Function In Yeast Cells Research Articles

Coupling DNA Replication and Spindle Function in Saccharomyces cerevisiae.

In the yeast Saccharomyces cerevisiae DNA replication and spindle assembly can overlap. Therefore, signaling mechanisms modulate spindle dynamics in order to ensure correct timing of chromosome segregation relative to genome duplication, especially when replication is incomplete or the DNA becomes damaged. This review focuses on the molecular mechanisms that coordinate DNA replication and spindle dynamics, as well as on the role of spindle-dependent forces in DNA repair. Understanding the coupling between genome duplication and spindle function in yeast cells can provide important insights into similar processes operating in other eukaryotic organisms, including humans.

Multi-omics based strategy for toxicity analysis of acrylamide in Saccharomyces cerevisiae model

Although the toxicity of acrylamide (ACR) has been extensively investigated in different experimental models, its perturbations to multiple nodes of the cellular signaling network have not been systematically associated. In this study, changes at different omics layers in ACR exposed Saccharomyces cerevisiae cells were monitored using a multi-omics strategy. The results of the analysis highlighted the impairment of oxidative-reductive balance, energy metabolism, lipid metabolism, nucleotide metabolism, and ribosome function in yeast cells. Response to acute ACR damage, glutathione synthesis was upregulated, the process of protein degradation was accelerated, and the autophagy flux was initiated. Meanwhile, yeast upregulates gene expression levels of enzymes in carbohydrate metabolism and speeds up the oxidation process of fatty acids to compensate for energy depletion. Importantly, the multi-omics strategy captures features that have rarely been addressed in previous studies on the toxicology of ACR, including blocked de novo nucleotide synthesis, decreased levels of metabolic enzyme cofactors thiamine and D-biotin, increased intracellular concentrations of neurotoxic N-methyl d-aspartic acid and l-glutamic acid, and release of death mediators ceramide. The ACR perturbation network constructed in this work and the discovery of new damage features provide a theoretical basis for subsequent point-to-point toxicological studies.

Mentha piperita L. essential oil inactivates spoilage yeasts in fruit juices through the perturbation of different physiological functions in yeast cells

This study evaluated the efficacy of the essential oil from Mentha piperita L. (MPEO) to inactivate cells of the potentially spoilage yeasts Candida albicans, Candida tropicalis, Pichia anomala and Saccharomyces cerevisiae in cashew, guava, mango and pineapple juices during 72 h of refrigerated storage. Damage in different physiological functions caused by MPEO in S. cerevisiae in cashew and guava juices were investigated using flow cytometry (FC). The effects of the incorporation of an effective anti-yeast MPEO dose on sensory characteristics of juices were also evaluated. MPEO displayed minimum inhibitory concentration of 1.875 μL/mL against all tested yeasts. A >5 log reduction in counts of C. albicans, P. anomala and S. cerevisiae was observed in cashew and guava juices with 7.5 and 3.75 μL/mL MPEO. Tested MPEO concentrations (1.875, 3.75 and 7.5 μL/mL) were not effective to cause >5 log reduction in counts of target yeasts in mango and pineapple juices during 72 h of exposure. Incorporation of 1.875 μL/mL MPEO in cashew and guava juices strongly compromised membrane permeability, membrane potential, enzymatic activity and efflux pump activity in S. cerevisiae cells. This same MPEO concentration did not affect appearance, odor and viscosity in fruit juices, but negatively affected their taste and aftertaste. These results show the efficacy of MPEO to inactivate potentially spoilage yeasts in fruit juices through disturbance of different physiological functions in yeast cells. However, the combined use of MPEO with other technologies should be necessary to decrease its effective anti-yeast dose in fruit juices and, consequently, the possible negative impacts on specific sensory properties of these products.

Dispersion of Endoplasmic Reticulum-associated Compartments by 4-phenyl Butyric Acid in Yeast Cells.

