Saccharomyces evolution and Biotechnological applications
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Saccharomyces evolution and Biotechnological applications
The Saccharomyces genus is a complex group of yeast, so important at evolutionary level (basic research) and with important biotechnological applications. In this topic I will try to update with the most recent studies about this exciting group of yeasts which show similar nucleotide divergences as Humans (taking S. cerevisiae as a reference) and Birds (taking S. eubayanus and S. uvarum cluster).
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Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae

Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae | Saccharomyces evolution and Biotechnological applications | Scoop.it
Author Summary The yeast Saccharomyces cerevisiae is being genetically engineered to produce renewable biofuels from sustainable plant material. Efficient biofuel production from plant material requires conversion of the complex suite of sugars found in plant material, including the five-carbon sugar xylose. Because it does not efficiently metabolize xylose, S. cerevisiae has been engineered with a minimal set of genes that should overcome this problem; however, additional genetic changes are required for optimal fermentative conversion of xylose into biofuel. Despite extensive knowledge of the regulatory networks controlling glucose metabolism, less is known about the regulation of xylose metabolism and how to rewire these networks for effective biofuel production. Here we report genetic mutations that enabled the conversion of xylose into bioethanol by a previously ineffective yeast strain. By comparing altered protein and metabolite abundance within yeast cells containing these mutations, we determined that the mutations synergistically alter metabolic pathways to improve the rate of xylose conversion. One change in a gene with well-characterized aerobic mitochondrial functions was found to play an unexpected role in anaerobic conversion of xylose into ethanol. The results of this work will allow others to rapidly generate yeast strains for the conversion of xylose into biofuels and other products.
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Distinct Domestication Trajectories in Top-Fermenting Beer Yeasts and Wine Yeasts

Distinct Domestication Trajectories in Top-Fermenting Beer Yeasts and Wine Yeasts | Saccharomyces evolution and Biotechnological applications | Scoop.it
Beer is one of the oldest alcoholic beverages and is produced by the fermentation of sugars derived from starches present in cereal grains. Contrary to lager beers, made by bottom-fermenting strains of Saccharomyces pastorianus, a hybrid yeast, ale beers are closer to the ancient beer type and are fermented by S. cerevisiae, a top-fermenting yeast. Here, we use population genomics to investigate (1) the closest relatives of top-fermenting beer yeasts; (2) whether top-fermenting yeasts represent an independent domestication event separate from those already described; (3) whether single or multiple beer yeast domestication events can be inferred; and (4) whether top-fermenting yeasts represent non-recombinant or recombinant lineages. Our results revealed that top-fermenting beer yeasts are polyphyletic, with a main clade composed of at least three subgroups, dominantly represented by the German, British, and wheat beer strains. Other beer strains were phylogenetically close to sake, wine, or bread yeasts. We detected genetic signatures of beer yeast domestication by investigating genes previously linked to brewing and using genome-wide scans. We propose that the emergence of the main clade of beer yeasts is related with a domestication event distinct from the previously known cases of wine and sake yeast domestication. The nucleotide diversity of the main beer clade more than doubled that of wine yeasts, which might be a consequence of fundamental differences in the modes of beer and wine yeast domestication. The higher diversity of beer strains could be due to the more intense and different selection regimes associated to brewing.
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Complex Ancestries of Lager-Brewing Hybrids Were Shaped by Standing Variation in the Wild Yeast Saccharomyces eubayanus

Author Summary Yeasts are key industrial microbes, most notably Saccharomyces cerevisiae , which is used to make a variety of products, including bread, wine, and ale-style beers. However, lager-style beers are brewed with interspecies hybrids of S . cerevisiae x Saccharomyces eubayanus . After its discovery in South America in 2011, rare strains of S . eubayanus have also been isolated outside of South America. Here we compare the genome sequences of several new and recent isolates of S . eubayanus from South America, North America, Australasia, and Asia to unravel the relationships of these wild isolates and their domesticated European hybrids. Two South American populations have the highest genetic diversity. One of these populations is closely related to a relatively low-diversity lineage that is spread across the Northern Hemisphere and includes the S . eubayanus parents of lager yeasts. Interestingly, we find that none of the wild isolates of S . eubayanus is the sole closest relative of lager-brewing hybrids. Instead, we show that standing variation among wild S . eubayanus strains contributed to the genetic makeup of lager yeasts. Our findings highlight the complex ancestries of lager yeasts and the importance of broader sampling of wild yeasts to illuminate our understanding of the sources of genetic variation among industrial hybrids.
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Cervezas de laboratorio

