Cluster analysis and display of genome-wide expression profiles in dimethyl sulfoxide treatment

Murata, Yoshinori; Momose, Yuko; Hasegawa, Mika; Iwahashi, Hitoshi; Komatsu, Yasuhiko

doi:10.1273/cbij.2.18

Cited by 10 publications

(13 citation statements)

References 34 publications

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“…The expression profiling of Me 2 SO-treated cells was compared with the expression data for the various culture incubation periods. Gene expression in response to Me 2 SO treatment was similar to the transcriptional profiles at the stationary phase (21). This suggests that in response to Me 2 SO treatment, the increase in the transcriptional level of SAM2 was greater than that of SAM1.…”

Section: Me 2 So Concentration and Duration Of Exposure-s Cerevisiaementioning

confidence: 53%

“…E. coli is capable of inducing specialized respiratory chains comprising a primary dehydrogenase when grown anaerobically with respiratory oxidants such as nitrate and Me 2 SO (1). In our DNA microarray experiments, the genes having a high similarity to the AAD gene of the lignin-degrading fungus Phanerochaete chrysosporium were induced by Me 2 SO treatment (21). The function of AAD in yeast is unclear, but it may metabolize Me 2 SO to generate DMS.…”

Section: Me 2 So Concentration and Duration Of Exposure-s Cerevisiaementioning

confidence: 85%

“…Preparation of Total RNA and mRNA-Total RNA was extracted from Me 2 SO-treated or non-treated cells by the hot phenol method (21). Poly(A) ϩ RNA was purified from total RNA with an Oligotex-dT30 mRNA purification kit (Takara Otsu, Shiga, Japan).…”

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

Dimethyl Sulfoxide Exposure Facilitates Phospholipid Biosynthesis and Cellular Membrane Proliferation in Yeast Cells

Murata¹,

Watanabe²,

Sato³

et al. 2003

Journal of Biological Chemistry

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Me 2 SO is a polar solvent that is widely used in biochemistry, pharmacology, and industry. Although there are several reports in the literature concerning the biological effects of Me 2 SO, the total cellular response remains unclear. In this paper, DNA microarray technology combined with the hierarchical clustering bioinformatics tool was used to assess the effects of Me 2 SO on yeast cells. We found that yeast exposed to Me 2 SO increased phospholipid biosynthesis through up-regulated gene expression. It was confirmed by Northern blotting that the level of INO1 and OPI3 gene transcripts, encoding key enzymes in phospholipid biosynthesis, were significantly elevated following treatment with Me 2 SO. Furthermore, the phospholipid content of the cells increased during exposure to Me 2 SO as shown by conspicuous incorporation of a lipophilic fluorescent dye (3,3 -dihexyloxacarbocyanine iodide) into the cell membranes. From these results we propose that Me 2 SO treatment induces membrane proliferation in yeast cells to alleviate the adverse affects of this chemical on membrane integrity.Dimethyl sulfoxide (Me 2 SO) 1 is widely used as a solvent in the chemical industry and as a cryoprotectant in biotechnology. It is present in the environment as a waste product of the paper industry and from the production of dimethyl sulfide (DMS) and also arises from the degradation of sulfur-containing pesticides (1). In addition, Me 2 SO forms naturally from photooxidation of DMS in the atmosphere and from degradation of DMS by phytoplankton in the marine environment (2). Because Me 2 SO has low volatility and is highly hygroscopic, it is rapidly scavenged from the atmosphere by rain and returned to earth, and thereby plays a role in the global sulfur cycle (1, 3).Microorganisms, including both prokaryotes and eukaryotes, have the capability of reducing Me 2 SO and can utilize it as a terminal electron acceptor during anaerobic growth (4 -6). Me 2 SO reductase from Escherichia coli and Rhodobacter sphaeroides catalyzes the reduction of Me 2 SO to DMS (7-9). This enzyme, which contains a molybdenum cofactor at the active center, is well characterized at the biochemical, biophysical, and molecular level and provides an excellent model system for investigating the structure and mechanism of electron transfer chain complexes (1, 10). Saccharomyces cerevisiae has a number of NADPH-dependent enzymes that, in conjunction with methionine sulfoxide reductase (MXR1), can reduce Me 2 SO to DMS (11).In E. coli, the combination of divalent cations as Ca 2ϩ and Me 2 SO has been shown to stimulate the efficiency of DNA transfer into the cell (12). In the case of mammalian cells, it is reported that the transfection efficiency is increased by Me 2 SO treatment after electroporation (13). The exact mechanism of how Me 2 SO increases membrane permeability leading to DNA uptake is unclear.In mammalian cells Me 2 SO (2% (v/v)) can induce morphological changes, for example in mouse erythroleukemic cells (14), or cause differentiation, for example ...

