Role of yeast <em>  HAP4 </em> gene in mitochondrial function, oxidative phosphorylation, and apoptosis in response to dna damage

Van Ngoc Bui; Duong Huy Nguyen

doi:10.15625/2615-9023/21232

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Authors

Bui Van Ngoc Institute of Biotechnology https://orcid.org/0000-0002-4659-7338
Nguyen Huy Duong Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam

DOI:

https://doi.org/10.15625/2615-9023/21232

Keywords:

apoptosis, DNA damage, HAP4, mitochondria, ROS, yeast

Abstract

Apoptosis plays a crucial role in the normal development and differentiation of multicellular organisms and is essential for embryogenesis, metamorphosis, and elimination of unwanted cells. Like mammalian cells, yeast cells have evolved a number of cellular surveillance mechanisms including DNA damage checkpoint, stimulation of DNA repair, tolerance of DNA damage, and initiation of apoptosis. In Saccharomyces cerevisiae, the HAP4 gene encodes the Hap4 protein which is a subunit of the heme-activated, glucose-repressed Hap2p/3p/4p/5p complex. This complex plays a crucial role in controlling the TCA cycle, the mitochondrial electron transport chain, ATP production and mitochondria biogenesis. Thus, the purpose of this study is to investigate the role of the HAP4 gene by using the BY4742 (wild type) and specific knock-out yeast strains (∆hap4) to elucidate the role of this gene in mitochondrial function and respiration, ATP synthesis, and apoptosis in response to DNA damage triggered by methyl methanesulfonate (MMS) treatment. The findings suggested that the fully functional mitochondria enhanced oxygen consumption and mitochondrial activity, attenuated ROS accumulation, and enabled efficient electron transport and ATP synthesis. High mitochondrial activity is performed as a cellular protective mechanism against oxidative stress. In contrast, deletion of the HAP4 gene (∆hap4), the main regulatory gene for the expression of respiratory proteins, caused a block of the electron transport chain, persistent inhibition of mitochondrial activity, thereby leading to a reduction of oxygen consumption. Low mitochondrial activity resulted in the development of oxidative stress, enhancement of sensitivity to DNA damaging agents. High intracellular ROS levels in ∆hap4 cells posed a significant threat to mitochondrial DNA damage, impairment of mitochondrial respiration, inhibition of glycolytic enzymes (GAPDH, PYK), repression of ATP synthesis, and subsequent induction of cell death (apoptosis).

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References

Bonowski F., Kitanovic A., Ruoff P., Holzwarth J., Kitanovic I., Bui N., Lederer E., Wölfl S., 2010. Computer controlled automated assay for comprehensive studies of enzyme kinetic parameters. PLoS ONE, 5(5): e10727. https://doi.org/10.1371/ journal.pone.0010727

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. Journal of invertebrate pathology, 206: 108164. United States. https://doi.org/10.1016/j.jip.2024.108164

Callender L. A., Schroth J., Carroll E. C., Garrod-Ketchley C., Romano L. E. L., Hendy E., Kelly A., Lavender P., Akbar A. N., Chapple J. P., Henson S. M., 2021. GATA3 induces mitochondrial biogenesis in primary human CD4+ T cells during DNA damage. Nature Communications, 12(1): 3379. https://doi.org/10.1038/ s41467-021-23715-7

Capps D., Hunter A., Chiang M., Pracheil T., Liu Z., 2022. Ubiquitin-Conjugating Enzymes Ubc1 and Ubc4 Mediate the Turnover of Hap4., a Master Regulator of Mitochondrial Biogenesis in Saccharomyces cerevisiae. Microorganisms, 10(12): 2370. https://doi.org/10.3390/microorganisms10122370

Carrillo-Garmendia A., Martinez-Ortiz C., Martinez-Garfias J. G., Suarez-Sandoval S. E., González-Hernández J. C., Nava G. M., Dufoo-Hurtado M. D., Madrigal-Perez L. A., 2022. Snf1p/Hxk2p/Mig1p pathway regulates hexose transporters transcript levels., affecting the exponential growth and mitochondrial respiration of Saccharomyces cerevisiae. Fungal Genetics and Biology, 161: 103701. https://doi.org/10.1016/j.fgb.2022.103701

