Genetic and Epigenetic Strategies Potentiate Gal4 Activation to Enhance Fitness in Recently Diverged Yeast Species

Abstract

Summary Certain genes show rapid reactivation after several generations of repression, a conserved phenomenon called epigenetic transcriptional memory. Following previous growth in galactose, GAL gene transcriptional memory confers a strong fitness benefit in Saccharomyces cerevisiae adapting to growth in galactose for up to 8 generations. A genetic screen for mutants defective for GAL gene memory revealed new insights into the molecular mechanism, adaptive consequences and evolutionary history of memory. A point mutation in the Gal1 coactivator that disrupts the interaction with the Gal80 inhibitor specifically and completely disrupted memory. This mutation confirms that cytoplasmically-inherited Gal1 produced during previous growth in galactose directly interferes with Gal80 repression to promote faster induction of GAL genes. This mitotically heritable mode of regulation is recently evolved; in a diverged Saccharomyces species, GAL genes show constitutively faster activation due to genetically-encoded basal expression of Gal1. Thus, recently diverged species utilize either epigenetic or genetic strategies to regulate the same molecular mechanism. The screen also revealed that the central domain of the Gal4 transcription factor both regulates the stochasticity of GAL gene expression and potentiates stronger GAL gene activation in the presence of Gal1. The central domain is critical for GAL gene transcriptional memory; Gal4 lacking the central domain fails to potentiate GAL gene expression and is unresponsive to previous Gal1 expression.

Repeated Cis-Regulatory Tuning of a Metabolic Bottleneck Gene during Evolution

“…2016 ; Roop et al. 2016 ; Sood and Brickner 2017 ). To determine which, if any, genetic and molecular features were associated with quantitative variation in galactose growth between species, we examined 19 DNA sequence features of the GAL networks of 17 species from the family Saccharomycetaceae.…”

“…2013 ; Roop et al. 2016 ; Sood and Brickner 2017 ). Mutations in coding regions have been frequently shown to lead to the acquisition of novel enzymatic activities and radical modifications in specificity ( Thomson et al.…”

“…2016 ; Roop et al. 2016 ; Sood and Brickner 2017 ). The GAL network of S. cerevisiae encodes three enzymes in the galactose-specific Leloir pathway (Gal1, Gal7, and Gal10), a transporter (Gal2), and three regulators (Gal3, Gal4, and Gal80) ( fig.…”

Mediator subunit Med15 dictates the conserved “fuzzy” binding mechanism of yeast transcription activators Gal4 and Gcn4

“…In the absence of galactose, Gal4 activation function is blocked by the repressor Gal80, while in the presence of galactose, Gal4 activates the transcription of genes required for galactose catabolism. Gal4 consists of an N-terminal DNA binding domain that targets the upstream activating sequence (UAS) of Gal4-regulated genes, a large central domain that likely plays a regulatory role, and a C-terminal transcription activation domain (AD) (Keegan et al, 1986; Ma and Ptashne, 1987b; Sood and Brickner, 2017; Stone and Sadowski, 1993; Wu et al, 1996). Under non-inducing conditions, Gal80 binds the Gal4 AD tightly and blocks its function (Johnston et al, 1987; Ma and Ptashne, 1987a).…”

The past determines the future: sugar source history and transcriptional memory

“…These studies revealed that there can be significant variability in an initial induction leading to bimodal expression depending on the galactose concentration due to feedback loops. Zacharioudakis et al and Sood et al showed that transcriptional memory reduces this variability, allowing the population to have a uniform response during reinduction (Sood and Brickner 2017 ; Zacharioudakis et al 2007 ). Sood et al further used fluorescence-activated cell sorting (FACS) to identify a Gal1p mutant that specifically affects memory by disrupting its interaction with Gal80p.…”