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Author ORCID Identifier
https://orcid.org/ 0000-0001-9766-8928
AccessType
Campus-Only Access for Five (5) Years
Document Type
dissertation
Degree Name
Doctor of Philosophy (PhD)
Degree Program
Plant Biology
Year Degree Awarded
2024
Month Degree Awarded
February
First Advisor
Elsbeth L. Walker
Subject Categories
Bioinformatics | Computational Biology | Genomics | Laboratory and Basic Science Research | Molecular Biology | Plant Biology | Plant Sciences | Systems Biology
Abstract
Iron is an essential micronutrient for plant development and is required in many enzymatic processes. Because excess iron could cause oxidative damage in cells, plants strictly regulate iron uptake to ensure that only the required amount of iron is present in cells and tissues. For these reasons, plants have developed complex mechanisms to tightly regulate iron uptake, use, and storage while adapting to changes in iron concentration in their environment. The primary objective of this dissertation is to explore the mechanisms underlying iron homeostasis in Arabidopsis thaliana. While working on iron signaling, I explored potential signals in the phloem, as well as key genes that regulate metal concentrations in vascular tissues, where iron sensing is hypothesized to occur.
The first chapter details the discovery of a novel long non-coding RNA (lncRNA), CAN OF SPINACH (COS), which regulates iron deficiency responses in Arabidopsis. Transcriptome analysis of whole shoots during iron deficiency led to the discovery of COS and also provided a broad overview of gene expression changes in response to iron levels in whole shoots. Using genetic analysis of COS mutants, the subtle but significant roles of this novel lncRNA were uncovered.
The second chapter investigates the small RNA landscape in the phloem sap of Arabidopsis, focusing on the sRNAs altered in response to iron deficiency. I identified a group of small RNAs with altered expression in phloem sap during iron-deficient conditions. This work also established for the first time that most sRNA in Arabidopsis phloem exudates are tRNA-derived fragments, specifically 5’ tRFs and 5’ tRNA halves. The results from this chapter suggest that there is selectivity for loading, or perhaps for retaining, particular sRNAs in the phloem sap.
In the last chapter, I characterized the roles and interplay of iron transporters YSL1, YSL3, and OPT3 in the vascular system of Arabidopsis. Through the use of transgenic plants, confocal microscopy, genetic crosses, and careful phenotyping, I revealed the contributions of these transporters in iron redistribution and cellular iron availability, thereby offering new insights into the complex regulation of iron in Arabidopsis.
These findings collectively contribute to a more nuanced and comprehensive understanding of iron homeostasis in Arabidopsis. They hold significant implications for plant molecular genetics and agriculture, where soil nutrient management is crucial for sustainable crop production. My Ph.D. research may open avenues for targeted genetic modifications to improve iron uptake and storage in crop plants, potentially addressing issues of nutrient deficiency in agriculture.
DOI
https://doi.org/10.7275/36423051
Recommended Citation
Bakirbas, Ahmet, "Elucidating Mechanisms of Shoot-to-root Iron Deficiency Signaling in Arabidopsis thaliana" (2024). Doctoral Dissertations. 3029.
https://doi.org/10.7275/36423051
https://scholarworks.umass.edu/dissertations_2/3029
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 License.