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Section: Me 2 So Concentration and Duration Of Exposure-s Cerevisiaementioning

confidence: 53%

Section: Me 2 So Concentration and Duration Of Exposure-s Cerevisiaementioning

confidence: 85%

See 1 more Smart Citation

Dimethyl Sulfoxide Exposure Facilitates Phospholipid Biosynthesis and Cellular Membrane Proliferation in Yeast Cells

Murata¹,

Watanabe²,

Sato³

et al. 2003

Journal of Biological Chemistry

Self Cite

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“…Hierarchical clustering was carried out by using Gene Spring [15] [16]. The settings for the calculations were as follows: The similarity was measured by standard correlation, the separation ratio was 1.0, and the minimum distance was 0.001 [15] [16].…”

Section: Hierarchical Clusteringmentioning

confidence: 99%

“…The settings for the calculations were as follows: The similarity was measured by standard correlation, the separation ratio was 1.0, and the minimum distance was 0.001 [15] [16]. For the calculation, 3874 genes were used.…”

Section: Hierarchical Clusteringmentioning

confidence: 99%

Bioassay of Pesticide Lindane Using Yeast-DNA Microarray Technology

Parveen

Momose

Kitagawa

et al. 2003

CBIJ

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We analysed the gene expression pattern of Saccharomyces cerevisiae in response to lindane, a strong toxicant widely used as a pesticide in agriculture and by public health services. cDNA preparations from untreated cells and from cells treated with lindane were used to screen the DNA microarrays of about 6,000 genes. A total of 288 genes showed >2-fold induction in transcript levels, out of which 112 have not yet been characterized. The functional analysis of most known genes indicates that genes involved with mitochondrial dysfunction, oxidative stress, ionic homeostasis, mitochondrial organization, or biogenesis responded to lindane-mediated stress. In addition, several induced genes were shown to contribute to ER-mediated degradation and quality control. However, no significant changes in the transcript levels of ORFs related to DNA damage and repair were observed. Furthermore, the mRNA levels of some uncharacterized genes are significantly high, and the unveiling of these genes, along with that of known genes, might provide the opportunity to illustrate how yeast responds to environmental perturbation. This analysis will also facilitate the identification of some specific genes that could be used as biomarkers for a toxicity assay of lindane or other similar environmental pollutants.

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Toxicity of anionic detergents determined by Saccharomyces cerevisiae microarray analysis

et al. 2004

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Cluster analysis and display of genome-wide expression profiles in dimethyl sulfoxide treatment

Cited by 10 publications

References 34 publications

Dimethyl Sulfoxide Exposure Facilitates Phospholipid Biosynthesis and Cellular Membrane Proliferation in Yeast Cells

Dimethyl Sulfoxide Exposure Facilitates Phospholipid Biosynthesis and Cellular Membrane Proliferation in Yeast Cells

Bioassay of Pesticide Lindane Using Yeast-DNA Microarray Technology

Toxicity of anionic detergents determined by Saccharomyces cerevisiae microarray analysis

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