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Evolution of Robustness to Protein Mistranslation by Accelerated Protein Turnover.

Kalapis D, Bezerra AR, Farkas Z, Horvath P, Bódi Z, Daraba A, Szamecz B, Gut I, Bayes M, Santos MA, Pál C - PLoS Biol. (2015)

Bottom Line: As a consequence of rapid elimination of erroneous protein products, evolution reduced the extent of toxic protein aggregation in mistranslating cells.We conclude that adjustment of proteome homeostasis to mistranslation evolves rapidly, but this adaptation has several side effects on cellular physiology.Our work also indicates that translational fidelity and the ubiquitin-proteasome system are functionally linked to each other and may, therefore, co-evolve in nature.

View Article: PubMed Central - PubMed

Affiliation: Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary.

ABSTRACT
Translational errors occur at high rates, and they influence organism viability and the onset of genetic diseases. To investigate how organisms mitigate the deleterious effects of protein synthesis errors during evolution, a mutant yeast strain was engineered to translate a codon ambiguously (mistranslation). It thereby overloads the protein quality-control pathways and disrupts cellular protein homeostasis. This strain was used to study the capacity of the yeast genome to compensate the deleterious effects of protein mistranslation. Laboratory evolutionary experiments revealed that fitness loss due to mistranslation can rapidly be mitigated. Genomic analysis demonstrated that adaptation was primarily mediated by large-scale chromosomal duplication and deletion events, suggesting that errors during protein synthesis promote the evolution of genome architecture. By altering the dosages of numerous, functionally related proteins simultaneously, these genetic changes introduced large phenotypic leaps that enabled rapid adaptation to mistranslation. Evolution increased the level of tolerance to mistranslation through acceleration of ubiquitin-proteasome-mediated protein degradation and protein synthesis. As a consequence of rapid elimination of erroneous protein products, evolution reduced the extent of toxic protein aggregation in mistranslating cells. However, there was a strong evolutionary trade-off between adaptation to mistranslation and survival upon starvation: the evolved lines showed fitness defects and impaired capacity to degrade mature ribosomes upon nutrient limitation. Moreover, as a response to an enhanced energy demand of accelerated protein turnover, the evolved lines exhibited increased glucose uptake by selective duplication of hexose transporter genes. We conclude that adjustment of proteome homeostasis to mistranslation evolves rapidly, but this adaptation has several side effects on cellular physiology. Our work also indicates that translational fidelity and the ubiquitin-proteasome system are functionally linked to each other and may, therefore, co-evolve in nature.

No MeSH data available.


Related in: MedlinePlus

Evolution of mistranslation rate.(A) Mutations in the variable arm of the tS(AGA)D3 serine tRNAs. The variable arm mutated in three lines independently (lines 6, 9, and 10). The identity elements for the SerRS are indicated in red (discriminator base G73 and the GC base pairs in the variable arm). Structure of the molecule was predicted by tRNAscan-SE analysis. (B) Evolution of mistranslation rate. The figure shows β-galactosidase enzyme activities in the ancestor and evolved lines, all of which carry the mistranslation causing tRNACAGSer construct. The ancestor is isogenic to the wild type, with the only exception being that the latter carries an empty vector instead of tRNACAGSer. Enzyme activities were normalized to the enzyme activity measured in wild-type control carrying no tRNACAGSer by normalization to the total amount of β-galactosidase protein (quantified by western blot). The bars indicate mean ± 95% confidence interval. Mann-Whitney U test was used to assess difference in fitness between ancestor and evolved lines. **/*** indicates p < 0.01/0.001, respectively. (C) β-galactosidase enzyme activities in the ancestor and the evolved lines carrying no tRNACAGSer. Enzyme activities were normalized to the enzyme activity measured in the wild type after normalization to the total amount of β-galactosidase protein quantified using western blot. The bars indicate mean ± 95% confidence interval. Mann-Whitney U test was used to assess difference in fitness between ancestor and evolved lines */** indicates p < 0.05/0.01, respectively.
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pbio.1002291.g004: Evolution of mistranslation rate.(A) Mutations in the variable arm of the tS(AGA)D3 serine tRNAs. The variable arm mutated in three lines independently (lines 6, 9, and 10). The identity elements for the SerRS are indicated in red (discriminator base G73 and the GC base pairs in the variable arm). Structure of the molecule was predicted by tRNAscan-SE analysis. (B) Evolution of mistranslation rate. The figure shows β-galactosidase enzyme activities in the ancestor and evolved lines, all of which carry the mistranslation causing tRNACAGSer construct. The ancestor is isogenic to the wild type, with the only exception being that the latter carries an empty vector instead of tRNACAGSer. Enzyme activities were normalized to the enzyme activity measured in wild-type control carrying no tRNACAGSer by normalization to the total amount of β-galactosidase protein (quantified by western blot). The bars indicate mean ± 95% confidence interval. Mann-Whitney U test was used to assess difference in fitness between ancestor and evolved lines. **/*** indicates p < 0.01/0.001, respectively. (C) β-galactosidase enzyme activities in the ancestor and the evolved lines carrying no tRNACAGSer. Enzyme activities were normalized to the enzyme activity measured in the wild type after normalization to the total amount of β-galactosidase protein quantified using western blot. The bars indicate mean ± 95% confidence interval. Mann-Whitney U test was used to assess difference in fitness between ancestor and evolved lines */** indicates p < 0.05/0.01, respectively.