Cervezas de laboratorio | Saccharomyces evolution and Biotechnological applications | Scoop.it
Un nuevo método que utiliza ingeniería genética para cruzar levaduras promete crear un sinfín de bebidas a la carta.
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Enological characterization of Spanish Saccharomyces kudriavzevii strains, one of the closest relatives to parental strains of winemaking and brewing Saccharomyces cerevisiae × S. kudriavzevii hybrids

Enological characterization of Spanish Saccharomyces kudriavzevii strains, one of the closest relatives to parental strains of winemaking and brewing Saccharomyces cerevisiae × S. kudriavzevii hybrids | Saccharomyces evolution and Biotechnological applications | Scoop.it
Peris's insight:

How few genetic differences among European/Iberian Saccharomyces kudriavzevii strains, species from Saccharomyces genus where the winemaking Saccharomyces cerevisiae belongs, can be translated in different fermentative profiles.

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The Genome Sequence of Saccharomyces eubayanus and the Domestication of Lager-Brewing Yeasts

The Genome Sequence of Saccharomyces eubayanus and the Domestication of Lager-Brewing Yeasts | Saccharomyces evolution and Biotechnological applications | Scoop.it
Peris's insight:

We had extensive debate around the number of hybridization events behind the origin of the most economically important yeast (lager yeast). The unique hybridization model and the multiple hybridization model have been fighting for the last ten years based in different molecular data. In this recent paper, the improvement of genome sequence of the second parent of lager brewing yeast, S. eubayanus, has allowed us to infer which is the most potential scenario originating the lager brewing hybrids. The different number of neutral mutation when both parents are compared, S. cerevisiae and S. eubayanus, indicates that the parental contributors for Saaz and Frohberg lineages were diverge previous to the hybridization, supporting for a multiple origin scenario.

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Basic principles of yeast genomics, a personal recollection

Basic principles of yeast genomics, a personal recollection | Saccharomyces evolution and Biotechnological applications | Scoop.it
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A walkthrough in yeast genomics, past, recent findings and future. A very interesting review, written by Bernard Dujon.

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Genetic improvement of non-GMO wine yeasts: Strategies, advantages and safety

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Public is not prepared for accepting industrial Genetic Modified Organisms making the governments to impose strict laws for the usage of GMOs. For that reason, other techniques are used for the improvement of relevant yeast with winemaking interest. This review explain the restriction to GMOs in Europe and other countries and explore alternatives to GMOs. Although, the review is focus to the wine industry we can apply those concepts to other biotechnological applications, such as brewing and biofuel.

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Forever Rising

Forever Rising | Saccharomyces evolution and Biotechnological applications | Scoop.it
We depend on yeasts for products ranging from beer and biofuel to forage and pharmaceuticals. But according to Chris Todd Hittinger and his colleagues at CALS, we’ve only begun to understand and mi...
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Genomic Insights into the Saccharomyces sensu stricto Complex

Genomic Insights into the Saccharomyces sensu stricto Complex | Saccharomyces evolution and Biotechnological applications | Scoop.it
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A review that explores the genomic information we already have about the different Saccharomyces species.

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The ecology and evolution of non-domesticated Saccharomyces species - Boynton - 2014 - Yeast - Wiley Online Library

The ecology and evolution of non-domesticated Saccharomyces species - Boynton - 2014 - Yeast - Wiley Online Library | Saccharomyces evolution and Biotechnological applications | Scoop.it
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A review integrating our actual knowledge about the Saccharomyces lineages in an ecological context.

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Saccharomyces pastorianus: genomic insights inspiring innovation for industry - Gibson - Yeast - Wiley Online Library

Saccharomyces pastorianus: genomic insights inspiring innovation for industry - Gibson - Yeast - Wiley Online Library | Saccharomyces evolution and Biotechnological applications | Scoop.it
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I bring a review about one of the most important strain in the production of lager beers.

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A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum : Nature Communications : Nature Publishing Group

A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum : Nature Communications : Nature Publishing Group | Saccharomyces evolution and Biotechnological applications | Scoop.it
Peris's insight:

As a continuation of a series of papers studying the phylogeography of Saccharomyces species, today I bring a paper exploring Saccharomyces uvarum. The authors have found:

1. A high frequency rate of isolation of S. uvarum in Nothofagus trees compared with previous isolations in oak trees.

2. They have described 3 clades: A (Holartic), B (South America) and C (Australasian). The nucleotide divergence among C vs A-B is about 4.4%, associated with clear phenotypic differences between A and B, when sugar consumption and temperature profiles are explored.

3. Intermediate levels of spore viability between crosses C x A or C x B . The spore viability of S. uvarum from outside South America crossed with S. eubayanus was higher than S. uvarum from South America x S. eubyanus South America indicating a reinforcement of reproductive isolation between both species from the same location.

