[show abstract][hide abstract] ABSTRACT: There is increasing evidence that certain Vps proteins, factors that mediate vesicular protein trafficking, have additional roles in regulating transcription factors at the endosome. We found that yeast mutants lacking the PI(3)P kinase Vps34 or its associated protein kinase Vps15 display multiple phenotypes indicating impaired transcription elongation. These phenotypes include reduced mRNA production from long or G+C-rich coding sequences (CDS) without affecting the associated GAL1 promoter activity, and a reduced rate of RNA polymerase II (Pol II) progression through lacZ CDS in vivo. Consistent with reported genetic interactions with mutations affecting the histone acetyltransferase complex NuA4, vps15Δ and vps34Δ mutations reduce NuA4 occupancy in certain transcribed CDS. vps15Δ and vps34Δ mutants also exhibit impaired localization of the induced GAL1 gene to the nuclear periphery. We found unexpectedly that, similar to known transcription elongation factors, these and several other Vps factors can be cross-linked to the CDS of genes induced by Gcn4 or Gal4 in a manner dependent on transcriptional induction and stimulated by Cdk7/Kin28-dependent phosphorylation of the Pol II CTD. We also observed co-localization of a fraction of Vps15-GFP and Vps34-GFP with nuclear pores at nucleus-vacuole (NV) junctions in live cells. These findings suggest that Vps factors enhance the efficiency of transcription elongation in a manner involving their physical proximity to nuclear pores and transcribed chromatin.
[show abstract][hide abstract] ABSTRACT: In response to severe environmental stresses eukaryotic cells shut down translation and accumulate components of the translational machinery in stress granules (SGs). Since they contain mainly mRNA, translation initiation factors and 40S ribosomal subunits, they have been referred to as dominant accumulations of stalled translation preinitiation complexes. Here we present evidence that the robust heat shock-induced SGs of also contain translation elongation factors eEF3 (Yef3p) and eEF1Bγ2 (Tef4p) as well as translation termination factors eRF1 (Sup45p) and eRF3 (Sup35p). Despite the presence of the yeast prion protein Sup35 in heat shock-induced SGs, we found out that its prion-like domain is not involved in the SGs assembly. Factors eEF3, eEF1Bγ2 and eRF1 were accumulated and co-localized with Dcp2 foci even upon a milder heat shock at 42°C independently of P-bodies scaffolding proteins. We also show that eEF3 accumulations at 42°C determine sites of the genuine SGs assembly at 46°C. We suggest that identification of translation elongation and termination factors in SGs might help to understand the mechanism of the eIF2α factor phosphorylation-independent repression of translation and SGs assembly.
PLoS ONE 01/2013; 8(2):e57083. · 3.73 Impact Factor
[show abstract][hide abstract] ABSTRACT: As we have shown previously, yeast Mmi1 protein translocates from the cytoplasm to the outer surface of mitochondria when vegetatively growing yeast cells are exposed to oxidative stress. Here we analyzed the effect of heat stress on Mmi1 distribution. We performed domain analyses and found that binding of Mmi1 to mitochondria is mediated by its central alpha-helical domain (V-domain) under all conditions tested. In contrast, the isolated N-terminal flexible loop domain of the protein always displays nuclear localization. Using immunoelectron microscopy we confirmed re-location of Mmi1 to the nucleus and showed association of Mmi1 with intact and heat shock-altered mitochondria. We also show here that mmi1Δ mutant strains are resistant to robust heat shock with respect to clonogenicity of the cells. To elucidate this phenotype we found that the cytosolic Mmi1 holoprotein re-localized to the nucleus even in cells heat-shocked at 40°C. Upon robust heat shock at 46°C, Mmi1 partly co-localized with the proteasome marker Rpn1 in the nuclear region as well as with the cytoplasmic stress granules defined by Rpg1 (eIF3a). We co-localized Mmi1 also with Bre5, Ubp3 and Cdc48 which are involved in the protein de-ubiquitination machinery, protecting protein substrates from proteasomal degradation. A comparison of proteolytic activities of wild type and mmi1Δ cells revealed that Mmi1 appears to be an inhibitor of the proteasome. We conclude that one of the physiological functions of the multifunctional protein module, Mmi1, is likely in regulating degradation and/or protection of proteins thereby indirectly regulating the pathways leading to cell death in stressed cells.
