Mutation of yeast PEX6 gene inhibits glycolysis and mitochondrial respiratory chain but promotes glycogen and trehalose biosynthesis and necrosis
Author affiliations
DOI:
https://doi.org/10.15625/2615-9023/22551Keywords:
DNA damage, glycolytic enzyme, glycogen, mitochondria, necrosis, trehalose, PEX6Abstract
In yeast, Pex6 (peroxisomal biogenesis factor 6) encoded by the PEX6 gene plays a crucial role in peroxisomal protein import, cell viability, and necrosis. Moreover, the activity of some key glycolytic enzymes is changed due to DNA damage or oxidative stress, leading to the diversion of metabolic flux into other biochemical pathways, such as the pentose phosphate pathway (ppp), hexosamine biosynthesis pathway (HBP), and glycogen and trehalose synthesis.
Thus, the present study aims to examine the role of the PEX6 gene by using the BY4741 (wild type) and specific knock-out yeast strains (∆pex6). The activity of this gene in these biochemical pathways in response to DNA damage triggered by methyl methanesulfonate (MMS) treatment would be elucidated by using enzymatic, Gloxo, and OxoPlate® assays, flow cytometry, and chromatography.
The findings obtained show that DNA damage significantly inhibited the activity of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and pyruvate kinase (PYK), mitochondrial respiration, cell growth, and ATP synthesis. However, DNA damage intensively promotes the activity of glucose-6-phosphate dehydrogenase (G6PDH) and the synthesis of uridine-diphosphoglucose-N-acetylglucosamine (UDP-NacGlu). Subsequently, the glucose flux was not diverted to the TCA cycle due to prohibited mitochondrial activity and oxygen consumption, but to the ppp as a result of increased G6PDH activity and to glycogen/trehalose accumulation because of enhanced UDP-NacGlu levels. The cells, especially the mutant ∆pex6, utilize glycogen/trehalose as major energy reserves to maintain their energy and survival, and induce necrosis as a cellular defense mechanism in response to DNA damage. These results suggest that a fully functional PEX6 plays a major role in cell proliferation, energy metabolism, and the cellular defense mechanism in response to DNA damage.
Downloads
References
Ali B. A., Judy R. M., Chowdhury S., Jacobsen N. K., Castanzo D. T., Carr K. L., Richardson C. D., Lander G. C., Martin A., Gardner B. M., 2023. The Pex6 N1 domain is required for Pex15 binding and proper assembly with Pex1. bioRxiv. https://doi.org/10.1101/2023.09.15.557798
Berg J. M., Tymoczko J. L., Stryer L., 2002. Biochemistry, Fifth Edition: W.H. Freeman.
Bonowski F., Kitanovic A., Ruoff P., Holzwarth J., Kitanovic I., Bui V. N., Lederer E., Wolfl S., 2010. Computer controlled automated assay for comprehensive studies of enzyme kinetic parameters. PLoS One, 5(5): e10727. doi: 10.1371/journal.pone.0010727
Bui V. N., & Nguyen D. H., 2025. Role of yeast HAP4 gene in mitochondrial function, oxidative phosphorylation, and apoptosis in response to DNA damage. Academia Journal of Biology, 47(1): 111–125. https://doi.org/10.15625/2615-9023/21232
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. doi: 10.1016/j.jip.2024.108164
Cerella C., D'Alessio M., Cristofanon S., De Nicola M., Radogna F., Dicato M., Diederich M., Ghibelli L., 2009. Subapoptogenic oxidative stress strongly increases the activity of the glycolytic key enzyme glyceraldehyde 3-phosphate dehydrogenase. Ann N Y Acad Sci, 1171: 583−590. https://doi.org/10.1111/j.1749-6632.2009.04723.x