Mentions: Several mutated genes were involved in the regulation of tRNA transcription (RNA polymerase III), tRNA export (SOL1 [S000005317]), tRNA surveillance and degradation (TRF5 [S000005243]). A serine tRNA was also repeatedly mutated, mostly in the variable arm of this molecule (Fig 4A, S4 Table), which is recognized by the seryl-tRNA synthetase (SerRS). Indeed, the yeast SerRS recognizes the three G-C base-pairs of the variable arm of serine tRNAs and the discriminator base at position 73 (G73). Based on these observations, we assumed that evolution has acted to alter tRNA stability and cellular abundance. Changes in the tRNA pool could subsequently reduce the rate of mistranslation during the evolution period.


Evolution of Robustness to Protein Mistranslation by Accelerated Protein Turnover.

Kalapis D, Bezerra AR, Farkas Z, Horvath P, Bódi Z, Daraba A, Szamecz B, Gut I, Bayes M, Santos MA, Pál C - PLoS Biol. (2015)

Evolution of mistranslation rate.(A) Mutations in the variable arm of the tS(AGA)D3 serine tRNAs. The variable arm mutated in three lines independently (lines 6, 9, and 10). The identity elements for the SerRS are indicated in red (discriminator base G73 and the GC base pairs in the variable arm). Structure of the molecule was predicted by tRNAscan-SE analysis. (B) Evolution of mistranslation rate. The figure shows β-galactosidase enzyme activities in the ancestor and evolved lines, all of which carry the mistranslation causing tRNACAGSer construct. The ancestor is isogenic to the wild type, with the only exception being that the latter carries an empty vector instead of tRNACAGSer. Enzyme activities were normalized to the enzyme activity measured in wild-type control carrying no tRNACAGSer by normalization to the total amount of β-galactosidase protein (quantified by western blot). The bars indicate mean ± 95% confidence interval. Mann-Whitney U test was used to assess difference in fitness between ancestor and evolved lines. **/*** indicates p < 0.01/0.001, respectively. (C) β-galactosidase enzyme activities in the ancestor and the evolved lines carrying no tRNACAGSer. Enzyme activities were normalized to the enzyme activity measured in the wild type after normalization to the total amount of β-galactosidase protein quantified using western blot. The bars indicate mean ± 95% confidence interval. Mann-Whitney U test was used to assess difference in fitness between ancestor and evolved lines */** indicates p < 0.05/0.01, respectively.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4636289&req=5

