Predicting 22 protein localizations in budding yeast

According to the recent experiments, proteins in budding yeast can be distinctly classified into 22 subcellular locations. Of these proteins, some bear the multi-locational feature, i.e., occur in more than one location. However, so far all the existing methods in predicting protein subcellular location were developed to deal with only the mono-locational case where a query protein is assumed to belong to one, and only one, subcellular location. To stimulate the development of subcellular location prediction, an augmentation procedure is formulated that will enable the existing methods to tackle the multi-locational problem as well. It has been observed thru a jackknife cross-validation test that the success rate obtained by the augmented GO-FnD-PseAA algorithm [BBRC 320 (2004) 1236] is overwhelmingly higher than those by the other augmented methods. It is anticipated that the augmented GO-FunD-PseAA predictor will become a very useful tool in predicting protein subcellular localization for both basic research and practical application.     

Automated image analysis of protein localization in budding yeast

MOTIVATION: The yeast Saccharomyces cerevisiae is the first eukaryotic organism to have its genome completely sequenced. Since then, several large-scale analyses of the yeast genome have provided extensive functional annotations of individual genes and proteins. One fundamental property of a protein is its subcellular localization, which provides critical information about how this protein works in a cell. An important project therefore was the creation of the yeast GFP fusion localization database by the University of California, San Francisco, USA (UCSF). This database provides localization data for 75% of the proteins believed to be encoded by the yeast genome. These proteins were classified into 22 distinct subcellular location categories by visual examination. Based on our past success at building automated systems to classify subcellular location patterns in mammalian cells, we sought to create a similar system for yeast. RESULTS: We developed computational methods to automatically analyze the images created by the UCSF yeast GFP fusion localization project. The system was trained to recognize the same location categories that were used in that study. We applied the system to 2640 images, and the system gave the same label as the previous assignments to 2139 images (81%). When only the highest confidence assignments were considered, 94.7% agreement was observed. Visual examination of the proteins for which the two approaches disagree suggests that at least some of the automated assignments may be more accurate. The automated method provides an objective, quantitative and repeatable assignment of protein locations that can be applied to new collections of yeast images (e.g. for different strains or the same strain under different conditions). It is also important to note that this performance could be achieved without requiring colocalization with any marker proteins. AVAILABILITY: The original images analyzed in this article are available at http://yeastgfp.ucsf.edu, and source code and results are available at http://murphylab.web.cmu.edu/software.     

芽殖酵母ASH1 mRNA的定位机制

mRNA定位是一种基因转录后水平的重要调控机制,对细胞的生理活动和分化发育都有着极其重要的作用。在芽殖酵母有丝分裂中,ASH1 mRNA在子细胞芽尖因不对称定位表达抑制了子细胞交配类型的转换。本综述介绍了芽殖酵母ASH1 mRNA定位的分子机制。     

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.     

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.     

PKA-dependent regulation of Cdc25 RasGEF localization in budding yeast

In Saccharomyces cerevisiae the Cdc25/Ras/cAMP pathway is involved in cell growth and proliferation regulation. Ras proteins are regulated by Ira1/2 GTPase activating proteins (GAPs) and Cdc25/Sdc25 guanine nucleotide exchange factors (GEFs).Most of cytosolic Cdc25 protein was found on internal membranes in exponentially growing cells, while upon incubation in a buffer with no nutrients it is re-localized to plasma membrane. The overexpression of Tpk1 PKA catalytic subunit also induces Cdc25 export from the nucleus, involving two serine residues near the Nuclear Localization Site (NLS): mutation of Ser⁸²⁵ and Ser⁸²⁶ to glutamate is sufficient to exclude physiologically expressed Cdc25 from the nucleus, mimicking Tpk1 overproduction effect. Mutation of these Ser residues to Ala abolishes the effect of nuclear export induced by Tpk1 overexpression on a Cdc25eGFP fusion. Moreover, mutation of these residues affects PKA-related phenotypes such as heat shock resistance, glycogen content and cell volume.     

Intracellular localization of mannan synthetase activity in budding baker's yeast

In extracts from budding yeast cells mannan synthetase is present at a much higher activity than in extracts from stationary cells. This activity is largely sedimentable. It is associated with fragments of the plasmalemma, with vesicles known to be involved in the local secretion of glucanases at the site of budding, and with ‘light membranes’ representing a mixed fraction which probably contains fragments of the endoplasmic reticulum. The possible involvement of these structures in the synthesis and secretion of mannanprotein is discussed.     