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
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 Syst, 6(5): 569−578. https://doi.org/10.1016/j.cels.2018.04.009
Ebberink M. S., Kofster J., Wanders R. J., Waterham H. R., 2010. Spectrum of PEX6 mutations in Zellweger syndrome spectrum patients. Hum Mutat, 31(1): E1058−1070. https://doi.org/10.1002/humu.21153
Francois J., & Parrou J. L., 2001. Reserve carbohydrates metabolism in the yeast Saccharomyces cerevisiae. FEMS Microbiol Rev, 25(1): 125−145. https://doi.org/ 10.1111/j.1574-6976.2001.tb00574.x
Geisbrecht B. V., Collins C. S., Reuber B. E., Gould S. J., 1998. Disruption of a PEX1-PEX6 interaction is the most common cause of the neurologic disorders Zellweger syndrome, neonatal adrenoleukodystrophy, and infantile Refsum disease. Proc Natl Acad Sci U S A, 95(15): 8630−8635. https://doi.org/ 10.1073/pnas.95.15.8630
Gomes A. M. V., Orlandi A., Parachin N. S., 2020. Deletion of the trehalose tps1 gene in Kluyveromyces lactis does not impair growth in glucose. FEMS Microbiol Lett, 367(10). doi: 10.1093/femsle/fnaa072
Grimm I., Saffian D., Platta H. W., Erdmann R., 2012. The AAA-type ATPases Pex1p and Pex6p and their role in peroxisomal matrix protein import in Saccharomyces cerevisiae. Biochim Biophys Acta, 1823(1): 150−158. https://doi.org/ 10.1016/j.bbamcr.2011.09.005
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
Grüning N. M., Rinnerthaler M., Bluemlein K., Mülleder M., Wamelink M. M., Lehrach H., Jakobs C., Breitenbach M., Ralser M., 2011. Pyruvate kinase triggers a metabolic feedback loop that controls redox metabolism in respiring cells. Cell Metab, 14(3): 415−427. https://doi.org/ 10.1016/j.cmet.2011.06.017
Halim A., Larsen I. S., Neubert P., Joshi H. J., Petersen B. L., Vakhrushev S. Y., Strahl S., Clausen H., 2015. Discovery of a nucleocytoplasmic O-mannose glycoproteome in yeast. Proc Natl Acad Sci U S A, 112(51): 15648−15653. https://doi.org/10.1073/pnas.1511743112
Hara M. R., Thomas B., Cascio M. B., Bae B. I., Hester L. D., Dawson V. L., Dawson T. M., Sawa A., Snyder S. H., 2006. Neuroprotection by pharmacologic blockade of the GAPDH death cascade. Proc Natl Acad Sci U S A, 103(10): 3887–3889. https://doi.org/10.1073/pnas.0511321103
Hildebrandt T., Knuesting J., Berndt C., Morgan B., Scheibe R., 2015. Cytosolic thiol switches regulating basic cellular functions: GAPDH as an information hub? Biol Chem, 396(5): 523−537. https://doi.org/10.1515/hsz-2014-0295
Huang Y. L., Pan W. L., Cai W. W., Ju J. Q., Sun S. C. 2021. Exposure to citrinin induces DNA damage, autophagy, and mitochondria dysfunction during first cleavage of mouse embryos. Environ Toxicol, 36(11): 2217−2224. https://doi.org/10.1002/tox.23335
Jungwirth H., Ring J., Mayer T., Schauer A., Büttner S., Eisenberg T., Carmona-Gutierrez D., Kuchler K., Madeo F., 2008. Loss of peroxisome function triggers necrosis. FEBS Lett, 582(19): 2882−2886. doi: 10.1016/j.febslet.2008.07.023
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
Kwun M. S., & Lee D. G., 2020. Quercetin-induced yeast apoptosis through mitochondrial dysfunction under the accumulation of magnesium in Candida albicans. Fungal Biol, 124(2): 83−90. doi: 10.1016/j.funbio.2019.11.009
