Content area
As sessile organisms, vascular plants have evolved to sense and respond to environmental changes by adjusting their growth, development, and metabolism to survive abiotic and biotic challenges. Changes in gene expression regulate the link between sensing stress and activating the specific mitigating response. This regulation occurs on multiple levels, from chromosomal organization to transcription and translation in a temporal and spatial context. In recent years, it has become apparent that the regulation of RNA abundance and structure of protein-coding genes is not only regulated by transcription factors but also by non-coding RNAs (ncRNAs) that contribute to and control the regulation of transcription, splicing, RNA stability, and localization, as well as modification of DNA. Circular RNAs (circRNAs) are a class of endogenous noncoding RNAs characterized by a covalently closed-loop structure, allowing them to act as gene regulators through diverse mechanisms. This work investigates the role of circRNAs in biotic and abiotic conditions using Lotus japonicus and Camelina Sativa.
Chapter 1 provides an overview of circRNAs and their implications in abiotic and biotic conditions. This chapter will also touch on sustainable agriculture and the role of public perception.
Chapter 2 establishes methods for circRNA identification in root and leaf tissues of Lotus japonicus. Two methods are described: 1) short-read (SR) Illumina sequencing and 2) circRNA-enriched long-read sequencing with Nanopore (CEnLR). Both methods identified ~6,000 putative circRNAs. While each method identified distinct pools with little overlap, we validated circRNAs from both, demonstrating reliable methods at identifying real circRNAs. This chapter serves as the first study of the identification of circRNAs in Lotus japonicus.
Chapter 3 establishes the connection between circRNAs and the Common Symbiosis Pathway, essential for symbiotic relationships between plants and microbes. Lotus japonicus was grown under nutrient sufficient and deficient conditions and in association with symbiotic partners Mesorhizobium loti (rhizobium) and Arbuscular mycorrhizal fungi (AMF). We identified ~15,000 unique nuclear circRNAs. We also describe the novel plant concept, backsplice regulated microRNA response elements (bsrMREs). This paper provides a first step in understanding the role of circRNAs in the well-studied interactions of symbiosis with rhizobia and AMF.
Chapter 4 investigates the role of circRNAs in germination, light, and lipid metabolism. Camelina sativa, is an allohexaploid, studied for its promising ability to serves jet biofuel. Lightgrown and etiolated seedlings were sequenced identifying 3,447 circRNAs. Several key lipid metabolism genes were identified as having circRNAs, and we conformed one circRNA from Kas II. This chapter is the first circRNA detection of circRNAs in C. sativa, providing insights on how circRNAs may function in polyploids and suggest roles for circRNAs in lipid metabolism.
Chapter 5 is an interdisciplinary chapter that explores the responsible development of agricultural innovations. Organic farming, the use of biofertilizers and synthetic fertilizers and all facets of synthetic biology are all proposed approaches to ensuring food security for a growing population. Although controversy around the technical effectiveness of these approaches is of concern, this chapter explores how well agricultural innovations align with the principles of Responsible Research and Innovation.