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Vasicova P, Rinnerthaler M, Haskova D, Novakova L, Malcova I, Breitenbach M, Hasek J. Formaldehyde fixation is detrimental to actin cables in glucose-depleted S. cerevisiae cells. MICROBIAL CELL 2016; 3:206-214. [PMID: 28357356 PMCID: PMC5349148 DOI: 10.15698/mic2016.05.499] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Actin filaments form cortical patches and emanating cables in fermenting cells of
Saccharomyces cerevisiae. This pattern has been shown to be
depolarized in glucose-depleted cells after formaldehyde fixation and staining
with rhodamine-tagged phalloidin. Loss of actin cables in mother cells was
remarkable. Here we extend our knowledge on actin in live glucose-depleted cells
co-expressing the marker of actin patches (Abp1-RFP) with the marker of actin
cables (Abp140-GFP). Glucose depletion resulted in appearance of actin patches
also in mother cells. However, even after 80 min of glucose deprivation these
cells showed a clear network of actin cables labeled with Abp140-GFP in contrast
to previously published data. In live cells with a mitochondrial dysfunction
(rho0 cells), glucose depletion resulted in almost immediate
appearance of Abp140-GFP foci partially overlapping with Abp1-RFP patches in
mother cells. Residual actin cables were clustered in patch-associated bundles.
A similar overlapping “patchy” pattern of both actin markers was observed upon
treatment of glucose-deprived rho+ cells with FCCP (the inhibitor of
oxidative phosphorylation) and upon treatment with formaldehyde. While the
formaldehyde-targeted process stays unknown, our results indicate that published
data on yeast actin cytoskeleton obtained from glucose-depleted cells after
fixation should be considered with caution.
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Affiliation(s)
- Pavla Vasicova
- Laboratory of Cell Reproduction, Institute of Microbiology of the CAS, v.v.i., Prague, Czech Republic
| | - Mark Rinnerthaler
- Department of Cell Biology, Division of Genetics, University of Salzburg, Salzburg, Austria
| | - Danusa Haskova
- Laboratory of Cell Reproduction, Institute of Microbiology of the CAS, v.v.i., Prague, Czech Republic
| | - Lenka Novakova
- Laboratory of Cell Reproduction, Institute of Microbiology of the CAS, v.v.i., Prague, Czech Republic
| | - Ivana Malcova
- Laboratory of Cell Reproduction, Institute of Microbiology of the CAS, v.v.i., Prague, Czech Republic
| | - Michael Breitenbach
- Department of Cell Biology, Division of Genetics, University of Salzburg, Salzburg, Austria
| | - Jiri Hasek
- Laboratory of Cell Reproduction, Institute of Microbiology of the CAS, v.v.i., Prague, Czech Republic
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Oeck S, Malewicz NM, Hurst S, Rudner J, Jendrossek V. The Focinator - a new open-source tool for high-throughput foci evaluation of DNA damage. Radiat Oncol 2015; 10:163. [PMID: 26238507 PMCID: PMC4554354 DOI: 10.1186/s13014-015-0453-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 07/05/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The quantitative analysis of foci plays an important role in many cell biological methods such as counting of colonies or cells, organelles or vesicles, or the number of protein complexes. In radiation biology and molecular radiation oncology, DNA damage and DNA repair kinetics upon ionizing radiation (IR) are evaluated by counting protein clusters or accumulations of phosphorylated proteins recruited to DNA damage sites. Consistency in counting and interpretation of foci remains challenging. Many current software solutions describe instructions for time-consuming and error-prone manual analysis, provide incomplete algorithms for analysis or are expensive. Therefore, we aimed to develop a tool for costless, automated, quantitative and qualitative analysis of foci. METHODS For this purpose we integrated a user-friendly interface into ImageJ and selected parameters to allow automated selection of regions of interest (ROIs) depending on their size and circularity. We added different export options and a batch analysis. The use of the Focinator was tested by analyzing γ-H2.AX foci in murine prostate adenocarcinoma cells (TRAMP-C1) at different time points after IR with 0.5 to 3 Gray (Gy). Additionally, measurements were performed by users with different backgrounds and experience. RESULTS The Focinator turned out to be an easily adjustable tool for automation of foci counting. It significantly reduced the analysis time of radiation-induced DNA-damage foci. Furthermore, different user groups were able to achieve a similar counting velocity. Importantly, there was no difference in nuclei detection between the Focinator and ImageJ alone. CONCLUSIONS The Focinator is a costless, user-friendly tool for fast high-throughput evaluation of DNA repair foci. The macro allows improved foci evaluation regarding accuracy, reproducibility and analysis speed compared to manual analysis. As innovative option, the macro offers a combination of multichannel evaluation including colocalization analysis and the possibility to run all analyses in a batch mode.
