A particulate form of alkaline phosphatase in the yeast, Saccharomyces cerevisiae

[Saccharomyces cerevisiae invasive infection: The first reported case in Morocco]

Saccharomyces cerevisiae is a cosmopolitan yeast, widely used in agro-alimentary and pharmaceutical industry. Its impact in human pathology is rare, but maybe still underestimated compared to the real situation. This yeast is currently considered as an emerging and opportunistic pathogen. Risk factors are immunosuppression and intravascular device carrying. Fungemias are the most frequent clinical forms. We report the first case of S. cerevisiae invasive infection described in Morocco, and to propose a review of the literature cases of S. cerevisiae infections described worldwide. A 77-year-old patient, with no notable medical history, who was hospitalized for a upper gastrointestinal stenosis secondary to impassable metastatic gastric tumor. Its history was marked by the onset of septic shock, with S. cerevisiae in his urine and in his blood, with arguments for confirmation of invasion: the presence of several risk factors in the patient, positive direct microbiological examination, abundant and exclusive culture of S. cerevisiae from clinical samples. Species identification was confirmed by the study of biochemical characteristics of the isolated yeast. Confirmation of S. cerevisiae infection requires a clinical suspicion in patients with risk factors, but also a correct microbiological diagnosis.

Assays for the biochemical and ultrastructural measurement of selective and nonselective types of autophagy in the yeast Saccharomyces cerevisiae

Autophagy is a conserved intracellular catabolic pathway that degrades unnecessary or dysfunctional cellular components. Components destined for degradation are sequestered into double-membrane vesicles called autophagosomes, which subsequently fuse with the vacuole/lysosome delivering their cargo into the interior of this organelle for turnover. Autophagosomes are generated through the concerted action of the autophagy-related (Atg) proteins. The yeast Saccharomyces cerevisiae has been key in the identification of the corresponding genes and their characterization, and it remains one of the leading model systems for the investigation of the molecular mechanism and functions of autophagy. In particular, it is still pivotal for the study of selective types of autophagy. The objective of this review is to present detailed protocols of the methods available to monitor the progression of both nonselective and selective types of autophagy, and to discuss their advantages and disadvantages. The ultimate aim is to provide researchers with the information necessary to select the optimal approach to address their biological question.

The quantitative Pho8Delta60 assay of nonspecific autophagy

The measurement of autophagic flux is critical in understanding the regulation of autophagy. The Pho8Delta60 assay employs a very sensitive enzymatic assay that provides a high signal-to-noise ratio and allows for precise quantification of autophagic flow in yeast. Pho8, alkaline phosphatase, is a resident vacuolar enzyme that is delivered to the vacuole membrane through a portion of the secretory pathway. The assay utilizes a genetically engineered version of Pho8 that lacks the N-terminal transmembrane domain that allows for translocation into the endoplasmic reticulum. Accordingly, Pho8Delta60 remains in the cytosol and is delivered to the vacuole only through autophagy. Once in the vacuole lumen, the C-terminal propeptide is proteolytically removed, which results in activation. Thus, the alkaline phosphatase activity reflects the amount of the cytosol delivered to the vacuole through nonspecific autophagy.

Monitoring autophagy in yeast: the Pho8Delta60 assay

Autophagy is an ubiquitous degradative process in eukaryotic cells. It is involved in various developmental programs and is also implicated in human pathophysiology. The basic process involves the formation of a cytosolic double membrane vesicle, termed an autophagosome. The autophagosome sequesters bulk cytosol, and after completion its outside membrane fuses with the limiting membrane of the lysosome/vacuole. The fusion event releases the inner single-membrane vesicle into the lysosome/vacuole lumen where the vesicle is now termed an autophagic body. The autophagic body and its cargo are typically degraded, and the resulting micromolecules are recycled for subsequent use in the cytosol. Autophagy is the only pathway with the capacity to degrade entire organelles. Accordingly, it may play a critical role in preventing pathologies that results from damaged organelles including the mitochondria, or from the accumulation of large protein aggregates, such as occur in certain types of neurodegenerative diseases. This article describes an assay to monitor bulk autophagy in yeast. The marker protein is a cytosolic derivative of the vacuolar enzyme alkaline phosphatase, Pho8. Following uptake into the vacuole, the precursor enzyme is cleaved at the C terminus to generate the active form. Cells expressing the cytosolic form of Pho8, Pho8Delta60, are assayed for alkaline phosphatase activity before and after shifting to conditions that induce autophagy.

