Functional genomics in the study of yeast cell polarity: moving in the right direction

Abstract

The budding yeast Saccharomyces cerevisiae has been used extensively for the study of cell polarity, owing to both its experimental tractability and the high conservation of cell polarity and other basic biological processes among eukaryotes. The budding yeast has also served as a pioneer model organism for virtually all genome-scale approaches, including functional genomics, which aims to define gene function and biological pathways systematically through the analysis of high-throughput experimental data. Here, we outline the contributions of functional genomics and high-throughput methodologies to the study of cell polarity in the budding yeast. We integrate data from published genetic screens that use a variety of functional genomics approaches to query different aspects of polarity. Our integrated dataset is enriched for polarity processes, as well as some processes that are not intrinsically linked to cell polarity, and may provide new areas for future study.

Keywords: Saccharomyces cerevisiae; functional genomics; genetics; microscopy; polarity; proteomics.

Figure 1.

An overview of Cdc42 regulation during polarized bud growth. (a) Budding occurs when the cell switches from isotropic to apical cell growth, leading to the formation of a bud. (b) Bud-site selection protein Rsr1 activates the GEF Cdc24, which converts Cdc42 to its active GTP-bound state. Activated Cdc42 binds to numerous effectors, promoting actin patch nucleation, actin cable assembly and septin/actomyosin ring assembly.

Figure 2.

An overview of Cdc42 regulation during mating. (a) Mating begins after exposure to mating pheromone from cells of the opposite mating type, which leads to the outgrowth of a mating projection, or ‘shmoo’. (b) The same Cdc42-based machinery used in budding drives polarized cell growth and shmoo formation during mating. In addition to regulating polarized secretion, Cdc42 also regulates the mating MAPK signalling pathway to turn on mating-specific genes required for cell fusion and the cyclin-dependent kinase inhibitor Far1, leading to G1 arrest.

Figure 3.

An overview of Cdc42 regulation during filamentous growth. (a) Filamentous growth occurs when cells elongate and exhibit enhanced cell adhesion, leading to a switch from yeast cell form to filamentous form. (b) Filamentation occurs when nitrogen starvation is sensed by Sho1 and Msb2, leading to the activation of Cdc42 and the downstream activation of the MAPK pathway. This leads to both cell elongation via a G2 delay as well as the expression of the flocculin Flo11 and other adhesion proteins.

Figure 4.

An overview of functional genomics approaches in the study of polarity. This review focuses on the use of genomic, cell biological and proteomic assays to study polarity in yeast.

Figure 5.

Biological processes enriched in genomic polarity screens. A network diagram was created with Cytoscape and BiNGO to visualize biological GO Slim processes that are enriched in a set of 35 genome-wide genetic polarity screens (n = 485).