NSF Postdoctoral Fellowship in Biology

This action funds an NSF Plant Genome Postdoctoral Research Fellowship in Biology for FY 2022. The fellowship supports a research and training plan in a host laboratory for the Fellow who also presents a plan to broaden participation in biology. The title of the research and training plan for this fellowship to Rachael DeTar is "Plant Organelle RNA Secondary Structure and Post-Transcriptional Modification".

The host institution for the fellowship is the Colorado State University Biology Department and the sponsoring scientist is Dr. Daniel Sloan.

RNAs are often described as intermediary sets of instructions copied from the genome (DNA) and ferried to the cellular machinery which produces proteins. However, RNA is more than just a mobile mimic of genomic DNA - one unique property of RNA is that it is typically single-stranded, which allows it to fold upon itself into specific 3-D structures based on the sequence.

The structures that RNAs adopt can influence if and how they are used by the cell to make proteins. RNA folding is often also influenced by environmental conditions, especially temperature. Thus, RNA folding could be a built-in switch for changing cell activities in response to the environment.

In some systems such as plant chloroplasts and mitochondria, RNAs can also be edited so that their sequence reads differently than the genomic DNA. Thus, this research aims to answer two questions: 1) Does RNA editing affect the secondary structure of plant mitochondria and chloroplast RNAs? 2) How do changes in RNA editing, and structure influence a plant’s ability to survive under stressful conditions?

This PGRP fellowship project will investigate these questions using computational modeling techniques and Next-Generation sequencing in a diverse array of plants, including crop species. This research is important for society because it will provide insights into how plants cope with temperature stress on the molecular level, which will inform the breeding of stress-tolerant crops.

In the short term, this project will have broader impacts on undergraduate education by initiating an internship program for students with disabilities.

The overarching goal of this research is to test the hypothesis that the relationship between post-transcriptional modifications and RNA secondary structure has fundamentally shaped plant organelle gene expression and adaptability to abiotic stress. Many RNA editing events in plant organelle transcriptomes result in non-synonymous changes to transcript codons and revert amino acid sequence.

Yet, it is unclear if these edits would also meaningfully influence RNA secondary structure. The first experiment will be to run a large-scale analysis of RNA editing and secondary structure in diverse plant and green algal lineages to predict if editing events result in conserved RNA secondary structure in non-coding sequences and at synonymous sites.

This will be accomplished by first cataloging organelle RNA editing sites using preexisting annotations and publicly available genome and transcriptome data. Then, an array of structure prediction tools will determine if putative editing events reliably result in the conserved secondary structure of transcripts across lineages. Next up, the link between RNA editing, structure, and stress adaptation will be addressed empirically using secondary structure mapping via DMS-MaPseq on organelle RNA.

This experiment will compare the “editome” and “structurome” of Arabidopsis thaliana and related extremophiles cold-tolerant Eutrema salsuginum and heat-tolerant Anastatica hierochuntica grown over a range of temperatures. Research deliverables including high-resolution organelle transcriptomes and new computational and empirical methods for RNA secondary structure prediction will be uploaded to the NCBI Sequence Read Archive or be deposited on the public science database Zenodo. Keywords: plant organelle, RNA editing, RNA secondary structure.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.