RNA chaperones buffer deleterious mutations in E. coli

Both proteins and RNAs can misfold into non-native conformations that are incompatible with function. Protein chaperones can promote the folding of nascent polypeptides towards the native state and catalyze re-folding of misfolded species1, thereby buffering the effects of mutations that compromise structural stability and jeopardize function2,3. Similarly, RNA chaperones can aid conformational transitions and rescue misfolded RNA species4-6, but whether they can act in a manner analogous to protein chaperones, mitigating the impact of deleterious mutations across a broad array of RNA substrates, remains unknown. Here we show that RNA chaperones can act as bona fide mutation buffers with repercussions for cellular fitness. Using classic competition assays7, we show that overexpression of select RNA chaperones, including three DEAD box RNA helicases (CsdA, SrmB, RhlB) and the cold shock protein CspA, enhances competitive fitness in an E. coli mutator strain that has accumulated deleterious mutations over ~40,000 generations of evolution in the laboratory. For DEAD box RNA helicases, which can prise apart short RNA helices and thereby potentiate productive re-folding8, we show that buffering relies on helicase activity, implicating RNA structural remodelling in the buffering process. We further observe fitness gains in a second evolved mutator strain that carries an independent set of mutations, ruling out simple complementation. Mutation buffering in trans by protein chaperones has implications for understanding the persistence of cryptic variation in natural populations9,10, protein evolvability3 and incomplete penetrance11. Our results suggest that some RNA chaperones possess a similar, perhaps mechanistically analogous capacity to alleviate the effect of mutations that affect RNA structure and might therefore have similar relevance for understanding RNA evolution, evolvability, and function.