Deletion of yeast YCA1 gene inhibits mitochondrial respiratory complex activity and induces apoptosis
Author affiliations
DOI:
https://doi.org/10.15625/2615-9023/22493Keywords:
Apoptosis, ATP, DNA damage, mitochondria, ROS, YCA1Abstract
Mitochondria play a central role in energy metabolism and the respiratory chain. They also play a major role in programmed cell death or apoptosis. Reactive oxygen species (ROS) are generated through both exogenous and endogenous pathways and pose a significant damage to DNA, lipids, and protein. Mitochondrial DNA (mtDNA) damage could result in loss of expression of mitochondrial polypeptides, inhibition of mitochondrial activity, induction of apoptosis. Thus, the purpose of the present study is to investigate the role of the YCA1 gene by using the BY4741 (wild type) and specific knock-out yeast strains (∆yca1). The activity of this gene in the mitochondrial respiratory chain and cellular apoptosis in response to DNA damage triggered by methyl methanesulfonate (MMS) treatment would be elucidated by using flow cytometry, chromatography, and OxoPlate® assay.
The findings indicated that fully functional yeast caspase-1 encoded by YCA1 significantly attenuates the intracellular ROS level, while deletion of YCA1 (∆yca1) results in gradual ROS accumulation upon MMS treatment, thereby introducing damage to mtDNA, leading to inhibition of mitochondrial activity and oxygen consumption. Subsequently, the absence of YCA1 leads to blockage in the mitochondrial electron transport chain (mtETC), repression of ATP synthesis, and fluctuation of cellular energy status (AEC). Altogether, high mitochondrial activity of the wild type acts as a protective mechanism against oxidative stress (ROS), whereas low mitochondrial activity of the ∆yca1 enhances susceptibility to ROS that strongly induce apoptosis. These findings suggest that fully functional YCA1 plays a major role in the protection of cell from DNA damage, while mutation of the YCA1 gene results in a reduction of the living mutant ∆yca1 cells accompanied with cell nucleic apoptosis.
Downloads
References
Amigoni L., Frigerio G., Martegani E., Colombo S., 2016. Involvement of Aif1 in apoptosis triggered by lack of Hxk2 in the yeast Saccharomyces cerevisiae. FEMS Yeast Res., 16(3). https://doi.org/10.1093/ femsyr/fow016
Atkinson D. E., 1968. The energy charge of the adenylate pool as a regulatory parameter. Interaction with feedback modifiers. Biochemistry, 7(11): 4030−4034. https://doi.org/10.1021/bi00851a033
Belli G., Colomina N., Castells-Roca L., Lorite N. P., 2022. Post-translational modifications of PCNA: Guiding for the best DNA damage tolerance choice. J. Fungi (Basel), 8(6). https://doi.org/10.3390/jof8060621
Berg J. M., Tymoczko J. L., Stryer L., 2002. Biochemistry, Fifth Edition: W.H. Freeman. pp. 1100.
Bui V. N., Le T. H., 2024. Regulation of yeast RAD9 gene in energy charge, intracellular ROS, and cell cycle arrest in response to DNA damage. Vietnam Journal of Biotechnology, 22: 507−522. https://doi.org/ 10.15625/vjbt-21211
Bui V. N., Nguyen T. P. T., Nguyen H. D., Phi Q. T., Nguyen T. N., Chu H. H., 2024. Bioactivity responses to changes in mucus-associated bacterial composition between healthy and bleached Porites lobata corals. J. Invertebr. Pathol., 206: 108164. https://doi.org/10.1016/j.jip.2024. 108164
Canete J. A., Andres S., Munoz S., Zamarreno J., Rodriguez S., Diaz-Cuervo H., Bueno A., Sacristan M. P., 2023. Fission yeast Cdc14-like phosphatase Flp1/Clp1 modulates the transcriptional response to oxidative stress. Sci. Rep., 13(1): 14677. https://doi.org/ 10.1038/s41598-023-41869-w
Canete J. A., Andrés S., Muñoz S., Zamarreño J., Rodríguez S., Díaz-Cuervo H., Bueno A., Sacristán M. P., 2023. Fission yeast Cdc14-like phosphatase Flp1/Clp1 modulates the transcriptional response to oxidative stress. Sci. Rep., 13(1): 14677. https://doi.org/ 10.1038/s41598-023-41869-w