In yeast Saccharomyces cerevisiae cells, some aberrant multimembrane-spanning proteins are not transported to the cell surface but form and are accumulated in endoplasmic reticulum (ER)-derived subcompartments, known as the ER-associated compartments (ERACs), which are observed as puncta under fluorescence microscopy. Here we show that a mutant of the cell surface protein Pma1, Pma1-2308, was accumulated in the ERACs, as well as the heterologously expressed mammalian cystic fibrosis transmembrane conductance regulator (CFTR), in yeast cells. Pma1-2308 and CFTR were located on the same ERACs. We also note that treatment of cells with 4-phenyl butyric acid (4-PBA) compromised the ERAC formation by Pma1-2308 and CFTR, suggesting that 4-PBA exerts a chaperone-like function in yeast cells. Intriguingly, unlike ER stress induced by the canonical ER stressor tunicamycin, ER stress that was induced by Pma1-2308 was aggravated by 4-PBA. We assume that this observation demonstrates a beneficial aspect of ERACs, and thus propose that the ERACs are formed through aggregation of aberrant transmembrane proteins and work as the accumulation sites of multiple ERAC-forming proteins for their sequestration.Key words: protein aggregation, organelle, unfolded protein response, ER stress, 4-PBA.

Over‐expression of the molecular chaperone Hsp104 in Saccharomyces cerevisiae results in the malpartition of [PSI+] propagons

The ability of a yeast cell to propagate [PSI+ ], the prion form of the Sup35 protein, is dependent on the molecular chaperone Hsp104. Inhibition of Hsp104 function in yeast cells leads to a failure to generate new propagons, the molecular entities necessary for [PSI+ ] propagation in dividing cells and they get diluted out as cells multiply. Over-expression of Hsp104 also leads to [PSI+ ] prion loss and this has been assumed to arise from the complete disaggregation of the Sup35 prion polymers. However, in conditions of Hsp104 over-expression in [PSI+ ] cells we find no release of monomers from Sup35 polymers, no monomerization of aggregated Sup35 which is not accounted for by the proportion of prion-free [psi- ] cells present, no change in the molecular weight of Sup35-containing SDS-resistant polymers and no significant decrease in average propagon numbers in the population as a whole. Furthermore, they show that over-expression of Hsp104 does not interfere with the incorporation of newly synthesised Sup35 into polymers, nor with the multiplication of propagons following their depletion in numbers while growing in the presence of guanidine hydrochloride. Rather, they present evidence that over-expression of Hsp104 causes malpartition of [PSI+ ] propagons between mother and daughter cells in a sub-population of cells during cell division thereby generating prion-free [psi- ] cells.

Three Candida albicans potassium uptake systems differ in their ability to provide Saccharomyces cerevisiae trk1trk2 mutants with necessary potassium.

Yeasts usually have one or two high-affinity potassium transporters. Two complete and one interrupted gene encoding three types of putative potassium uptake system exist in Candida albicans SC5314. As high intracellular potassium is essential for many yeast cell functions, the existence of three transporters with differing transport mechanisms (Trk uniporter, Hak cation-proton symporter, Acu ATPase) may help pathogenic C. albicans cells to acquire the necessary potassium in various organs and tissues of the host. When expressed in Saccharomyces cerevisiae lacking their own potassium uptake systems, all three putative transporters were able to provide cells with the ability to grow with low amounts of potassium over a broad range of external pH. Only CaTrk1 was properly recognized and secreted to the plasma membrane. Nevertheless, even the small number of CaHak1 and mainly CaAcu1 molecules which reached the plasma membrane resulted in an improved growth of cells in low potassium concentrations, suggesting a high affinity and capacity of the transporters. A single-point mutation restored the complete CaACU1 gene, and the resulting protein not only provided cells with the necessary potassium but also improved their tolerance to toxic lithium. In contrast to its known homologues, CaAcu1 did not seem to transport sodium.

Pathogenic Candida species differ in the ability to grow at limiting potassium concentrations.

A high intracellular concentration of potassium (200-300 mmol/L) is essential for many yeast cell functions, such as the regulation of cell volume and pH, maintenance of membrane potential, and enzyme activation. Thus, cells use high-affinity specific transporters and expend a lot of energy to acquire the necessary amount of potassium from their environment. In Candida genomes, genes encoding 3 types of putative potassium uptake systems were identified: Trk uniporters, Hak symporters, and Acu ATPases. Tests of the tolerance and sensitivity of C. albicans, C. dubliniensis, C. glabrata, C. krusei, C. parapsilosis, and C. tropicalis to various concentrations of potassium showed significant differences among the species, and these differences were partly dependent on external pH. The species most tolerant to potassium-limiting conditions were C. albicans and C. krusei, while C. parapsilosis tolerated the highest KCl concentrations. Also, the morphology of cells changed with the amount of potassium available, with C. krusei and C. tropicalis being the most influenced. Taken together, our results confirm potassium uptake and accumulation as important factors for Candida cell growth and suggest that the sole (and thus probably indispensable) Trk1 potassium uptake system in C. krusei and C. glabrata may serve as a target for the development of new antifungal drugs.

