An Evolutionary Perspective on the Crabtree Effect

View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Frontiers - Publisher Connector PERSPECTIVE ARTICLE published: 21 October 2014 MOLECULAR BIOSCIENCES doi: 10.3389/fmolb.2014.00017 An evolutionary perspective on the Crabtree effect Thomas Pfeiffer* and Annabel Morley New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand Edited by: The capability to ferment sugars into ethanol is a key metabolic trait of yeasts. Thomas Nägele, University of Crabtree-positive yeasts use fermentation even in the presence of oxygen, where they Vienna, Austria could, in principle, rely on the respiration pathway. This is surprising because fermentation Reviewed by: has a much lower ATP yield than respiration (2 ATP vs. approximately 18 ATP per Luciana Hannibal, Cleveland Clinic, USA glucose). While genetic events in the evolution of the Crabtree effect have been identified, Bas Teusink, VU University the selective advantages provided by this trait remain controversial. In this review we Amsterdam, Netherlands analyse explanations for the emergence of the Crabtree effect from an evolutionary and *Correspondence: game-theoretical perspective. We argue that an increased rate of ATP production is likely Thomas Pfeiffer, New Zealand the most important factor behind the emergence of the Crabtree effect. Institute for Advanced Study, Massey University, Private Bag Keywords: yeast energy metabolism, Crabtree effect, evolution of metabolism, respiro-fermentation, evolutionary 102904, North Shore Mail Centre, game theory Auckland 0745, New Zealand e-mail: [email protected] INTRODUCTION all organisms (Berg et al., 2002). In the initial reactions of Adenosine triphosphate (ATP) is a key compound in cellular glycolysis, 2 ATP are consumed per glucose, and the result- energy metabolism, where it drives free-energy dependent pro- ing fructose 1,6-bisphosphate is transformed into two 3-carbon cesses such as motion, transport, biosynthesis and growth. Yeasts sugars. In the downstream reactions, the 3-carbon sugars are can typically use two different pathways to produce ATP from degraded to pyruvate, each yielding 2 ATP and 1 NADH. sugars, namely respiration and fermentation (Figure 1). While Pyruvate can then be further degraded either through the respiration results in a high yield of ATP (in Saccharomyces cere- respiration pathway or the fermentation pathway. In alcoholic visiae approximately 18 ATP per glucose), fermentation has a fermentation, pyruvate is transformed into ethanol by pyruvate much lower ATP yield (2 ATP per glucose) but does not require decarboxylase (Pdc) and alcohol dehydrogenase (Adh), resulting oxygen. At high levels of sugar and oxygen, yeasts can pro- in a net gain of 2 ATP per glucose. Adh recycles the NADH that duce ATP via respiration, fermentation, or a concurrent use of is formed in lower glycolysis back into NAD+ and thus alcoholic both pathways. Two strategies are commonly observed and relate fermentation can operate in the absence of oxygen. to the well-known Crabtree effect (De Deken, 1966; Postma In the respiration pathway, pyruvate is transformed by pyru- and Verduyn, 1989; Van Urk et al., 1990):theexclusiveuseof vate dehydrogenase (Pdh) into acetyl-Coenzyme A, which is then respiration in Crabtree-negative yeasts, and the simultaneous oxidized in the TCA cycle to CO2. This yields further GTP,NADH use of fermentation and respiration in Crabtree-positive yeasts. and other reduced co-enzymes which are then oxidized in the Crabtree-positive yeasts likely emerged around the same time as mitochondrion to produce ATP. Overall, the respiration pathway flowering plants, whose sugar-rich fruits and nectar might have can in eukaryotes produce up to 38 molecules of ATP from one provided a novel niche to ancestral yeast species (Piškur et al., molecule of glucose, including the two produced by glycolysis. 2006). A number of genetic events, such as a whole-genome This value is substantially lower for organisms with a low P/O duplication, regulatory rewiring of yeast energy metabolism and ratio in oxidative phosphorylation. For S. cerevisiae,whereaP/O hexose transporter duplications, have likely contributed to the ratio of about 1.2 has been estimated, the resulting yield of res- Crabtree effect (Wolfe and Shields, 1997; Piškur et al., 2006; piration is about 18 ATP per glucose (Verduyn et al., 1991; van Conant and Wolfe, 2007; Hagman et al., 2013). Yet, despite this Gulik and Heijnen, 1995; de Kok et al., 2012). mechanistic knowledge, the evolutionary forces behind the emer- While the capability of degrading sugars via fermentation gence of the Crabtree effect remain unclear. We here review allows yeasts to adapt to anoxic environments, the use of fer- explanations for the emergence of