Horizontally acquired oligopeptide transporters favour adaptation of <i>Saccharomyces cerevisiae</i> wine yeast to oenological environment

Marsit, Souhir; Sanchez, Isabelle; Galeote, Virginie; Dequin, Sylvie

doi:10.1111/1462-2920.13117

Cited by 42 publications

(52 citation statements)

References 74 publications

(95 reference statements)

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“…Horizontal Gene Transfer (HGT) has been reported as a mechanism of adaptative evolution in fungal species and to have contributed to the domestication of S. cerevisiae [56][57][58]. Similarly, an HGT event is predicted to have conferred the ability to utilize sucrose as a carbon source to B. bruxellensis and B. anomalus via the incorporation of a bacterially-derived invertase.…”

Section: Discussionmentioning

confidence: 99%

New genome assemblies reveal patterns of domestication and adaptation across Brettanomyces (Dekkera) species

Roach

Borneman

2020

BMC Genomics

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Background: Yeasts of the genus Brettanomyces are of significant interest, both for their capacity to spoil, as well as their potential to positively contribute to different industrial fermentations. However, considerable variance exists in the depth of research and knowledgebase of the five currently known species of Brettanomyces. For instance, Brettanomyces bruxellensis has been heavily studied and many resources are available for this species, whereas Brettanomyces nanus is rarely studied and lacks a publicly available genome assembly altogether. The purpose of this study is to fill this knowledge gap and explore the genomic adaptations that have shaped the evolution of this genus. Results: Strains for each of the five widely accepted species of Brettanomyces (Brettanomyces anomalus, B. bruxellensis, Brettanomyces custersianus, Brettanomyces naardenensis, and B. nanus) were sequenced using a combination of long-and short-read sequencing technologies. Highly contiguous assemblies were produced for each species. Structural differences between the species' genomes were observed with gene expansions in fermentation-relevant genes (particularly in B. bruxellensis and B. nanus) identified. Numerous horizontal gene transfer (HGT) events in all Brettanomyces species', including an HGT event that is probably responsible for allowing B. bruxellensis and B. anomalus to utilize sucrose were also observed. Conclusions: Genomic adaptations and some evidence of domestication that have taken place in Brettanomyces are outlined. These new genome assemblies form a valuable resource for future research in Brettanomyces.

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Section: Discussionmentioning

confidence: 99%

New genome assemblies reveal patterns of domestication and adaptation across Brettanomyces (Dekkera) species

Roach

Borneman

2020

BMC Genomics

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“…High affinity sugar transporters were overexpressed in a moment when sugar was still at elevated concentration in the medium, as well as the oligopeptide transporter coding gene OPT1, which have been recently identified among the upregulated genes of wine S. cerevisiae in co-culture with Oenococcus oeni (Rossouw et al, 2012). Oligopeptides transporters activation could be a mechanism for nitrogen resources increased acquisition (Marsit et al, 2016). Moreover, the nodes obtained for the control of gene expression in response to competition at 20 C are very similar to those found for S. cerevisiae, pointing to a similar response which would be temperature dependent.…”

Section: Discussionmentioning

confidence: 99%

Dominance of wine Saccharomyces cerevisiae strains over S. kudriavzevii in industrial fermentation competitions is related to an acceleration of nutrient uptake and utilization

Alonso-del-Real

Pérez‐Torrado

Querol

et al. 2019

Environmental Microbiology

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Summary Grape must is a sugar‐rich habitat for a complex microbiota which is replaced by Saccharomyces cerevisiae strains during the first fermentation stages. Interest on yeast competitive interactions has recently been propelled due to the use of alternative yeasts in the wine industry to respond to new market demands. The main issue resides in the persistence of these yeasts due to the specific competitive activity of S. cerevisiae. To gather deeper knowledge of the molecular mechanisms involved, we performed a comparative transcriptomic analysis during fermentation carried out by a wine S. cerevisiae strain and a strain representative of the cryophilic S. kudriavzevii, which exhibits high genetic and physiological similarities to S. cerevisiae, but also differences of biotechnological interest. In this study, we report that transcriptomic response to the presence of a competitor is stronger in S. cerevisiae than in S. kudriavzevii. Our results demonstrate that a wine S. cerevisiae industrial strain accelerates nutrient uptake and utilization to outcompete the co‐inoculated yeast, and that this process requires cell‐to‐cell contact to occur. Finally, we propose that this competitive phenotype evolved recently, during the adaptation of S. cerevisiae to man‐manipulated fermentative environments, since a non‐wine S. cerevisiae strain, isolated from a North American oak, showed a remarkable low response to competition.

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“…These findings also suggest that a subset of accessory genes was not vertically inherited from the species ancestor. These genes that were acquired by introgression, horizontal gene transfer, and de novo gene emergence probably represent a key source of evolutionary innovation and phenotypic diversity (Marsit et al, ; Marsit, Sanchez, Galeote, & Dequin, ; Novo et al, ). Overall, it has been found that human‐related environments foster expansion and loss of genes resulting in rampant variation in genome content.…”

Section: From One To More Than a Thousand S Cerevisiae Genomesmentioning

confidence: 99%

André Goffeau's imprinting on second generation yeast “genomologists”

Fairhead

Fischer

Liti

et al. 2019

Yeast

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All authors of the present paper have worked in labs that participated to the sequencing effort of the Saccharomyces cerevisiae reference genome, and we owe to this the fact that we have all chosen to work on genomics of yeasts. S. cerevisiae has been a popular model species for genetics since the 20th century as well as being a model for general eukaryotic cellular processes. Although it has also been used empirically in fermentation for millennia, there was until recently, a lack of knowledge about the natural and evolutionary history of this yeast. The achievement of the international effort to sequence its genome was the foundation for understanding many eukaryotic biological processes but also represented the first step towards the study of the genome and ecological diversity of yeast populations worldwide. We will describe recent advances in yeast comparative and population genomics that find their origins in the S. cerevisiae genome project initiated and pursued by André Goffeau.

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Horizontally acquired oligopeptide transporters favour adaptation of Saccharomyces cerevisiae wine yeast to oenological environment

Cited by 42 publications

References 74 publications

New genome assemblies reveal patterns of domestication and adaptation across Brettanomyces (Dekkera) species

New genome assemblies reveal patterns of domestication and adaptation across Brettanomyces (Dekkera) species

Dominance of wine Saccharomyces cerevisiae strains over S. kudriavzevii in industrial fermentation competitions is related to an acceleration of nutrient uptake and utilization

André Goffeau's imprinting on second generation yeast “genomologists”

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