4. A recent migration from South America to North Hemisphere, being the SA-A the ancestor of North Hemisphere strains.

5. Holarctic strains displayed introgression from many Saccharomyces species and this introgressions occurred in Europe as a result of domestication.

 

I have to note that spore crosses involve few strains but future studies will improve the statistics of this analysis. Also, the implementation of microtitter assays could help to make better assesments about glucose consumption.

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Novel brewing yeast hybrids: creation and application

Novel brewing yeast hybrids: creation and application | Saccharomyces evolution and Biotechnological applications | Scoop.it
The natural interspecies Saccharomyces cerevisiae × Saccharomyces eubayanus hybrid yeast is responsible for global lager beer production and is one of the most important industrial microorganisms. Its
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Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts

Whereas domestication of livestock, pets, and crops is well documented, it is still unclear to what extent microbes associated with the production of food have also undergone human selection and where the plethora of industrial strains originates from. Here, we present the genomes and phenomes of 157 industrial Saccharomyces cerevisiae yeasts. Our analyses reveal that today’s industrial yeasts can be divided into five sublineages that are genetically and phenotypically separated from wild strains and originate from only a few ancestors through complex patterns of domestication and local divergence. Large-scale phenotyping and genome analysis further show strong industry-specific selection for stress tolerance, sugar utilization, and flavor production, while the sexual cycle and other phenotypes related to survival in nature show decay, particularly in beer yeasts. Together, these results shed light on the origins, evolutionary history, and phenotypic diversity of industrial yeasts and provide a resource for further selection of superior strains.
Peris's insight:
A nice paper showing potential multiple domestication events for brewing Saccharomyces cerevisiae strains. In addition, authors report the importance of the inactivation of two genes for the improvement of beer flavor.
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Population genomics of yeasts: towards a comprehensive view across a broad evolutionary scale - Peter - 2016 - Yeast - Wiley Online Library

Population genomics of yeasts: towards a comprehensive view across a broad evolutionary scale - Peter - 2016 - Yeast - Wiley Online Library | Saccharomyces evolution and Biotechnological applications | Scoop.it
Abstract With the advent of high-throughput technologies for sequencing, the complete description of the genetic variation that occurs in populations, also known as population genomics, is foreseeable [...]...
Peris's insight:
For a long time, most of the research about population genomics in yeast has been focused in S. cerevisiae. Although this continue being true, this trend is changing for the study of other Saccharomycotina yeasts. Peter and Joseph bring us a review about the insights of population genomics in budding yeasts.
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Efficient engineering of marker-free synthetic allotetraploids of Saccharomyces

Efficient engineering of marker-free synthetic allotetraploids of Saccharomyces | Saccharomyces evolution and Biotechnological applications | Scoop.it
Peris's insight:

Alcoholic and biofuel industry make their products by using yeasts. During the fermentation process for the production of wine, beer and bioethanol Saccharomyces cerevisiae is the main workhorse. However, recent investigations are showing how the combination of genomic traits of different non-cerevisiae species can innovate or improve the fermentation process, generating new aromas (wine and beer) or increasing the tolerance to lignocellulosic toxins (biofuels). In most cases, the combination of those traits is performed by the production of haploid x haploid hybrids, restricting the genomic landscape. In other cases, allotetraploids (diploid x diploid) has been generated but the frequency of these hybrids is low because it depends on a molecular mechanism that occurs rarely in the cell (also known as rare-mating). Here, we constructed a series of plasmids to facilitate the molecular mechanism, showing a higher frequency of allotetraploid generation (technique called HyPr -> Hybrid Production). HyPr open the door to a more efficient exploration of the genotypic landscape of different Saccharomyces genome combinations for the improvement of alcoholic and bioethanol production.

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A population genomics insight into the Mediterranean origins of wine yeast domestication - Almeida - 2015 - Molecular Ecology - Wiley Online Library

A population genomics insight into the Mediterranean origins of wine yeast domestication - Almeida - 2015 - Molecular Ecology - Wiley Online Library | Saccharomyces evolution and Biotechnological applications | Scoop.it
Peris's insight:

A recent paper explaining the close relationship between Saccharomyces cerevisiae from wine and Mediterranean oaks. This might indicate that the wild stock of domesticated wine Saccharomyces cerevisiae strains is from Mediterranean oaks. I wonder if we would like to do some home-made wine, probably we want to visit Mediterranean oaks and try to use their yeast for performing the fermentation.

