Research Article
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Year 2020, Volume: 29 Issue: 1, 8 - 17, 30.06.2020
https://doi.org/10.38042/biost.2020.29.01.02

Abstract

References

  • Assou, S., Le Carrour, T., Tondeur, S., Ström, S., Gabelle, A., Marty, S., Nadal, L., Pandesco, V., Reme, T. Hugnot, J. P., Gasca, S., Hovatta, O., Hamamah, S., Klein, B., & De Vos, J. (2007). A meta‐analysis of human embryonic stem cells transcriptome integrated into a web‐based expression atlas. Stem cells, 25(4), 961-973.
  • Bhasin, M. K., Ndebele, K., Bucur, O., Yee, E. U., Otu, H. H., Plati, J., Bullock, A., Gu, X., Castan, E., Zhang, P., Najarian, R., Muraru, M. S., Miksad, R., Khosravi-Far, R., & Libermann, T. A. (2016). Meta-analysis of transcriptome data identifies a novel 5-gene pancreatic adenocarcinoma classifier. Oncotarget, 7(17), 23263.
  • Breuer, U., Terentiev, Y., Kunze, G., & Babel, W. (2002). Yeasts as producers of polyhydroxyalkanoates: genetic engineering of Saccharomyces cerevisiae. Macromolecular bioscience, 2(8), 380-386.
  • Borresen, E. C., Henderson, A. J., Kumar, A., Weir, T. L., & Ryan, E. P. (2012). Fermented foods: patented approaches and formulations for nutritional supplementation and health promotion. Recent patents on food, nutrition & agriculture, 4(2), 134-140.
  • Cabiscol, E., Piulats, E., Echave, P., Herrero, E., & Ros, J. (2000). Oxidative stress promotes specific protein damage in Saccharomyces cerevisiae. Journal of Biological Chemistry, 275(35), 27393-27398.
  • Carbon, S., Ireland, A., Mungall, C. J., Shu, S., Marshall, B., Lewis, S., the Amigo Hub, & the Web Presence Working Group. (2009). AmiGO: online access to ontology and annotation data. Bioinformatics, 25(2), 288-289.
  • Cardona, C. A., Orrego, C. E., & Paz, I. C. (2009). The Potential for production of bioethanol and bioplastics from potato starch in Colombia. Fruit, Vegetable and Cereal Science and Biotechnology, 3, 102-114.
  • Carmel‐Harel, O., Stearman, R., Gasch, A. P., Botstein, D., Brown, P. O., & Storz, G. (2001). Role of thioredoxin reductase in the Yap1p‐dependent response to oxidative stress in Saccharomyces cerevisiae. Molecular microbiology, 39(3), 595-605.
  • Cheng, C., Tang, R. Q., Xiong, L., Hector, R. E., Bai, F. W., & Zhao, X. Q. (2018). Association of improved oxidative stress tolerance and alleviation of glucose repression with superior xylose-utilization capability by a natural isolate of Saccharomyces cerevisiae. Biotechnology for biofuels, 11(1), 28.
  • Christodoulou, D., Link, H., Fuhrer, T., Kochanowski, K., Gerosa, L., & Sauer, U. (2018). Reserve flux capacity in the pentose phosphate pathway enables Escherichia coli's rapid response to oxidative stress. Cell systems, 6(5), 569-578.
  • Cyrne, L., us Martins, L., Fernandes, L., & Marinho, H. S. (2003). Regulation of antioxidant enzymes gene expression in the yeast Saccharomyces cerevisiae during stationary phase. Free Radical Biology and Medicine, 34(3), 385-393.
  • Davies, J. M., Lowry, C. V., & Davies, K. J. (1995). Transient adaptation to oxidative stress in yeast. Archives of biochemistry and biophysics, 317(1), 1-6.
  • Diezmann, S. (2014). Oxidative stress response and adaptation to H2O2 in the model eukaryote Saccharomyces cerevisiae and its human pathogenic relatives Candida albicans and Candida glabrata. Fungal Biology Reviews, 28(4), 126-136.
  • Douglas, K. T. (1987). Mechanism of action of glutathione‐ dependent enzymes. Advances in enzymology and related areas of molecular biology, 59, 103-167.
  • Farrugia, G., Azzopardi, M., Saliba, C., Grech, G., Gross, A. S., Pistolic, J., Benes, V., Vassallo, N., Borg, J., Madeo, F., Eisenberg, T., & Balzan, R. (2019). Aspirin impairs acetyl-coenzyme A metabolism in redox-compromised yeast cells. Scientific reports, 9(1), 1-13.
  • Flattery-O'Brien, J., Collinson, L. P., & Dawes, I. W. (1993). Saccharomyces cerevisiae has an inducible response to menadione which differs from that to hydrogen peroxide. Microbiology, 139(3), 501-507.
  • Gasch, A. P., Spellman, P. T., Kao, C. M., Carmel-Harel, O., Eisen, M. B., Storz, G., Botstein, D., & Brown, P. O. (2000). Genomic expression programs in the response of yeast cells to environmental changes. Molecular biology of the cell, 11(12), 4241-4257.
  • Giaever, G., Chu, A. M., Ni, L., Connelly, C., Riles, L., Véronneau, S., Dow, S., Lucau-Danila, A., Anderson, K., Andre, B., Arkin, A. P., Astromoff, A., Bakkoury, M. E., Bangham, R., Benito, R., Brachat, S., Campanaro, S., Curtiss, M., … & Johnston, M. (2002). Functional profiling of the Saccharomyces cerevisiae genome. Nature, 418(6896), 387-391.
  • Godon, C., Lagniel, G., Lee, J., Buhler, J. M., Kieffer, S., Perrot, M., Boucherie, H., Toledano, M. B., & Labarre, J. (1998). The H2O2 stimulon in Saccharomyces cerevisiae. Journal of Biological Chemistry, 273(35), 22480-22489.
  • Gopalacharyulu, P. V., Velagapudi, V. R., Lindfors, E., Halperin, E., & Orešič, M. (2009). Dynamic network topology changes in functional modules predict responses to oxidative stress in yeast. Molecular BioSystems, 5(3), 276-287.
  • Grant, C. M., MacIver, F. H., & Dawes, I. W. (1996). Glutathione is an essential metabolite required for resistance to oxidative stress in the yeastSaccharomyces cerevisiae. Current genetics, 29(6), 511-515.
  • Grant, C. M., Perrone, G., & Dawes, I. W. (1998). Glutathione and catalase provide overlapping defenses for protection against hydrogen peroxide in the yeastsaccharomyces cerevisiae. Biochemical and biophysical research communications, 253(3), 893-898.
  • Harding, H. P., Zhang, Y., Zeng, H., Novoa, I., Lu, P. D., Calfon, M., Sadri, N., Yun, C., Popko, B., Paules, R., Stojdl, D. F., Bell, J. C., Hettmann, T., Leiden, J. M., & Ron, D. (2003). An integrated stress response regulates amino acid metabolism and resistance to oxidative stress. Molecular cell, 11(3), 619-633.
  • Hartwell, L. H. (1974). Saccharomyces cerevisiae cell cycle. Bacteriological reviews, 38(2), 164.
  • Hruz, T., Laule, O., Szabo, G., Wessendorp, F., Bleuler, S., Oertle, L., Widmayer, P., Gruissem, W., & Zimmermann, P. (2008). Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes. Advances in bioinformatics. 2008, 420747.
  • Inzé, D., & Van Montagu, M. (1995). Oxidative stress in plants. Current Opinion in Biotechnology, 6(2), 153-158.
  • Jamieson, D. J. (1992). Saccharomyces cerevisiae has distinct adaptive responses to both hydrogen peroxide and menadione. Journal of bacteriology, 174(20), 6678-6681.