Phosphorylation and spindle pole body localization of the Cdc15p mitotic regulatory protein kinase in budding yeast

Cdc15p is an essential protein kinase and functions with a group of late mitotic proteins that includes Lte1p, Tem1p, Cdc14p and Dbf2p/Dbf20p to inactivate Cdc28p-Clb2p at the end of mitosis in budding yeast [1] [2]. Cdc14p is activated and released from the nucleolus at late anaphase/telophase to dephosphorylate important regulators of Cdc28p-Clb2p such as Hct1p/Cdh1p, Sic1p and Swi5p in a CDC15-dependent manner [3] [4] [5] [6] [7]. How Cdc15p itself is regulated is not known. Here, we report that both the phosphorylation and localization of Cdc15p are cell cycle regulated. The extent of phosphorylation of Cdc15p gradually increases during cell-cycle progression until some point during late anaphase/telophase when it is rapidly dephosphorylated. We provide evidence suggesting that Cdc14p is the phosphatase responsible for the dephosphorylation of Cdc15p. Using a Cdc15p fusion protein coupled at its carboxyl terminus to green fluorescent protein (GFP), we found that Cdc15p, like its homologue Cdc7p [8] in fission yeast, localizes to the spindle pole bodies (SPBs) during mitosis. At the end of telophase, a portion of Cdc15p is located at the mother-bud neck, suggesting a possible role for Cdc15p in cytokinesis.     

The budding yeast RasGEF Cdc25 reveals an unexpected nuclear localization

The mechanisms regulating the activity of Saccharomyces cerevisiae Ras-GEF Cdc25 are still largely unknown. While the catalytical function of the C-terminal domain has been thoroughly studied, only recently a role of negative control on the protein activity has been suggested for the dispensable N-terminal domain. In order to investigate Cdc25 localization and the role of its different domains, several fusion proteins were constructed using the full length Cdc25 or different fragments of the protein with the green fluorescent protein. Unexpectedly, even if only slightly overexpressed, the full protein was not located in the cell plasma membrane, but accumulates inside the cell and also into the nucleus. Moreover, the endogenous Cdc25, tagged with HA, was also found in purified nuclear extracts. The fusions spanning aa 353-875, aa 876-1100 or aa 353-1100 localize heavily in the nucleus, concentrating in the nuclear peripheral area, in a region distinct from the nucleolus. This could be related to the presence of two predicted nuclear localization signals (NLS) in positions 547 and 806, but also to the contribution of another region, spanning residues 876-1100. This localization is likely to be physiological, since the fusion proteins can be efficiently exported and then imported back into the nucleus.     

A myosin light chain mediates the localization of the budding yeast IQGAP-like protein during contractile ring formation

Cytokinesis in animal cells is accomplished through constriction of an actomyosin ring [1] [2] [3], which must assemble at the correct time and place in order to ensure proper division of genetic material and organelles. Budding yeast is a useful model system for determining the biochemical pathway of contractile ring assembly. The budding yeast IQGAP-like protein, Cyk1/Iqg1p, has multiple roles in the assembly and contraction of the actomyosin ring [4] [5] [6]. Previously, the IQ motifs of Cyk1/Iqg1p were shown to be required for the localization of this protein at the bud neck [6]. We have investigated the binding partner of the IQ motifs, which are predicted to interact with calmodulin-like proteins. Mlc1p was originally identified as a light chain for a type V myosin, Myo2p; however, a cytokinesis defect associated with disruption of the MLC1 gene suggested that the essential function of Mlc1p may involve interactions with other proteins [7]. We show that Mlc1p binds the IQ motifs of Cyk1/Iqg1p and present evidence that this interaction recruits Cyk1/Iqg1p to the bud neck. Immunofluorescence staining shows that Mlc1p is localized to sites of polarized cell growth as well as the bud neck before and independently of Cyk1p. These results demonstrate that Mlc1p is important for the assembly of the actomyosin ring in budding yeast and that this function is mediated through interaction with Cyk1/Iqg1p.     

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.     

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.     

Insight into Tor2, a budding yeast microdomain protein

The plasma membrane of eukaryotic organisms is compartmentalized into microdomains. The budding yeast Saccharomyces cerevisiae presents three laterally distinct microdomains: membrane compartment containing Can1 (MCC), membrane compartment containing Pma1 (MCP), and membrane compartment containing Tor2 (MCT). Tor2 and its corresponding protein complex, target of rapamycin complex 2 (TORC2), has been of particular interest in recent years. Tor2, the main organizer of TORC2, is a highly conserved kinase that has proved to be an important regulator of multiple cellular functions including cell growth, actin polymerization, endocytosis, and sphingolipid synthesis. Despite significant advancements, the full understanding of the Tor2 signaling networks is incomplete. Here we review the most compelling evidences for the function and physiological significance of Tor2, as well as discuss possible implications and explanations for observed phenomena.     