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Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage

Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage | Saccharomyces evolution and Biotechnological applications | Scoop.it
The ancient whole-genome duplication in the Saccharomyces cerevisiae lineage has been a paradigm for the study of genome duplications in eukaryotes. This article presents evidence for the existence of an interspecies hybridization event shortly before the duplication, with deep implications for the functional and evolutionary consequences of this genome doubling.
Peris's insight:

For the last 20 years, data has supported for a Whole Genome Duplication occurring around 100mya. The WGD originated 6 of the clades belonging to the Ascomycetes family where Saccharomyces genus, which contain the baker and brewing yeast, is one of them. For several years the mechanism (autopoliploidization or allopoliploidization) driving to the WGD was not clear. In this work, Marcet-Houben and Gabaldón have been able to solve the mystery by phylogenomics approaches. They were able to support hybridization (allopoliploidization) as the most plausible mechanism generating the WGD and being responsible to generate the huge diversity we can nowadays observe in those post-WGD clades.

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Diversity and adaptive evolution of Saccharomyces wine yeast: a review

Diversity and adaptive evolution of Saccharomyces wine yeast: a review | Saccharomyces evolution and Biotechnological applications | Scoop.it
Peris's insight:

A review exploring the knowledge of Saccharomyces, mostly S. cerevisiae, in the application to the wine industry. Genomic insights, hybridization and horizontal gene transfer are also detailed due to their importance for the acquisition of winery traits.

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Comparative Genomics of Saccharomyces cerevisiae Natural Isolates for Bioenergy Production

Comparative Genomics of Saccharomyces cerevisiae Natural Isolates for Bioenergy Production | Saccharomyces evolution and Biotechnological applications | Scoop.it
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Mining tolerance and biofuel traits from three Saccharomyces cerevisiae stress tolerant strains.

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Temperature and host preferences drive the diversification of Saccharomyces and other yeasts: a survey and the discovery of eight new yeast species.

Temperature and host preferences drive the diversification of Saccharomyces and other yeasts: a survey and the discovery of eight new yeast species. | Saccharomyces evolution and Biotechnological applications | Scoop.it
Peris's insight:

Exploration of the natural sources of yeast species of important for understanding the mechanism driving the evolution of yeast. This survey explores several sources in North America, describing the potential mechanisms driving the diversification of Saccharomyces and other yeasts, and how far we are of the identification of most of yeast species.

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New lager yeast strains generated by interspecific hybridization - Online First - Springer

New lager yeast strains generated by interspecific hybridization - Online First - Springer | Saccharomyces evolution and Biotechnological applications | Scoop.it
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How important Saccharomyces hybrids can be in the innovation of industrial products is well known. Here, authors have generated interespecific hybrids for finding new lager flavours to bring new brewing products.

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The interaction of Saccharomyces paradoxus with its natural competitors on oak bark - Kowallik - Molecular Ecology - Wiley Online Library

The interaction of Saccharomyces paradoxus with its natural competitors on oak bark - Kowallik - Molecular Ecology - Wiley Online Library | Saccharomyces evolution and Biotechnological applications | Scoop.it
Peris's insight:

In the case of Saccharomyces strains few studies have shown how wild yeast strains interacts with their competitors in natural environments. Here the authors explore how the growth of S. paradoxus will depend on the microbial species surronding them.

 

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Saccharomyces eubayanus and Saccharomyces uvarum associated with the fermentation of Araucaria araucana seeds in Patagonia - Rodríguez - 2014 - FEMS Yeast Research - Wiley Online Library

Saccharomyces eubayanus and Saccharomyces uvarum associated with the fermentation of Araucaria araucana seeds in Patagonia - Rodríguez - 2014 - FEMS Yeast Research - Wiley Online Library | Saccharomyces evolution and Biotechnological applications | Scoop.it
Peris's insight:

Saccharomyces eubayanus, the non-cerevisiae parent of the lager brewing strain S. pastorianus, is under a gold period. Three recent studies have found S. eubayanus in South America, North America and Asia. The interest of this strain is clear, the biotechnological application and consequences in the production of lager beer. In the recent study, where I will be focus in S. eubayanus, the authors have isolated new strains of S. eubayanus. The most important results are:

S. eubayanus have been isolated from Araucaria araucana, which seed are used by Mapuches to produce an alcoholic beverage named Mudai. This result expand the recent described ecological niches of S. eubayanus (Nothofagus, Acer, Fagus and Oak trees) to the bark and seed of A. araucana.Description of the RFLP patterns for the identification and differentiation of S. eubayanus and S.uvarum strains.The importance of the isolation of yeasts from the raw material where surprisingly S. eubayanus and S. uvarum where the most prevalent yeast strains, indicating that they could be the responsible of ancient fermentation, nowadays replace by S. cerevisiae.

Notes: although a non-proper population survey was conducted the phylogenetic results using the S. eubayanus strains could indicate that they belong to the two recent described populations from South America, Patagonia A and Patagonia B/Lager. This new findings, again, highlight the importance of ancient fermentation procedures using native Saccharomyces strains.

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