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Jure Piskur – 1st expert on this subject based on the ideXlab platform
coevolution with bacteria drives the evolution of Aerobic Fermentation in lachancea kluyveriPLOS ONE, 2017Co-Authors: Nerve Zhou, Krishna B S Swamy, Michael J Mcdonald, Silvia Galafassi, Concetta Compagno, Jure PiskurAbstract:
The Crabtree positive yeasts, such as Saccharomyces cerevisiae, prefer Fermentation to respiration, even under fully Aerobic conditions. The selective pressures that drove the evolution of this trait remain controversial because of the low ATP yield of Fermentation compared to respiration. Here we propagate experimental populations of the weak-Crabtree yeast Lachancea kluyveri, in competitive co-culture with bacteria. We find that L. kluyveri adapts by producing quantities of ethanol lethal to bacteria and evolves several of the defining characteristics of Crabtree positive yeasts. We use precise quantitative analysis to show that the rate advantage of Fermentation over Aerobic respiration is insufficient to provide an overall growth advantage. Thus, the rapid consumption of glucose and the utilization of ethanol are essential for the success of the Aerobic Fermentation strategy. These results corroborate that selection derived from competition with bacteria could have provided the impetus for the evolution of the Crabtree positive trait.
a study on the fundamental mechanism and the evolutionary driving forces behind Aerobic Fermentation in yeastPLOS ONE, 2015Co-Authors: Arne Hagman, Jure PiskurAbstract:
Baker’s yeast Saccharomyces cerevisiae rapidly converts sugars to ethanol and carbon dioxide at both anAerobic and Aerobic conditions. The later phenomenon is called Crabtree effect and has been described in two forms, long-term and short-term effect. We have previously studied under fully controlled Aerobic conditions forty yeast species for their central carbon metabolism and the presence of long-term Crabtree effect. We have also studied ten steady-state yeast cultures, pulsed them with glucose, and followed the central carbon metabolism and the appearance of ethanol at dynamic conditions. In this paper we analyzed those wet laboratory data to elucidate possible mechanisms that determine the fate of glucose in different yeast species that cover approximately 250 million years of evolutionary history. We determine overflow metabolism to be the fundamental mechanism behind both long- and short-term Crabtree effect, which originated approximately 125–150 million years ago in the Saccharomyces lineage. The “invention” of overflow metabolism was the first step in the evolution of Aerobic Fermentation in yeast. It provides a general strategy to increase energy production rates, which we show is positively correlated to growth. The “invention” of overflow has also simultaneously enabled rapid glucose consumption in yeast, which is a trait that could have been selected for, to “starve” competitors in nature. We also show that glucose repression of respiration is confined mainly among S. cerevisiae and closely related species that diverged after the whole genome duplication event, less than 100 million years ago. Thus, glucose repression of respiration was apparently “invented” as a second step to further increase overflow and ethanol production, to inhibit growth of other microbes. The driving force behind the initial evolutionary steps was most likely competition with other microbes to faster consume and convert sugar into biomass, in niches that were semi-anAerobic.
Wenhsiung Li – 2nd expert on this subject based on the ideXlab platform
Identifying Cis-Regulatory Changes Involved in the Evolution of Aerobic Fermentation in YeastsGenome Biology and Evolution, 2013Co-Authors: Tzi-yuan Wang, Bing Shi Tsai, Fang Ting Wu, Fu Jung Yu, Yu Jung Tseng, Huang Mo Sung, Wenhsiung LiAbstract:
Gene regulation change has long been recognized as an important mechanism for phenotypic evolution. We used the evolution of yeast Aerobic Fermentation as a model to explore how gene regulation has evolved and how this process has contributed to phenotypic evolution and adaptation. Most eukaryotes fully oxidize glucose to CO2 and H2O in mitochondria to maximize energy yield, whereas some yeasts, such as Saccharomyces cerevisiae and its relatives, predominantly ferment glucose into ethanol even in the presence of oxygen, a phenomenon known as Aerobic Fermentation. We examined the genome-wide gene expression levels among 12 different yeasts and found that a group of genes involved in the mitochondrial respiration process showed the largest reduction in gene expression level during the evolution of Aerobic Fermentation. Our analysis revealed that the downregulation of these genes was significantly associated with massive loss of binding motifs of Cbf1p in the fermentative yeasts. Our experimental assays confirmed the binding of Cbf1p to the predicted motif and the activator role of Cbf1p. In summary, our study laid a foundation to unravel the long-time mystery about the genetic basis of evolution of Aerobic Fermentation, providing new insights into understanding the role of cis-regulatory changes in phenotypic evolution.
expansion of hexose transporter genes was associated with the evolution of Aerobic Fermentation in yeastsMolecular Biology and Evolution, 2011Co-Authors: Wenhsiung LiAbstract:
The genetic basis of organisms’ adaptation to different environments is a central issue of molecular evolution. The budding yeast Saccharomyces cerevisiae and its relatives predominantly ferment glucose into ethanol even in the presence of oxygen. This was suggested to be an adaptation to glucose-rich habitats, but the underlying genetic basis of the evolution of Aerobic Fermentation remains unclear. In S. cerevisiae, the first step of glucose metabolism is transporting glucose across the plasma membrane, which is carried out by hexose transporter proteins. Although several studies have recognized that the rate of glucose uptake can affect how glucose is metabolized, the role of HXT genes in the evolution of Aerobic Fermentation has not been fully explored. In this study, we identified all members of the HXT gene family in 23 fully sequenced fungal genomes, reconstructed their evolutionary history to pinpoint gene gain and loss events, and evaluated their adaptive significance in the evolution of Aerobic Fermentation. We found that the HXT genes have been extensively amplified in the two fungal lineages that have independently evolved Aerobic Fermentation. In contrast, reduction of the number of HXT genes has occurred in Aerobic respiratory species. Our study reveals a strong positive correlation between the copy number of HXT genes and the strength of Aerobic Fermentation, suggesting that HXT gene expansion has facilitated the evolution of Aerobic Fermentation.
