Elsevier

Gene

Volume 366, Issue 2, 1 February 2006, Pages 343-351
Gene

Genome-wide scan reveals that genetic variation for transcriptional plasticity in yeast is biased towards multi-copy and dispensable genes

https://doi.org/10.1016/j.gene.2005.10.042Get rights and content

Abstract

One of the most important aspects of the evolution of development and physiology is the interplay between gene expression and the environment, by which traits become altered in response to environmental triggers. This feature is known as phenotypic plasticity. When different genotypes show different levels of plasticity for a trait, then they show genotype-by-environment interaction, or GEI. It is now clear that gene expression plays an important role in organismic-level phenotypic plasticity, but we know very little about whether gene expression itself is subject to genetic variation for phenotypic plasticity (GEI). Given that gene regulation is likely to have evolved to respond to environmental changes, it is of central importance to understand how environmental and genetic variation interact to produce variation in gene expression. Here we investigate genetic variation for phenotypic plasticity in the yeast transcriptome for the whole genome. Six strains of Saccharomyces cerevisiae were grown in four different environments representing a continuum of rich and poor natural conditions. Using DNA-microarray data and an ANOVA analysis with a stringent criterion of significance, we found significant genetic variation for transcriptional plasticity (GEI) among strains for ∼5% of the genes in the genome. There are about twice as many genes that show genetic variation for phenotypic plasticity as show genetic variation in transcription level independent of the environment. We also found that genes with genetic variation for plasticity were less likely to be essential and were significantly biased towards genes that have paralogs.

Introduction

Understanding the genetic bases of complex diseases and adaptive traits are among the fundamental goals of medical and evolutionary genetics. The environment is usually seen as the agent of natural selection, selecting the fittest genotypes in a given population. But the environment is far from constant. Moreover, genetic and environmental effects may interact with each other and may produce complex evolutionary trajectories. For instance, phenotypic changes in response to environmental changes–known as phenotypic plasticity–can themselves be genetically variable. Also, the evolution of robustness against environmental perturbations can lead to the evolution of robustness also against genetic perturbations, consequently redrawing the maps that connect genotype and environment with phenotype and fitness (Waddington, 1942, Hartman et al., 2001, Meiklejohn and Hartl, 2002). Consideration of both genetic and environmental perturbations is therefore necessary for a more complete understanding of evolutionary processes (Levins, 2004).

Genetic variation for phenotypic plasticity emerges from the non-additive interaction between the genotypes of organisms and variation in the environment. In the presence of such interactions, different genotypes respond differently to the same environmental change, so there is genotype-by-environment interaction (GEI). Sensitivity to therapeutic drugs in individuals with some genotypes but not others is a manifestation of GEI in pharmacogenomics. The visualization of GEI can be facilitated through the use of norms of reaction—a mapping of the phenotype onto the genotype as a function of the environment, depicted graphically as a plot of phenotypic values against environmental values (Stearns, 1992, Fig. 1). GEI refers to genetic variation in the shape of those norms of reaction. Different hypothetical norms of reaction are illustrated in Fig. 1, in which each color represents a different genotype. Panel (A) shows a trait with genetic variation but no phenotypic plasticity, and panel (B) shows a trait with phenotypic plasticity but no genetic variation. The trait in panel (C) exhibits both genetic variation and phenotypic plasticity, but there is no genetic variation in phenotypic plasticity: each genotype responds in the same way to each environment. The only trait in Fig. 1 that shows genetic variation for phenotypic plasticity (GEI) is that depicted in panel (D), where the norms of reaction of the different genotypes are not parallel.

The machinery of gene regulation can exhibit an exquisite response to the environment because it has evolved to allow transcription to be induced, repressed, or modulated in response to environmental cues (Suiter et al., 2003). The transcriptional response can be at the level of individual cells, tissues, or the whole organism. In fact, a large fraction of phenotypic diversity within species may result from phenotypic plasticity controlled at the level of differential gene expression (Pigliucci, 1996, Abouheif and Wray, 2002). Studying gene regulation is therefore key to our understanding of the genetic and environmental dissection of complex phenotypes, and this in the perspective of better understanding phenotypic evolution, which is a grand challenge facing evolutionary biology (Singh, 2003). To this end, microarray technologies have become valuable tools because they enable the survey of gene expression at a genomic scale and this quantitatively (e.g., Gibson, 2002).

In order to quantify the extent of genetic variation for transcriptional plasticity, we studied gene expression in Saccharomyces cerevisiae. This unicellular fungus is particularly well suited for such an experiment because the time scale of environmental changes can be much shorter than the generation time (e.g., Gasch and Werner-Washburne, 2002), a condition known to favor the evolution of phenotypic plasticity (Schlichting and Smith, 2002). Additionally, transcriptional responses in microorganisms are at the organismic-level and do not include confounding factors of differential responses in distinct tissues or organs. Finally, the metabolism of microorganisms is relatively tightly linked to genetic regulatory gene networks whose transcriptional state can be estimated by assaying mRNA levels. In yeast, genetic variation in gene expression in a single environment has been documented (e.g. Cavalieri et al., 2000, Townsend et al., 2003), as have changes in gene expression in different environments (e.g., Gasch et al., 2000, Causton et al., 2001). There is also evidence that different strains show different responses to chemical agents (Fay et al., 2004). What is lacking, however, is a large-scale assay for GEI, which would reveal how much genetic variation is present in the transcriptional response to environmental changes and what genetic characteristics of this species favor or limit the diversity of transcriptional responses to environmental triggers. Because genetic variation for phenotypic plasticity emerges from the interaction between genotypes and environments, it can be assayed only by examining the transcriptional response of multiple genotypes across several environments. This can now be carried out on a genomic scale.

In this study, we used cDNA microarrays to examine genetic variation for phenotypic plasticity in genome-wide gene expression in six isolates of S. cerevisiae grown in four different environments, either in standard rich medium or any of three alternative media simulating environmental stress. The specific objective was to reveal which general classes of genes show genetic variation for phenotypic plasticity. We also hoped to identify factors that might constrain or favor the diversity of norms of reaction in the genome of S. cerevisiae.

Section snippets

Genotypes and environments

Six diploid prototrophic strains were studied: Ds288c, EM93, Sgu52, Sgu407, Sgu421, and Sg60. Ds288c is a diploid heterothallic strain derived from a cross of two S288c derivatives isolated in the 1980s. EM93 was originally isolated from a fig in Mercedes, California, in the early days of yeast genetics (Mortimer and Johnston, 1986). The other strains are from the Polsinelli collection of Italian yeast isolates: Sgu52, Sgu407, and Sgu421 were isolated from grapes in the Chianti region, and Sg60

Variation in gene expression across environments

Gene expression was estimated in replicate experiments in which each strain of yeast was grown in four environmental conditions: aerobic growth in YPD medium, a typical rich laboratory condition; anaerobic growth in synthetic wine must (SWM), which mimics wine fermentation conditions; and either 4 or 24 h of anaerobic growth with nitrogen starvation (NS) in medium in which proline was the main source of nitrogen. These environmental conditions simulate the progression of environments that yeast

Acknowledgments

We would like to thank Nadia Aubin-Horth and Cristian Castillo-Davis for comments on an earlier version of the manuscript and members of the Hartl lab for discussions on the work. We would also like thank Ping Ma for helpful discussions about statistical issues and Hao Wu for information about the use of MAANOVA, Keith Morneau for lab assistance and Mario Polsinelli for providing the strains for this work. CRL is a Frank Knox Memorial fellow at Harvard University and is supported by graduate

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    Present address: Department of Biological Sciences, Stanford University, Stanford CA, USA.

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