Evolutionary Selection on Barrier Activity: Bar1 Is an Aspartyl Protease with Novel Substrate Specificity

Limiting the Broadcast Range of a Secreting Cell during Intercellular Signaling Using Protease-Mediated Degradation

Synthetic biology is revolutionizing our approaches to biocomputing, diagnostics, and environmental monitoring through the use of designed genetic circuits that perform a function within a single cell. More complex functions can be performed by multiple cells that coordinate as they perform different subtasks. Cell-cell communication using molecular signals is particularly suited for aiding in this communication, but the number of molecules that can be used in different communication channels is limited. Here we investigate how proteases can limit the broadcast range of communicating cells. We find that adding barrierpepsin to Saccharomyces cerevisiae cells in two-dimensional multicellular networks that use α-factor signaling prevents cells beyond a specific radius from responding to α-factor signals. Such limiting of the broadcast range of cells could allow multiple cells to use the same signaling molecules to direct different communication processes and functions, provided that they are far enough from one another. These results suggest a means by which complex synthetic cellular networks using only a few signals for communication could be created by structuring a community of cells to create distinct broadcast environments.

Multiplex substrate profiling by mass spectrometry for proteases

Proteolysis is a central regulator of many biological pathways and the study of proteases has had a significant impact on our understanding of both native biology and disease. Proteases are key regulators of infectious disease and misregulated proteolysis in humans contributes to a variety of maladies, including cardiovascular disease, neurodegeneration, inflammatory diseases, and cancer. Central to understanding a protease's biological role, is characterizing its substrate specificity. This chapter will facilitate the characterization of individual proteases and complex, heterogeneous proteolytic mixtures and provide examples of the breadth of applications that leverage the characterization of misregulated proteolysis. Here we present the protocol of Multiplex Substrate Profiling by Mass Spectrometry (MSP-MS), a functional assay that quantitatively characterizes proteolysis using a synthetic library of physiochemically diverse, model peptide substrates, and mass spectrometry. We present a detailed protocol as well as examples of the use of MSP-MS for the study of disease states, for the development of diagnostic and prognostic tests, for the generation of tool compounds, and for the development of protease-targeted drugs.

Quantitative analysis of the yeast pheromone pathway

The pheromone response pathway of the yeast Saccharomyces cerevisiae is a well-established model for the study of G proteins and mitogen-activated protein kinase (MAPK) cascades. Our longstanding ability to combine sophisticated genetic approaches with established functional assays has provided a thorough understanding of signalling mechanisms and regulation. In this report, we compare new and established methods used to quantify pheromone-dependent MAPK phosphorylation, transcriptional induction, mating morphogenesis, and gradient tracking. These include both single-cell and population-based assays of activity. We describe several technical advances, provide example data for benchmark mutants, highlight important differences between newer and established methodologies, and compare the advantages and disadvantages of each as applied to the yeast model. Quantitative measurements of pathway activity have been used to develop mathematical models and reveal new regulatory mechanisms in yeast. It is our expectation that experimental and computational approaches developed in yeast may eventually be adapted to human systems biology and pharmacology.

Asymmetric diversification of mating pheromones in fission yeast

In fungi, mating between partners depends on the molecular recognition of two peptidyl mating pheromones by their respective receptors. The fission yeast Schizosaccharomyces pombe (Sp) has two mating types, Plus (P) and Minus (M). The mating pheromones P-factor and M-factor, secreted by P and M cells, are recognized by the receptors mating type auxiliary minus 2 (Mam2) and mating type auxiliary plus 3 (Map3), respectively. Our recent study demonstrated that a few mutations in both M-factor and Map3 can trigger reproductive isolation in S. pombe. Here, we explored the mechanism underlying reproductive isolation through genetic changes of pheromones/receptors in nature. We investigated the diversity of genes encoding the pheromones and their receptor in 150 wild S. pombe strains. Whereas the amino acid sequences of M-factor and Map3 were completely conserved, those of P-factor and Mam2 were very diverse. In addition, the P-factor gene contained varying numbers of tandem repeats of P-factor (4–8 repeats). By exploring the recognition specificity of pheromones between S. pombe and its close relative Schizosaccharomyces octosporus (So), we found that So-M-factor did not have an effect on S. pombe P cells, but So-P-factor had a partial effect on S. pombe M cells. Thus, recognition of M-factor seems to be stringent, whereas that of P-factor is relatively relaxed. We speculate that asymmetric diversification of the two pheromones might be facilitated by the distinctly different specificities of the two receptors. Our findings suggest that M-factor communication plays an important role in defining the species, whereas P-factor communication is able to undergo a certain degree of flexible adaptation–perhaps as a first step toward prezygotic isolation in S. pombe.