Cornett K., Puderbaugh A., Back O., Craven R., 2022. GAPDH in neuroblastoma: Functions in metabolism and survival. Frontiers in Oncology, 12: 979683. https://doi.org/10.3389/fonc.2022.979683

Cui H., Kong Y., Zhang H., 2012. Oxidative Stress., Mitochondrial Dysfunction., and Aging. Journal of Signal Transduction, 2012(1): 646354. https://doi.org/10.1155/ 2012/646354

Dahal S., Dubey S., Raghavan S. C., 2018. Homologous recombination-mediated repair of DNA double-strand breaks operates in mammalian mitochondria. Cellular and Molecular Life Sciences, 75(9): 1641–1655. https://doi.org/10.1007/ s00018-017-2702-y

Dastoor Z., Dreyer J. L., 2001. Potential role of nuclear translocation of glyceraldehyde-3-phosphate dehydrogenase in apoptosis and oxidative stress. Journal of Cell Science, 114(9): 1643–1653. https://doi.org/10.1242/ jcs.114.9.1643

Fang J., Zhou G., Zhao H., Xie D., Zhang J., Kües U., Xiao Y., Fang Z., Liu J., 2024. An apoptosis-inducing factor controls programmed cell death and laccase expression during fungal interactions. Applied Microbiology and Biotechnology, 108(1): 135. https://doi.org/10.1007/ s00253-023-12988-1

Fu X., Wan S., Lyu Y. L., Liu L. F., Qi H., 2008. Etoposide induces ATM-dependent mitochondrial biogenesis through AMPK activation. PLoS ONE, 3(4): e2009. https://doi.org/10.1371/journal.pone.0002009

Garcia I., Jones E., Ramos M., Innis-Whitehouse W., Gilkerson R., 2017. The little big genome: The organization of mitochondrial DNA. Frontiers in Bioscience - Landmark, 22(4): 710–721. https://doi.org/10.2741/4511

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? Environmental Pollution, 218: 402–409. https://doi.org/ 10.1016/j.envpol.2016.07.019

Guaragnella N., Palermo V., Galli A., Moro L., Mazzoni C., Giannattasio S., 2014. The expanding role of yeast in cancer research and diagnosis: Insights into the function of the oncosuppressors p53 and BRCA1/2. FEMS Yeast Research, 14(1): 2−16. https://doi.org/10.1111/1567-1364.12094

Van Houten B., Woshner V., Santos J. H., 2006. Role of mitochondrial DNA in toxic responses to oxidative stress. DNA Repair, 5(2): 145−152. https://doi.org/10.1016/ j.dnarep.2005.03.002

Kassis S., Grondin M., Averill-Bates D. A., 2021. Heat shock increases levels of reactive oxygen species., autophagy and apoptosis. Biochimica et Biophysica Acta - Molecular Cell Research, 1868(3): 118924. https://doi.org/10.1016/j.bbamcr. 2020.118924

Kawai K., Kanesaki Y., Yoshikawa H., Hirasawa T., 2019. Identification of metabolic engineering targets for improving glycerol assimilation ability of Saccharomyces cerevisiae based on adaptive laboratory evolution and transcriptome analysis. Journal of Bioscience and Bioengineering, 128(2): 162−169. https://doi.org/10.1016/j.jbiosc. 2019.02.001

Kitanovic A., Walther T., Loret M. O., Holzwarth J., Kitanovic I., Bonowski F., Bui N. Van., Francois J. M., Wölfl S., 2009. Metabolic response to MMS-mediated DNA damage in Saccharomyces cerevisiae is dependent on the glucose concentration in the medium. FEMS Yeast Research, 9(4): 535–551. https://doi.org/ 10.1111/j.1567-1364.2009.00505.x

Krasovec G., Pottin K., Rosello M., Quéinnec É., Chambon J. P., 2021. Apoptosis and cell proliferation during metamorphosis of the planula larva of Clytia hemisphaerica (Hydrozoa., Cnidaria). Developmental Dynamics, 250(12): 1739−1758. https://doi.org/10.1002/dvdy.376