PLoS ONE 01/2013; 8(10):e77791. · 3.73 Impact Factor
[show abstract][hide abstract] ABSTRACT: The protein Isw1 of Saccharomyces cerevisiae is an imitation-switch chromatin-remodeling factor. We studied the mechanisms of its nuclear import and found that the nuclear localization signal (NLS) mediating the transport of Isw1 into the nucleus is located at the end of the C-terminus of the protein (aa1079-1105). We show that it is an atypical bipartite signal with an unconventional linker of 19 aa (KRIR X(19) KKAK) and the only nuclear targeting signal within the Isw1 molecule. The efficiency of Isw1 nuclear import was found to be modulated by changes to the amino-acid composition in the vicinity of the KRIR motif, but not by the linker length. Live-cell imaging of various karyopherin mutants and in vitro binding assays of Isw1NLS to importin-α revealed that the nuclear translocation of Isw1 is mediated by the classical import pathway. Analogous motifs to Isw1NLS are highly conserved in Isw1 homologues of other yeast species, and putative bipartite cNLS were identified in silico at the end of the C-termini of ISWI proteins from higher eukaryotes. We suggest that the C-termini of the ISWI family proteins play an important role in their nuclear import.
[show abstract][hide abstract] ABSTRACT: The large protein superfamily of NADPH oxidases (NOX enzymes) is found in members of all eukaryotic kingdoms: animals, plants, fungi, and protists. The physiological functions of these NOX enzymes range from defense to specialized oxidative biosynthesis and to signaling. In filamentous fungi, NOX enzymes are involved in signaling cell differentiation, in particular in the formation of fruiting bodies. On the basis of bioinformatics analysis, until now it was believed that the genomes of unicellular fungi like Saccharomyces cerevisiae and Schizosaccharomyces pombe do not harbor genes coding for NOX enzymes. Nevertheless, the genome of S. cerevisiae contains nine ORFs showing sequence similarity to the catalytic subunits of mammalian NOX enzymes, only some of which have been functionally assigned as ferric reductases involved in iron ion transport. Here we show that one of the nine ORFs (YGL160W, AIM14) encodes a genuine NADPH oxidase, which is located in the endoplasmic reticulum (ER) and produces superoxide in a NADPH-dependent fashion. We renamed this ORF YNO1 (yeast NADPH oxidase 1). Overexpression of YNO1 causes YCA1-dependent apoptosis, whereas deletion of the gene makes cells less sensitive to apoptotic stimuli. Several independent lines of evidence point to regulation of the actin cytoskeleton by reactive oxygen species (ROS) produced by Yno1p.
Proceedings of the National Academy of Sciences 05/2012; 109(22):8658-63. · 9.74 Impact Factor
[show abstract][hide abstract] ABSTRACT: Environmental stresses inducing translation arrest are accompanied by the deposition of translational components into stress granules (SGs) serving as mRNA triage sites. It has recently been reported that, in Saccharomyces cerevisiae, formation of SGs occurs as a result of a prolonged glucose starvation. However, these SGs did not contain eIF3, one of hallmarks of mammalian SGs. We have analyzed the effect of robust heat shock on distribution of eIF3a/Tif32p/Rpg1p and showed that it results in the formation of eIF3a accumulations containing other eIF3 subunits, known yeast SG components and small but not large ribosomal subunits and eIF2alpha/Sui2p. Interestingly, under these conditions, Dcp2p and Dhh1p P-body markers also colocalized with eIF3a. Microscopic analyses of the edc3Deltalsm4DeltaC mutant demonstrated that different scaffolding proteins are required to induce SGs upon robust heat shock as opposed to glucose deprivation. Even though eIF2alpha became phosphorylated under these stress conditions, the decrease in polysomes and formation of SGs occurred independently of phosphorylation of eIF2alpha. We conclude that under specific stress conditions, such as robust heat shock, yeast SGs do contain eIF3 and 40S ribosomes and utilize alternative routes for their assembly.
