Identification of a complex genetic network underlying Saccharomyces cerevisiae colony morphology

Abstract

When grown on solid substrates, different microorganisms often form colonies with very specific morphologies. Whereas the pioneers of microbiology often used colony morphology to discriminate between species and strains, the phenomenon has not received much attention recently. In this study, we use a genome-wide assay in the model yeast Saccharomyces cerevisiae to identify all genes that affect colony morphology. We show that several major signalling cascades, including the MAPK, TORC, SNF1 and RIM101 pathways play a role, indicating that morphological changes are a reaction to changing environments. Other genes that affect colony morphology are involved in protein sorting and epigenetic regulation. Interestingly, the screen reveals only few genes that are likely to play a direct role in establishing colony morphology, with one notable example being FLO11, a gene encoding a cell-surface adhesin that has already been implicated in colony morphology, biofilm formation, and invasive and pseudohyphal growth. Using a series of modified promoters for fine-tuning FLO11 expression, we confirm the central role of Flo11 and show that differences in FLO11 expression result in distinct colony morphologies. Together, our results provide a first comprehensive look at the complex genetic network that underlies the diversity in the morphologies of yeast colonies.

Aneuploidy underlies a multicellular phenotypic switch

“…Our results are consistent with either of two models. First, because numerous biological processes are required to form a fluffy colony (26)(27)(28), these five chromosomes could each contain dosage sensitive genes necessary for the function or regulation of key processes. Alternatively, the fluffy state could be sensitive to some more general aspect of aneuploidy, such as the DNA content of the cell.…”

“…The surprisingly large number of chromosomes able to modulate the phenotypic toggle between fluffy and smooth may be proportional to the relatively large number of pathways required for the fluffy morphology (26)(27)(28) or may indicate that the trait is particularly sensitive to changes in gene dosage. In either case, the fact that aneuploidy provides cells multiple routes to the same phenotypic endpoint has fundamental implications for understanding how organisms respond to environmental perturbations.…”

“…These "fluffy" colonies possess properties similar to those of microbial biofilms, including the secretion and maintenance of an extracellular matrix (21)(22)(23), localized expression of drug efflux pumps (23), increased adherence (24), and the use of cell-cell communication (25). Fluffy colony formation requires the function and coordination of numerous pathways that underlie the trait, and the deletion of key factors produces a smooth colony phenotype (26)(27)(28). Fluffy colonies may benefit from both rapid acquisition of larger territories as well as an increased capacity for nutrient and water transport (21).…”

Global Regulation of a Differentiation MAPK Pathway in Yeast

“…An ordered collection of 4072 deletion mutants constructed in the filamentous (MATa S1278b) background (provided by the Boone Lab, Toronto, ON; Ryan et al 2012) was screened for changes in colony morphology (Granek and Magwene 2010;Voordeckers et al 2012) and invasive growth based on the plate-washing assay (Roberts and Fink 1994) to identify regulators of filamentous growth. These assays provide a readout of filamentous growth that correlate with the activity of the filamentous growth MAPK pathway ( Figure 1B; Roberts and Fink 1994).…”

“…The plate washing (Roberts and Fink 1994) and single-cell invasive growth assays (Cullen and Sprague 2000) were used to measure filamentous growth. Colony morphology was examined by visual inspection on YEPD media (Granek and Magwene 2010;Voordeckers et al 2012). Functional analysis of the MAPK regulatory genes came from SGD (http://www.yeastgenome.org).…”