Microbiology

Functional yeast genomics

In our group we aim for an understanding how predacious yeasts manage to infect fungal prey cells and kill them. This specific behaviour is unique to a group of yeasts belonging to the genus Saccharomycopsis. We have begun to study the biology of the predatory yeasts, which were isolated and reported by André Lachance in 1997. Key events in a predation event are predator-prey cell-cell attachment, penetration peg formation, prey cell invasion and killing of the prey.

Comparative and evolutionary genomics are used to provide insight into the genome make-up of predator yeasts. Our goal is to determine key genes and gene families involved in predator-prey recognition and successful predation. As genetically tractable preys we use the yeast Saccharomyces cerevisiae and the filamentous fungus Ashbya gossypii.

The host range of predator yeasts, i.e. the range of fungal species that can successfully be killed, is apparently quite wide and also includes serious plant pathogenic fungi, e.g. Fusarium. Further understanding of the predation mechanisms and the host range of predatory yeasts will promote their development into antifungal biocontrol agents in sustainable agricultural pest management.

Currently we concentrate on two central themes:

1. Genomics and transcriptomics of predator yeasts

We have generated several high quality draft genome sequences of predator yeasts using Illumina HighSeq next-generation sequencing and currently refine the genome annotations. In collaboration Maitreya Dunham's group (University of Washington, Seattle) we have determined the position of predator yeast centromere loci using chromatin conformation capture sequencing, Hi-C. For further refinement of our genome annotation we use PacBio sequencing.The identification of key genes required for predation is tackled by using RNAseq.

2. Development of tools for functional analysis of predator genes

Molecular studies on predator yeasts have been very limited. Therefore, we are currently establishing functional analysis tools to be able to characterize the role of target genes for predation. This includes designing synthetic marker genes, e.g. SAK1 conferring resistance to the antibiotic G418, identifying promoters for constitutive and regulated gene expression as well as establishing in vivo protein localization tools, e.g GFP and LifeAct.

Previously, we have used comparative and evolutionary genomics to gain insight into the adaptive evolution of fungal species. Here, we put our efforts on the genus Eremothecium within the Saccharomyces clade that harbors filamentous fungi closely related to yeasts.

Genomics of lager yeasts indentified key differences within the two groups of lager yeasts. This promotes genome based molecular yeast breeding that opens new routes to non-GMO production strain enhancement, e.g. with increased flavor production, increased fermentation speed, co-fermentations, more/less ethanol production, genome streamlining or increased fertility. Our current focus in this area is on flavor regulation and enhancement of flavor notes in lager yeast strains.

Our prime models for studying developmental biology and fungal growth have been Ashbya gossypii and Candida albicans. The current focus of our research is on sporulation, spore germination and colony development in Ashbya gossypii. We have determined the set of sporulation genes in A. gossypii using an RNAseq approach combined with functional analysis of key sporulation genes. This has identified a central role of the cAMP-protein kinase A pathway for sporulation.

Synthetic biology uses basic research knowledge to generate novel machines or improve platform production strains. This provides novel opportunities to enhance the use of yeasts in biotechnology, which we are beginning to exploit. We have generated a S. cerevisiae yeast strain that can utilize N-Acetyl-glucosamine (building block for chitin) by transferring four genes from Candida albicans into Saccharomyces cerevisiae. To generate novel strains a set of strain builder tools is required based on the use of platform strains as hosts for new funtionalities.

 

Recent Publications:

  • Volume Editor of MYCOTA Vol I, 3rd edition: Growth, Differentiation and Sexuality (2016).
  • Bertheussen, E., Verdaguer-Casadevall, A., Ravasio, D., Montoya, J.H., Trimarco, D.B., Roy, C., Meier, S., Wendland, J., Nørskov, J.K., Stephens, I.E.L., Chorkendorff, I. (2016). “Acetaldehyde as an Intermediate in the Electroreduction of Carbon Monoxide to Ethanol on Oxide-derived Copper.” Angewandte Chemie, 55:1450-1454.
  • Wasserstrom, L., Lengeler, K.B., Walther, A. and Wendland, J. (2015). “Developmental growth control exerted via the A Kinase Tpk2 in Ashbya gossypii.” Eukaryotic Cell, 14:593-601.
  • Walther; A., Ravasio, D., Qin, F., Wendland, J. and Meier, S. (2015). “Development of brewing science in (and since) the late 19th century: Molecular profiles of 110–130 year old beers”. Food Chemistry 183:227–234

 

Previous publications:

Yeast Genomics

  • Wendland, J. and Walther, A. (2014). “Chromosome number reduction by two telomere-to-telomere fusions in the Eremothecium coryli genome”. Genome Biology and Evolution; 6:1186-98.
  • Walther, A., Hesselbart, A. and Wendland, J. (2014). “Genome sequence of Saccharomyces carlsbergensis, the world’s first pure culture lager yeast”. G3: Genes Genomes, Genetics; 4:783-93.
  • Wendland, J. and Walther, A. (2011). “Genome evolution in the Eremothecium clade of the Saccharomyces complex revealed by comparative genomics”. G3: Genes Genomes, Genetics; 1:539-548.

