Abstract
As one of the most diverse ecosystems in the world, coral reefs provide humans with various benefits, including goods, services, coastal protection, and so on. However, they are facing challenges from global climate change and environmental pollution. Coral bleaching is occurring more frequently over time, causing the global decline of coral reefs. Natural stress-tolerant coral species are regarded as the future of coral reefs. Stress tolerance can be shaped under the high pressure of natural selection, but the underlying mechanisms remain poorly understood. Subtropical corals, Platygyra carnosa, is a stress-tolerant species that can withstand the high environmental fluctuations in Hong Kong. Therefore, in this thesis, it was used to investigate the environmental adaptation mechanisms by using in-depth proteomic profiling, together with transcriptomics and phosphoproteomics analysis.Firstly, a robust workflow for investigating the coral proteome is essential for understanding coral biology. Here I investigated different preparative workflows and characterized the proteome of P. carnosa. I found that a combination of bead homogenization with suspension trapping (S-Trap) preparation could yield more than 2,700 proteins from coral samples. Annotation using a P. carnosa transcriptome database revealed that the majority of these proteins were from the coral host cells (2,140, 212, and 427 proteins from host coral, dinoflagellate, and other compartments, respectively). Label-free quantification and functional annotation of the proteins indicated that a high proportion were involved in protein and redox homeostasis. Furthermore, the S-Trap method achieved good reproducibility in quantitative analysis. Although yielding a low symbiont:host ratio, this method is efficient in characterizing the coral host proteomic landscape, which provides a foundation to study the molecular responses of coral host tissues to environmental stressors.
Secondly, I investigated the seasonal proteome dynamics of P. carnosa by integrating the S-Trap workflow with offline peptide fractionation, achieving a 150% increase in coral protein identification. More than 5,000 coral proteins were quantitatively analyzed using natural samples collected in the months of wet and dry seasons with distinct environmental conditions. Correlation network analysis revealed protein modules underpinning coral adaptations related to environmental stressors, including temperature, pH, dissolved oxygen, salinity, and turbidity. More importantly, these modules were organized into scale-free networks coordinated by hub proteins that are strongly correlated with stressors, suggesting their key roles in environmental adaptation. Using coral cultures in the laboratory, I validated the hub proteins of the temperature-responsive modules, including HSP90B1 and HSPA5 that are implicated in stress response and protein homeostasis.
Thirdly, to further explore the molecular responses of stress-tolerance corals under temperature changes, I mimed the warming and cooling processes faced by subtropical corals in the laboratory and analyzed the molecular changes by multi-omics approaches. The study identified a total of 22061 protein-coding transcripts, 3013 proteins, and 829 phosphorylated proteins from coral samples collected across ten temperature gradients, revealing rapid and sensitive transcriptomic and phosphoproteomic responses that are likely crucial for the environmental adaptation of coral hosts. However, proteomic resilience may play a significant role in coral tolerance. The findings further suggest that subtropical corals are more vulnerable to cooling stress, although both warming and cooling can induce stress in coral hosts. Cooling was found to impede growth-related processes while enhancing immune-responsive gene expression in response to stresses, whereas warming activated immune responses and increased the expression of growth-related genes. The study also highlighted the potential involvement of NF-kappaB signaling as a central regulator of thermal responses in coral hosts.
The coral proteomic workflow established in this thesis provides a foundation to study the molecular responses of coral host tissues to environmental stressors. I investigated the stony coral proteome with unprecedented depth and breadth and revealed co-regulated coral protein modules that respond to environmental stressors. Moreover, I investigated the thermal responses of stress-tolerance corals using a multi-omics approach and revealed that protein homeostasis was critical for coral tolerance. Taken together, the research in this thesis provides a research workflow and multi-omics datasets of the adaptive responses of corals to environmental changes, setting the stage for multi-omics-based approaches in promoting climate change resilience on coral reefs, and further leading to more informed conservation and restoration efforts.
| Date of Award | 8 May 2023 |
|---|---|
| Original language | English |
| Awarding Institution |
|
| Supervisor | Lai Leo CHAN (Supervisor) & Liang ZHANG (Co-supervisor) |