Morphologically-structured models of growing budding yeast populations

It has been well recognized that many key aspects of cell cycle regulation are encoded into the size distributions of growing budding yeast populations due to the tight coupling between cell growth and cell division present in this organism. Several attempts have been made to model the cell size distribution of growing yeast populations in order to obtain insight on the underlying control mechanisms, but most were based on the age structure of asymmetrically dividing populations. Here we propose a new framework that couples a morphologically-structured representation of the population with population balance theory to formulate a dynamic model for the size distribution of growing yeast populations. An advantage of the presented framework is that it allows derivation of simpler models that are directly identifiable from experiments. We show how such models can be derived from the general framework and demonstrate their utility in analyzing yeast population data. Finally, by employing a recently proposed numerical scheme, we proceed to integrate numerically the full distributed model to provide predictions of dynamics of the cell size structure of growing yeast populations.     

Structural heterogeneity in populations of the budding yeast Saccharomyces cerevisiae.

Bud scar analysis integrated with mathematical analysis of DNA and protein distributions obtained by flow microfluorometry have been used to analyze the cell cycle of the budding yeast Saccharomyces cerevisiae. In populations of this yeast growing exponentially in batch at 30 degrees C on different carbon and nitrogen sources with duplication times between 75 and 314 min, the budded period is always shorter (approximately 5 to 10 min) than the sum of the S + G2 + M + G1* phases (determined by the Fried analysis of DNA distributions), and parent cells always show a prereplicative unbudded period. The analysis of protein distributions obtained by flow microfluorometry indicates that the protein level per cell required for bud emergence increases at each new generation of parent cells, as observed previously for cell volume. A wide heterogeneity of cell populations derives from this pattern of budding, since older (and less frequent) parent cells have shorter generation times and produce larger (and with shorter cycle times) daughter cells. A possible molecular mechanism for the observed increase with genealogical age of the critical protein level required for bud emergence is discussed.     

Steady-State growth of budding yeast populations in well-mixed continous-flow microbial reactors

A population-balance mathematical model of microbial growth in a flow reactor is formulated which incorporates an asymmetric-division, budding-cycle model of coordinated cell and nuclear division cycles for the budding yeast Saccharomyces cerevisiae. Analytical solutions are obtained for limiting nutrient and cell-number concentrations in the reactor as functions of basic cell cycle parameters. Frequency functions for cell mass and DNA content in the resident yeast population are also derived under different assumptions concerning cell mass and DNA synthesis and bud scar accumulation. These results, which correspond to experimentally observable medium and population variables, provide new bases for evaluating budding-yeast-cell cycle models and for deducing kinetics of mass and DNA synthesis in single cells growing in steady-state, asynchronous populations.     

Plasmid stability in budding yeast populations: Steady-state growth with selection pressure

Plasmid gene product accumulation in a cell population depends on the fraction of plasmid-containing cells and the distribution of single-cell plasmid content. These important population properties have been related to plasmid replication regulation and kinetics and to plasmid segregation rules at the single-cell level using population balance mathematical models. Budding yeast populations are considered in detail because of the practical potential of yeast host-vector systems and because of the model complications introduced by the asymmetric division pattern observed for Saccharomyces cerevisiae at all but the largest growth rates. Solutions are presented for several different reasonable models of plasmid replication and segregation. The results offer potential for identification of important qualitative features of yeast plasmid replication and of model parameter values from average and segregated experimental data on yeast populations.     

A note on modelling the dynamics of budding yeast populations using branching processes

A multitype branching process is proposed as a model for the behaviour of populations of the budding yeast Saccharomyces Cerevisiae. Using the idea of branching processes counted by random characteristics, we are able to obtain explicit expressions describing different aspects of the asymptotic composition of such populations. The main purpose of this note is to show that the branching process approach is an alternative to deterministic population models based on differential equation methods.Supported by the Swedish Natural Science Research Council     

Transient sister chromatid separation and elastic deformation of chromosomes during mitosis in budding yeast

The accurate segregation of chromosomes at mitosis requires that all pairs of chromatids bind correctly to microtubules prior to the dissolution of sister cohesion and the initiation of anaphase. By analyzing the motion of GFP-tagged S. cerevisiae chromosomes, we show that kinetochore-microtubule attachments impose sufficient tension on sisters during prometaphase to transiently separate centromeric chromatin toward opposite sides of the spindle. Transient separations of 2-10 min duration occur in the absence of cohesin proteolysis, are characterized by independent motion of the sisters along the spindle, and are followed by the apparent reestablishment of sister linkages. The existence of transient sister separation in yeast explains the unusual bilobed localization of kinetochore proteins and supports an alternative model for spindle structure. By analogy with animal cells, we propose that yeast centromeric chromatin acts as a tensiometer.     