Lapshina E. A., Sudnikovich E. J., Maksimchik J. Z., Zabrodskaya S. V., Zavodnik L. B., Kubyshin V. L., Nocun M., Kazmierczak P., Dobaczewski M., Watala C., Zavodnik I. B., 2006. Antioxidative enzyme and glutathione S-transferase activities in diabetic rats exposed to long-term ASA treatment. Life Sci, 79(19): 1804−1811. https://doi.org/ 10.1016/j.lfs.2006.06.008
Liang J., Cao R., Wang X., Zhang Y., Wang P., Gao H., Li C., Yang F., Zeng R., Wei P., Li D., Li W., Yang W., 2017. Mitochondrial PKM2 regulates oxidative stress-induced apoptosis by stabilizing Bcl2. Cell Res, 27(3): 329−351. https://doi.org/10.1038/cr.2016.159
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
Lucaccioni L., Righi B., Cingolani G. M., Lugli L., Della Casa E., Torcetta F., Iughetti L., Berardi A., 2020. Overwhelming sepsis in a neonate affected by Zellweger syndrome due to a compound heterozygosis in PEX 6 gene: a case report. BMC Med Genet, 21(1): 229. doi: 10.1186/s12881-020-01175-y
Matte A., Federti E., Kung C., Kosinski P. A., Narayanaswamy R., Russo R., Federico G., Carlomagno F., Desbats M. A., Salviati L., Leboeuf C., Valenti M. T., Turrini F., Janin A., Yu S., Beneduce E., Ronseaux S., Iatcenko I., Dang L., Ganz T., Jung C. L., Iolascon A., Brugnara C., De Franceschi L., 2021. The pyruvate kinase activator mitapivat reduces hemolysis and improves anemia in a β-thalassemia mouse model. J Clin Invest, 131(10). https://doi.org/10.1172/jci144206
Mendelow B. V. (2008). Molecular medicine for clinicians. Johannesburg, South Africa: Wits University Press.
Min K., Son H., Lee J., Choi G. J., Kim J. C., Lee Y. W., 2012. Peroxisome function is required for virulence and survival of Fusarium graminearum. Mol Plant Microbe Interact, 25(12): 1617−1627. https://doi.org/10.1094/mpmi-06-12-0149-r
Muronetz V. I., Melnikova A. K., Saso L., Schmalhausen E. V., 2020. Influence of Oxidative Stress on Catalytic and Non-glycolytic Functions of Glyceraldehyde-3-phosphate Dehydrogenase. Curr Med Chem, 27(13): 2040−2058. https://doi.org/ 10.2174/0929867325666180530101057
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. doi: 10.1038/s41598-020-61477-2
Parrou J. L., Teste M. A., Francois J., 1997. Effects of various types of stress on the metabolism of reserve carbohydrates in Saccharomyces cerevisiae: genetic evidence for a stress-induced recycling of glycogen and trehalose. Microbiology (Reading), 143 ( Pt 6): 1891−1900. doi: 10.1099/00221287-143-6-1891
Prakasam G., Singh R. K., Iqbal M. A., Saini S. K., Tiku A. B., Bamezai R. N. K., 2017. Pyruvate kinase M knockdown-induced signaling via AMP-activated protein kinase promotes mitochondrial biogenesis, autophagy, and cancer cell survival. J Biol Chem, 292(37): 15561−15576. https://doi.org/10.1074/ jbc.M117.791343
Ralser M., Wamelink M. M., Kowald A., Gerisch B., Heeren G., Struys E. A., Klipp E., Jakobs C., Breitenbach M., Lehrach H., Krobitsch S., 2007. Dynamic rerouting of the carbohydrate flux is key to counteracting oxidative stress. J Biol, 6(4): 10. https://doi.org/10.1186/jbiol61
Renaud M., Guissart C., Mallaret M., Ferdinandusse S., Cheillan D., Drouot N., Muller J., Claustres M., Tranchant C., Anheim M., Koenig M., 2016. Expanding the spectrum of PEX10-related peroxisomal biogenesis disorders: slowly progressive recessive ataxia. J Neurol, 263(8): 1552−1558. https://doi.org/ 10.1007/s00415-016-8167-3