Chenna S., Koopman W. J. H., Prehn J. H. M., Connolly N. M. C., 2022. Mechanisms and mathematical modeling of ROS production by the mitochondrial electron transport chain. Am. J. Physiol. Cell Physiol., 323(1): C69-C83. https://doi.org/10.1152/ajpcell.00455.2021
Du L., Su Y., Sun D., Zhu W., Wang J., Zhuang X., Zhou S., Lu Y., 2008. Formic acid induces Yca1p-independent apoptosis-like cell death in the yeast Saccharomyces cerevisiae. FEMS Yeast Res., 8(4): 531−539. https://doi.org/10.1111/j.1567-1364.2008.00375.x
Gomes M. P., Juneau P., 2016. Oxidative stress in duckweed (Lemna minor L.) induced by glyphosate: Is the mitochondrial electron transport chain a target of this herbicide? Environ. Pollut., 218: 402−409. https://doi.org/10.1016/ j.envpol.2016.07.019
Greetham D., Kritsiligkou P., Watkins R. H., Carter Z., Parkin J., Grant C. M., 2013. Oxidation of the yeast mitochondrial thioredoxin promotes cell death. Antioxid. Redox Signal., 18(4): 376−385. https://doi.org/10.1089/ars.2012.4597
Groth P., Auslander S., Majumder M. M., Schultz N., Johansson F., Petermann E., Helleday T., 2010. Methylated DNA causes a physical block to replication forks independently of damage signalling, O(6)-methylguanine or DNA single-strand breaks and results in DNA damage. J. Mol. Biol., 402(1): 70−82. https://doi.org/ 10.1016/j.jmb.2010.07.010
Khan M. A., Chock P. B., Stadtman E. R., 2005. Knockout of caspase-like gene, YCA1, abrogates apoptosis and elevates oxidized proteins in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U. S. A., 102(48): 17326−17331. https://doi.org/ 10.1073/pnas.0508120102
Kitanovic A., Walther T., Loret M. O., Holzwarth J., Kitanovic I., Bonowski F., Van Bui N., Francois J. M., Wolfl S., 2009. Metabolic response to MMS-mediated DNA damage in Saccharomyces cerevisiae is dependent on the glucose concentration in the medium. FEMS Yeast Res., 9(4): 535−551. https://doi.org/ 10.1111/j.1567-1364.2009.00505.x
Lam D. K., Sherlock G., 2023. Yca1 metacaspase: diverse functions determine how yeast live and let die. FEMS Yeast Res: 23. https://doi.org/10.1093/femsyr/ foad022
Leadsham J. E., Gourlay C. W., 2010. cAMP/PKA signaling balances respiratory activity with mitochondria dependent apoptosis via transcriptional regulation. BMC Cell Biol., 11: 92. https://doi.org/ 10.1186/1471-2121-11-92
Lee J. Y., Jun D. Y., Park J. E., Kwon G. H., Kim J. S., Kim Y. H., 2017. Pro-apoptotic role of the human YPEL5 gene identified by functional complementation of a yeast moh1delta mutation. J. Microbiol. Biotechnol., 27(3): 633−643. https://doi.org/ 10.4014/jmb.1610.10045
Lee Y. J., Hoe K. L., Maeng P. J., 2007. Yeast cells lacking the CIT1-encoded mitochondrial citrate synthase are hypersusceptible to heat- or aging-induced apoptosis. Mol. Biol. Cell, 18(9): 3556−3567. https://doi.org/10.1091/mbc. e07-02-0118
Loret M. O., Pedersen L., François J., 2007. Revised procedures for yeast metabolites extraction: application to a glucose pulse to carbon-limited yeast cultures, which reveals a transient activation of the purine salvage pathway. Yeast, 24(1): 47−60. https://doi.org/10.1002/yea.1435
Madeo F., Herker E., Maldener C., Wissing S., Lächelt S., Herlan M., Fehr M., Lauber K., Sigrist S. J., Wesselborg S., Fröhlich K. U., 2002. A caspase-related protease regulates apoptosis in yeast. Mol. Cell., 9(4): 911−917. https://doi.org/10.1016/ s1097-2765(02)00501-4
Mazzoni C., Falcone C., 2008. Caspase-dependent apoptosis in yeast. Biochim. Biophys. Acta., 1783(7): 1320−1327. https://doi.org/10.1016/j.bbamcr.2008.02.015
Mendelow B. V., 2009. Molecular medicine for clinicians (Second Edition ed.). Johannesburg, South Africa: Wits University Press, pp. 300.