An asymmetric pheromone/receptor system in the fission yeast Schizosaccharomyces pombe might allow flexible adaptation of pheromones to mutational changes while maintaining stringent recognition for mating partners, perhaps as a first step toward prezygotic mating isolation.

The emergence of a new species might occur when two groups can no longer mate. Although such reproductive isolation is considered a key evolutionary process, the mechanisms by which it actually occurs have been confined to conjecture. The two sexes (Plus [P] and Minus [M]) of S. pombe each secrete a pheromone (P-factor and M-factor), which binds to a corresponding receptor (mating type auxiliary minus 2 [Mam2] and mating type auxiliary plus 3 [Map3]) on cells of the opposite sex. The interaction between a pheromone and its receptor is essential for successful mating. Here, we explored conservation of the mating pheromone communication system among 150 wild S. pombe strains of different geographical origins and the closely related species S. octosporus. We found that 1) the M-factor/Map3 interaction was completely conserved, whereas the P-factor/Mam2 interaction was very diverse in the strains investigated, and 2) most of the P-factor variants were functional across species. Thus, we have revealed an asymmetric pheromone/receptor system in fungal mating: namely, whereas M-factor communication operates extremely stringently, P-factor communication has the flexibility to create variations, perhaps facilitating prezygotic isolation in S. pombe.

Structure-Activity Relationship of α Mating Pheromone from the Fungal Pathogen Fusarium oxysporum

During sexual development ascomycete fungi produce two types of peptide pheromones termed a and α. The α pheromone from the budding yeast Saccharomyces cerevisiae, a 13-residue peptide that elicits cell cycle arrest and chemotropic growth, has served as paradigm for the interaction of small peptides with their cognate G protein-coupled receptors. However, no structural information is currently available for α pheromones from filamentous ascomycetes, which are significantly shorter and share almost no sequence similarity with the S. cerevisiae homolog. High resolution structure of synthetic α-pheromone from the plant pathogenic ascomycete Fusarium oxysporum revealed the presence of a central β-turn resembling that of its yeast counterpart. Disruption of the-fold by d-alanine substitution of the conserved central Gly6-Gln7 residues or by random sequence scrambling demonstrated a crucial role for this structural determinant in chemoattractant activity. Unexpectedly, the growth inhibitory effect of F. oxysporum α-pheromone was independent of the cognate G protein-coupled receptors Ste2 and of the central β-turn but instead required two conserved Trp1-Cys2 residues at the N terminus. These results indicate that, despite their reduced size, fungal α-pheromones contain discrete functional regions with a defined secondary structure that regulate diverse biological processes such as polarity reorientation and cell division.

Environmental Factors Can Influence Mitochondrial Inheritance in the Saccharomyces Yeast Hybrids

Mitochondria play a critical role in the generation of metabolic energy and are crucial for eukaryotic cell survival and proliferation. In most sexual eukaryotes, mitochondrial DNA (mtDNA) is inherited from only one parent in non-Mendelian inheritance in contrast to the inheritance of nuclear DNA. The model organism Saccharomyces cerevisiae is commonly used to study mitochondrial biology. It has two mating types: MATa and MATα. Previous studies have suggested that the mtDNA inheritance patterns in hybrid diploid cells depend on the genetic background of parental strains. However, the underlying mechanisms remain unclear. To elucidate the mechanisms, we examined the effects of environmental factors on the mtDNA inheritance patterns in hybrids obtained by crossing S. cerevisiae with its close relative S. paradoxus. The results demonstrated that environmental factors can influence mtDNA transmission in hybrid diploids, and that the inheritance patterns are strain dependent. The fitness competition assay results showed that the fitness differences can explain the mtDNA inheritance patterns under specific conditions. However, in this study, we found that fitness differences cannot fully be explained by mitochondrial activity in hybrids under stress conditions.

Hyphal chemotropism in fungal pathogenicity

The ability to grow as filamentous hyphae defines the lifestyle of fungi. Hyphae are exposed to a variety of chemical stimuli such as nutrients or signal molecules from mating partners and host organisms. How fungi sense and process this chemical information to steer hyphal growth is poorly understood. Saccharomyces cerevisiae and Neurospora crassa have served as genetic models for the identification of cellular components functioning in chemotropism. A recent study in the pathogen Fusarium oxysporum revealed distinct MAPK pathways governing hyphal growth towards nutrient sources and sex pheromones or plant signals, suggesting an unanticipated complexity of chemosensing during fungus-host interactions.