[show abstract][hide abstract] ABSTRACT: Strains of Saccharomyces cerevisiae lacking Isw2, the catalytic subunit of the Isw2 chromatin remodeling complex, show the mating type-independent activation of the cell wall integrity (CWI) signaling pathway. Since the CWI pathway activation usually reflects cell wall defects, we searched for the cell wall-related genes changed in expression. The genes DSE1, CTS1, and CHS1 were upregulated as a result of the absence of Isw2, according to previously published gene expression profiles (I. Frydlova, M. Basler, P. Vasicova, I. Malcova, and J. Hasek, Curr. Genet. 52:87-95, 2007). Western blot analyses of double deletion mutants, however, did not indicate the contribution of the chitin metabolism-related genes CTS1 and CHS1 to the CWI pathway activation. Nevertheless, the deletion of the DSE1 gene encoding a daughter cell-specific protein with unknown function suppressed CWI pathway activation in isw2Delta cells. In addition, the deletion of DSE1 also abolished the budding-within-the-birth-scar phenotype of isw2Delta cells. The plasmid-driven overexpression proved that the deregulation of Dse1 synthesis was also responsible for CWI pathway activation and manifestation of the budding-within-the-birth-scar phenotype in wild-type cells. The overproduced Dse1-green fluorescent protein localized to both sides of the septum and persisted in unbudded cells. Although the exact cellular role of this daughter cell-specific protein has to be elucidated, our data point to the involvement of Dse1 in bud site selection in haploid cells.
[show abstract][hide abstract] ABSTRACT: Fröhlich postulated coherent polar oscillations as a fundamental biophysical property of biological systems. Recently, Pelling et al. (2004, 2005) detected mechanical vibrations of yeast cell membrane with atomic force microscope (AFM) and analyzed by Fourier analysis in the frequency range 0.5-2 kHz with amplitudes of the order of 1 nm. This article describes the measurement of electric activity of yeast cells in the acoustic frequency range and of mechanical vibrations of cell membrane. Spectrum analyzer and electrically and electromagnetically screened box with point sensor and amplifiers fed by batteries were used for measurement of synchronized and non synchronized tubulin mutants of yeast cells. We show that the electric activity of synchronized cells in the M phase is greater that of non synchronized cells. That corresponds to the findings of Pohl et al. (1981). Obtained results of measurement of cell electric activity are in good agreement with AFM findings.
Electromagnetic Biology and Medicine 01/2009; 28(2):223-32. · 0.81 Impact Factor
[show abstract][hide abstract] ABSTRACT: The late endosome (MVB) plays a key role in coordinating vesicular transport of proteins between the Golgi complex, vacuole/lysosome, and plasma membrane. We found that deleting multiple genes involved in vesicle fusion at the MVB (class C/D vps mutations) impairs transcriptional activation by Gcn4, a global regulator of amino acid biosynthetic genes, by decreasing the ability of chromatin-bound Gcn4 to stimulate preinitiation complex assembly at the promoter. The functions of hybrid activators with Gal4 or VP16 activation domains are diminished in class D mutants as well, suggesting a broader defect in activation. Class E vps mutations, which impair protein sorting at the MVB, also decrease activation by Gcn4, provided they elicit rapid proteolysis of MVB cargo proteins in the aberrant late endosome. By contrast, specifically impairing endocytic trafficking from the plasma membrane, or vesicular transport to the vacuole, has a smaller effect on Gcn4 function. Thus, it appears that decreasing cargo proteins in the MVB through impaired delivery or enhanced degradation, and not merely the failure to transport cargo properly to the vacuole or downregulate plasma membrane proteins by endocytosis, is required to attenuate substantially transcriptional activation by Gcn4.
Molecular and cellular biology 10/2008; 28(22):6796-818. · 6.06 Impact Factor
[show abstract][hide abstract] ABSTRACT: Hypothesis of coherent vibration states in biological systems based on nonlinear interaction between longitudinal elastic and electric polarization fields with metabolic energy supply was formulated by Frohlich. Conditions for excitation of coherent states and generation of electromagnetic fields are satisfied in microtubules which form electrical polar structures. Numerical models are used for analysis of Frohlich's vibration states in cells. Reduction of activity and of energy production in mitochondria, and disintegration of cytoskeleton structures by phosphorylation on the pathway of cancer trasformation can diminish excitation of the Frohlich's vibration states and of the generated electromagnetic field, which results in disturbances of the interaction forces between cells. Interaction forces between cancer cells may be smaller than interaction forces between healthy cells and cancer cells as follows from numerical models. Mechanism of malignity, i.e. local invasion, detachment of cancer cells, and metastasis, is assumed to depend on the electromagnetic field.