The Evolution of Aerobic Fermentation in Schizosaccharomyces pombe Was Associated with Regulatory Reprogramming but not Nucleosome ReorganizationMolecular Biology and Evolution, 2010Co-Authors: Wenhsiung LiAbstract:
Aerobic Fermentation has evolved independently in two yeast lineages, the Saccharomyces cerevisiae and the Schizosaccharomyces pombe lineages. In the S. cerevisiae lineage, the evolution of Aerobic Fermentation was shown to be associated with transcriptional reprogramming of the genes involved in respiration and was recently suggested to be linked to changes in nucleosome occupancy pattern in the promoter regions of respiration-related genes. In contrast, little is known about the genetic basis for the evolution of Aerobic Fermentation in the Sch. pombe lineage. In particular, it is not known whether respiration-related genes in Sch. pombe have undergone a transcriptional reprogramming or changes in nucleosome occupancy pattern in their promoter regions. In this study, we compared genome-wide gene expression profiles of Sch. pombe with those of S. cerevisiae and the Aerobic respiration yeast Candida albicans. We found that the expression profile of respiration-related genes in Sch. pombe is similar to that of S. cerevisiae, but different from that of C. albicans, suggesting that their transcriptional regulation has been reprogrammed during the evolution of Aerobic Fermentation. However, we found no significant nucleosome organization change in the promoter of respiration-related gene in Sch. pombe.
Cris Kuhlemeier – 3rd expert on this subject based on the ideXlab platform
Ethanolic Fermentation: new functions for an old pathwayTrends in Plant Science, 1999Co-Authors: Million Tadege, Isabelle Dupuis, Cris KuhlemeierAbstract:
Abstract Ethanolic Fermentation is an ancient metabolic pathway. In plants, it is a major route of ATP production under anAerobic conditions. In addition, recent developments suggest that the pathway has important functions in the presence of oxygen. Both of the enzymes required for the production of acetaldehyde and ethanol, pyruvate decarboxylase and alcohol dehydrogenase, are highly abundant in pollen, resulting in Fermentation in fully oxygenated cells. Acetaldehyde toxicity is an inevitable side effect of Aerobic Fermentation. Could acetaldehyde be the elusive pollen factor that contributes to male sterility in cmsT maize? The versatility of this ancient pathway is also illustrated by the induction of Aerobic Fermentation by environmental stress and activation of a defense response by overexpression of pyruvate decarboxylase.
Aerobic Fermentation during tobacco pollen developmentPlant Molecular Biology, 1997Co-Authors: Million Tadege, Cris KuhlemeierAbstract:
In vegetative organs of plants, the metabolic switch from respiration to Fermentation is dictated by oxygen availability. The two genes dedicated to ethanolic Fermentation, pyruvate decarboxylase and alcohol dehydrogenase, are induced by oxygen deprivation and the gene products are active under oxygen stress. In pollen, these two genes are expressed in a stage-specific manner and transcripts accumulate to high levels, irrespective of oxygen availability. We have examined the expression pattern of pyruvate decarboxylase and alcohol dehydrogenase at the protein level in developing pollen and show that the active proteins are localized to the gametophytic tissue and begin to accumulate at microspore mitosis. A flux through the ethanolic Fermentation pathway could already be detected very early in pollen development, occurring in all stages from premeiotic buds to mature pollen. This flux was primarily controlled not by oxygen availability, but rather by sugar supply. At a high rate of sugar metabolism, respiration and Fermentation took place concurrently in developing and germinating pollen. We propose that Aerobic Fermentation provides a shunt from pyruvate to acetyl-CoA to accommodate the increased demand for energy and biosynthetic intermediates during pollen development and germination. A possible undesirable side-effect is the potential accumulation of toxic acetaldehyde. Our results support a model for cms-T-type male sterility in maize, in which degeneration of the tapetum is caused by the toxic effects of acetaldehyde on mitochondria weakened by the presence of the URF13 protein.
Aerobic Fermentation in tobacco pollenPlant Molecular Biology, 1995Co-Authors: Marcel Bucher, Karl A. Brander, Sandro Sbicego, Therese Mandel, Cris KuhlemeierAbstract:
We characterized the genes coding for the two dedicated enzymes of ethanolic Fermentation, alcohol dehydrogenase (ADH) and pyruvate decarboxylase (PDC), and show that they are functional in pollen. Two PDC-encoding genes were isolated, which displayed reciprocal regulation: PDC1 was anAerobically induced in leaves, whereas PDC2 mRNA was absent in leaves, but constitutively present in pollen. A flux through the ethanolic Fermentation pathway could be measured in pollen under all tested environmental and developmental conditions. Surprisingly, the major factor influencing the rate of ethanol production was not oxygen availability, but the composition of the incubation medium. Under optimal conditions for pollen tube growth, approximately two-thirds of the carbon consumed was fermented, and ethanol accumulated into the surrounding medium to a concentration exceeding 100 mM.