Leadsham J. E., Gourlay C. W., 2010. CAMP/PKA signaling balances respiratory activity with mitochondria dependent apoptosis via transcriptional regulation. BMC Cell Biology, 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 moh1Δ mutation. Journal of Microbiology and Biotechnology, 27(3): 633−643. https://doi.org/10.4014/jmb.1610.10045

Lesko M. A., Chandrashekarappa D. G., Jordahl E. M., Oppenheimer K. G., Bowman R. W., Shang C., Durrant J. D., Schmidt M. C., O’Donnell A. F., 2023. Changing course: Glucose starvation drives nuclear accumulation of Hexokinase 2 in S. cerevisiae. PLoS Genetics, 19(5): e1010745. https://doi.org/10.1371/journal. pgen.1010745

Liu Y., Sun Y., Guo Y., Shi X., Chen X., Feng W., Wu L. L., Zhang J., Yu S., Wang Y., Shi Y., 2023. An Overview: The Diversified Role of Mitochondria in Cancer Metabolism. International Journal of Biological Sciences, 19(3): 897−915. https://doi.org/10.7150/ijbs.81609

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

Mentel M., Illová M., Krajčovičová V., Kroupová G., Mannová Z., Chovančíková P., Polčic P., 2023. Yeast Bax Inhibitor (Bxi1p/Ybh3p) Is Not Required for the Action of Bcl-2 Family Proteins on Cell Viability. International Journal of Molecular Sciences, 24(15): 12011. https://doi.org/10.3390/ijms241512011

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. Scientific Reports, 10(1): 5575. https://doi.org/10.1038/s41598-020-61477-2

Nie F., Yan J., Ling Y., Liu Z., Fu C., Li X., Qin Y., 2021. Effect of Shuangdan Mingmu capsule., a Chinese herbal formula., on oxidative stress-induced apoptosis of pericytes through PARP/GAPDH pathway. BMC Complementary Medicine and Therapies, 21(1): 118. https://doi.org/ 10.1186/s12906-021-03238-w

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. Journal of Chromatography B: Analytical Technologies in the Biomedical and Life Sciences, 843(2): 216–226. https://doi.org/ 10.1016/j.jchromb.2006.06.004

Rong Z., Tu P., Xu P., Sun Y., Yu F., Tu N., Guo L., Yang Y., 2021. The Mitochondrial Response to DNA Damage. Frontiers in cell and developmental biology, 9: 669379. https://doi.org/ 10.3389/fcell.2021.669379

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. Journal of Microbiological Methods, 127: 77−81. https://doi.org/10.1016/j.mimet. 2016.05.023

Shokolenko I., Venediktova N., Bochkareva A., Wilson G. I., Alexeyev M. F., 2009. Oxidative stress induces degradation of mitochondrial DNA. Nucleic Acids Research, 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., Ärengård T., Ghiaci P., Larsson-Berglund L., Zackrisson M., Smits S., Hallin J., Höög L. L., Molin M., Liti G., Omholt S. W., Warringer J., 2022. Genetically controlled mtDNA deletions prevent ROS damage by arresting oxidative phosphorylation. eLife, 8(11): e76095. https://doi.org/10.7554/ elife.76095

Whalley N. A., Walters S., Hammond K., 2018. Molecular Cell Biology. Molecular Medicine for Clinicians: 37−49. https://doi.org/10.18772/22008014655.9

Yakes F. M., Van Houten B. 1997., Mitochondrial DNA damage is more extensive and persists longer than nuclear DNA damage in human cells following oxidative stress. Proceedings of the National Academy of Sciences of the United States of America, 94(2): 514−519. https://doi.org/10.1073/pnas.94.2.514

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, 9(8): 914−921. https://doi.org/ 10.1016/j.dnarep.2010.06.005

Zhang Y., Li B. X., Mao Q. Z., Zhuo J. C., Huang H. J., Lu J. B., Zhang C. X., Li J. M., Chen J. P., Lu G., 2023. The JAK-STAT pathway promotes persistent viral infection by activating apoptosis in insect vectors. PLoS Pathogens, 19(3): e1011266. https://doi.org/10.1371/journal.ppat.1011266