Transcriptomic and proteomic profiling of Arabidopsis flower and leaf under sufficient or limited water conditions
Restricted (Penn State Only)
- Author:
- Ma, Xinwei
- Graduate Program:
- Biology
- Degree:
- Doctor of Philosophy
- Document Type:
- Dissertation
- Date of Defense:
- February 21, 2023
- Committee Members:
- Michael Axtell, Chair of Committee
Hong Ma, Major Field Member & Dissertation Advisor
Jesse Lasky, Major Field Member
Teh-Hui Kao, Outside Unit & Field Member
Stephen Schaeffer, Professor in Charge/Director of Graduate Studies - Keywords:
- Drought
Proteomics
Transcriptomics
Plant reproduction - Abstract:
- Drought is one of the most common environmental stresses that negatively affect plant growth, development and yield. Previous analyses demonstrated that plants during reproductive development are more sensitive to adverse environmental conditions comparing with plants during vegetative development, since plants need to devote more resources and energy, and allocate these resources and energy properly to push through reproduction and produce even limited number of seeds. Traditional genetics demonstrated the importance of a small number of genes under drought stress during flower development, while microarray revealed the gene expression changes in the reproductive tissue induced by drought stress on a large scale. However, studies on plant drought responsiveness on the protein level are much lacking, not to mention addressing the proteomic changes in the reproductive tissues. Additionally, considering the complexity of reproductive development which includes 20 consecutive stages, a more detailed and high-throughput transcriptomic analysis is necessary to obtain more details on the changes at the transcriptomic level. This dissertation utilized a parallel well-watered flower and leaf proteomic analysis as a comparison, which integrated a nuclear enrichment process as an attempt to identify more low abundant proteins, and compared for the differences on proteome between reproductive and vegetative tissues. This study provides new implications for flower and leaf development from the protein level under standard lab growth conditions. The above analyses then serve as a foundation for the subsequent comparisons between well-watered and drought-treated proteomes in flower and leaf. Of the 11,769 proteins detected under drought stress, the vast majority of the proteins identified under drought stress were also present under well-watered conditions, with 228 proteins only detected under drought conditions. Additionally, a total of 231 proteins showed drought-induced differential expression, of which 79 were up-regulated and 152 were down-regulated. The inconsistency between the number of differentially expressed genes/proteins and the degree of differential expression between the transcriptome and the proteome suggests that drought disrupts the correlation between mRNA and protein levels, and that multiple aspects of gene expression regulation might be subjected onto the transcriptional level, post-transcriptional level, translational level, post-translational level, and protein stability in flower and leaf under drought stress. Moreover, different sets of proteins with diverse biological functions were responsive to drought stress in flower and leaf and are important for flower and leaf specific functions, indicating tissue specificity in response to drought. This is the first document of a large-scale proteomic profiling of Arabidopsis flower and leaf under drought stress. From another perspective, previous transcriptome studies on flower development under drought used microarray, which is not as sensitive as RNA-sequencing, and whole inflorescences as their materials, which did not address the stage differences. A developmental-stage dependent drought transcriptome of Arabidopsis reproductive tissues was performed, and it demonstrated that under different drought conditions flowers at different developmental states required unique drought-responsive genes, involving transcriptional regulation and drought response during early stage, lipid storage during middle stage, and pollen and seed development and metabolism during late stage; developmentally-regulated genes under different water conditions shared similar biological functions belonging to different gene families, suggesting that the effect of drought stress on different levels of gene expression in reproductive tissue. Together, this study provides a reservoir of potential regulators for drought response, flower development, and connections between these seemingly not related biological processes.