Meta-analysis of transcriptome data on oxidative stress response in Saccharomyces cerevisiae cells underlines regulation of carbon, redox and glutathione metabolism

Year 2020, Volume: 29 Issue: 1, 8 - 17, 30.06.2020
https://doi.org/10.38042/biost.2020.29.01.02

Abstract

Environmental stress adversely affects living systems within medical as well as industrial context, causing either diseases or resulting in e.g. underperforming production processes. In particular oxidative stress in industrial biotechnology context, manifested as the imbalance in generation of reactive oxygen species and antioxidant capacity causes yield losses both in growth and production in baker’s yeast. Oxidative stress response studies for Saccharomyces cerevisiae at transcriptome level are using either direct induction methods such as treatment with peroxides or indirect induction methods such as treatment with drugs or toxins. To extract common response mechanisms integrating all conditions is of high value. To this end, this study collects, processes and aggregates published transcriptome data from studies that examined the response using both direct and indirect oxidative stress induction methods. Interestingly, carbon metabolism, oxidation reduction processes and glutathione metabolic process were found to be the common mechanisms involved in oxidative stress response. However, ion homeostasis and hexose transport mechanisms have been shown to be affected from direct induction using peroxides. This result illustrates bioinformatics analysis for large, aggregated transcriptome datasets, as a steppingstone for finding common features and further metabolic engineering targets were developed.