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Affiliation(s)
- Sebastian Oeck
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Medical School, Virchowstrasse 173, 45122, Essen, Germany.
| | - Nathalie M Malewicz
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Medical School, Virchowstrasse 173, 45122, Essen, Germany.
| | - Sebastian Hurst
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Medical School, Virchowstrasse 173, 45122, Essen, Germany.
| | - Justine Rudner
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Medical School, Virchowstrasse 173, 45122, Essen, Germany.
| | - Verena Jendrossek
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Medical School, Virchowstrasse 173, 45122, Essen, Germany.
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Pokorný J, Hašek J, Jelínek F, Šaroch J, Palán B. ELECTROMAGNETIC ACTIVITY OF YEAST CELLS IN THE M PHASE. ACTA ACUST UNITED AC 2009. [DOI: 10.1081/jbc-100108577] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Malone RE, Haring SJ, Foreman KE, Pansegrau ML, Smith SM, Houdek DR, Carpp L, Shah B, Lee KE. The signal from the initiation of meiotic recombination to the first division of meiosis. EUKARYOTIC CELL 2005; 3:598-609. [PMID: 15189982 PMCID: PMC420144 DOI: 10.1128/ec.3.3.598-609.2004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Two of the unique events that occur in meiosis are high levels of genetic recombination and the reductional division. Our previous work demonstrated that the REC102, REC104, REC114, and RAD50 genes, required to initiate meiotic recombination in Saccharomyces cerevisiae, are needed for the proper timing of the first meiotic (MI) division. If these genes are absent, the MI division actually begins at an earlier time. This paper demonstrates that the meiotic recombination genes MER2/REC107, SPO11, and MRE2 and the synaptonemal complex genes HOP1 and RED1 are also required for the normal delay of the MI division. A rec103/ski8 mutant starts the MI division at the same time as in wild-type cells. Our data indicate no obvious correlation between the timing of premeiotic S phase and the timing of the first division in Rec- mutants. Cells with rec102 or rec104 mutations form MI spindles before wild-type cells, suggesting that the initiation signal acts prior to spindle formation. Neither RAD9 nor RAD24 is needed to transduce the signal, which delays the first division. The timing of the MI division in RAD24 mutants indicates that the pachytene checkpoint is not active in Rec+ cells and suggests that the coordination between recombination and the MI division in wild-type cells may occur primarily due to the initiation signal. Finally, at least one of the targets of the recombination initiation signal is the NDT80 gene, a transcriptional regulator of middle meiotic gene expression required for the first division.
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Affiliation(s)
- Robert E Malone
- Department of Biological Sciences and Program in Genetics, University of Iowa, Iowa City, IA 52242, USA.
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Váchová L, Palková Z. Physiological regulation of yeast cell death in multicellular colonies is triggered by ammonia. ACTA ACUST UNITED AC 2005; 169:711-7. [PMID: 15939758 PMCID: PMC2171614 DOI: 10.1083/jcb.200410064] [Citation(s) in RCA: 146] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The existence of programmed cell death (PCD) in yeast and its significance to simple unicellular organisms is still questioned. However, such doubts usually do not reflect the fact that microorganisms in nature exist predominantly within structured, multicellular communities capable of differentiation, in which a profit of individual cells is subordinated to a profit of populations. In this study, we show that some PCD features naturally appear during the development of multicellular Saccharomyces cerevisiae colonies. An ammonia signal emitted by aging colonies triggers metabolic changes that localize yeast death only in the colony center. The remaining population can exploit the released nutrients and survives. In colonies defective in Sok2p transcription factor that are unable to produce ammonia (Váchová, L., F. Devaux, H. Kucerova, M. Ricicova, C. Jacq, and Z. Palková. 2004. J. Biol. Chem. 279:37973–37981), death is spread throughout the whole population, thus decreasing the lifetime of the colony. The absence of Mca1p metacaspase or Aif1p orthologue of mammalian apoptosis-inducing factor does not prevent regulated death in yeast colonies.
