Nanopore sequencing and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization

Salazar, Alex N.; Vries, Arthur R. Gorter de; Broek, Marcel van den; Brouwers, Nick; Cortés, Pilar de la Torre; Kuijpers, Niels G. A.; Daran, Jean‐Marc; Abeel, Thomas

doi:10.1101/603480

Cited by 8 publications

(7 citation statements)

References 101 publications

(110 reference statements)

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“…The recent release of the first long-read sequencing assembly of S. pastorianus enabled a precise chromosomal mapping of the maltose metabolism genes (54) and showed that the Frohberg-type S. pastorianus strain CBS 1483 harbored one copy of SeAGT1 on the S.…”

Section: Discussionmentioning

confidence: 99%

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Himalayan Saccharomyces eubayanus Genome Sequences Reveal Genetic Markers Explaining Heterotic Maltotriose Consumption by Saccharomyces pastorianus Hybrids

Brouwers

Brickwedde

Vries

et al. 2019

Appl Environ Microbiol

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S. pastorianus, an S. cerevisiae × S. eubayanus hybrid, is used for production of lager beer, the most produced alcoholic beverage worldwide. It emerged by spontaneous hybridization and colonized early lager brewing processes. Despite accumulation and analysis of genome sequencing data of S. pastorianus parental genomes, the genetic blueprint of industrially relevant phenotypes remains unresolved. Assimilation of maltotriose, an abundant sugar in wort, has been postulated to be inherited from the S. cerevisiae parent. Here, we demonstrate that although Asian S. eubayanus isolates harbor a functional maltotriose transporter SeAGT1 gene, they are unable to grow on α-oligoglucosides, but expression of S. cerevisiae regulator MAL13 (ScMAL13) was sufficient to restore growth on trisaccharides. We hypothesized that the S. pastorianus maltotriose phenotype results from regulatory interaction between S. cerevisiae maltose transcription activator and the promoter of SeAGT1. We experimentally confirmed the heterotic nature of the phenotype, and thus these results provide experimental evidence of the evolutionary origin of an essential phenotype of lager brewing strains.

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Section: Discussionmentioning

confidence: 99%

“…eubayanus ChrXV section (as in CDFM21L.1) of the chimeric chromosome formed from S. eubayanus ChrXV ( Se ChrXV) and Se ChrVIII (54).…”

Section: Discussionmentioning

confidence: 99%

Himalayan Saccharomyces eubayanus Genome Sequences Reveal Genetic Markers Explaining Heterotic Maltotriose Consumption by Saccharomyces pastorianus Hybrids

Brouwers

Brickwedde

Vries

et al. 2019

Appl Environ Microbiol

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“…This may have been facilitated by the occurrence of multiple copies of the SeAGT1 gene in the S. eubayanus ancestor, which could act as a sequence buffer to counteracting adverse effects of gene copy loss. The recent release of the first long-read sequencing assembly of S. pastorianus enabled a precise chromosomal mapping of the maltose-metabolism genes (Salazar et al 2019) and showed that the Frohberg type S. pastorianus strains CBS 1483 harbored one copy of SeAGT1 on the S. eubayanus CHRXV section (as in CDFM21L.1) of the chimeric chromosome formed from SeCHRXV and SeCHRVIII (Salazar et al 2019).…”

Section: Discussionmentioning

confidence: 99%

Maltotriose consumption by hybridSaccharomyces pastorianusis heterotic and results from regulatory cross-talk between parental sub-genomes