Motility and segregation of Hsp104-associated protein aggregates in budding yeast

During yeast cell division, aggregates of damaged proteins are segregated asymmetrically between the bud and the mother. It is thought that protein aggregates are cleared from the bud via actin cable-based retrograde transport toward the mother and that Bni1p formin regulates this transport. Here, we examined the dynamics of Hsp104-associated protein aggregates by video microscopy, particle tracking, and image correlation analysis. We show that protein aggregates undergo random walk without directional bias. Clearance of heat-induced aggregates from the bud does not depend on formin proteins but occurs mostly through dissolution via Hsp104p chaperon. Aggregates formed naturally in aged cells also exhibit random walk but do not dissolve during observation. Although our data do not disagree with a role for actin or cell polarity in aggregate segregation, modeling suggests that their asymmetric inheritance can be a predictable outcome of aggregates' slow diffusion and the geometry of yeast cells.     

Subtelomere-binding protein Tbf1 and telomere-binding protein Rap1 collaborate to inhibit localization of the Mre11 complex to DNA ends in budding yeast

Chromosome ends, known as telomeres, have to be distinguished from DNA double-strand breaks that activate DNA damage checkpoints. In budding yeast, the Mre11-Rad50-Xrs2 (MRX) complex associates with DNA ends and promotes checkpoint activation. Rap1 binds to double-stranded telomeric regions and recruits Rif1 and Rif2 to telomeres. Rap1 collaborates with Rif1 and Rif2 and inhibits MRX localization to DNA ends. This Rap1-Rif1-Rif2 function becomes attenuated at shortened telomeres. Here we show that Rap1 acts together with the subtelomere-binding protein Tbf1 and inhibits MRX localization to DNA ends. The placement of a subtelomeric sequence or TTAGGG repeats together with a short telomeric TG repeat sequence inhibits MRX accumulation at nearby DNA ends in a Tbf1-dependent manner. Moreover, tethering of both Tbf1 and Rap1 proteins decreases MRX and Tel1 accumulation at nearby DNA ends. This Tbf1- and Rap1-dependent pathway operates independently of Rif1 or Rif2 function. Depletion of Tbf1 protein stimulates checkpoint activation in cells containing short telomeres but not in cells containing normal-length telomeres. These data support a model in which Tbf1 and Rap1 collaborate to maintain genomic stability of short telomeres.     

Lipid rafts in protein sorting and cell polarity in budding yeast Saccharomyces cerevisiae

Cellular membranes contain many types and species of lipids. One of the most important functional consequences of this heterogeneity is the existence of microdomains within the plane of the membrane. Sphingolipid acyl chains have the ability of forming tightly packed platforms together with sterols. These platforms or lipid rafts constitute segregation and sorting devices into which proteins specifically associate. In budding yeast, Saccharomyces cerevisiae, lipid rafts serve as sorting platforms for proteins destined to the cell surface. The segregation capacity of rafts also provides the basis for the polarization of proteins at the cell surface during mating. Here we discuss some recent findings that stress the role of lipid rafts as key players in yeast protein sorting and cell polarity.     

Dynamics of Sir3 spreading in budding yeast: secondary recruitment sites and euchromatic localization

Chromatin domains are believed to spread via a polymerization-like mechanism in which modification of a given nucleosome recruits a modifying complex, which can then modify the next nucleosome in the polymer. In this study, we carry out genome-wide mapping of the Sir3 component of the Sir silencing complex in budding yeast during a time course of establishment of heterochromatin. Sir3 localization patterns do not support a straightforward model for nucleation and polymerization, instead showing strong but spatially delimited binding to silencers, and weaker and more variable Ume6-dependent binding to novel secondary recruitment sites at the seripauperin (PAU) genes. Genome-wide nucleosome mapping revealed that Sir binding to subtelomeric regions was associated with overpackaging of subtelomeric promoters. Sir3 also bound to a surprising number of euchromatic sites, largely at genes expressed at high levels, and was dynamically recruited to GAL genes upon galactose induction. Together, our results indicate that heterochromatin complex localization cannot simply be explained by nucleation and linear polymerization, and show that heterochromatin complexes associate with highly expressed euchromatic genes in many different organisms.     

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.