An extracellular matrix composed of a layered meshwork of β-glucans, chitin, and mannoproteins encapsulates cells of the yeast Saccharomyces cerevisiae. This organelle determines cellular morphology and plays a critical role in maintaining cell integrity during cell growth and division, under stress conditions, upon cell fusion in mating, and in the durable ascospore cell wall. Here we assess recent progress in understanding the molecular biology and biochemistry of cell wall synthesis and its remodeling in S. cerevisiae. We then review the regulatory dynamics of cell wall assembly, an area where functional genomics offers new insights into the integration of cell wall growth and morphogenesis with a polarized secretory system that is under cell cycle and cell type program controls.

Cell Wall Assembly in Saccharomyces cerevisiae

Function and regulation in MAPK signaling pathways: Lessons learned from the yeast Saccharomyces cerevisiae

Availability of key nutrients, such as sugars, amino acids, and nitrogen compounds, dictates the developmental programs and the growth rates of yeast cells. A number of overlapping signaling networks—those centered on Ras/protein kinase A, AMP-activated kinase, and target of rapamycin complex I, for instance—inform cells on nutrient availability and influence the cells’ transcriptional, translational, posttranslational, and metabolic profiles as well as their developmental decisions. Here I review our current understanding of the structures of the networks responsible for assessing the quantity and quality of carbon and nitrogen sources. I review how these signaling pathways impinge on transcriptional, metabolic, and developmental programs to optimize survival of cells under different environmental conditions. I highlight the profound knowledge we have gained on the structure of these signaling networks but also emphasize the limits of our current understanding of the dynamics of these signaling networks. Moreover, the conservation of these pathways has allowed us to extrapolate our finding with yeast to address issues of lifespan, cancer metabolism, and growth control in more complex organisms.

https://www.genetics.org/content/genetics/192/1/73.full.pdf

Nutritional Control of Growth and Development in Yeast

Yeast cells sense the amount and quality of external nutrients through multiple interconnected signaling networks, which allow them to adjust their metabolism, transcriptional profile and developmental program to adapt readily and appropriately to changing nutritional states. We present our current understanding of the nutritional sensing networks yeast cells rely on for perceiving the nutritional landscape, with particular emphasis on those sensitive to carbon and nitrogen sources. We describe the means by which these networks inform the cell's decision among the different developmental programs available to them-growth, quiescence, filamentous development, or meiosis/sporulation. We conclude that the highly interconnected signaling networks provide the cell with a highly nuanced view of the environment and that the cell can interpret that information through a sophisticated calculus to achieve optimum responses to any nutritional condition.

How Saccharomyces Responds to Nutrients

The SNF1/AMPK family of protein kinases is highly conserved in eukaryotes and is required for energy homeostasis in mammals, plants, and fungi. SNF1 protein kinase was initially identified by genetic analysis in the budding yeast Saccharomyces cerevisiae. SNF1 is required primarily for the adaptation of yeast cells to glucose limitation and for growth on carbon sources that are less preferred than glucose, but is also involved in responses to other environmental stresses. SNF1 regulates transcription of a large set of genes, modifies the activity of metabolic enzymes, and controls various nutrient-responsive cellular developmental processes. Like AMPK, SNF1 protein kinase is heterotrimeric. It is phosphorylated and activated by the upstream kinases Sak1, Tos3, and Elm1 and is inactivated by the Reg1-Glc7 protein phosphatase 1. Further regulation of SNF1 is achieved through autoinhibition and through control of its subcellular localization. Here we review the current understanding of SNF1 protein kinase pathways in Saccharomyces cerevisiae and other yeasts.

SNF1/AMPK pathways in yeast.

Simple fungi have evolved sophisticated mechanisms to sense and respond to environmental cues by activating developmental switches that result in coordinated changes in cell physiology, morphology and cell adherence. Critical depletion of nutrients often induces growth arrest to form spores capable of tolerating a wide range of environmental stresses. However, an alternative response is the dimorphic switch to filamentous growth, characterized by branching networks of chains of cells or hyphae to form a mycelium (Gancedo, 2001; Kron & Gow, 1995). Filamentous growth is considered an important adaptive response that functions analogously to cell motility in allowing a starving fungal colony to forage for nutrients (Lee & Elion, 1999). Branching filaments permit wider exploration of the environment at a lower biomass (energy) cost than nonfilamentous growth. Cell–cell adherence and highly polarized growth promote invasion of the substrate (Gancedo, 2001). Further, the high surface-to-volume ratio of filaments may facilitate transport of nutrients. The dimorphic switch is essentially modular and may be activated by a wide range of stimuli appropriate to the lifestyle of the fungus. Typically, the dimorphic switch in pathogenic fungi is tuned such that cells elongate or increase cell–cell adherence when exposed to their host (San-Blas et al., 2000; Sanchez-Martinez & Perez-Martin, 2001). Such regulated dimorphism has been established as an important virulence factor, determining invasion and colonization by pathogenic organisms such as Candida albicans, Magnaporthe grisea (rice blast) and Ustilago maydis (corn smut) (Lengeler et al., 2000; Sanchez-Martinez & PerezMartin, 2001). Thus the dimorphic switch may prove to be an attractive target for chemical intervention in the prophylaxis and treatment of fungal infections in medicine and agriculture. In turn, many industrial biochemical processes employ dimorphic yeasts and filamentous fungi to drive production of desired chemical compounds. Fermentation of carbohydrates in fruits, grains and other biomass to ethanol by Saccharomyces cerevisiae is the critical process for a wide range of products from fine wines to gasoline additives (Bothast et al., 1999; Pretorius, 2000). S. cerevisiae and other simple fungi are also widely utilized in industrial production of small-molecule metabolites such as citrate and amino acids, bioremediation of toxic contaminants, fermentation of foodstuffs, production of complex organic compounds such as antibiotics, growth of starting material for protein purifications, and expression of heterologous proteins for vaccines, drugs and enzymes (Bennett, 1998; Chartrain et al., 2000; Ostergaard et al., 2000). The manner of organism proliferation, whether in a dispersed or aggregated form, is potentially a limiting factor in production of the desired metabolite(s), utilization of the growth medium and}or separation of cell mass from the soluble product. The classic example of self-clearing of beers at the end of the fermentation by the flocculation and settling of ale yeast underlines that control over cell morphology and}or cell–cell adhesion is a highly desirable characteristic of an industrial micro-organism (Hammond, 1995; Straver et al., 1993). A detailed understanding of how metabolite sensing and signalling leads to changes in physical properties of cells will be critical for cellular engineering approaches to control dimorphism. For example, maintaining cell dispersion is desired during a fermentation to maximize mass transport and reaction rates but inducing flocculation can facilitate separation of the cells from fermentation products. In turn, it should be kept inmind that adhesion and morphology are not the only characteristics that change during the dimorphic transition. Many fungi also switch their patterns of metabolic conversions, gene expression and protein secretion (Viard & Kuriyama,

