Polymorphisms in the yeast galactose sensor underlie a natural continuum of nutrient-decision phenotypes

Abstract

In nature, microbes often need to “decide” which of several available nutrients to utilize, a choice that depends on a cell’s inherent preference and external nutrient levels. While natural environments can have mixtures of different nutrients, phenotypic variation in microbes’ decisions of which nutrient to utilize is poorly studied. Here, we quantified differences in the concentration of glucose and galactose required to induce galactose-responsive (GAL) genes across 36 wild S. cerevisiae strains. Using bulk segregant analysis, we found that a locus containing the galactose sensor GAL3 was associated with differences in GAL signaling in eight different crosses. Using allele replacements, we confirmed that GAL3 is the major driver of GAL induction variation, and that GAL3 allelic variation alone can explain as much as 90% of the variation in GAL induction in a cross. The GAL3 variants we found modulate the diauxic lag, a selectable trait. These results suggest that ecological constraints on the galactose pathway may have led to variation in a single protein, allowing cells to quantitatively tune their response to nutrient changes in the environment.Author summaryIn nature, microbes often need to decide which of many potential nutrients to consume. This decision making process is complex, involving both intracellular constraints and the organism’s perception of the environment. To begin to mimic the complexity of natural environments, we grew cells in mixtures of two sugars, glucose and galactose. We find that in mixed environments, the sugar concentration at which cells decides to induce galactose-utilizing (GAL) genes is highly variable in natural isolates of yeast. By analyzing crosses of phenotypically different strains, we identified a locus containing the galactose sensor, a gene that in theory could allow cells to tune their perception of the environment. We confirmed that the galactose sensor can explain upwards of 90% of the variation in the decision to induce GAL genes. Finally, we show that the variation in the galactose sensor can modulate the time required for cells to switch from utilizing glucose to galactose. Our results suggest that signaling pathways can be highly variable across strains and thereby might allow for rapid adaption in fluctuating environments.

Assigning function to natural allelic variation via dynamic modeling of gene network induction

“…A previous study identified GAL3 as an important genetic determinant for this decision: The concentration ratio at which cells turn GAL expression ON differs between strains harboring different natural alleles of GAL3 (Lee et al, 2017). We asked if this variation, visible in the steady-state exposure to both glucose and galactose, was correlated with the variation observed on the dynamics of network induction upon exposure to galactose only.…”

“…We asked if this variation, visible in the steady-state exposure to both glucose and galactose, was correlated with the variation observed on the dynamics of network induction upon exposure to galactose only. We chose four strains that showed different decision thresholds because of different GAL3 alleles (Lee et al, 2017; Fig 5B), and we monitored their dynamics of induction at three different concentrations of galactose (with no glucose). We then used our model to assign q Gal3 and K Gal parameter values to each strain.…”

“…Genotype was validated by PCR and sequencing. Strains of Fig 5 were MPJ125-E06 (GAL3 BY ), MPJ143-H01 (GAL3 YJM428 ), MPJ143-F01 (GAL3 YJM421 ), and MPJ125-A07 (GAL3 BC187 ), which were described in another study (Lee et al, 2017); they all derived from a S288c hoD::GAL1pr-YFP-mTagBFP2-kanMX4; gal3Δ::hphNT1 parental strain. Strains GY2180 and GY2181 carrying mutations GAL3 W117A and GAL3 W117T , respectively, were obtained using CRISPR/Cas9: Oligonucleotides 1P29 and 1P30 were annealed and cloned in the SwaI, BclI sites of the pML104 plasmid (Laughery et al, 2015) to produce pGY514.…”

“…Expression of GAL3 is itself under Gal4p/Gal80p control (positive feedback). In addition, the sequence of GAL3 differs between natural isolates of S. cerevisiae and this allelic variation was recently associated with different sensitivities of the network to galactose (Lee et al, 2017). There are multiple ways that a GAL3 variant could affect the dynamics of induction: by modifying the production or degradation rates of the Gal3p protein or of its messenger RNA, by changing the affinity of Gal3p to galactose or ATP, by changing the capacity of Gal3p to dimerize, by changing the nucleocytoplasmic ratio of Gal3p molecules, or by changing the affinity of Gal3p to Gal80p.…”

Decoupling transcription factor expression and activity enables dimmer-switch gene regulation

“…We next sought to determine if natural isolates have genetic variants that independently 5 affect the rheostat and the switch. We have shown that there is natural variation in both the rheostats and switch (24,25). We chose two isolates, S288C and DBVPG1106 ( Fig.…”