E.coli Hokb (ecHokb) gene containing tRNA-like CTACGAA sequence, which has been reported to be highly edited by ecTadA at RNA levels [14], into a CMV promoter-driven vector. Then, this reporter was co-transfected with a sgRNA targeting HEK site 3 and ABEmax or its mutated variants, and the A-to-G editing e ciencies in ecHokb cDNA (reversely transcribed from mRNA) or genomic DNA (gDNA) were determined by deep sequencing on ecHokb cDNA or gDNA amplicons.…”

Adenosine to inosine mRNA editing in fungi and how it may relate to fungal pathogenesis

“…Liu and colleagues [ 11 ] suggested that adenosine deaminases acting on tRNA (ADATs) may mediate mRNA editing in fungi, possibly together with specific cofactors. Indeed, ADATs were recently shown to catalyze the deamination of adenosines in both tRNA and mRNA in bacteria [ 18 ]. However, deletion of the F .…”

“…There, editing targets evolutionary conserved toxin—antitoxin pairs. Editing of the hokB toxin transcript increased toxicity and was conserved in the pathogenic bacteria Klebsiella pneumoniae and Yersinia enterocolitica [ 18 ], revealing another correlation of editing and pathogenicity.…”