Abstract
The combination of a changing climate and growing population necessitate new ways to improve photosynthesis; this thesis adresses this by examining the poorly-explored class of regulatory RNAs called long non-coding RNAs (lncRNAs). LncRNAs have diverse mechanisms of action, from transcriptional and translational inhibition, to interacting directly with proteins. While the molecular roles of lncRNAs have been established in eukaryotes including plants, their role in photosynthesis and stress response remains poorly understood. This thesis uses T-DNA insertional mutants of high light (HL)-responsive lncRNAs in Arabidopsis thaliana to identify aberrant photosynthetic phenotypes through high-throughput imaging coupled to transcriptomics.
I first identify homozygous mutants, then examine a wide variety of phenotypes, demonstrating broadly unchanged growth, morphology and leaf composition in the mutants compared to wild type (WT) plants. Using pulse amplitude modulation (PAM) fluorometry, I find a range of photosynthetic behaviours that differ from WT. Mutant alleles showed traits such as altered induction kinetics (e.g. lncrna9b), altered relaxation kinetics (e.g. lncrna14a), or constitutively higher photosynthetic efficiency (e.g. lncrna7b). Chief among these mutants is lncrna9b, which showed highly aberrant non-photochemical quenching (NPQ) quantum yield (ΦNPQ) kinetics post-stress. Whereas WT and the other mutants increase NPQ after 1 hour of HL stress, lncrna9b experiences a significant reduction in ΦNPQ. This is coupled with a post-stress rise in photosynthetic efficiency (ΦPSII)—an inversion of WT behaviour. lncrna9b also shows accelerated ΦNPQ induction. These results identify lncRNAs as effectors of photosynthesis with resulting stress-responsive phenotypes. lncrna9b, in particular, has disturbed energy-dependent quenching (qE).
Transcriptomic profiles of the mutants of interest (lncrna9b, lncrna14a, lncrna7b) show varied transcriptomic fingerprints for the phenotypes observed, however I prioritised lncrna9b for deeper investigation due to the strongly divergent phenotype. lncrna9b has increased gene expression among chromatin and PPR genes, the latter of which affects organellar transcription, providing a potential mechanism affecting nucleus-to-organellar (anterograde) signalling and underpinning the phenotype.
Overall, this thesis identifies specific HL-responsive lncRNAs as effectors of photosynthesis, likely through modulating photosynthetic genes. Further work is needed to identify the underlying qE component, or the precise mechanism by which lncrna9b affects chromatin and PPR protein expression. Such elucidations will provide new understanding of photosynthesis regulation and potential targets for crop uplift if the lncRNA is conserved among crop species such as Canola/Rapeseed (Brassica napus).
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