Cooperative binding of the cytoplasm to vacuole targeting pathway proteins, Cvt13 and Cvt20, to phosphatidylinositol 3-phosphate at the pre-autophagosomal structure is required for selective autophagy

Autophagy is a catabolic membrane-trafficking mechanism involved in cell maintenance and development. Most components of autophagy also function in the cytoplasm to vacuole targeting (Cvt) pathway, a constitutive biosynthetic pathway required for the transport of aminopeptidase I (Ape1). The protein components of autophagy and the Cvt pathway include a putative complex composed of Apg1 kinase and several interacting proteins that are specific for either the Cvt pathway or autophagy. A second required complex includes a phosphatidylinositol (PtdIns) 3-kinase and associated proteins that are involved in its activation and localization. The majority of proteins required for the Cvt and autophagy pathways localize to a perivacuolar pre-autophagosomal structure. We show that the Cvt13 and Cvt20 proteins are required for transport of precursor Ape1 through the Cvt pathway. Both proteins contain phox homology domains that bind PtdIns(3)P and are necessary for membrane localization to the pre-autophagosomal structure. Functional phox homology domains are required for Cvt pathway function. Cvt13 and Cvt20 interact with each other and with an autophagy-specific protein, Apg17, that interacts with Apg1 kinase. These results provide the first functional connection between the Apg1 and PtdIns 3-kinase complexes. The data suggest a role for PtdIns(3)P in the Cvt pathway and demonstrate that this lipid is required at the pre-autophagosomal structure.

Acclimation of Chlamydomonas reinhardtii to its nutrient environment

To cope with low nutrient availability in nature, organisms have evolved inducible systems that enable them to scavenge and efficiently utilize the limiting nutrient. Furthermore, organisms must have the capacity to adjust their rate of metabolism and make specific alterations in metabolic pathways that favor survival when the potential for cell growth and division is reduced. In this article I will focus on the acclimation of Chlamydomonas reinhardtii, a unicellular, eukaryotic green alga to conditions of nitrogen, sulfur and phosphorus deprivation. This organism has a distinguished history as a model for classical genetic analyses, but it has recently been developed for exploitation using an array of molecular and genomic tools. The application of these tools to the analyses of nutrient limitation responses (and other biological processes) is revealing mechanisms that enable Chlamydomonas to survive harsh environmental conditions and establishing relationships between the responses of this morphologically simple, photosynthetic eukaryote and those of both nonphotosynthetic organisms and vascular plants.

The newly identified yeast GRD genes are required for retention of late-Golgi membrane proteins

Processing of A-ALP, a late-Golgi membrane protein constructed by fusing the cytosolic domain of dipeptidyl aminopeptidase A to the transmembrane and lumenal domains of alkaline phosphatase (ALP), serves as a convenient assay for loss of retention of late-Golgi membrane proteins in Saccharomyces cerevisiae. In this study, a large group of novel grd (for Golgi retention defective) yeast mutants, representing 18 complementation groups, were identified on the basis of their mislocalization of A-ALP to the vacuole, where it was proteolytically processed and thus became enzymatically activated. All of the grd mutants exhibited significant mislocalization of A-ALP, as measured by determining the kinetics of A-ALP processing and by analyzing its

Thioredoxin is required for vacuole inheritance in Saccharomyces cerevisiae

The vacuole of Saccharomyces cerevisiae projects a stream of tubules a and vesicles (a "segregation structure") into the bud in early S phase. We have described an in vitro reaction, requiring physiological temperature, ATP, and cytosol, in which isolated vacuoles form segregation structures and fuse. This in vitro reaction is defective when reaction components are prepared from vac mutants that are defective in this process in vivo, Fractionation of the cytosol reveals at least three components, each of which can support the vacuole fusion reaction, and two stimulatory fractions. Purification of one "low molecular weight activity" (LMA1) yields a heterodimeric protein with a thioredoxin subunit. Most of the thioredoxin of yeast is in this complex rather than the well-studied monomer. A deletion of both S. cerevisiae thioredoxin genes causes a striking vacuole inheritance defect in vivo, establishing a role for thioredoxin as a novel factor in this trafficking reaction.

