Two Distinct Pathways for Trehalose Assimilation in the Yeast Saccharomyces cerevisiae

The yeast Saccharomyces cerevisiae can synthesize trehalose and also use this disaccharide as a carbon source for growth. However, the molecular mechanism by which extracellular trehalose can be transported to the vacuole and degraded by the acid trehalase Ath1p is not clear. By using an adaptation of the assay of invertase on whole cells with NaF, we showed that more than 90% of the activity of Ath1p is extracellular, splitting of the disaccharide into glucose. We also found that Agt1p-mediated trehalose transport and the hydrolysis of the disaccharide by the cytosolic neutral trehalase Nth1p are coupled and represent a second, independent pathway, although there are several constraints on this alternative route. First, the AGT1/MAL11 gene is controlled by the MAL system, and Agt1p was active in neither non-maltose-fermenting nor maltose-inducible strains. Second, Agt1p rapidly lost activity during growth on trehalose, by a mechanism similar to the sugar-induced inactivation of the maltose permease. Finally, both pathways are highly pH sensitive and effective growth on trehalose occurred only when the medium was buffered at around pH 5.0. The catabolism of trehalose was purely oxidative, and since levels of Ath1p limit the glucose flux in the cells, batch cultures on trehalose may provide a useful alternative to glucose-limited chemostat cultures for investigation of metabolic responses in yeast.     

Non-repair Pathways for Minimizing Protein Isoaspartyl Damage in the Yeast Saccharomyces cerevisiae

The spontaneous degradation of asparaginyl and aspartyl residues to isoaspartyl residues is a common type of protein damage in aging organisms. Although the protein-l-isoaspartyl (d-aspartyl) O-methyltransferase (EC 2.1.1.77) can initiate the repair of l-isoaspartyl residues to l-aspartyl residues in most organisms, no gene homolog or enzymatic activity is present in the budding yeast Saccharomyces cerevisiae. Therefore, we used biochemical approaches to elucidate how proteins containing isoaspartyl residues are metabolized in this organism. Surprisingly, the level of isoaspartyl residues in yeast proteins (50–300 pmol of isoaspartyl residues/mg of protein extract) is comparable with organisms with protein-l-isoaspartyl (d-aspartyl) O-methyltransferase, suggesting a novel regulatory pathway. Interfering with common protein quality control mechanisms by mutating and inhibiting the proteasomal and autophagic pathways in vivo did not increase isoaspartyl residue levels compared with wild type or uninhibited cells. However, the inhibition of metalloproteases in in vitro aging experiments by EDTA resulted in an ∼3-fold increase in the level of isoaspartyl-containing peptides. Characterization by mass spectrometry of these peptides identified several proteins involved in metabolism as targets of isoaspartyl damage. Further analysis of these peptides revealed that many have an N-terminal isoaspartyl site and originate from proteins with short half-lives. These results suggest that one or more metalloproteases participate in limiting isoaspartyl formation by robust proteolysis.     

Vacuole Biogenesis in Saccharomyces cerevisiae: Protein Transport Pathways to the Yeast Vacuole

Delivery of proteins to the vacuole of the yeast Saccharomyces cerevisiae provides an excellent model system in which to study vacuole and lysosome biogenesis and membrane traffic. This organelle receives proteins from a number of different routes, including proteins sorted away from the secretory pathway at the Golgi apparatus and endocytic traffic arising from the plasma membrane. Genetic analysis has revealed at least 60 genes involved in vacuolar protein sorting, numerous components of a novel cytoplasm-to-vacuole transport pathway, and a large number of proteins required for autophagy. Cell biological and biochemical studies have provided important molecular insights into the various protein delivery pathways to the yeast vacuole. This review describes the various pathways to the vacuole and illustrates how they are related to one another in the vacuolar network of S. cerevisiae.     

Ascospore Formation in the Yeast Saccharomyces cerevisiae

Sporulation of the baker's yeast Saccharomyces cerevisiae is a response to nutrient depletion that allows a single diploid cell to give rise to four stress-resistant haploid spores. The formation of these spores requires a coordinated reorganization of cellular architecture. The construction of the spores can be broadly divided into two phases. The first is the generation of new membrane compartments within the cell cytoplasm that ultimately give rise to the spore plasma membranes. Proper assembly and growth of these membranes require modification of aspects of the constitutive secretory pathway and cytoskeleton by sporulation-specific functions. In the second phase, each immature spore becomes surrounded by a multilaminar spore wall that provides resistance to environmental stresses. This review focuses on our current understanding of the cellular rearrangements and the genes required in each of these phases to give rise to a wild-type spore.     

