First Advisor
Jason Podrabsky
Term of Graduation
January 2025
Date of Publication
1-1-2025
Document Type
Dissertation
Language
English
Subjects
Anoxia, Epigenetics, Killifish, Mass spectrometry, Stress tolerance
Physical Description
1 online resource ( pages)
Abstract
Most organisms are ill-equipped to survive anoxia, but some organisms have developed molecular strategies to mitigate the cellular stressors associated with a lack of oxygen. While it is established that anoxic survival is contingent on metabolic suppression, it is unclear what mechanisms support this change in gene expression. Gene expression is regulated by a variety of mechanisms within in the cell, including alteration of chromatin structure through histone modifications and protein modifications which contribute to the ever-changing proteomic landscape of the cell. Protein modifications such as ubiquitylation can lead to the degradation of proteins, while modifications to transcription factors can change the relative abundance of proteins within the cell by upregulating or downregulating transcription. These mechanisms can be influenced by extracellular stimuli, allowing them to modulate the cellular phenotypes in response to environmental stressors. Embryos of the annual killifish Austrofundulus limnaeus have the greatest tolerance to anoxia of all vertebrates, making them the ideal model to study the cellular mechanisms necessary for anoxia tolerance. Understanding how epigenetic modification of histones may regulate gene expression may provide insight into how A. limnaeus cells utilize specific biological pathways to successfully survive and recover from anoxia.Quantitative label-free mass spectrometry-based proteomics was used to quantify histone isoform abundance and histone post-translational modifications in developing embryos exposed to anoxia, and in an anoxia-tolerant cell line (PSU-AL-WS40NE) isolated from embryos of A. limnaeus. The proteomic landscape of WS40NE cells was profiled in response to anoxia and recovery from anoxia. Given the extreme nature of anoxic assault, I hypothesized that the epigenetic landscape and the proteome would be statistically significantly modified in response to anoxia. Subsequently, we expected statistically significant changes in protein abundance as a consequence of depressed cellular metabolism. In particular, I expected a downregulation of proteins that could trigger aberrant responses (e.g. dysregulated mitosis) and thus promote survival of anoxic stress. My research found WS40NE cells experience drastic changes to the proteome during both anoxia and anoxic recovery, suggesting that gene expression is being altered at both the epigenetic and the proteomic level. Surprisingly, the histone global landscape of A. limnaeus embryos did not change in response to 24 hours of anoxia. This may be due to a need for epigenetic stability during embryonic development. Additionally, resolution at the cellular level is not possible with this type of analysis, as such work represents an aggregate of cell types. However, the histone landscape statistically significantly changed both globally and in a residue-specific manner in WS40NE cells exposed to changing oxygen availability. Both histone isoform abundance and histone post-translational modifications were differentially expressed during anoxia and aerobic recovery, suggesting that these histone post-translational modifications may be at least partially responsible for the alterations in the proteomic landscape. This research provides a foundation to understand the epigenetic and proteomic changes that may be key mechanisms of anoxia tolerance in this species, and may provide insights into how nontolerant species could be altered to survive anoxia.
Rights
In Copyright. URI: http://rightsstatements.org/vocab/InC/1.0/ This Item is protected by copyright and/or related rights. You are free to use this Item in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you need to obtain permission from the rights-holder(s).
Recommended Citation
Hughes, Chelsea Jordan, "Breaking the Rules: Post-Translational Modifications and Proteome Dynamics During Anoxia" (2025). Dissertations and Theses. Paper 6878.