Indian journal of experimental biology 06/2008; 46(5):310-21. · 1.20 Impact Factor
[show abstract][hide abstract] ABSTRACT: This paper presents results from the measurement of the electrical activity cold sensitive beta-tubulin mutant tub2-401 of yeast cells in frequency region 0.4 - 1.6 kHz. 25 measurements of both synchronized and nonsynchronized cells show that the synchronized cells have higher electrical activity which corresponds to the findings of Pohl et al. Local nanomechanical vibrations of yeast cell membrane have been measured by Pelling et al. with Atomic Force Microscopy in same frequency region. Mechanical oscillations of electrically polar structures in cell may give rise to electric oscillations we measured.
[show abstract][hide abstract] ABSTRACT: Frohlich postulated coherent polar oscillations as a fundamental biophysical property of biological systems. Pelling et al. detected recently mechanical vibrations of yeast cell membrane in the frequency range 0.5-2 kHz with atomic force microscope (AFM). This paper describes the measurement of electric activity of yeast cells at frequencies around 1 kHz and of mechanical vibrations of cell membrane. Synchronized and non- synchronized tubulin mutants of yeast cells were measured. The paper includes a description of the laboratory equipment with a platinum wire point sensor and a spectrum analyzer. Obtained results are in good agreement with AFM findings.
[show abstract][hide abstract] ABSTRACT: The ability to invade a solid substrate is an important phenomenon due to its connection with pathogenic activity of fungi. We report here on invasion displayed by MATalpha cells of Saccharomyces cerevisiae lacking Isw2p, a subunit of the ISW2 chromatin remodelling complex. We found that on minimal medium, where the isw2Delta MATalpha mutant is not invasive, additional absence of another ISW2 complex subunit, Dls1p or Dpb4p, promoted invasion. Our microarray data showed that derepression of MAT a-specific genes caused by absence of Isw2p is very low. Their expression is increased only by the autocrine activation of the mating pathway. Invasion of isw2Delta MATalpha cells thus resembles the pheromone-induced invasion, including dependence on Fig2p. We show here that another pheromone-induced protein, mating agglutinin Aga1p, can play a role in the agar adhesion necessary for invasion. In contrast with MAT a-cells invading agar under low alpha-pheromone concentration, the invasive growth of isw2Delta cells specifically requires Fus3 kinase. Its function in the invasion of isw2Delta MATalpha cells cannot be completely substituted by Kss1 kinase, which plays a basic role in invasive growth signalling. We suggest that partial dependence of the isw2Delta MATalpha invasion on Fus3p and Aga1p corresponds to a weaker pheromone response of this mutant.
Current Genetics 09/2007; 52(2):87-95. · 2.41 Impact Factor
[show abstract][hide abstract] ABSTRACT: This paper discusses the possibility of using a device composed of a resonant cavity, preamplifiers, and a spectrum analyzer to detect electromagnetic emission of yeast cells at a frequency of about 42 GHz. Measurement in this frequency range is based on the Frohlich's postulate of coherent polar oscillations as a fundamental biophysical property of biological systems and on the experiments of Grundler and Keilmann who disclosed effects of exposure to the electromagnetic field at 42 GHz on the growth rate of yeast cells. This article includes a detailed description of the laboratory equipment and the methods used to evaluate the obtained results.