REVIEW ARTICLE Sensing, signalling and integrating physical processes during Saccharomyces cerevisiae invasive and filamentous growth

Sensing, signalling and integrating physical processes during Saccharomyces cerevisiae invasive and filamentous growth

Under inducing conditions, haploid Saccharomyces cerevisiae perform a dimorphic transition from yeast-form growth on the agar surface to invasive growth, where chains of cells dig into the solid growth medium. Previous work on signaling cascades that promote agar invasion has demonstrated upregulation of FLO11, a cell-surface flocculin involved in cell-cell adhesion. We find that increasing FLO11 transcription is sufficient to induce both invasive and filamentous growth. A genetic screen for repressors of FLO11 isolated mutant strains that dig into agar (dia) and identified mutations in 35 different genes: ELM1, HSL1, HSL7, BUD3, BUD4, BUD10, AXL1, SIR2, SIR4, BEM2, PGI1, GND1, YDJ1, ARO7, GRR1, CDC53, HSC82, ZUO1, ADH1, CSE2, GCR1, IRA1, MSN5, SRB8, SSN3, SSN8, BPL1, GTR1, MED1, SKN7, TAF25, DIA1, DIA2, DIA3, and DIA4. Indeed, agar invasion in 20 dia mutants requires upregulation of the endogenous FLO11 promoter. However, 13 mutants promote agar invasion even with FLO11 clamped at a constitutive low-expression level. These FLO11 promoter-independent dia mutants establish distinct invasive growth pathways due to polarized bud site selection and/or cell elongation. Epistasis with the STE MAP kinase cascade and cytokinesis/budding checkpoint shows these pathways are targets of DIA genes that repress agar invasion by FLO11 promoter-dependent and -independent mechanisms, respectively.

https://www.genetics.org/content/genetics/156/3/1005.full.pdf

Genetic analysis reveals that FLO11 upregulation and cell polarization independently regulate invasive growth in Saccharomyces cerevisiae.

Haploid Saccharomyces cerevisiae cells growing on media lacking glucose but containing high concentrations of carbon sources such as fructose, galactose, raffinose, and ethanol exhibit enhanced agar invasion. These carbon sources also promote diploid filamentous growth in response to nitrogen starvation. The enhanced invasive and filamentous growth phenotypes are suppressed by the addition of glucose to the media and require the Snf1 kinase. Mutations in the PGI1 and GND1 genes encoding carbon source utilization enzymes confer enhanced invasive growth that is unaffected by glucose but requires active Snf1. Carbon source does not modulate FLO11 flocculin expression, but enhanced polarized bud site selection is necessary for invasion on certain carbon sources. Interestingly, deletion of SNF1 blocks invasion without affecting bud site selection. Snf1 is also required for formation of spokes and hubs in multicellular mats. To examine glucose repression of invasive growth more broadly, we performed genome-wide microarray expression analysis in wild-type cells growing on glucose and galactose, and snf1 Delta cells on galactose. SNF1 probably mediates glucose repression of multiple genes potentially involved in invasive and filamentous growth. FLO11-independent cell-cell attachment, cell wall integrity, and/or polarized growth are affected by carbon source metabolism. In addition, derepression of cell cycle genes and signalling via the cAMP-PKA pathway appears to depend upon SNF1 activity during growth on galactose.

https://www.onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-2958.2002.03024.x

Archita S. Parikh

Papers

REVIEW ARTICLE Sensing, signalling and integrating physical processes during Saccharomyces cerevisiae invasive and filamentous growth

Sensing, signalling and integrating physical processes during Saccharomyces cerevisiae invasive and filamentous growth

Genetic analysis reveals that FLO11 upregulation and cell polarization independently regulate invasive growth in Saccharomyces cerevisiae.

Depression of Saccharomyces cerevisiae invasive growth on non-glucose carbon sources requires the Snf1 kinase