the Crabtree effect from an mentation is not confined to such conditions. Some yeast species evolutionary and game-theoretical point of view. We start by giv- such as S. cerevisiae use fermentation even in the presence of ing an introduction of the metabolic system that underlies the oxygen, when glucose concentrations are sufficiently high. The respiro-fermentative metabolism of yeasts. use of fermentation in the presence of oxygen and at high glucose concentrations is referred to as the Crabtree effect (Crabtree, RESPIRO-FERMENTATION AND THE CRABTREE EFFECT IN 1929). Yeasts that display a Crabtree effect are Crabtree-positive; YEASTS yeasts that do not display a Crabtree effect are Crabtree-negative. Sugars such as glucose are converted into pyruvate through gly- Examples and growth data for Crabtree-positive and Crabtree- colysis, a metabolic pathway employed with deviations in nearly negative yeasts are given in Hagman et al. (2013). www.frontiersin.org October 2014 | Volume 1 | Article 17 | 1 Pfeiffer and Morley Evolution of the Crabtree effect uptake rate of glucose starts saturating around 500 mg/l), though this might vary from species to species and depend on the spe- cific conditions. The sharp drop in biomass yield associated with fermentation raises the question of why Crabtree-positive yeasts use the “wasteful” fermentation pathway if they could in principle rely solely on respiration for ATP production. EVOLUTION OF THE CRABTREE EFFECT A major event in the evolution of the S. cerevisiae lineage was a whole genome duplication (Wolfe and Shields, 1997; Kellis et al., FIGURE 1 | Yeast energy metabolism. Yeasts have two pathways for ATP 2004) that occurred approximately 100 million years ago (mya) production from glucose, respiration, and fermentation. Both pathways and doubled the number of chromosomes from 8 to 16. The tim- start with glycolysis, which results in the production of two molecules of ing of the whole-genome duplication (WGD) coincides with the pyruvate and ATP per glucose. In fermentation, pyruvate is then turned into diversification of angiosperms (Wing and Boucher, 1998)which ethanol. This process does not produce additional ATP but recycles the NAD+ consumed in glycolysis and thereby provides a way of might have provided a novel niche for the ancestral yeasts. It oxygen-independent ATP production. In respiration, pyruvate is completely has thus been argued that an increased flux in glycolysis has oxidized to CO2 through the TCA cycle and oxidative phosphorylation been an evolutionary beneficial outcome of the WGD (Liti and (OXPHOS), which yields additional ATP but requires oxygen. Crabtree Louis, 2005; Merico et al., 2007). On the other hand, a compar- positive yeasts, at sufficient levels of oxygen and glucose, use fermentation and respiration simultaneously. The ethanol that accumulates in the ative analysis of yeast species covering over 150 million years of environment can be recycled for ATP production once glucose has been yeast evolutionary history has also shown that while post-WGD depleted. This process, however, yields less ATP than the direct oxidation lineages have a pronounced Crabtree effect, aerobic fermenta- of pyruvate because the synthesis of Acetyl-CoA from ethanol requires ATP. tion is not confined to these lineages (Merico et al., 2007). A number of additional evolutionary events have likely contributed in shaping the sugar metabolism of yeasts and are reviewed in The Crabtree effect can be easily demonstrated in chemo- Conant and Wolfe (2007); Merico et al. (2007); Hagman et al. stat (Postma and Verduyn, 1989) and batch culture (Verduyn (2013). et al., 1984). In glucose-limited chemostat culture and at low One event that has received particular attention is the dupli- dilution rates, CO2 production equals O2 uptake. The biomass cation of alcohol dehydrogenase, giving rise to two distinctive yield is high under such conditions (about 0.5 g/g) and the resid- enzymes, Adh1 and Adh2. This duplication event has led to ual glucose concentration is low. As the dilution rate increases, one avenue of explanation for the use of “wasteful” fermen- the population is forced to replicate faster to maintain a steady tation by Crabtree-positive yeasts, a theory referred to as the state population size in the chemostat. This implicates an increase “make-accumulate-consume” strategy (Piškur et al., 2006). The in the residual glucose concentration. Both CO2 production and idea behind the “make-accumulate-consume” strategy (in short O2 uptake increase with increasing dilution rate, but remain cou- MAC) is that yeasts ferment glucose in order to defend sugar rich pled until a critical point is reached. When the dilution rate is resources such as fruit from

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