ORCID

https://orcid.org/0000-0002-5985-2027

Date of Award

2023

Document Type

Dissertation

Degree Name

Philosophy (Ph.D)

Department

Biological Sciences

First Advisor

ALES VANCURA

Second Advisor

MATTEO RUGGIU

Third Advisor

YONG YU

Abstract

The DNA damage response (DDR) is an evolutionarily conserved process essential for cell survival. Major part of DDR is coordinated by DNA damage checkpoint (DDC). In addition to DDC, eukaryotic cells also have DNA replication checkpoint (DRC) that is distinct from the DDC and specifically signals slowly progressing or arrested replication forks. DDR involves stalling or arrest of the cell cycle, initiation of DNA repair, and altered regulation of transcription, translation, and the ubiquitin-proteasome system. DDR also triggers transcription shut-off of histone genes. One of the key outcomes of DDC/DRC activation is the increased synthesis of the deoxyribonucleoside triphosphates (dNTPs), which is a prerequisite for normal progression through the S phase and for effective DNA repair. Previously, our laboratory found that decreased histone expression activates mitochondrial electron transport chain (ETC) and oxidative metabolism, raising the question of whether the DDC/DRC also stimulate ETC. Here, we show that DDC activation in the budding yeast Saccharomyces cerevisiae, either via genetic manipulation or by growth in the presence of genotoxic chemicals, induces ETC. We observed that this induction is conferred by checkpoint kinase Rad53p-mediated inhibition of histone gene transcription and globally decreased DNA nucleosome occupancy. This globally altered chromatin structure increased the expression of genes encoding enzymes of tricarboxylic acid cycle (TCA), ETC, and oxidative phosphorylation (OXPHOS) and elevated oxygen consumption and ATP synthesis. The elevated ATP levels resulting from DDC-stimulated ETC drove the enlargement of dNTP pools; cells with a defect in ETC failed to increase dNTP synthesis and exhibited reduced fitness in the presence of DNA damage. Together, our results revealed an unexpected connection between ETC and the DDC and indicated that the benefit of increased dNTP synthesis in the face of DNA damage outweighs possible cellular damage due to increased oxygen metabolism. Unlike DDC, DRC does not inhibit transcription of histone genes but activates ETC and oxidative metabolism by a checkpoint kinase Dun1p-dependent mechanism. DRC induces transcription of RNR1-4 genes and elevates mtDNA copy number, leading to ETC activation. This mechanism contrasts with the Dun1p-independent mechanism employed by DDC, whereby DDC represses transcription of histone genes, leading to altered chromatin structure and increased expression of respiratory genes. However, since DDC also triggers Dun1p activation and increased transcription of RNR genes, it is very likely that both mechanisms function redundantly during DDC activation.

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