Effects of an antipsoriatic agent, dithranol, on mitochondrial and nuclear functions in yeast cells

Respiration-deficient (petite) cells are much more resistant than respiration-competent (grande) cells of Saccharomyces cerevisae to the killing effect of dithranol at concentrations of 2 times 10-6 — 10 times 10-6M. The high proportions of cytoplasmic petites found in cultures of yeast treated at these concentrations are mainly due to this selective killing. However, at lower concentrations with little killing effect on grandes a strong net increase of the number of cytoplasmic petites was found. Dithranol can act as a photosensitizer. Results from photodynamic treatment indicate that the resistance of petites depends on their inability to take up dithranol. Cells grown in media with glycerol as carbon source were more resistant to the petite-inducing effect of dithranol than cells grown with glucose. Kinetic studies showed that both killing and petites can be induced by very short treatments, the maximal effect being obtained within 2–5 min. Reconstruction experiments showed that the dithranol available in the treatment solution was quickly bound to the cells. Dithranol was found to be much more effective than ethidium bromide in inducing petites by treatments under no-growth conditions in phosphate buffer. Mitotic recombination and gene conversion were not increased by treatment with dithranol in the dark. Light + dithranol gave a small increase of the frequency of mitotic gene conversion.

Membrane association and functional regulation of Sec3 by phospholipids and Cdc42

The exocyst is an octameric protein complex implicated in tethering post-Golgi secretory vesicles at the plasma membrane in preparation for fusion. However, it is not clear how the exocyst is targeted to and physically associates with specific domains of the plasma membrane and how its functions are regulated at those regions. We demonstrate that the N terminus of the exocyst component Sec3 directly interacts with phosphatidylinositol 4,5-bisphosphate. In addition, we have identified key residues in Sec3 that are critical for its binding to the guanosine triphosphate–bound form of Cdc42. Genetic analyses indicate that the dual interactions of Sec3 with phospholipids and Cdc42 control its function in yeast cells. Disrupting these interactions not only blocks exocytosis and affects exocyst polarization but also leads to defects in cell morphogenesis. We propose that the interactions of Sec3 with phospholipids and Cdc42 play important roles in exocytosis and polarized cell growth.

SAGA-mediated H2B deubiquitination controls the development of neuronal connectivity in the Drosophila visual system

Nonstop, which has previously been shown to have homology to ubiquitin proteases, is required for proper termination of axons R1-R6 in the optic lobe of the developing Drosophila eye. Herein, we establish that Nonstop actually functions as an ubiquitin protease to control the levels of ubiquitinated histone H2B in flies. We further establish that Nonstop is the functional homolog of yeast Ubp8, and can substitute for Ubp8 function in yeast cells. In yeast, Ubp8 activity requires Sgf11. We show that in Drosophila, loss of Sgf11 function causes similar photoreceptor axon-targeting defects as loss of Nonstop. Ubp8 and Sgf11 are components of the yeast SAGA complex, suggesting that Nonstop function might be mediated through the Drosophila SAGA complex. Indeed, we find that Nonstop does associate with SAGA components in flies, and mutants in other SAGA subunits display nonstop phenotypes, indicating that SAGA complex is required for accurate axon guidance in the optic lobe. Candidate genes regulated by SAGA that may be required for correct axon targeting were identified by microarray analysis of gene expression in SAGA mutants.

Dimerization of Hsp90 Is Required for in Vivo Function

Heat shock protein 90 (Hsp90) plays a central role in signal transduction and has emerged as a promising target for anti-cancer therapeutics, but its molecular mechanism is poorly understood. At physiological concentration, Hsp90 predominantly forms dimers, but the function of full-length monomers in cells is not clear. Hsp90 contains three domains: the N-terminal and middle domains contribute directly to ATP binding and hydrolysis and the C domain mediates dimerization. To study the function of Hsp90 monomers, we used a single-chain strategy that duplicated the C-terminal dimerization domain. This novel monomerization strategy had the dual effect of stabilizing the C domain to denaturation and hindering intermolecular association of the ATPase domain. The resulting construct was predominantly monomeric at physiological concentration and did not function to support yeast viability as the sole Hsp90. The monomeric construct was also defective at ATP hydrolysis and the activation of a kinase and steroid receptor substrate in yeast cells. The ability to support yeast growth was rescued by the addition of a coiled-coil dimerization domain, indicating that the parental single-chain construct is functionally defective because it is monomeric.