Evolution of Osmosensory MAP Kinase Signaling Pathways

Mitogen-activated protein (MAP) kinases constitute a large familyof proteins with many functions. They are represented by a multitudeof paralogous isoforms in yeast, vertebrates, and other eukaryotes.A phylogenetically conserved function of MAP kinases is to carryosmotic signals from sensory to target elements of cells. Eventhough this function of MAP kinases is ubiquitous and characteristicof unicellular and multicellular eukaryotes alike the contingenciesbetween individual MAP kinases, sensor elements, and targetelements have been subject to vast modification during evolution.Extensive networking of MAP kinase cascades with other signalingpathways is reflected by the large number of diverse signalsthat can be carried by a single MAP kinase pathway and flexibleactivation kinetics. It is emerging that the most importantfunction of MAP kinase networks may not be signal amplificationbut integration of information about the setpoint of environmentalparameters (including osmolality) with other physiological processesto control cell function. Insight into how this cellular integrationof information is achieved by MAP kinase networks will shedlight on the principles of cell dynamics and adaptation.     

Atg9 Trafficking in Yeast Saccharomyces cerevisiae

Autophagy can be divided into selective and non-selective modes. This process is considered selective when a precise cargo is specifically and exclusively incorporated into autophagosomes, the double-membrane vesicles that are the hallmark of autophagy. In contrast, during nonselective, bulk autophagy, cytoplasmic components are randomly enwrapped into autophagosomes. To date, approximately 30 autophagy-related genes called ATG have been identified. Sixteen of them compose the general basic machinery catalyzing the formation of double-membrane vesicles in all eukaryotic cells. The rest of them are often not conserved between species and cooperate with the basic Atg proteins during either selective or nonselective autophagy. Atg9 is the only integral membrane component of the conserved Atg machinery and appears to be a crucial organizational element.5 Recent studies in the S. cerevisiae have shown that Atg9 transport is differentially regulated depending on the autophagy mode. In this addendum, we will review and discuss what has recently been unveiled about yeast S. cerevisiae Atg9 trafficking, its modulators and its potential role in double-membrane vesicle biogenesis.

Addendum to:

Atg9 Sorting from Mitochondria is Impaired in Early Secretion and VFT Complex Mutants in Saccharomyces cerevisiae

F. Reggiori and D.J. Klionsky

J Cell Sci 2006: 119:2903-11     

Analysis of Meiotic Recombination Pathways in the Yeast Saccharomyces Cerevisiae

In the yeast, Saccharomyces cerevisiae, several genes appear to act early in meiotic recombination. HOP1 and RED1 have been classified as such early genes. The data in this paper demonstrate that neither a red1 nor a hop1 mutation can rescue the inviable spores produced by a rad52 spo13 strain; this phenotype helps to distinguish these two genes from other early meiotic recombination genes such as SPO11, REC104, or MEI4. In contrast, either a red1 or a hop1 mutation can rescue a rad50S spo13 strain; this phenotype is similar to that conferred by mutations in the other early recombination genes (e.g., REC104). These two different results can be explained because the data presented here indicate that a rad50S mutation does not diminish meiotic intrachromosomal recombination, similar to the mutant phenotypes conferred by red1 or hop1. Of course, RED1 and HOP1 do act in the normal meiotic interchromosomal recombination pathway; they reduce interchromosomal recombination to ~10% of normal levels. We demonstrate that a mutation in a gene (REC104) required for initiation of exchange is completely epistatic to a mutation in RED1. Finally, mutations in either HOP1 or RED1 reduce the number of double-strand breaks observed at the HIS2 meiotic recombination hotspot.     