 

Fungal growth and physiology:

  • Wasserstrom, L., Lengeler, K.B., Walther, A. and Wendland, J. (2013). „Molecular Determinants of Sporulation in Ashbya gossypii”. GENETICS, 195(1):87-99.
  • Walther, A. and Wendland, J. (2012). “Yap1-dependent oxidative stress response provides a link to riboflavin production in Ashbya gossypii”. Fungal Genetics & Biology, 49(9):697-707.
  • Lengeler, K.B., Wasserstrom, L., Walther, A. and Wendland, J. (2013). “Impact of the cell wall integrity pathway on hyphal growth, colony morphogenesis, and riboflavin production in Ashbya gossypii”. Microbiological Research, 168:607-614.
  • Wendland, J., Dünkler, A., and Walther, A. (2011). “Characterization of components of the Ashbya gossypii mating pheromone response pathway”. FEMS Yeast Research, 11(5):418-29.
  • Jorde, S., Walther, A., and Wendland, J. (2011). „The Ashbya gossypii fimbrin SAC6 is required for fast polarized hyphal tip growth and endocytosis”. Microbiological Research, 166:137-45.
  • Borth, N., Walther, A., Reijnst, P., Jorde, S., Schaub, Y., and Wendland, J. (2010). „Candida albicans Vrp1 is required for polarized morphogenesis and interacts with Wal1 and Myo5”. Microbiology, 156: 2962-2969.
  • Grünler, A., Walther, A., Lämmel, J., and Wendland, J. (2010) “ Analysis of flocculins in Ashbya gossypii reveals FIG2 regulation by TEC1”. Fungal Genetics & Biology, 47:619-628.
  • Epp, J., Walther, A., Lépine, G., Leon, Z., Mullick, A., Raymond, M., Wendland, J., and Whiteway; M. (2010) “Forward genetics in Candida albicans that reveals the Arp2/3 complex is required for hyphal formation, but not endocytosis.” Molecular Microbiology, 75:1182-98.

 

SynMicro, Methods and Tools

  • Wendland, J., Schaub, Y., and Walther, A. (2009). „GlcNAc utilization by Saccharomyces cerevisiae based on the expression of Candida albicans NAG-genes.” Applied and Environmental Microbiology, 75: 5840-5845.
  • Walther, A. and Wendland, J. (2008). PCR-based gene targeting in Candida albicans. Nature Protocols, 3:1414-24.
  • Reijnst, P., Walther, A., and Wendland, J. (2011) “Dual-colour fluorescence microscopy using yEmCherry-/GFP-tagging of eisosome components Pil1 and Lsp1 in Candida albicans.” Yeast, 28: 331-338
  • Schaub, Y., Dünkler, A., Walther, A., and Wendland, J. (2006). New pFA-cassettes for PCR-based gene manipulation in Candida albicans. J. Basic Microbiol., 46: 417-430.
  • Gola, S., Martin, R., Walther, A., Dünkler, A., and Wendland, J. (2003) New modules for PCR-based gene targeting in Candida albicans: Rapid and efficient gene targeting using 100bp of flanking homology region. Yeast, 20:1339-1347.

 

Molecular Yeast Breeding

  • Ravasio, D., Walther, A. and Wendland, J. (2014). “Major contribution of the Ehrlich Pathway for 2-phenylethanol/ rose flavor production in Ashbya gossypii”. FEMS Yeast Research, 2014 Jun 11. doi: 10.1111/1567-1364.12172.
  • Ravasio, D., Walther, A., Trost, K., Vrhovsek, U. and Wendland, J. (2014). “An indirect assay for volatile compound production in yeast strains”. Scientific Reports, 4:3707.
  • Garcia Sanchez, R., Solodovnikova, N. and Wendland, J. (2012). "Breeding of lager yeast with Saccharomyces cerevisiae improves stress resistance and fermentation performance”. Yeast,.29: 343-355

 

Reviews:

  • Wendland, J. (2014). “Lager yeast comes of age”. Eukaryotic Cell, 13(10):1256-1265.
  • Perez-Nadales E., Almeida Nogueira M.F., Baldin C., Castanheira S., El Ghalid M., Grund E., Lengeler K., Marchegiani E., Mehrotra P.V., Moretti M., Naik V., Oses-Ruiz M., Oskarsson T., Schäfer K., Wasserstrom L., Brakhage A.A., Gow N.A., Kahmann R., Lebrun M.H., Perez-Martin J., Di Pietro A., Talbot N.J., Toquin V., Walther A. and Wendland J. (2014). “Fungal model systems and the elucidation of pathogenicity determinants”. Fungal Genetics & Biology, 70C:42-67.
  • Nicolas Rispail, Darren Soanes, Cemile Ant, Robert Czajkowsky, Anke Grünler, Romain Huguet, Elena Perez-Nadales, Anna Poli, Elodie Sartorel, Vito Valiante, Meng Yang, Roland Beffa, Axel A. Brakhage, Neil A. R. Gow, Regine Kahmann, Marc-Henri Lebrun, Helena Lenasi, José Perez-Martin, Nicholas J. Talbot, Jürgen Wendland, Antonio Di Pietro. (2009). Comparative genomics of MAP kinase and calcium-calcineurin signalling components in fungal plant and human pathogens. Fungal Genetics & Biologgy, 46: 287-298.
  • Wendland, J. and Walther, A. (2008). Hyphal growth and virulence in Candida albicans. THE MYCOTA Vol. II., Ed A. Brakhage and R. Zipfel, Springer, Heidelberg, Germany, pp 95-114.
  • Wendland J. and Walther A. (2005) Ashbya gossypii: a model for fungal developmental biology. Nature Reviews Microbiology, 3: 421-429.
  • Wendland, J. (2003) PCR-based methods facilitate targeted gene manipulations and cloning procedures. Current Genetics, 44(3):115-123.
  • Walther, A. and Wendland, J. (2003) An improved transformation protocol for the human fungal pathogen Candida albicans. Current Genetics, 42(6):339-343.