Sociobiology of the budding yeast

Social theory has provided a useful framework for research with microorganisms. Here I describe the advantages and possible risks of using a well-known model organism, the unicellular yeast Saccharomyces cerevisiae, for sociobiological research. I discuss the problems connected with clear classification of yeast behaviour based on the fitness-based Hamilton paradigm. Relevant traits include different types of communities, production of flocculins, invertase and toxins, and the presence of apoptosis.     

The centromere of budding yeast

Stable maintenance of genetic information during meiosis and mitosis is dependent on accurate chromosome transmission. The centromere is a key component of the segregational machinery that couples chromosomes with the spindle apparatus. Most of what is known about the structure and function of the centromeres has been derived from studies on yeast cells. In Saccharomyces cerevisiae, the centromere DNA requirements for mitotic centromere function have been defined and some of the proteins required for an active complex have been identified. Centromere DNA and the centromere proteins form a complex that has been studied extensively at the chromatin level. Finally, recent findings suggest that assembly and activation of the centromere are integrated in tethe cell cycle.     

Single-cell phenomics in budding yeast

The demand for phenomics, a high-dimensional and high-throughput phenotyping method, has been increasing in many fields of biology. The budding yeast Saccharomyces cerevisiae, a unicellular model organism, provides an invaluable system for dissecting complex cellular processes using high-resolution phenotyping. Moreover, the addition of spatial and temporal attributes to subcellular structures based on microscopic images has rendered this cell phenotyping system more reliable and amenable to analysis. A well-designed experiment followed by appropriate multivariate analysis can yield a wealth of biological knowledge. Here we review recent advances in cell imaging and illustrate their broad applicability to eukaryotic cells by showing how these techniques have advanced our understanding of budding yeast.     

酵母菌与其“芽体”

从细胞生物学和分子生物学的层面对酵母菌的芽体形成过程及芽体与母体细胞的相关性作了综合评述。     

Clathrin-mediated endocytosis in budding yeast

Clathrin-mediated endocytosis in the budding yeast Saccharomyces cerevisiae involves the ordered recruitment, activity and disassembly of nearly 60 proteins at distinct sites on the plasma membrane. Two-color live-cell fluorescence microscopy has proven to be invaluable for in vivo analysis of endocytic proteins: identifying new components, determining the order of protein arrival and dissociation, and revealing even very subtle mutant phenotypes. Yeast genetics and functional genomics facilitate identification of complex interaction networks between endocytic proteins and their regulators. Quantitative datasets produced by these various analyses have made theoretical modeling possible. Here, we discuss recent findings on budding yeast endocytosis that have advanced our knowledge of how -60 endocytic proteins are recruited, perform their functions, are regulated by lipid and protein modifications, and are disassembled, all with remarkable regularity.     

Nutrient-regulated protein kinases in budding yeast

The ability of cells to react appropriately to nutritional cues is of fundamental importance, and in budding yeast, a small number of intracellular protein kinases, PKA, Snf1p/AMP-activated kinase, TOR, Gcn2p, and the cyclin-dependent kinase Pho85p have key roles. A recently characterized enzyme, PAS kinase, may be a new member of this group of nutritional transducers.     

Vacuolar dynamics in synchronously budding yeast

Summary A simple and rapid method for obtaining synchronously budding cultures of Saccharomyces cerevisiae is described. Synchronous cultures were started with homogeneous cell fractions isolated from exponentially growing cultures by isopycnic centrifugation in osmotically inactive media. The technique of fractionation is based on changes of cell density throughout the budding cycle. These changes are correlated with vacuolar changes observed in the light and electron microscope. During bud initiation the large vacuoles in late budding cells shrink and fragment into small vacuoles. Simultaneously the density of the cells increases. Later stages of the budding cycle are characterized by the distribution of the small vacuoles between mother and daughter cell, followed by their fusion and expansion, and by a decreasing density of the cells. The relative changes in cell density and dry weight and in the content of different macromolecules during the budding cycle suggest a cyclic change between utilization of endogenous and exogenous substrates. This is discussed in terms of a cyclic consumption and accumulation of vacuolar pools.     