References

  • Assou, S., Le Carrour, T., Tondeur, S., Ström, S., Gabelle, A., Marty, S., Nadal, L., Pandesco, V., Reme, T. Hugnot, J. P., Gasca, S., Hovatta, O., Hamamah, S., Klein, B., & De Vos, J. (2007). A meta‐analysis of human embryonic stem cells transcriptome integrated into a web‐based expression atlas. Stem cells, 25(4), 961-973.
  • Bhasin, M. K., Ndebele, K., Bucur, O., Yee, E. U., Otu, H. H., Plati, J., Bullock, A., Gu, X., Castan, E., Zhang, P., Najarian, R., Muraru, M. S., Miksad, R., Khosravi-Far, R., & Libermann, T. A. (2016). Meta-analysis of transcriptome data identifies a novel 5-gene pancreatic adenocarcinoma classifier. Oncotarget, 7(17), 23263.
  • Breuer, U., Terentiev, Y., Kunze, G., & Babel, W. (2002). Yeasts as producers of polyhydroxyalkanoates: genetic engineering of Saccharomyces cerevisiae. Macromolecular bioscience, 2(8), 380-386.
  • Borresen, E. C., Henderson, A. J., Kumar, A., Weir, T. L., & Ryan, E. P. (2012). Fermented foods: patented approaches and formulations for nutritional supplementation and health promotion. Recent patents on food, nutrition & agriculture, 4(2), 134-140.
  • Cabiscol, E., Piulats, E., Echave, P., Herrero, E., & Ros, J. (2000). Oxidative stress promotes specific protein damage in Saccharomyces cerevisiae. Journal of Biological Chemistry, 275(35), 27393-27398.
  • Carbon, S., Ireland, A., Mungall, C. J., Shu, S., Marshall, B., Lewis, S., the Amigo Hub, & the Web Presence Working Group. (2009). AmiGO: online access to ontology and annotation data. Bioinformatics, 25(2), 288-289.
  • Cardona, C. A., Orrego, C. E., & Paz, I. C. (2009). The Potential for production of bioethanol and bioplastics from potato starch in Colombia. Fruit, Vegetable and Cereal Science and Biotechnology, 3, 102-114.
  • Carmel‐Harel, O., Stearman, R., Gasch, A. P., Botstein, D., Brown, P. O., & Storz, G. (2001). Role of thioredoxin reductase in the Yap1p‐dependent response to oxidative stress in Saccharomyces cerevisiae. Molecular microbiology, 39(3), 595-605.
  • Cheng, C., Tang, R. Q., Xiong, L., Hector, R. E., Bai, F. W., & Zhao, X. Q. (2018). Association of improved oxidative stress tolerance and alleviation of glucose repression with superior xylose-utilization capability by a natural isolate of Saccharomyces cerevisiae. Biotechnology for biofuels, 11(1), 28.
  • Christodoulou, D., Link, H., Fuhrer, T., Kochanowski, K., Gerosa, L., & Sauer, U. (2018). Reserve flux capacity in the pentose phosphate pathway enables Escherichia coli's rapid response to oxidative stress. Cell systems, 6(5), 569-578.
  • Cyrne, L., us Martins, L., Fernandes, L., & Marinho, H. S. (2003). Regulation of antioxidant enzymes gene expression in the yeast Saccharomyces cerevisiae during stationary phase. Free Radical Biology and Medicine, 34(3), 385-393.
  • Davies, J. M., Lowry, C. V., & Davies, K. J. (1995). Transient adaptation to oxidative stress in yeast. Archives of biochemistry and biophysics, 317(1), 1-6.
  • Diezmann, S. (2014). Oxidative stress response and adaptation to H2O2 in the model eukaryote Saccharomyces cerevisiae and its human pathogenic relatives Candida albicans and Candida glabrata. Fungal Biology Reviews, 28(4), 126-136.
  • Douglas, K. T. (1987). Mechanism of action of glutathione‐ dependent enzymes. Advances in enzymology and related areas of molecular biology, 59, 103-167.