G-protein ligands inhibit in vitro reactions of vacuole inheritance

During budding in Saccharomyces cerevisiae, maternal vacuole material is delivered into the growing daughter cell via tubular or vesicular structures. One of the late steps in vacuole inheritance is the fusion in the bud of vesicles derived from the maternal vacuole. This process has been reconstituted in vitro and requires isolated vacuoles, a physiological temperature, cytosolic factors, and ATP (Conradt, B., J. Shaw, T. Vida, S. Emr, and W. Wickner. 1992. J. Cell Biol. 119:1469-1479). We now report a simple and reliable assay to quantify vacuole-to-vacuole fusion in vitro. This assay is based on the maturation and activation of vacuole membrane-bound pro-alkaline phosphatase by vacuolar proteinase A after vacuole-to-vacuole fusion. In vitro fusion allowed maturation of 30 to 60% of pro-alkaline phosphatase. Vacuoles prepared from a mutant defective in vacuole inheritance in vivo (vac2-1) were inactive in this assay. Vacuole fusion in vitro required a vacuole membrane potential. Inhibition by nonhydrolyzable guanosine derivatives, mastoparans, and benzalkonium chloride suggest that GTP-hydrolyzing G proteins may play a key role in the in vitro fusion events.

Determination of four biochemically distinct, sequential stages during vacuole inheritance in vitro

Vacuole inheritance in Saccharomyces cerevisiae can be reconstituted in vitro using isolated organelles, cytosol, and ATP. Using the requirements of the reaction and its susceptibility to inhibitors, we have divided the in vitro reaction into four biochemically distinct, sequential subreactions. Stage I requires exposure of vacuoles to solutions of moderate ionic strength. Stage II requires "stage I" vacuoles and cytosol. In stage III, stage II vacuoles react with ATP. Finally, during stage IV, stage III vacuoles at a certain, minimal concentration complete the fusion reaction without further requirement for any soluble components. Reagents that inhibit the overall vacuole inheritance reaction block distinct stages. Stage III of the reaction is sensitive to the proton ionophore CCCP, to inhibitors of the vacuolar ATPase such as bafilomycin A1, and to the ATP-hydrolyzing enzyme apyrase, suggesting that an electrochemical potential across the vacuolar membrane is required during this stage. Inhibition studies with the amphiphilic peptide mastoparan and GTP gamma S suggest that GTP-hydrolyzing proteins might also be involved during this stage. Microcystin-LR, a specific inhibitor of protein phosphatases of type 1 and 2A, inhibits stage IV of the inheritance reaction, indicating that a protein dephosphorylation event is necessary for fusion. The definition of these four stages may allow the development of specific assays for the factors which catalyze each of the consecutive steps of the in vitro reaction.

Use of microbial spores as a biocatalyst

Endospores of a bacterium Bacillus subtilis and ascospores of a yeast Saccharomyces cerevisiae contained almost all the activities for the same enzymes as vegetative cells. The biotechnological potential of spores was studied by selecting adenosine 5'-triphosphatase and alkaline phosphatase in bacterial and yeast spores, respectively, as model enzymes. The activity of both enzymes was efficiently expressed when the spores were treated by physical (sonication or electric field pulse) and chemical (organic solvents or detergents) methods. The yeast spores were immobilized in polyacrylamide gel without any appreciable loss of activity. The immobilized spores were packed in a column and used successfully for the continuous reactions of alkaline phosphatase and glyoxalase I. The microbial spores were confirmed to be promising as a biocatalyst for the production of useful chemicals in bioreactor systems.

Exocytosis in electropermeabilized neutrophils. Responsiveness to calcium and guanosine 5'-[gamma-thio]triphosphate

Electropermeabilized neutrophils were used to study the exocytotic response in rabbit neutrophils. Enzyme release from electropermeabilized neutrophils could be induced by elevating the Ca2+ concentration. Ca(2+)-induced secretion was significantly enhanced by guanosine 5'-[gamma-thio]triphosphate (GTP[S]) in a concentration-dependent manner. The effect of GTP[S] could be blocked by guanosine 5'-[beta-thio]diphosphate (GDP[S]) and was not affected by pertussis toxin. GTP[S] did not induce enzyme release in the absence of Ca2+. Induction of an exocytotic response did not require addition of ATP. However, neutrophils permeabilized in the absence of ATP became refractory to stimulation due to a reduction in their affinity for Ca2+. Responsiveness to the effectors Ca2+ or Ca2+ + GTP[S] could be prolonged or restored by ATP. ATP was not the only agent that prolonged responsiveness; other nucleotides and inorganic phosphates were also effective. The protein kinase C inhibitors staurosporine and 1-O-hexadecyl-2-methyl-sn-glycerol did not inhibit exocytosis and had only a small effect on the prolongation and restoration of responsiveness by ATP. A hypothesis is presented suggesting that the loss of responsiveness is caused by dephosphorylation and that the restoration or prolongation of responsiveness is not mediated by protein kinase C. It is possible that an as yet unidentified Ca(2+)-binding protein is dephosphorylated, resulting in a decrease in Ca2+ affinity.