Modulation of Spc1 stress-activated protein kinase activity by methylglyoxal through inhibition of protein phosphatase in the fission yeast Schizosaccharomyces pombe

Methylglyoxal, a ubiquitous metabolite derived from glycolysis has diverse physiological functions in yeast cells. Previously, we have reported that extracellularly added methylglyoxal activates Spc1, a stress-activated protein kinase (SAPK), in the fission yeast Schizosaccharomyces pombe [Y. Takatsume, S. Izawa, Y. Inoue, J. Biol. Chem. 281 (2006) 9086–9092]. Phosphorylation of Spc1 by treatment with methylglyoxal in S. pombe cells defective in glyoxalase I, an enzyme crucial for the metabolism of methylglyoxal, continues for a longer period than in wild-type cells. Here we show that methylglyoxal inhibits the activity of the protein phosphatase responsible for the dephosphorylation of Spc1 in vitro. In addition, we found that methylglyoxal inhibits human protein tyrosine phosphatase 1B (PTP1B) also. We propose a model for the regulation of the activity of the Spc1-SAPK signaling pathway by methylglyoxal in S. pombe.

Structure of the Papillomavirus DNA-Tethering Complex E2:Brd4 and a Peptide that Ablates HPV Chromosomal Association

Many DNA viruses that are latent in dividing cells are noncovalent passengers on mitotic chromosomes and require specific viral-encoded and cellular factors for this activity. The chromosomal protein Brd4 is implicated in the hitchhiking of bovine papillomavirus-1 (BPV-1), and the viral protein E2 binds to both plasmids and Brd4. Here, we present the X-ray crystal structure of the carboxy-terminal domain of Brd4 in complex with HPV-16 E2, and with this information have developed a Brd4-Tat fusion protein that is efficiently taken up by different transformed cells harboring HPV plasmids. In cells treated with these fusion proteins for only 2 hr and arrested in metaphase, the HPV DNA, either HPV-16 or -31, is displaced from mitotic chromosomes. Mutant Brd4 peptides are deficient in ablating this association. We suggest that such peptides may lead to the development of inhibitors of latency for many, if not all, papillomaviruses.

TheYCR079wgene confers a rapamycin-resistant function and encodes the sixth type 2C protein phosphatase inSaccharomyces cerevisiae

Type 2C protein phosphatase (PP2C) is a monomeric enzyme and requires Mg(2+) or Mn(2+) for its activity. Up to now, seven PP2C-like genes have been identified in the genome of Saccharomyces cerevisiae. However, the protein encoded by the sixth PP2C-like gene, YCR079w, has not been demonstrated to have PP2C activity. In this study, we show that YCR079w confers a rapamycin-resistant function in yeast cells, and we also demonstrate that the YCR079w-encoded protein exhibits characteristics of a typical PP2C. Therefore, YCR079w encodes the sixth PP2C, PTC6, in budding yeast.

A novel family of Ca2+/calmodulin-binding proteins involved in transcriptional regulation: interaction with fsh/Ring3 class transcription activators.