Brouwers

Brickwedde

et al. 2019

Preprint

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S. pastorianus strains are hybrids of S. cerevisiae and S. eubayanus that have been domesticated for several centuries in lager-beer brewing environments. As sequences and structures of S. pastorianus genomes are being resolved, molecular mechanisms and evolutionary origin of several industrially relevant phenotypes remain unknown. This study investigates how maltotriose metabolism, a key feature in brewing, may have arisen in early S. eubayanus × S. cerevisiae hybrids. To address this question, we generated a near-complete genome assembly of Himalayan S. eubayanus strains of the Holarctic subclade. This group of strains have been proposed to be the origin of the S. eubayanus subgenome of current S. pastorianus strains. The Himalayan S. eubayanus genomes harbored several copies of a SeAGT1 α-oligoglucoside transporter gene with high sequence identity to genes encountered in S. pastorianus. Although Himalayan S. eubayanus strains are unable to grown on maltose and maltotriose, their maltose-hydrolase and SeMALT1 and SeAGT1 maltose-transporter genes complemented the corresponding null mutants of S. cerevisiae. Expression, in a Himalayan S. eubayanus strain, of a functional S. cerevisiae maltose-metabolism regulator gene (MALx3) enabled growth on oligoglucosides. The hypothesis that the maltotriose-positive phenotype in S. pastorianus is a result of heterosis was experimentally tested by constructing a S. cerevisiae × S. eubayanus laboratory hybrid with a complement of maltose-metabolism genes that resembles that of current S. pastorianus strains. The ability of this hybrid to consume maltotriose in brewer’s wort demonstrated regulatory cross talk between sub-genomes and thereby validated this hypothesis. These results provide experimental evidence of the evolutionary origin of an essential phenotype of lager-brewing strains and valuable knowledge for industrial exploitation of laboratory-made S. pastorianus-like hybrids.ImportanceS.pastorianus, a S.cerevisiae X S.eubayanus hybrid, is used for production of lager beer, the most produced alcoholic beverage worldwide It emerged by spontaneous hybridization and have colonized early lager-brewing processes. Despite accumulation and analysis of genome sequencing data of S.pastorianus parental genomes, the genetic blueprint of industrially relevant phenotypes remains unknown. Assimilation of wort abundant sugar maltotriose has been postulated to be inherited from S.cerevisiae parent. Here, we demonstrate that although Asian S.eubayanus isolates harbor a functional maltotriose transporter SeAGT1 gene, they are unable to grow on α-oligoglucosides, but expression of S. cerevisae regulator ScMAL13 was sufficient to restore growth on trisaccharides. We hypothesized that S. pastorianus maltotriose phenotype results from regulatory interaction between S.cerevisae maltose transcription activator and the promoter of SeAGT1. We experimentally confirmed the heterotic nature of the phenotype and thus this results provide experimental evidence of the evolutionary origin of an essential phenotype of lager-brewing strains.

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“…A number of clades have become adapted to the production of fermented beverages or foods and these are regarded as prime examples of microbe domestication that quite often led to the existence of polyploid and/or aneuploid lineages (Strope et al 2015;Gallone et al 2016;Duan et al 2018;Peter et al 2018;Steensels et al 2019). The most widespread yeast-fermented product worldwide that uses another yeast "species" is lager beer, where fermentation is carried out by domesticated hybrids of S. cerevisiae and S. eubayanus (known as S. pastorianus and S. carlsbergensis) (Gallone et al 2019;Langdon et al 2019;Salazar et al 2019).…”

Section: Introductionmentioning

confidence: 99%

How to characterize a strain? The neglected influence of clonal heterogeneity on the phenotypes of industrialSaccharomyces

Rácz

Mukhtar

Imre

et al. 2020

Preprint

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Populations of microbes are constantly evolving heterogeneity that selection acts upon, yet heterogeneity is non-trivial to assess methodologically. The practice of isolating single cell colonies for establishing, transferring, and using a strain results in single-cell bottlenecks with a generally neglected effect on the characteristics of the strain. We used six industrial yeasts to assess the level of heterogeneity in clonal populations, especially in terms of stress tolerance. First, we uncovered the existence of genome structure variants in available sequenced genomes of clonal lineages of thes strains. Subsequent phenotyping of strains and their newly isolated subclones showed that single-cell bottlenecks during isolation can considerably influence the observable phenotype. Next, we decoupled fitness distributions on the level of individual cells from clonal interference by plating single cell colonies. We used the obtained data on colony area for statistical modeling of the heterogeneity in phenotypes. One strain was further used to show how individual subclonal lineages are remarkably different not just in phenotype, but also in the level of heterogeneity. Thereby we call attention to the fact that choosing an initial clonal lineage from an industrial yeast strain may vastly influence downstream performances and observations on geno- and phenotype, and also on heterogeneity.

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Nanopore sequencing and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization

Abstract: 22Background 23

Cited by 8 publications

References 101 publications

Himalayan Saccharomyces eubayanus Genome Sequences Reveal Genetic Markers Explaining Heterotic Maltotriose Consumption by Saccharomyces pastorianus Hybrids

Himalayan Saccharomyces eubayanus Genome Sequences Reveal Genetic Markers Explaining Heterotic Maltotriose Consumption by Saccharomyces pastorianus Hybrids

Maltotriose consumption by hybridSaccharomyces pastorianusis heterotic and results from regulatory cross-talk between parental sub-genomes

How to characterize a strain? The neglected influence of clonal heterogeneity on the phenotypes of industrialSaccharomyces

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