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Affiliation(s)
- Libuse Váchová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, 142 20 Prague-4, Czech Republic
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Malínská K, Malínský J, Opekarová M, Tanner W. Visualization of protein compartmentation within the plasma membrane of living yeast cells. Mol Biol Cell 2003; 14:4427-36. [PMID: 14551254 PMCID: PMC266762 DOI: 10.1091/mbc.e03-04-0221] [Citation(s) in RCA: 220] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Different distribution patterns of the arginine/H+ symporter Can1p, the H+ plasma membrane ATPase Pma1p, and the hexose transport facilitator Hxt1p within the plasma membrane of living Saccharomyces cerevisiae cells were visualized using fluorescence protein tagging of these proteins. Although Hxt1p-GFP was evenly distributed through the whole cell surface, Can1p-GFP and Pma1p-GFP were confined to characteristic subregions in the plasma membrane. Pma1p is a well-documented raft protein. Evidence is presented that Can1p, but not Hxt1p, is exclusively associated with lipid rafts, too. Double labeling experiments with Can1p-GFP- and Pma1p-RFP-containing cells demonstrate that these proteins occupy two different nonoverlapping membrane microdomains. The size of Can1p-rich (Pma1p-poor) areas was estimated to 300 nm. These domains were shown to be stable in growing cells for >30 min. To our knowledge, this is the first observation of a cell polarization-independent lateral compartmentation in the plasma membrane of a living cell.
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Affiliation(s)
- Katerina Malínská
- Universität Regensburg, Lehrstuhl für Zellbiologie und Pflanzenphysiologie, 93040 Regensburg, Germany
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Hasek J, Trachtulcová P, Kohlwein SD, Streiblová E. Colocalization of cortical microtubules and F-actin in Dipodascus magnusii using confocal laser scanning microscopy. Folia Microbiol (Praha) 2003; 48:177-82. [PMID: 12800500 DOI: 10.1007/bf02930952] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Distribution of microtubules and F-actin in aerobically growing cells of Dipodascus magnusii, belonging to the class Saccharomycetes was analyzed using immunofluorescence microscopy and labeling with rhodamine-tagged phalloidin. A conspicuous system of permanent cytoplasmic microtubules was observed in association with multiple nuclei. In elongating cells, helices of cytoplasmic microtubules appeared at the cell cortex. In cells approaching cytokinesis transversely oriented microtubules were revealed at incipient division sites. Confocal laser scanning microscopy showed a continuity of these transverse microtubules with the remaining microtubule network. The actin system of D. magnusii consisted of patches and filaments. Patches were found to accumulate at the tips of growing cells. Bands of fine actin filaments were usually observed before F-actin rings were established. A close cortical association of microtubules with the F-actin ring was documented on individual optical sections of labeled cells. Cells with developing septa showed medial F-actin discs associated at both sides with microtubules. Colocalization of cytoplasmic microtubules with actin filaments at the cortex of dividing cells supports a role of both cytoskeletal components in controlling cell wall growth and septum formation in D. magnusii.
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Affiliation(s)
- J Hasek
- Institute of Microbiology, Academy of Sciences of the Czech Republic, 142 20 Prague, Czechia.
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Hendrychová J, Vítová M, Bisová K, Wiche G, Zachleder V. Plectin-like proteins are present in cells of Chlamydomonas eugametos (Volvocales). Folia Microbiol (Praha) 2002; 47:535-9. [PMID: 12503400 DOI: 10.1007/bf02818794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Using both monoclonal and polyclonal antibodies against mammalian plectin (multifunctional protein cross-linking cytoskeletal structures, mainly intermediate filaments, in mammalian cells), several putative isoforms of plectin-like proteins were found in protein extracts from the green alga Chlamydomonas eugametos (Volvocales). Immunofluorescence and immunoblotting revealed that some of the plectin-like proteins were present in perinuclear region or localized near the cell wall, probably being attached to the cytoplasmic membrane.
