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RNA chaperones buffer deleterious mutations in E. coli.

Rudan M, Schneider D, Warnecke T, Krisko A - Elife (2015)

Bottom Line: We identify strain-specific mutations that are deleterious and subject to buffering when introduced individually into the ancestral genotype.For DBRHs, we show that buffering requires helicase activity, implicating RNA structural remodelling in the buffering process.Our results suggest that RNA chaperones might play a fundamental role in RNA evolution and evolvability.

View Article: PubMed Central - PubMed

Affiliation: Mediterranean Institute for Life Sciences, Split, Croatia.

ABSTRACT
Both proteins and RNAs can misfold into non-functional conformations. Protein chaperones promote native folding of nascent polypeptides and refolding of misfolded species, thereby buffering mutations that compromise protein structure and function. Here, we show that RNA chaperones can also act as mutation buffers that enhance organismal fitness. Using competition assays, we demonstrate that overexpression of select RNA chaperones, including three DEAD box RNA helicases (DBRHs) (CsdA, SrmB, RhlB) and the cold shock protein CspA, improves fitness of two independently evolved Escherichia coli mutator strains that have accumulated deleterious mutations during short- and long-term laboratory evolution. We identify strain-specific mutations that are deleterious and subject to buffering when introduced individually into the ancestral genotype. For DBRHs, we show that buffering requires helicase activity, implicating RNA structural remodelling in the buffering process. Our results suggest that RNA chaperones might play a fundamental role in RNA evolution and evolvability.

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Relative fitness in competition experiments terminated in mid-exponential phase (REL606).DOI:http://dx.doi.org/10.7554/eLife.04745.004
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fig1s1: Relative fitness in competition experiments terminated in mid-exponential phase (REL606).DOI:http://dx.doi.org/10.7554/eLife.04745.004

Mentions: (A) Relationships between strains used in different competition assays. Short names of competed strains are given in bold; gen.: generations. (B) Relative fitness of the 20k and 40k genotypes, each competed against their REL606 ancestor. (C) Relative fitness of ancestral and evolved genotypes overexpressing one of three DEAD box RNA helicases (DBRHs) compared with identical strains carrying the empty control plasmid. E166K, E157K, and E158K: competitions in the 40k background where plasmids carried mutated versions of the respective DBRH. In each case, the central glutamic acid residue of the DEAD motif has been recoded to lysine, compromising the helicase activity. Bar heights indicate mean relative fitness across four biological replicates, with each mean derived by averaging over four technical replicates. Error bars represent standard errors of the mean. **p < 0.01, *p < 0.05 (one-sample t-test). Additional results for competitions terminated in mid-exponential phase (after 2 hr) are shown in Figure 1—figure supplement 1.


RNA chaperones buffer deleterious mutations in E. coli.

Rudan M, Schneider D, Warnecke T, Krisko A - Elife (2015)

Relative fitness in competition experiments terminated in mid-exponential phase (REL606).DOI:http://dx.doi.org/10.7554/eLife.04745.004
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4402597&req=5

fig1s1: Relative fitness in competition experiments terminated in mid-exponential phase (REL606).DOI:http://dx.doi.org/10.7554/eLife.04745.004
Mentions: (A) Relationships between strains used in different competition assays. Short names of competed strains are given in bold; gen.: generations. (B) Relative fitness of the 20k and 40k genotypes, each competed against their REL606 ancestor. (C) Relative fitness of ancestral and evolved genotypes overexpressing one of three DEAD box RNA helicases (DBRHs) compared with identical strains carrying the empty control plasmid. E166K, E157K, and E158K: competitions in the 40k background where plasmids carried mutated versions of the respective DBRH. In each case, the central glutamic acid residue of the DEAD motif has been recoded to lysine, compromising the helicase activity. Bar heights indicate mean relative fitness across four biological replicates, with each mean derived by averaging over four technical replicates. Error bars represent standard errors of the mean. **p < 0.01, *p < 0.05 (one-sample t-test). Additional results for competitions terminated in mid-exponential phase (after 2 hr) are shown in Figure 1—figure supplement 1.

Bottom Line: We identify strain-specific mutations that are deleterious and subject to buffering when introduced individually into the ancestral genotype.For DBRHs, we show that buffering requires helicase activity, implicating RNA structural remodelling in the buffering process.Our results suggest that RNA chaperones might play a fundamental role in RNA evolution and evolvability.

View Article: PubMed Central - PubMed

Affiliation: Mediterranean Institute for Life Sciences, Split, Croatia.

ABSTRACT
Both proteins and RNAs can misfold into non-functional conformations. Protein chaperones promote native folding of nascent polypeptides and refolding of misfolded species, thereby buffering mutations that compromise protein structure and function. Here, we show that RNA chaperones can also act as mutation buffers that enhance organismal fitness. Using competition assays, we demonstrate that overexpression of select RNA chaperones, including three DEAD box RNA helicases (DBRHs) (CsdA, SrmB, RhlB) and the cold shock protein CspA, improves fitness of two independently evolved Escherichia coli mutator strains that have accumulated deleterious mutations during short- and long-term laboratory evolution. We identify strain-specific mutations that are deleterious and subject to buffering when introduced individually into the ancestral genotype. For DBRHs, we show that buffering requires helicase activity, implicating RNA structural remodelling in the buffering process. Our results suggest that RNA chaperones might play a fundamental role in RNA evolution and evolvability.

Show MeSH
Related in: MedlinePlus