Mihoubi W., Sahli E., Gargouri A., Amiel C., 2017. FTIR spectroscopy of whole cells for the monitoring of yeast apoptosis mediated by p53 over-expression and its suppression by Nigella sativa extracts. PLoS One, 12(7): e0180680. https://doi.org/10.1371/ journal.pone.0180680
Muzaffar S., Chattoo B. B., 2017. Apoptosis-inducing factor (Aif1) mediates anacardic acid-induced apoptosis in Saccharomyces cerevisiae. Apoptosis, 22(3): 463−474. https://doi.org/10.1007/s10495-016-1330-6
Nadalutti C. A., Stefanick D. F., Zhao M. L., Horton J. K., Prasad R., Brooks A. M., Griffith J. D., Wilson S. H., 2020. Mitochondrial dysfunction and DNA damage accompany enhanced levels of formaldehyde in cultured primary human fibroblasts. Sci. Rep., 10(1): 5575. https://doi.org/10.1038/s41598-020-61477-2
Ritter J. B., Genzel Y., Reichl U., 2006. High-performance anion-exchange chromatography using on-line electrolytic eluent generation for the determination of more than 25 intermediates from energy metabolism of mammalian cells in culture. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci., 843(2): 216−226. https://doi.org/ 10.1016/j.jchromb.2006.06.004
Salmon T. B., Evert B. A., Song B., Doetsch P. W., 2004. Biological consequences of oxidative stress-induced DNA damage in Saccharomyces cerevisiae. Nucleic Acids Res., 32(12): 3712−3723. https://doi.org/ 10.1093/nar/gkh696
Senoo T., Yamanaka M., Nakamura A., Terashita T., Kawano S., Ikeda S., 2016. Quantitative PCR for detection of DNA damage in mitochondrial DNA of the fission yeast Schizosaccharomyces pombe. J. Microbiol. Methods, 127: 77−81. https://doi.org/10.1016/j.mimet.2016.05.023
Shokolenko I., Venediktova N., Bochkareva A., Wilson G. L., Alexeyev M. F., 2009. Oxidative stress induces degradation of mitochondrial DNA. Nucleic Acids Res., 37(8): 2539−2548. https://doi.org/10.1093/ nar/gkp100
Stenberg S., Li J., Gjuvsland A. B., Persson K., Demitz-Helin E., Gonzalez Pena C., Yue J. X., Gilchrist C., Arengard T., Ghiaci P., Larsson-Berglund L., Zackrisson M., Smits S., Hallin J., Hoog J. L., Molin M., Liti G., Omholt S. W., Warringer J., 2022. Genetically controlled mtDNA deletions prevent ROS damage by arresting oxidative phosphorylation. Elife: 11. https://doi.org/10.7554/eLife.76095
Van Houten B., Woshner V., Santos J. H., 2006. Role of mitochondrial DNA in toxic responses to oxidative stress. DNA Repair (Amst), 5(2): 145−152. https://doi.org/ 10.1016/j.dnarep.2005.03.002
van Soest D. M. K., Polderman P. E., den Toom W. T. F., Keijer J. P., van
Roosmalen M. J., Leyten T. M. F., Lehmann J., Zwakenberg S., De Henau S., van Boxtel R., Burgering B. M. T., Dansen T. B., 2024. Mitochondrial H(2)O(2) release does not directly cause damage to chromosomal DNA. Nat. Commun., 15(1): 2725. https://doi.org/ 10.1038/s41467-024-47008-x
Wang C. Q., Li X., Wang M. Q., Qian J., Zheng K., Bian H. W., Han N., Wang J. H., Pan J. W., Zhu M. Y., 2014. Protective effects of ETC complex III and cytochrome c against hydrogen peroxide-induced apoptosis in yeast. Free Radic. Res., 48(4): 435−444. https://doi.org/ 10.3109/10715762.2014.885116
Waterman D. P., Haber J. E., Smolka M. B., Test T. T., 2020. Checkpoint responses to DNA double-strand breaks. Annu. Rev. Biochem., 89: 103−133. https://doi.org/ 10.1146/annurev-biochem-011520-104722
Yang Y., Gordenin D. A., Resnick M. A., 2010. A single-strand specific lesion drives MMS-induced hyper-mutability at a double-strand break in yeast. DNA Repair (Amst), 9(8): 914−921. https://doi.org/ 10.1016/j.dnarep.2010.06.005
Yao S., Feng Y., Zhang Y., Feng J., 2021. DNA damage checkpoint and repair: From the budding yeast Saccharomyces cerevisiae to the pathogenic fungus Candida albicans. Comput. Struct. Biotechnol. J., 19: 6343−6354. https://doi.org/10.1016/j.csbj. 2021.11.033
Downloads
Published
How to Cite
Issue
Section
License
Copyright (c) 2025 Van Ngoc Bui, Duc Duy Nguyen

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
Academia Journal of Biology (AJB) is an open-access and peer-reviewed journal. The articles published in the AJB are licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC BY-NC-ND 4.0), which permits for immediate free access to the articles to read, download, copy, non-commercial use, distribution and reproduction in any medium, provided the work is properly cited (with a link to the formal publication through the relevant DOI), and without subscription charges or registration barriers. The full details of the CC BY-NC-ND 4.0 License are available at https://creativecommons.org/licenses/by-nc-nd/4.0/.