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Affiliation(s)
- J Hendrychová
- Division of Autotrophic Microorganisms, Institute of Microbiology, Academy of Sciences of the Czech Republic, 379 81 Trebon
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Lunde CS, Kubo I. Effect of polygodial on the mitochondrial ATPase of Saccharomyces cerevisiae. Antimicrob Agents Chemother 2000; 44:1943-53. [PMID: 10858359 PMCID: PMC89990 DOI: 10.1128/aac.44.7.1943-1953.2000] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/1999] [Accepted: 04/20/2000] [Indexed: 11/20/2022] Open
Abstract
The fungicidal mechanism of a naturally occurring sesquiterpene dialdehyde, polygodial, was investigated in Saccharomyces cerevisiae. In an acidification assay, polygodial completely suppressed the glucose-induced decrease in external pH at 3.13 microgram/ml, the same as the fungicidal concentration. Acidification occurs primarily through the proton-pumping action of the plasma membrane ATPase, Pma1p. Surprisingly, this ATPase was not directly inhibited by polygodial. In contrast, the two other membrane-bound ATPases in yeast were found to be susceptible to the compound. The mitochondrial ATPase was inhibited by polygodial in a dose-dependent manner at concentrations similar to the fungicidal concentration, whereas the vacuolar ATPase was only slightly inhibited. Cytoplasmic petite mutants, which lack mitochondrial DNA and are respiration deficient, were significantly less susceptible to polygodial than the wild type, as was shown in time-kill curves. A pet9 mutant which lacks a functional ADP-ATP translocator and is therefore respiration dependent was rapidly inhibited by polygodial. The results of these susceptibility assays link enzyme inhibition to physiological effect. Previous studies have reported that plasma membrane disruption is the mechanism of polygodial-induced cell death; however, these results support a more complex picture of its effect. A major target of polygodial in yeast is mitochondrial ATP synthase. Reduction of the ATP supply leads to a suppression of Pma1 ATPase activity and impairs adaptive responses to other facets of polygodial's cellular inhibition.
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Affiliation(s)
- C S Lunde
- Comparative Biochemistry Group, Policy, and Management, University of California, Berkeley, California 94720, USA.
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Bialek-Wyrzykowska U, Bauer BE, Wagner W, Kohlwein SD, Schweyen RJ, Ragnini A. Low levels of Ypt protein prenylation cause vesicle polarization defects and thermosensitive growth that can be suppressed by genes involved in cell wall maintenance. Mol Microbiol 2000; 35:1295-311. [PMID: 10760132 DOI: 10.1046/j.1365-2958.2000.01782.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Rab/Ypt small G proteins are essential for intracellular vesicle trafficking in mammals and yeast. The vesicle-docking process requires that Ypt proteins are located in the vesicle membrane. C-terminal geranylgeranyl anchors mediate the membrane attachment of these proteins. The Rab escort protein (REP) is essential for the recognition of Rab/Ypt small G proteins by geranylgeranyltransferase II (GGTase II) and for their delivery to acceptor membranes. What effect an alteration in the levels of prenylated Rab/Ypt proteins has on vesicle transport or other cellular processes is so far unknown. Here, we report the characterization of a yeast REP mutant, mrs6-2, in which reduced prenylation of Ypt proteins occurs even at the permissive temperature. A shift to the restrictive temperature does not alter exponential growth during the first 3 h. The amount of Sec4p, but not Ypt1p, bound to vesicle membranes is reduced 2.5 h after the shift compared with wild-type or mrs6-2 cells incubated at 25 degrees C. In addition, vesicles fail to be polarized towards the bud and small budded binucleate cells accumulate at this time point. Growth in 1 M sorbitol or overexpression of MLC1, encoding a myosin light chain able to bind the unconventional type V myosin Myo2, or of genes involved in cell wall maintenance, such as SLG1, GFA1 and LRE1, suppresses mrs6-2 thermosensitivity. Our data suggest that, at least at high temperature, a critical minimal level of Ypt protein prenylation is required for maintaining vesicle polarization.
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Affiliation(s)
- U Bialek-Wyrzykowska
- Vienna Biocenter, Institute of Microbiology and Genetics, University of Vienna, A-1030 Vienna, Austria
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Jelínek F, Pokorný J, Saroch J, Trkal V, Hasek J, Palán B. Microelectronic sensors for measurement of electromagnetic fields of living cells and experimental results. BIOELECTROCHEMISTRY AND BIOENERGETICS (LAUSANNE, SWITZERLAND) 1999; 48:261-6. [PMID: 10379538 DOI: 10.1016/s0302-4598(99)00017-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Microelectronic sensors are used for measurements of electromagnetic fields generated by synchronized cultures of yeast cells. Cold sensitive mutant tub2-401 of Saccharomyces cerevisiae is used. The measured electromagnetic signals in the frequency range from 8 to 9 MHz are compared with evolution of the reassembled microtubules. The detected signals peak in the time interval 25-30 min and 45-60 min after the release of the cells from the restrictive to the permissive temperature. The first maximum corresponds to the stage when the mitotic spindle is formed and binds chromatids. The second maximum is measured when the processes of anaphase A and of anaphase B take place.
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Affiliation(s)
- F Jelínek
- Institute of Radio Engineering and Electronics, Academy of Sciences of Czech Republic, Prague.
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