Predicting protein localization in budding yeast

MOTIVATION: Most of the existing methods in predicting protein subcellular location were used to deal with the cases limited within the scope from two to five localizations, and only a few of them can be effectively extended to cover the cases of 12-14 localizations. This is because the more the locations involved are, the poorer the success rate would be. Besides, some proteins may occur in several different subcellular locations, i.e. bear the feature of 'multiplex locations'. So far there is no method that can be used to effectively treat the difficult multiplex location problem. The present study was initiated in an attempt to address (1) how to efficiently identify the localization of a query protein among many possible subcellular locations, and (2) how to deal with the case of multiplex locations. RESULTS: By hybridizing gene ontology, functional domain and pseudo amino acid composition approaches, a new method has been developed that can be used to predict subcellular localization of proteins with multiplex location feature. A global analysis of the proteins in budding yeast classified into 22 locations was performed by jack-knife cross-validation with the new method. The overall success identification rate thus obtained is 70%. In contrast to this, the corresponding rates obtained by some other existing methods were only 13-14%, indicating that the new method is very powerful and promising. Furthermore, predictions were made for the four proteins whose localizations could not be determined by experiments, as well as for the 236 proteins whose localizations in budding yeast were ambiguous according to experimental observations. However, according to our predicted results, many of these 'ambiguous proteins' were found to have the same score and ranking for several different subcellular locations, implying that they may simultaneously exist, or move around, in these locations. This finding is intriguing because it reflects the dynamic feature of these proteins in a cell that may be associated with some special biological functions.     

The spindle cycle in budding yeast

The mitotic spindle of the budding yeast Saccharomyces cerevisiae will probably be the first such organelle to be understood in molecular detail. Here we describe the mitotic spindle cycle of budding yeast using electron-microscope-derived structures and dynamic live-cell imaging. Recent work has revealed that many general aspects of mitosis are conserved, making budding yeast an excellent model for the study of mitosis.     

Isolation of glucanase-containing vesicles from budding yeast

Summary In an investigation of the role of glucanases in modifying yeast cell walls at the location of new buds, vesicles derived from the endoplasmic reticulum, which are secreted locally into the cell wall of growing buds, and may be involved in the secretion of glucanases, have been isolated.In yeast, exo--1,3-glucanase is present both extra- and intracellularly. Exponentially growing cells contain at least 11% of the enzyme activity intracellularly (within the plasmalemma). Most of this intracellular glucanase is sedimentable. Of the three classes of subcellular particles that contain glucanase, one is almost completely absent from stationary phase cells and largely absent from cells of the late budding phase of the cell cycle. These particles were isolated from budding cells by combined differential and density gradient centrifugation. They contain exo- and endo--1,3-glucanases, mannan and protein. The isolate consists mainly of membrane-bounded vesicles with diameters corresponding to those of the secretory vesicles observed in situ. It is concluded that these particles are identical with the vesicles derived from the endoplasmic reticulum.     

Analysis of protein distribution in budding yeast

Flow cytometry is a fast and sensitive method that allows monitoring of different cellular parameters on large samples of a population. Protein distributons give relevant information on growth dynamics, since they are related to the age distribution and depend on the law of growth of the population and the law of protein accumulation during the cell cycle. We analyzed protein distributions to evaluate alternative growth models for the budding yeast Saccharomyces cerevisiae and to monitor the changes in population dynamics that result from environmental modifications; such an analysis could potentially give parameters useful in the control of biotechnological processes. Theoretical protein distributions (taking into account the unequal division of yeast cells and the exponential law of protein accumulation during a cell cycle) quantitatively fit experimental distributions, once appropriate variability sources are introduced. Best fits are obtained when the protein threshold required for bud emergence increases at each new generation of parent cells.