[show abstract][hide abstract] ABSTRACT: Phosphatidylinositol (PtdIns) phosphates are involved in signal transduction, cytoskeletal organization, and membrane traffic. PtdIns 4-phosphate [PtdIns(4)P], produced in yeast by PtdIns 4-kinase (Pik1p), appears to regulate Golgi secretory function. PtdIns(4)P is also produced by dephosphorylation of phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2], catalyzed by one of the three yeast Sjl proteins, homologs of the mammalian synaptic vesicle-associated PtdIns(4,5)P2 5-phosphatase, synaptojanin. To determine whether Pik1p and Sjl proteins operate in the same pathway or regulate the same process, we used a genetic approach. Mutation in the PIK1 gene displays synthetic genetic interactions with deletions of individual SJL genes. Deletion of SJL3 gene is synthetically lethal with pik1ts, and deletions of SJL1 or SJL2 genes in pik1ts cells exacerbate the temperature sensitivity, neomycin sensitivity, and defect in invertase secretion. A diminished level of PtdIns(4)P and increased level of PtdIns(4,5)P2 in pik1(ts)sjl1delta and pik1(ts)sjl2delta cells, compared with pik1ts cells, indicate that PtdIns(4)P is specifically required for secretion. Collectively, our results suggest that Pik1p and the Sjl proteins coordinately function to regulate the dynamic phosphorylation-dephosphorylation of the polar heads of phosphoinositides, and this process appears to be important for membrane trafficking pathways.
FEMS Yeast Research 03/2005; 5(4-5):363-71. · 2.46 Impact Factor
[show abstract][hide abstract] ABSTRACT: The Isw2p-Itc1p chromatin remodelling complex of Saccharomyces cerevisiae is a member of the ISWI class of ATPases with a nucleosome spacing activity, involved in regulation of expression of a broad spectrum of genes. Its absence causes derepression of a-specific genes and aberrant morphology in alpha-mating type cells. We report here that the deletion of the ISW2 gene in the originally non-invasive BY strain induces mating type-specific invasive growth strongly affected by nitrogen starvation. Although the Flo11 protein was postulated to be critical for haploid invasive growth, we showed that the invasive growth caused by the isw2 and itc1 deletions in alpha-mating type cells was Flo11p-independent. This type of invasive growth was proved to be a consequence of the activation of the pheromone response pathway. Our results suggest that Isw2 and Itc1 proteins do not have the same impact on the described phenomenon.
[show abstract][hide abstract] ABSTRACT: We performed detailed phenotypic analysis of the isw2 delta strains of the W303 genetic background and compared its results with those obtained previously in BY-derived genetic background. Shmoolike morphology was observed in the isw2 delta strain of alpha-mating type of the BY strains, but not in its W303-derived counterpart. On the other hand, derepression of a-specific genes in the isw2 delta (MAT alpha) strain was observed in both genetic backgrounds, although to a different extent. Unlike in BY-derived strain hyperactivation of the Ras2/cAMP pathway reduced invasiveness of the isw2 delta strain (MAT alpha) of the W303 background. Sensitivity to Calcofluor White indicating a cell wall-integrity defect was significantly increased in the isw2 delta strains of the W303 background in contrast to BY-derived strains. Our data indicate that the effects of the isw2 deletion strongly depend on the background in which the deletion, is made.
[show abstract][hide abstract] ABSTRACT: eIF3j/Hcr1p, a protein associated with eIF3, was shown to bind to, and stabilize, the multifactor complex containing eIFs 1, 2, 3, and 5 and Met-tRNA(i)(Met), whose formation is required for an optimal rate of translation initiation. Here we present evidence that eIF3j/Hcr1p is an RNA binding protein that enhances a late step in 40 S ribosome maturation involving cleavage of the 20 S precursor of 18 S rRNA in the cytoplasm. Immunofluorescence staining shows that eIF3j/Hcr1p is localized predominantly in the cytoplasm. The hcr1Delta mutant exhibits a decreased amount of 40 S subunits, hypersensitivity to paromomycin, and increased levels of 20 S pre-rRNA. Combining the hcr1Delta mutation with drs2Delta or rps0aDelta, deletions of two other genes involved in the same step of 40 S subunit biogenesis, produced a synthetic growth defect. p35, the human ortholog of eIF3j/Hcr1p, partially complemented the slow growth phenotype conferred by hcr1Delta when overexpressed in yeast. heIF3j/p35 was found physically associated with yeast eIF3 and 43 S initiation complexes in vitro and in vivo. Because it did not complement the 40 S biogenesis defect of hcr1Delta, it appears that heIF3j can substitute for eIF3j/Hcr1p only in translation initiation. We conclude that eIF3j/Hcr1p is required for rapid processing of 20 S to 18 S rRNA besides its role in translation initiation, providing an intriguing link between ribosome biogenesis and translation.
Journal of Biological Chemistry 12/2001; 276(46):43351-60. · 4.65 Impact Factor