Research Lab

Yeast Genomics

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Research Interests

We use yeasts to study basic and applied aspects of microbial physiology, fungal development and evolutionary ecology. We address questions related to sugar utilization in yeast fermentations, to the evolution of sex in early diverged lineages of Basidiomycetes, or to the distribution and ecology of wild Saccharomyces populations and their domestication by man. To do so we combine the awesome power of Next-Generation (whole-genome) Sequencing with in-depth physiological and ecological studies.

Our work includes computational and experimental methods and integrates genomics, evolutionary genetics, ecology, microbial diversity and physiology.

Research Highlights
Evidence for Loss and Reacquisition of alcoholic fermentation in yeasts (PI Paula Gonçalves)

Fructophily is a rare trait that consists of the preference for fructose over other carbon sources. We showed that in a yeast lineage comprised of fructophilic species thriving in the high-sugar floral niche, the acquisition of fructophily is concurrent with a wider remodelling of central carbon metabolism. Coupling comparative genomics with biochemical and genetic approaches, we gathered ample evidence for the loss of alcoholic fermentation in an ancestor of the W/S clade and subsequent reinstatement through either horizontal acquisition of homologous bacterial genes or modification of a pre-existing yeast gene.

Evidence for Loss and Reacquisition of alcoholic fermentation in yeasts

 

We found that early in their evolutionary history, fructophilic yeasts lost the genes that allowed them to conduct alcoholic fermentation (ADH1 and PDC1) . However, at a later point in time, these yeasts had to adapt to survive in flower nectar, a sugar rich environment. They then favored fructose as their source of energy, possibly because this sugar can compensate more effectively for the impact of the absence of alcoholic fermentation in central metabolism. Later, the yeasts horizontally acquired a gene from bacteria, which restored alcoholic fermentation again. This improved sugar metabolism further, impacting in particular glucose assimilation.
The multiscales of microbe domestication (PI José Paulo Sampaio)

Although it is known that yeasts, together with other microbes underwent a domestication process equivalent to those already known for plant crops and livestock, a detailed understanding of the genetic mechanisms of the transition from wild to domesticate has not yet been achieved. We revealed a scenario more complex than previously thought, with transitions from wild to domesticate combined with primary and secondary domestication states. (Barbosa et al. 2018).

Representative Projects

  • “Exploring unique metabolic traits of biotechnological interest in fructophilic yeasts”, FCT-MCTES, Total funding: €238,347, Unit funding: €182,997, Paula Gonçalves (PI)
  • “Advancing wine yeast genomics – exploring the evolutionary dimensions of domestication and the emergence of virulence”, FCT-MCTES, Total funding: € 239,997, Unit funding: €210,550, José Paulo Sampaio (PI).
  • “Contract Research Microbiology”, Victor Guedes SA, Total and Unit funding: €20,000, José Paulo Sampaio and Paula Gonçalves (PIs).
  • “Contract Research Microbiology”, Fermentis Lasaffre for Beverages, Total and Unit funding: €10,000, José Paulo Sampaio (PI).

Selected Publications

Pontes, A; Cadez, N; Goncalves, P; Sampaio, JP. 2019. A Quasi-Domesticate Relic Hybrid Population of Saccharomyces cerevisiae x S. paradoxus Adapted to Olive Brine. Frontiers in Genetics, 10, DOI: 10.3389/fgene.2019.00449
Sampaio, JP. 2018. Microbe Profile: Saccharomyces eubayanus, the missing link to lager beer yeasts. MICROBIOLOGY-SGM, 164, DOI: 10.1099/mic.0.000677
Nilsson, RH; Taylor, AFS; Adams, RI; Baschien, C; Bengtsson-Palme, J; Cangren, P; Coleine, C; Daniel, HM; Glassman, SI; Hirooka, Y; Irinyi, L; Irsenaite, R; Martin-Sanchez, PM; Meyer, W; Oh, SY; Sampaio, JP; Seifert, KA; Sklenar, F; Stubbe, D; Suh, SO; Summerbell, R; Svantesson, S; Unterseher, M; Visagie, CM; Weiss, M; Woudenberg, JHC; Wurzbacher, C; Van den Wyngaert, S; Yilmaz, N; Yurkov, A; Koljalg, U; Abarenkov, K. 2018. Taxonomic annotation of public fungal ITS sequences from the built environment - a report from an April 10-11, 2017 workshop (Aberdeen, UK). MycoKeys, DOI: 10.3897/mycokeys.28.20887
Pontes, A; Rohl, A; MaLdonado, C; Yurkov, AM; Sampaio, JP. 2017. Cryptotrichosporon argae sp nov., Cryptotrichosporon brontae sp nov and Cryptotrichosporon steropae sp nov., isolated from forest soils. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 67, DOI: 10.1099/ijsem.0.002177
Peris, D; Moriarty, RV; Alexander, WG; Baker, E; Sylvester, K; Sardi, M; Langdon, QK; Libkind, D; Wang, QM; Bai, FY; Leducq, JB; Charron, G; Landry, CR; Sampaio, JP; Goncalves, P; Hyma, KE; Fay, JC; Sato, TK; Hittinger, CT. 2017. Hybridization and adaptive evolution of diverse Saccharomyces species for cellulosic biofuel production. Biotechnology for Biofuels, 10, DOI: 10.1186/s13068-017-0763-7