The yeast galactose network as a quantitative model for cellular memory

Abstract

Recent experiments have revealed surprising behavior in the yeast galactose (GAL) pathway, one of the preeminent systems for studying gene regulation. Under certain circumstances, yeast cells display memory of their prior nutrient environments. We distinguish two kinds of cellular memory discovered by quantitative investigations of the GAL network and present a conceptual framework for interpreting new experiments and current ideas on GAL memory. Reinduction memory occurs when cells respond transcriptionally to one environment, shut down the response during several generations in a second environment, then respond faster and with less cell-to-cell variation when returned to the first environment. Persistent memory describes a long-term, arguably stable response in which cells adopt a bimodal or unimodal distribution of induction levels depending on their preceding environment. Deep knowledge of how the yeast GAL pathway responds to different sugar environments has enabled rapid progress in uncovering the mechanisms behind GAL memory, which include cytoplasmic inheritance of inducer proteins and positive feedback loops among regulatory genes. This network of genes, long used to study gene regulation, is now emerging as a model system for cellular memory.

Figure 1

The GAL network is controlled by interlocking positive and negative feedback loops. Asterisks indicate activation by intracellular galactose. Red indicates repressive effects; green represents inducers. Positive and negative feedback loops are marked with circled + and − signs, respectively. See text for details. Adapted with permission from [29].

Figure 2

Timecourses of reinduction memory experiments. Top: 12-hour reinduction memory [4, 32]. Bottom: 1-hour reinduction memory [20]. Timecourse curves are approximate. GAL1 and GAL3 mRNA and proteins are not on the same vertical scale. A) Primary induction after overnight glucose. A’) Primary induction after overnight raffinose. B, B’) Glucose repression. C) Secondary induction after 12 hours is faster than primary induction. C’) Secondary induction after 1 hour is faster than primary induction for wild-type. Secondary induction is the same as primary induction (A’) for swi2Δ, indicating loss of the memory phenotype in the mutant. D) Secondary induction after 15 hours is as slow as primary induction. Data sources (“WT” = wild-type): A) Gal1p: [4] fig. 1c, [14] fig. 6. GAL1 WT: [32] fig. 1a. A’) Gal1p: [58] fig. 4, in a neutral medium similar to raffinose. GAL1 WT: [20] fig. 6 (GAL1) and fig. 2 (GAL10, similar). GAL1 swi2Δ: [20] fig. 6. B, B’) Gal1p: [4] fig. S3A. GAL1: [33] fig. 2c. C) Gal1p: [4] fig. 1c. GAL1 WT: [32] fig. 1c, [20] fig. 1a. GAL1 swi2Δ: [20] fig. 1b. C’) GAL1 WT: [20] fig. 6 (GAL1), fig. 2 (GAL10, similar). GAL1 swi2Δ: [20] fig. 6c. D) Gal1p: [4] fig. S3B.

Figure 3

Reinduction and persistent memory. All histograms are flow cytometry measurements of single-cell fluorescence intensity of GAL gene reporters. Fluorescence intensity is on a log₁₀ scale. All strains are wild-type except for GAL reporters. A) Reinduction memory experiment (12-hour) [4]: glucose, galactose (slow GAL induction), glucose, galactose (fast GAL induction). B) Persistent memory experiment [5]: raffinose or glucose, then a mix of galactose and glucose (14h). C) Persistent memory experiment [6]: raffinose or high galactose, then low galactose (27h). D) Reinduction memory data. Timecourses of Gal1p-GFP fusion protein expression in cells growing in 2% galactose media. Left: Initial galactose induction after pre-growth in glucose (>24h). Right: Reinduction in galactose after pre-growth in glucose (>24h), galactose (24h), and glucose again (12h). The second induction is faster and unimodal, demonstrating reinduction memory. Adapted with permission from [4]. E) Persistent memory under weak repression, showing the effects of pre-growth history in glucose vs. raffinose. Following the pre-growth phase, cells were grown for 14h in 2% galactose plus the indicated concentration of glucose. Flow cytometry measurements show the fluorescence intensity of a GFP reporter of GAL1 promoter activity. In moderately repressing medium (center images), glucose-history cells are bimodally distributed; raffinose-history cells are unimodal and the ON peak displays a graded response to glucose repression. Adapted with permission from [5]. F) Persistent memory under weak induction, showing the effects of pre-growth for 12h in raffinose (blue) vs. 2% galactose (red). After pre-growth, cells were grown for 27h in the indicated concentration of galactose. Flow cytometry measurements show the fluorescence intensity of a YFP reporter of GAL1 promoter activity. Raffinose-history cells are bimodally distributed; galactose-history cells are unimodal and display a graded response to galactose concentration. Adapted with permission from [6].

Figure 4

The carbon landscape. The arrows summarize persistent memory experiments described in the text, which measured GAL1 reporter expression at various concentrations of galactose (GAL inducer) and glucose (GAL repressor) in wild-type yeast. Drawing is not to scale. “OFF” and “ON” refer to the expression level of GAL1 at the extremes of glucose and galactose concentration. Cells were incubated in one carbon source (arrow bases) and then transferred to a new medium (arrowheads) for 14-27h. Blue arrows indicate bimodal expression in the new medium, i.e., some cells are induced and others are not. Black arrows indicate a homogeneous (unimodal) cell population in the new medium. Partial circles highlight points on the carbon landscape where cellular memory of the sugar (carbon source) history affects steady-state GAL expression in the new medium (i.e., persistent memory). Acar: [6]. B&C: [5].