Nutrient-dependent regulation of histone homeostasis in Saccharomyces cerevisiae

Chatzitheodoridou, Dimitra (2024): Nutrient-dependent regulation of histone homeostasis in Saccharomyces cerevisiae. Dissertation, LMU München: Fakultät für Biologie

Abstract

Regulation of cellular protein homeostasis in response to environmental challenges such as nutrient availability is essential for maintaining cell function and viability. The surrounding nutrients strongly influence cell growth and biosynthetic capacity, dictating, among others, cellular growth rate, cell size and cell cycle progression. Ensuring protein homeostasis therefore requires cells to tightly control RNA and protein concentrations, even when cell growth and the cell cycle are significantly modulated by nutrient conditions. This poses a challenge, especially for genes whose expression is highly regulated throughout the cell cycle. A comprehensive picture of how cells achieve nutrient-dependent homeostasis of periodically expressed genes remains elusive. In this work, I study histone biogenesis in the model organism Saccharomyces cerevisiae to investigate how cells produce the appropriate amount of histones in different nutrient environments. Histones constitute an ideal model to understand differential regulation of cell cycle-regulated proteins, as their synthesis is strongly coordinated with the DNA replication during S-phase. Moreover, as building blocks of chromatin, histones are produced in proportion to the genome content, which requires accurate control of histone concentrations. To understand the regulatory processes underlying nutrient-dependent histone homeostasis, I perform population and single-cell analyses of histone expression at the protein and mRNA level. Using western blots, flow cytometry and live-cell imaging, I first show that cells maintain constant amounts of the core histone H2B in rich and poor nutrients, independent of changes in cell growth and cell cycle. As a result, H2B concentrations increase in poor growth media, due to the smaller cell volumes. Surprisingly, however, I find that histone mRNA concentrations are downregulated in poor compared to rich nutrients. smFISH analysis of histone promoter-driven mCitrine expression further reveals that the promoter can confer this nutrient-dependent transcript regulation, which depends on regulatory elements within the promoter, as well as the transcriptional activator Spt10. Furthermore, my results suggest that cells in poor growth media are more sensitive to excess histone accumulation than cells in rich growth media. By keeping histone transcript levels low, they may therefore minimize the risk of histone overexpression. Finally, I propose that cells compensate for the differentially regulated histone transcript concentrations by modulating the relative translation efficiency according to the nutrient conditions. Thereby, they can finely tune histone protein abundance across nutrients, while preventing high histone accumulation in poor growth media. Overall, I show that the decoupling of mRNA and protein concentrations enables nutrient-dependent histone homeostasis despite changes in cell growth and cell cycle phases. This work could lay the foundation for a deeper understanding of the differential regulation of cell cycle-regulated genes across changing nutrient environments.

• Dokumententyp: Dissertationen (Dissertation, LMU München)
• Themengebiete: 500 Naturwissenschaften und Mathematik ; 500 Naturwissenschaften und Mathematik > 570 Biowissenschaften, Biologie
• Fakultäten: Fakultät für Biologie
• Sprache der Hochschulschrift: Englisch
• Datum der mündlichen Prüfung: 8. Februar 2024
• 1. Bericht­erstatter:in: Falter-Braun, Pascal