啤酒酵母乙醇脱氢酶Ⅰ(ADHI)的遗传变异

在啤酒酵母(Saccharomyces cerevisiae)中观察到存在一种新的ADHI:ADHIF,电泳迁移率明显快于文献报道的ADHI:ADHIS。这种ADHIF在10％葡萄糖的培养条件下,以及在呼吸缺陷型菌株进行无氧呼吸时都能够出现。ADHIF性状的遗传分析表明,它受1个与结构基因ADC-1S(编码ADHIS)等位的基因ADC-1F控制。     

酿酒酵母胞质内NADH的代谢调控

酿酒酵母(Saccharomyces cerevisiae)的生长过程有大量的胞内NADH产生。有氧途径中,胞外的NADH脱氢酶、三磷酸甘油穿梭酶系是线粒体内NADH氧化的最主要机制。该文主要讨论以下三个方面的内容:不同生理环境下促成线粒体胞内NADH氧化的各主要机制的作用;借助电子传递链开启NADH从胞质脱氢酶到线粒体的通道,各代谢动力学的有序进行;各种酶形成超分子复合物,尤其是起关键调控作用的酶形成具相似生理功能的高整合性功能酶。     

Vacuolar Function in the Phosphate Homeostasis of the Yeast Saccharomyces cerevisiae

We studied physiological roles of the yeast vacuole in the phosphatemetabolism using ³¹P-in vivo nuclear magnetic resonance (NMR)spectroscopy. Under phosphate starvation wild-type yeast cellscontinued to grow for two to three generations, implying thatwild-type cells contain large phosphate pool to sustain thegrowth. During the first four hours under the phosphate starvedcondition, the cytosolic phosphate level was maintained almostconstant, while the vacuolar pool of phosphate decreased significantly.³¹P-NMR spectroscopy on the intact cells and perchloric acid(PCA) extracts showed that drastic decrease of polyphosphatetook place during this phase. In contrast,     

Protein Topology Prediction Algorithms Systematically Investigated in the Yeast Saccharomyces cerevisiae

Membrane proteins perform a variety of functions, all crucially dependent on their orientation in the membrane. However, neither the exact number of transmembrane domains (TMDs) nor the topology of most proteins have been experimentally determined. Due to this, most scientists rely primarily on prediction algorithms to determine topology and TMD assignments. Since these can give contradictory results, single‐algorithm‐based predictions are unreliable. To map the extent of potential misanalysis, the predictions of nine algorithms on the yeast proteome are compared and it is found that they have little agreement when predicting TMD number and termini orientation. To view all predictions in parallel, a webpage called TopologYeast: http://www.weizmann.ac.il/molgen/TopologYeast was created. Each algorithm is compared with experimental data and a poor agreement is found. The analysis suggests that more systematic data on protein topology are required to increase the training sets for prediction algorithms and to have accurate knowledge of membrane protein topology.     

Transposition of a Rice Mutator-Like Element in the Yeast Saccharomyces cerevisiae

Mutator-like transposable elements (MULEs) are widespread in plants and are well known for their high transposition activity as well as their ability to duplicate and amplify host gene fragments. Despite their abundance and importance, few active MULEs have been identified. In this study, we demonstrated that a rice (Oryza sativa) MULE, Os3378, is capable of excising and reinserting in yeast (Saccharomyces cerevisiae), suggesting that yeast harbors all the host factors for the transposition of MULEs. The transposition activity induced by the wild-type transposase is low but can be altered by modification of the transposase sequence, including deletion, fusion, and substitution. Particularly, fusion of a fluorescent protein to the transposase enhanced the transposition activity, representing another approach to manipulate transposases. Moreover, we identified a critical region in the transposase where the net charge of the amino acids seems to be important for activity. Finally, transposition efficiency is also influenced by the element and its flanking sequences (i.e., small elements are more competent than their large counterparts). Perfect target site duplication is favorable, but not required, for precise excision. In addition to the potential application in functional genomics, this study provides the foundation for further studies of the transposition mechanism of MULEs.     

Cytokinin Utilization by Adenine-Requiring Mutants of the Yeast Saccharomyces cerevisiae

By monitoring the growth of several adenine auxotrophs of the yeast Saccharomyces cerevisiae on cytokinin-supplemented media, we have demonstrated that this organism can utilize some of these derivatives as a source of adenine. Growth of a mutant lacking adenylosuccinate synthetase suggests that the conversion of cytokinins to adenine does not involve a hypoxanthine intermediate and may be catalyzed by an enzyme analogous to cytokinin oxidase.