The fungal vacuole: composition, function, and biogenesis

The fungal vacuole is an extremely complex organelle that is involved in a wide variety of functions. The vacuole not only carries out degradative processes, the role most often ascribed to it, but also is the primary storage site for certain small molecules and biosynthetic precursors such as basic amino acids and polyphosphate, plays a role in osmoregulation, and is involved in the precise homeostatic regulation of cytosolic ion and basic amino acid concentration and intracellular pH. These many functions necessitate an intricate interaction between the vacuole and the rest of the cell; the vacuole is part of both the secretory and endocytic pathways and is also directly accessible from the cytosol. Because of the various roles and properties of the vacuole, it has been possible to isolate mutants which are defective in various vacuolar functions including the storage and uptake of metabolites, regulation of pH, sorting and processing of vacuolar proteins, and vacuole biogenesis. These mutants show a remarkable degree of genetic overlap, suggesting that these functions are not individual, discrete properties of the vacuole but, rather, are closely interrelated.

Molecular characterization of a specific p-nitrophenylphosphatase gene, PHO13, and its mapping by chromosome fragmentation in Saccharomyces cerevisiae

The structural gene, PHO13, for the specific p-nitrophenyl phosphatase of Saccharomyces cerevisiae was cloned and its nucleotide sequence determined. The deduced PHO13 protein consists of 312 amino acids and its molecular weight is 34635. The disruption of the PHO13 gene produced no effect on cell growth, sporulation, or viability of ascospores. The PHO13 locus was mapped at 1.9 centimorgans from the HO locus on the left arm of chromosome IV. By chromosome fragmentation, the PHO13 locus was found to be located about 72 kb from the left-hand telomere of chromosome IV and distal to the HO locus.

PEP4 gene of Saccharomyces cerevisiae encodes proteinase A, a vacuolar enzyme required for processing of vacuolar precursors

The proteinase A structural gene of Saccharomyces cerevisiae was cloned by using an immunological screening procedure that allows detection of yeast cells which are aberrantly secreting vacuolar proteins (J. H. Rothman, C. P. Hunter, L. A. Valls, and T. H. Stevens, Proc. Natl. Acad. Sci. USA, 83:3248-3252, 1986). A second cloned gene was obtained on a multicopy plasmid by complementation of a pep4-3 mutation. The nucleotide sequences of these two genes were determined independently and were found to be identical. The predicted amino acid sequence of the cloned gene suggests that proteinase A is synthesized as a 405-amino-acid precursor which is proteolytically converted to the 329-amino-acid mature enzyme. Proteinase A shows substantial homology to mammalian aspartyl proteases, such as pepsin, renin, and cathepsin D. The similarities may reflect not only analogous functions but also similar processing and intracellular targeting mechanisms for the two proteins. The cloned proteinase A structural gene, even when it is carried on a single-copy plasmid, complements the deficiency in several vacuolar hydrolase activities that is observed in a pep4 mutant. A strain carrying a deletion in the genomic copy of the gene fails to complement a pep4 mutant of the opposite mating type. Genetic linkage data demonstrate that integrated copies of the cloned proteinase A structural gene map to the PEP4 locus. Thus, the PEP4 gene encodes a vacuolar aspartyl protease, proteinase A, that is required for the in vivo processing of a number of vacuolar zymogens.