pbio.1002291.g004: Evolution of mistranslation rate.(A) Mutations in the variable arm of the tS(AGA)D3 serine tRNAs. The variable arm mutated in three lines independently (lines 6, 9, and 10). The identity elements for the SerRS are indicated in red (discriminator base G73 and the GC base pairs in the variable arm). Structure of the molecule was predicted by tRNAscan-SE analysis. (B) Evolution of mistranslation rate. The figure shows β-galactosidase enzyme activities in the ancestor and evolved lines, all of which carry the mistranslation causing tRNACAGSer construct. The ancestor is isogenic to the wild type, with the only exception being that the latter carries an empty vector instead of tRNACAGSer. Enzyme activities were normalized to the enzyme activity measured in wild-type control carrying no tRNACAGSer by normalization to the total amount of β-galactosidase protein (quantified by western blot). The bars indicate mean ± 95% confidence interval. Mann-Whitney U test was used to assess difference in fitness between ancestor and evolved lines. **/*** indicates p < 0.01/0.001, respectively. (C) β-galactosidase enzyme activities in the ancestor and the evolved lines carrying no tRNACAGSer. Enzyme activities were normalized to the enzyme activity measured in the wild type after normalization to the total amount of β-galactosidase protein quantified using western blot. The bars indicate mean ± 95% confidence interval. Mann-Whitney U test was used to assess difference in fitness between ancestor and evolved lines */** indicates p < 0.05/0.01, respectively.
Mentions: Several mutated genes were involved in the regulation of tRNA transcription (RNA polymerase III), tRNA export (SOL1 [S000005317]), tRNA surveillance and degradation (TRF5 [S000005243]). A serine tRNA was also repeatedly mutated, mostly in the variable arm of this molecule (Fig 4A, S4 Table), which is recognized by the seryl-tRNA synthetase (SerRS). Indeed, the yeast SerRS recognizes the three G-C base-pairs of the variable arm of serine tRNAs and the discriminator base at position 73 (G73). Based on these observations, we assumed that evolution has acted to alter tRNA stability and cellular abundance. Changes in the tRNA pool could subsequently reduce the rate of mistranslation during the evolution period.

Bottom Line: As a consequence of rapid elimination of erroneous protein products, evolution reduced the extent of toxic protein aggregation in mistranslating cells.We conclude that adjustment of proteome homeostasis to mistranslation evolves rapidly, but this adaptation has several side effects on cellular physiology.Our work also indicates that translational fidelity and the ubiquitin-proteasome system are functionally linked to each other and may, therefore, co-evolve in nature.

View Article: PubMed Central - PubMed

Affiliation: Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary.

ABSTRACT
Translational errors occur at high rates, and they influence organism viability and the onset of genetic diseases. To investigate how organisms mitigate the deleterious effects of protein synthesis errors during evolution, a mutant yeast strain was engineered to translate a codon ambiguously (mistranslation). It thereby overloads the protein quality-control pathways and disrupts cellular protein homeostasis. This strain was used to study the capacity of the yeast genome to compensate the deleterious effects of protein mistranslation. Laboratory evolutionary experiments revealed that fitness loss due to mistranslation can rapidly be mitigated. Genomic analysis demonstrated that adaptation was primarily mediated by large-scale chromosomal duplication and deletion events, suggesting that errors during protein synthesis promote the evolution of genome architecture. By altering the dosages of numerous, functionally related proteins simultaneously, these genetic changes introduced large phenotypic leaps that enabled rapid adaptation to mistranslation. Evolution increased the level of tolerance to mistranslation through acceleration of ubiquitin-proteasome-mediated protein degradation and protein synthesis. As a consequence of rapid elimination of erroneous protein products, evolution reduced the extent of toxic protein aggregation in mistranslating cells. However, there was a strong evolutionary trade-off between adaptation to mistranslation and survival upon starvation: the evolved lines showed fitness defects and impaired capacity to degrade mature ribosomes upon nutrient limitation. Moreover, as a response to an enhanced energy demand of accelerated protein turnover, the evolved lines exhibited increased glucose uptake by selective duplication of hexose transporter genes. We conclude that adjustment of proteome homeostasis to mistranslation evolves rapidly, but this adaptation has several side effects on cellular physiology. Our work also indicates that translational fidelity and the ubiquitin-proteasome system are functionally linked to each other and may, therefore, co-evolve in nature.

No MeSH data available.


Related in: MedlinePlus