The cost of gene expression underlies a fitness trade-off in yeast

Abstract

Natural selection optimizes an organism's genotype within the context of its environment. Adaptations to one environment can decrease fitness in another, revealing evolutionary trade-offs. Here, we show that the cost of gene expression underlies a trade-off between growth rate and mating efficiency in the yeast Saccharomyces cerevisiae. During asexual growth, mutations that eliminate the ability to mate provide an approximately 2% per-generation growth-rate advantage. Some strains, including most laboratory strains, carry an allele of GPA1 (an upstream component of the mating pathway) that increases mating efficiency by approximately 30% per round of mating at the cost of an approximately 1% per-generation growth-rate disadvantage. In addition to demonstrating a trade-off between growth rate and mating efficiency, our results illustrate differences in the selective pressures defining fitness in the laboratory versus the natural environment and show that selection, acting on the cost of gene expression, can optimize expression levels and promote gene loss.

Fig. 1.

A subset of αF^R mutations provides a competitive growth-rate advantage. (A) Spontaneous αF^R mutants have a greater variance of growth-rate coefficients (s_g) and a higher average growth rate than unselected clones (P < 10⁻⁷, Wilcoxon rank sum test), whereas the distribution of s_g for Can^R mutants is similar to wild type (P > 0.05, Wilcoxon). The 8 clones with growth-rate disadvantages of at least 1% were excluded from the statistical analysis. (B) Targeted gene disruptions show that loss of the G_β subunit (Ste4), the MAP kinase kinase (Ste7), or the transcription factor (Ste12) increases growth rate (P = 2.8 × 10⁻⁵, 5.8 × 10⁻⁹, 2.2 × 10⁻⁶, respectively, t test); however, loss of the receptor (Ste2) or Far1 does not [P = 0.23, 0.03, respectively, t test (the value for far1Δ is not significant because we are testing 5 deletion mutants and thus require P < 0.05/5 = 0.01 to regard a result as significant)]. Values represent the mean and standard deviation of 5 to 7 independent gene deletions.

Fig. 2.

The growth-rate advantage of αF^R mutants correlates with the elimination of gene expression. (A) A schematic of the pheromone-induced signaling pathway. In a MATa yeast cell, the mating pheromone, αF, binds to the receptor, Ste2. Pheromone-induced signaling activates a heterotrimeric G protein (consisting of Gpa1, Ste18, and Ste4), which in turn, activates a MAP kinase cascade (consisting of the MAP kinase kinase kinase, Ste11, the MAP kinase kinase, Ste7, the MAP kinases Fus3 and Kss1, and the scaffolding protein, Ste5) ultimately leading to a cell-cycle arrest dependent on Far1 and a transcriptional response through the transcription factor, Ste12 (13). Expression of mating pathway genes in the absence of pheromone is maintained by basal signaling through the pathway, which is independent of the receptor (Ste2) or Far1. Identification of the mutations in 5 spontaneous αF^R mutants with a growth-rate advantage using yeast tiling arrays (42) identified Ste11^P656H, Ste5^C198S, and Ste7^L7ochre mutations in strains αF^R-2, αF^R-8, and αF^R-20, respectively. Using this method, we also identified Apc1^S838I and Eds1^P6L mutations in the strain αF^R-1. (B) αF^R strains with a growth-rate advantage reduce gene expression downstream of Ste12, whereas strains without a growth-rate advantage do not show the same reduction in gene expression. Strains are displayed in order of their growth-rate coefficient. The genes displayed are those whose expression changes significantly in the 7 spontaneous αF^R mutants with a competitive growth-rate advantage (Fig. S2) or known components of the mating pathway. Some of the apparent down-regulation in strains αF^R-36 and αF^R-41 may be an artifact because these strains acquire suppressor mutations that partially restore mating and αF arrest (Fig. S1B). From these arrays, the Ste7^E43ochre and Ste4^frameshift mutations were identified in strains αF^R-4 and αF^R-7, respectively, because the suppression of the expression of specific genes suggests nonsense-mediated decay of the transcripts.

Fig. 3.

A trade-off between growth rate and mating efficiency. (A) The wild-type allele of GPA1 down-regulates genes in the mating pathway producing an expression profile intermediate to that of deletions eliminating basal signaling (ste7Δ, ste4Δ, and ste12Δ) and those not affecting signaling (far1Δ and ste2Δ). Shown are 3 independent wild-type GPA1 allele replacement strains. (B) Wild-type GPA1 allele replacement strains have a growth-rate advantage relative to the GPA1-G1406T allele strains (s_g = 0.92% ± 0.35% and −0.17% ± 0.34% for the wild-type GPA1 allele and the GPA1-G1406T allele, respectively, P < 2.6 × 10⁻⁶, t test). The points represent 3 independent measurements for each of 3 independent transformants of each GPA1 allele. (C) Wild-type GPA1 allele replacement strains have a mating disadvantage relative to the GPA1-G1406T allele strains (s_m = −27.2% ± 6.5%). MATa strains carrying each allele were mixed and allowed to compete for a limiting number of MATα cells. The mating coefficients (s_m) were calculated as the change in the natural logarithm of the ratio of the 2 alleles: s_m = ln(wild-type GPA1/GPA1-G1406T)_postmating − ln(wild-type GPA1/GPA1-G1406T)_premating.

Fig. 4.

A schematic of the evolutionary dynamics between the 2 alleles of GPA1. The wild-type GPA1 allele has growth-rate advantage of ≈1% per generation, but a mating disadvantage of ≈30% per round of mating compared with the GPA1-G1406T allele. If these 2 strains are mixed and propagated in a regime where 1 round of mating occurs every 30 generations, these 2 strains would be equally fit (black trace). If mating occurs more frequently than every 30 generations, the GPA1-G1406T allele will win the competition (red trace). Conversely, if more than 30 generations pass between rounds of mating, the wild-type allele of GPA1 will win (blue trace). During long-term evolution, strains are typically propagated asexually. Under such a circumstance, sterile strains, which eliminate basal signaling through the mating pathway, will outcompete mating-proficient strains (green trace, on the secondary y axis to demonstrate the ≈2% advantage versus strains carrying the GPA1-G1406T allele).