Structural characteristics of the PHO8 gene encoding repressible alkaline phosphatase in Saccharomyces cerevisiae

The nucleotide sequence of a 3694-bp DNA fragment bearing the PHO8 gene encoding nonspecific repressible alkaline phosphatase (rALPase; EC 3.1.3.1) of Saccharomyces cerevisiae was determined. The sequence contains a 1698 bp open reading frame (ORF), and the major PHO8 transcription start point at 32 bp upstream from the ATG codon; several minor transcription start points are located between the major start point and ATG. The major start point is most responsive to the phosphate signals. The amino acid (aa) sequence deduced from the ORF contains several homologous regions in common with alkaline phosphatases of Escherichia coli and human placenta. A PHO8 DNA fragment previously isolated [Kaneko et al., Mol. Cell. Biol. 5 (1985) 248-252] was found to be truncated for the region encoding the 22 aa residues at the C terminus of the enzyme, which were replaced with 17 aa encoded by a pBR322 DNA. The modified gene could produce significant rALPase activity without the function of proteinase A which is required for the maturation of rALPase from its precursor.

PEP4 gene of Saccharomyces cerevisiae encodes proteinase A, a vacuolar enzyme required for processing of vacuolar precursors

The proteinase A structural gene of Saccharomyces cerevisiae was cloned by using an immunological screening procedure that allows detection of yeast cells which are aberrantly secreting vacuolar proteins (J. H. Rothman, C. P. Hunter, L. A. Valls, and T. H. Stevens, Proc. Natl. Acad. Sci. USA, 83:3248-3252, 1986). A second cloned gene was obtained on a multicopy plasmid by complementation of a pep4-3 mutation. The nucleotide sequences of these two genes were determined independently and were found to be identical. The predicted amino acid sequence of the cloned gene suggests that proteinase A is synthesized as a 405-amino-acid precursor which is proteolytically converted to the 329-amino-acid mature enzyme. Proteinase A shows substantial homology to mammalian aspartyl proteases, such as pepsin, renin, and cathepsin D. The similarities may reflect not only analogous functions but also similar processing and intracellular targeting mechanisms for the two proteins. The cloned proteinase A structural gene, even when it is carried on a single-copy plasmid, complements the deficiency in several vacuolar hydrolase activities that is observed in a pep4 mutant. A strain carrying a deletion in the genomic copy of the gene fails to complement a pep4 mutant of the opposite mating type. Genetic linkage data demonstrate that integrated copies of the cloned proteinase A structural gene map to the PEP4 locus. Thus, the PEP4 gene encodes a vacuolar aspartyl protease, proteinase A, that is required for the in vivo processing of a number of vacuolar zymogens.

Overproduction-induced mislocalization of a yeast vacuolar protein allows isolation of its structural gene

Using an immunological screening procedure that allows the detection of yeast cells aberrantly secreting vacuolar proteins, we have isolated a cloned DNA fragment containing the structural gene for the vacuolar enzyme proteinase A (PrA; EC 3.4.23.6). A large portion of PrA is misdirected to the cell surface in cells harboring the PrA structural gene on a multicopy plasmid. This mislocalized PrA traverses the late stages of the secretory pathway and differs slightly in apparent molecular weight from the vacuolar form. A deletion in the genomic copy of the PrA structural gene eliminates immunoreactive PrA as well as the enzymatic activities of at least three other vacuolar hydrolases. In the case of the vacuolar enzyme carboxypeptidase Y (EC 3.4.16.1), the lack of activity is due to the absence of proteolytic activation of the zymogen. Thus, PrA may be required for in vivo processing of a number of yeast vacuolar hydrolases.

Asparagine-linked carbohydrate does not determine the cellular location of yeast vacuolar nonspecific alkaline phosphatase

The nonspecific alkaline phosphatase of Saccharomyces sp. strain 1710 has been shown by phosphatase cytochemistry to be exclusively located in the vacuole, para-Nitrophenyl phosphate-specific alkaline phosphatase is not detected by this procedure because the activity of this enzyme is sensitive to the fixative agent, glutaraldehyde. To determine whether the oligosaccharide of nonspecific alkaline phosphatase is necessary to transport the enzyme into the vacuole, protoplasts were derepressed in the absence or in the presence of tunicamycin, an antibiotic which interferes with the glycosylation of asparagine residues in proteins. The location of the enzyme in the tunicamycin-treated protoplasts, as determined by electron microscopy and subcellular fractionation, was identical to its location in control protoplasts. In addition, carbohydrate-free alkaline phosphatase was found in vacuoles from tunicamycin-treated protoplasts. Our findings indicate that the asparagine-linked carbohydrate moiety does not determine the cellular location of the enzyme.