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
Rüttermann M., Koci M., Lill P., Geladas E. D., Kaschani F., Klink B. U., Erdmann R., Gatsogiannis C., 2023. Structure of the peroxisomal Pex1/Pex6 ATPase complex bound to a substrate. Nat Commun, 14(1): 5942. https://doi.org/10.1038/s41467-023-41640-9
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
Shimizu K., & Matsuoka Y., 2019. Redox rebalance against genetic perturbations and modulation of central carbon metabolism by the oxidative stress regulation. Biotechnol Adv, 37(8): 107441. https://doi.org/10.1016/j.biotechadv.2019.107441
Sousa B., Pereira J., Marques R., Grilo L. F., Pereira S. P., Sardão V. A., Schmitt F., Oliveira P. J., Paredes J., 2020. P-cadherin induces anoikis-resistance of matrix-detached breast cancer cells by promoting pentose phosphate pathway and decreasing oxidative stress. Biochim Biophys Acta Mol Basis Dis, 1866(12): 165964. doi: 10.1016/ j.bbadis.2020.165964
Ueda K., Nakajima T., Yoshikawa K., Toya Y., Matsuda F., Shimizu H., 2018. Metabolic flux of the oxidative pentose phosphate pathway under low light conditions in Synechocystis sp. PCC 6803. J Biosci Bioeng, 126(1): 38−43. https://doi.org/10.1016/j.jbiosc.2018.01.020
Valderrama R., Corpas F. J., Carreras A., Gomez-Rodriguez M. V., Chaki M., Pedrajas J. R., Fernandez-Ocana A., Del Rio L. A., Barroso J. B., 2006. The dehydrogenase-mediated recycling of NADPH is a key antioxidant system against salt-induced oxidative stress in olive plants. Plant Cell Environ, 29(7): 1449−1459. https://doi.org/10.1111/j.1365-3040.2006.01530.x
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
Vigetti D., Viola M., Karousou E., De Luca G., Passi A., 2014. Metabolic control of hyaluronan synthases. Matrix Biol, 35: 8−13. https://doi.org/10.1016/j.matbio. 2013.10.002
Virgilio S., Cupertino F. B., Ambrosio D. L., Bertolini M. C., 2017. Regulation of the reserve carbohydrate metabolism by alkaline pH and calcium in Neurospora crassa reveals a possible cross-regulation of both signaling pathways. BMC Genomics, 18(1): 457. https://doi.org/ 10.1186/s12864-017-3832-1
Wang H., Nicolay B. N., Chick J. M., Gao X., Geng Y., Ren H., Gao H., Yang G., Williams J. A., Suski J. M., Keibler M. A., Sicinska E., Gerdemann U., Haining W. N., Roberts T. M., Polyak K., Gygi S. P., Dyson N. J., Sicinski P., 2017. The metabolic function of cyclin D3-CDK6 kinase in cancer cell survival. Nature, 546(7658): 426−430. https://doi.org/ 10.1038/nature22797
Wang X., Ni H., Xu W., Wu B., Xie T., Zhang C., Cheng J., Li Z., Tao L., Zhang Y., 2021. Difenoconazole induces oxidative DNA damage and mitochondria mediated apoptosis in SH-SY5Y cells. Chemosphere, 283: 131160. https://doi.org/10.1016/ j.chemosphere.2021.131160
Wu X., Liu L., Zheng Q., Hao H., Ye H., Li P., Yang H., 2021. Protocatechuic aldehyde protects cardiomycoytes against ischemic injury via regulation of nuclear pyruvate kinase M2. Acta Pharm Sin B, 11(11): 3553−3566. https://doi.org/ 10.1016/j.apsb.2021.03.021
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
Downloads
Published
How to Cite
Issue
Section
License
Copyright (c) 2025 Van Ngoc Bui, Hoang Ha Chu
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/.