A novel CaM-binding protein was isolated through protein-protein interaction based screening of an Arabidopsis cDNA expression library using a 35S calmodulin (CaM) probe. There are four additional homologs in the Arabidopsis genome with similar structures: a BTB domain in the N-terminus and a Zf-TAZ domain in the C-terminus. Hence, they were designated as AtBT1-5 (Arabidopsis thaliana BTB and TAZ domain protein). CaM-binding experiments revealed that all five AtBTs are CaM-binding proteins, and their CaM-binding domains were mapped to the C-terminus. AtBT homologs are also present in rice, but are not present in human, animal, yeast or other organisms, suggesting that the BTB and TAZ domain proteins are plant-specific. The AtBT1-smGFP fusion protein expressed in tobacco BY-2 cells showed that AtBT1 targets the nucleus. Yeast two-hybrid screening using an AtBT1 fragment as bait identified two interacting proteins (AtBET10 and AtBET9) belonging to the family of fsh/Ring3 class transcription regulators. The BTB domain of the AtBTs is required for the interaction, and this protein-protein interaction was confirmed by GST pull-down. AtBET10 also interacts with AtBT2 and AtBT4, and exhibited a transcriptional activation function in yeast cells. AtBTs exhibit varying responses to different stress stimuli, but all five genes responded rapidly to H2O2 and salicylic acid (SA) treatments. These results suggest that AtBTs play a role in transcriptional regulation, and signal molecules such as Ca2+, H2O2, and SA affect transcriptional machinery by altering the expression and conformation of AtBTs which interact with transcriptional activators such as AtBET10.

Functional inactivation of the conserved Sem1p in yeast by intrabodies.

Intrabody technology was applied to characterize the function and intracellular localization of a highly conserved Saccharomyces cerevisiae Sem1 protein. DSS1, the mammalian homologue of Sem1p, is functionally conserved between yeast and mammalian cells, and in mammalian cells physically interacts with the strong tumour supressor BRCA2. Yeast and the generated intrabodies are thus expected to offer a useful system for studies on Sem1p/DSS1 function. Sem1p-specific antibody isolated from a phage display library was expressed intracellularily and targeted to either the cytosol or the nucleus of yeast cells. Analysis of the applicability of different antibody fragments as intrabodies showed that the Fab intrabody was expressed most efficiently. Expression of nuclear-targeted anti-Sem1p Fab intrabodies inhibited the growth of the sigma1278b yeast strain in a manner similar to deletion of the SEM1 gene. This indicates that the Fab intrabodies interact in vivo with Sem1p and result in inactivation of Sem1p. Localization of the Fab intrabody with or without the nuclear localization signal to the nucleus in Sem1p-dependent manner suggests that Sem1p mediates the nuclear transport of the intrabody without any targeting signal. Our results suggest that Sem1p function in yeast cells is in part manifested in the nucleus.

Arginine Residues 47 and 70 of Human Flap Endonuclease-1 Are Involved in DNA Substrate Interactions and Cleavage Site Determination

Flap endonuclease-1 (FEN-1) is a critical enzyme for DNA replication and repair. Intensive studies have been carried out on its structure-specific nuclease activities and biological functions in yeast cells. However, its specific interactions with DNA substrates as an initial step of catalysis are not defined. An understanding of the ability of FEN-1 to recognize and bind a flap DNA substrate is critical for the elucidation of its molecular mechanism and for the explanation of possible pathological consequences resulting from its failure to bind DNA. Using human FEN-1 in this study, we identified two positively charged amino acid residues, Arg-47 and Arg-70 in human FEN-1, as candidates responsible for substrate binding. Mutation of the Arg-70 significantly reduced flap endonuclease activity and eliminated exonuclease activity. Mutation or protonation of Arg-47 shifted cleavage sites with flap substrate and significantly reduced the exonuclease activity. We revealed that these alterations are due to the defects in DNA-protein interactions. Although the effect of the single Arg-47 mutation on binding activities is not as severe as R70A, its double mutation with Asp-181 had a synergistic effect. Furthermore the possible interaction sites of these positively charged residues with DNA substrates were discussed based on FEN-1 cleavage patterns using different substrates. Finally data were provided to indicate that the observed negative effects of a high concentration of Mg(2+) on enzymatic activity are probably due to the competition between the arginine residues and metal ions with DNA substrate since mutants were found to be less tolerant.

Helix 12 in the human estrogen receptor (hER) is essential for the hER function by overcoming nucleosome repression in yeast

