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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 (cspA).OE: overexpression; EP: empty plasmid.DOI:http://dx.doi.org/10.7554/eLife.04745.012
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fig4s1: Relative fitness in competition experiments terminated in mid-exponential phase (cspA).OE: overexpression; EP: empty plasmid.DOI:http://dx.doi.org/10.7554/eLife.04745.012

Mentions: Relative fitness of REL606- and MG1655-derived strains overexpressing CspA compared with strains of the same genotype carrying the empty control plasmid. F20L: competitions in the 40k and evolved ΔmutH backgrounds, respectively, where plasmids carried a mutated version of the cspA gene yielding a protein with compromised nucleic acid binding ability (Hilier et al., 1998). Bar heights and error bars are as described in Figure 1. **p < 0.01, *p < 0.05 (one-sample t-test). Additional results for competitions terminated in mid-exponential phase (after 2 hr) and competitions involving the lamB mutant in the evolved ΔmutH strain and the rplSsyn mutant in the 40k strain are shown in Figure 4—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 (cspA).OE: overexpression; EP: empty plasmid.DOI:http://dx.doi.org/10.7554/eLife.04745.012
© Copyright Policy
Related In: Results  -  Collection

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

fig4s1: Relative fitness in competition experiments terminated in mid-exponential phase (cspA).OE: overexpression; EP: empty plasmid.DOI:http://dx.doi.org/10.7554/eLife.04745.012
Mentions: Relative fitness of REL606- and MG1655-derived strains overexpressing CspA compared with strains of the same genotype carrying the empty control plasmid. F20L: competitions in the 40k and evolved ΔmutH backgrounds, respectively, where plasmids carried a mutated version of the cspA gene yielding a protein with compromised nucleic acid binding ability (Hilier et al., 1998). Bar heights and error bars are as described in Figure 1. **p < 0.01, *p < 0.05 (one-sample t-test). Additional results for competitions terminated in mid-exponential phase (after 2 hr) and competitions involving the lamB mutant in the evolved ΔmutH strain and the rplSsyn mutant in the 40k strain are shown in Figure 4—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