  • Farrugia, G., Azzopardi, M., Saliba, C., Grech, G., Gross, A. S., Pistolic, J., Benes, V., Vassallo, N., Borg, J., Madeo, F., Eisenberg, T., & Balzan, R. (2019). Aspirin impairs acetyl-coenzyme A metabolism in redox-compromised yeast cells. Scientific reports, 9(1), 1-13.
  • Flattery-O'Brien, J., Collinson, L. P., & Dawes, I. W. (1993). Saccharomyces cerevisiae has an inducible response to menadione which differs from that to hydrogen peroxide. Microbiology, 139(3), 501-507.
  • Gasch, A. P., Spellman, P. T., Kao, C. M., Carmel-Harel, O., Eisen, M. B., Storz, G., Botstein, D., & Brown, P. O. (2000). Genomic expression programs in the response of yeast cells to environmental changes. Molecular biology of the cell, 11(12), 4241-4257.
  • Giaever, G., Chu, A. M., Ni, L., Connelly, C., Riles, L., Véronneau, S., Dow, S., Lucau-Danila, A., Anderson, K., Andre, B., Arkin, A. P., Astromoff, A., Bakkoury, M. E., Bangham, R., Benito, R., Brachat, S., Campanaro, S., Curtiss, M., … & Johnston, M. (2002). Functional profiling of the Saccharomyces cerevisiae genome. Nature, 418(6896), 387-391.
  • Godon, C., Lagniel, G., Lee, J., Buhler, J. M., Kieffer, S., Perrot, M., Boucherie, H., Toledano, M. B., & Labarre, J. (1998). The H2O2 stimulon in Saccharomyces cerevisiae. Journal of Biological Chemistry, 273(35), 22480-22489.
  • Gopalacharyulu, P. V., Velagapudi, V. R., Lindfors, E., Halperin, E., & Orešič, M. (2009). Dynamic network topology changes in functional modules predict responses to oxidative stress in yeast. Molecular BioSystems, 5(3), 276-287.
  • Grant, C. M., MacIver, F. H., & Dawes, I. W. (1996). Glutathione is an essential metabolite required for resistance to oxidative stress in the yeastSaccharomyces cerevisiae. Current genetics, 29(6), 511-515.
  • Grant, C. M., Perrone, G., & Dawes, I. W. (1998). Glutathione and catalase provide overlapping defenses for protection against hydrogen peroxide in the yeastsaccharomyces cerevisiae. Biochemical and biophysical research communications, 253(3), 893-898.
  • Harding, H. P., Zhang, Y., Zeng, H., Novoa, I., Lu, P. D., Calfon, M., Sadri, N., Yun, C., Popko, B., Paules, R., Stojdl, D. F., Bell, J. C., Hettmann, T., Leiden, J. M., & Ron, D. (2003). An integrated stress response regulates amino acid metabolism and resistance to oxidative stress. Molecular cell, 11(3), 619-633.
  • Hartwell, L. H. (1974). Saccharomyces cerevisiae cell cycle. Bacteriological reviews, 38(2), 164.
  • Hruz, T., Laule, O., Szabo, G., Wessendorp, F., Bleuler, S., Oertle, L., Widmayer, P., Gruissem, W., & Zimmermann, P. (2008). Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes. Advances in bioinformatics. 2008, 420747.
  • Inzé, D., & Van Montagu, M. (1995). Oxidative stress in plants. Current Opinion in Biotechnology, 6(2), 153-158.
  • Jamieson, D. J. (1992). Saccharomyces cerevisiae has distinct adaptive responses to both hydrogen peroxide and menadione. Journal of bacteriology, 174(20), 6678-6681.
There are 27 citations in total.

Details

Primary Language English
Subjects Microbiology
Journal Section Research Articles
Authors

Ezgi Tanıl This is me

Burcu Şirin This is me

Emrah Nikerel This is me

Publication Date June 30, 2020
Published in Issue Year 2020 Volume: 29 Issue: 1

Cite

APA Tanıl, E., Şirin, B., & Nikerel, E. (2020). Meta-analysis of transcriptome data on oxidative stress response in Saccharomyces cerevisiae cells underlines regulation of carbon, redox and glutathione metabolism. Biotech Studies, 29(1), 8-17. https://doi.org/10.38042/biost.2020.29.01.02


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