When exogenous human estrogen receptor (hER) binds with estrogen, it can activate transcription of target genes in yeast cells. The estrogen dose-response expression patterns in yeast are very similar to those in human cells. This implies that hER may function in yeast cells via mechanisms similar to those in human cells. In this study, Saccharomyces cerevisiae was used to dissect mechanisms of hER-activated transcription in yeast. The hER contains two transcription activation domains: ER-AF-1 and ER-AF-2 (LBD or HBD). In both human and wild-type yeast cells, hER must bind with estrogen in order to activate transcription. In those cells, ER-AF-2 is independently active upon hormone binding, but ER-AF-1 by itself is inactive. In a mutagenesis screen, we found a mutant strain in which the ER-AF-1 was independently active. It was determined that this mutant strain carried a Tup1 mutation. More interestingly, a small hER fragment ER-AF-0, containing neither ER-AF-1 nor ER-AF-2, was also fully active in the DeltaTup1 cells. This suggests that in this strain, hormone binding is not required for transcription activation by hER. It is known that the Tup1/Ssn6 complex plays an important role in general transcription repression by protecting histone acetylation sites thus stabilizing nucleosomes. In the DeltaTup1 cells, nucleosomes are known to be unstable because histones can be easily accessed by acetylase and cause nucleosome disassociation. Two point mutations in helix 12 (H12) in ER-AF-2, which abolished hER function in human cells, also completely abolished hER function in the wild-type yeast cells. This suggested that H12 is essential for hER transcription activation function. However, hER with the H12 mutation is able to activate transcription in DeltaTup1 cells. This indicates that the normal function of H12 is required for transcription activation by hER only if nucleosomes are not acetylated and are therefore stable. The results of this work suggest that there is a close relationship between hER function and nucleosome remodeling. It also provides insight about H12 activity and its functional relationship with other domains in hER. We propose here that H12 is essential for hER function by recruiting strong nucleosome remodeling proteins to the promoter region thus overcoming nucleosome repression.

Genetic analysis of calmodulin and its targets in Saccharomyces cerevisiae.

Calmodulin, a small, ubiquitous Ca2+-binding protein, regulates a wide variety of proteins and processes in all eukaryotes. CMD1, the single gene encoding calmodulin in S. cerevisiae, is essential, and this review discusses studies that identified many of calmodulin's physiological targets and their functions in yeast cells. Calmodulin performs essential roles in mitosis, through its regulation of Nuf1p/Spc110p, a component of the spindle pole body, and in bud growth, by binding Myo2p, an unconventional class V myosin required for polarized secretion. Surprisingly, mutant calmodulins that fail to bind Ca2+ can perform these essential functions. Calmodulin is also required for endocytosis in yeast and participates in Ca2+-dependent, stress-activated signaling pathways through its regulation of a protein phosphatase, calcineurin, and the protein kinases, Cmk1p and Cmk2p. Thus, calmodulin performs important physiological functions in yeast cells in both its Ca2+-bound and Ca2+-free form.

Mutation in the beta-tubulin signature motif suppresses microtubule GTPase activity and dynamics, and slows mitosis.

We introduced a threonine-to-glycine point mutation at position 143 in the "tubulin signature motif" 140Gly-Gly-Gly-Thr-Gly-Ser-Gly146 of Saccharomyces cerevisiae beta-tubulin. In an electron diffraction model of the tubulin dimer, this sequence comes close to the phosphates of a guanine nucleotide bound in the beta-tubulin exchangeable E site. Both the GTP-binding affinity and the microtubule (MT)-dependent GTPase activity of tubulin isolated from haploid tub2-T143G mutant cells were reduced by at least 15-fold, compared to tubulin isolated from control wild-type cells. The growing and shortening dynamics of MTs assembled from alphabeta:Thr143Gly-mutated dimers were also strongly suppressed, compared to control MTs. The in vitro properties of the mutated MTs (slower growing and more stable) are consistent with the effects of the tub2-T143G mutation in haploid cells. The average length of MT spindles in large-budded mutant cells was only 3.7 +/- 0.2 microm, approximately half of the size of MT arrays in large-budded wild-type cells (average length = 7.1 +/- 0.4 microm), suggesting that there is a delay in mitosis in the mutant cells. There was also a higher proportion of large-budded cells with unsegregated nuclei in mutant cultures (30% versus 12% for wild-type cells), again suggesting such a delay. The results show that beta:Thr143 of the tubulin signature motif plays an important role in GTP binding and hydrolysis by the beta-tubulin E site and support the idea that tubulins belong to a family of proteins within the GTPase superfamily that are structurally distinct from the classic GTPases, such as EF-Tu and p21(ras). The data also suggest that MT dynamics are critical for MT function in yeast cells and that spindle MT assembly and disassembly could be coordinated with other cell-cycle events by regulating beta-tubulin GTPase activity.