Circadian clock control of biosynthetic gene clusters

Dekeya, Richard (2025) Circadian clock control of biosynthetic gene clusters. Doctoral thesis, University of East Anglia.

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Abstract

The circadian clock coordinates a range of plant biological process in alignment with the aily fluctuating environmental conditions. This includes the production of specialised metabolites involved in biotic and abiotic responses to the environment. Plant specialised metabolites iosynthesis is sometimes driven by specially constructed genetic structures known as biosynthetic gene clusters (BGCs).

I investigated the potential circadian regulation of BGCs using the well characterised thalianol BGC in Arabidopsis thaliana (Arabidopsis). I examined thalianol BGC transcript dynamics in Arabidopsis seedling roots under free running conditions. I also generated individual thalianol BGC promoter-LUCIFERASE reporter genotypes and monitored activity under free running conditions. I examined a number of potential regulatory mechanisms governing circadian clock control using superenhancer, circadian clock and accessory transcription factor mutants. Finally, I investigated the role of the circadian oscillator in thalianol pathway metabolite production and the implications on rhizosphere interactions through colonisation assays with Bacillus subtilis.

I uncovered a novel role of the circadian clock in the regulation of BGCs. The circadian clock coordinates thalianol BGC transcripts, together with the associated transporter (ABGC34), and I show in a preliminary analysis that this may extend to BGCs in Neurospora crassa, suggesting similar regulation in more than one kingdom of life. My findings suggest that circadian regulation of the thalianol BGC transcripts requires an embedded superenhancer element and this could explain the low promoter activity I observed. The circadian regulation of the thalianol BGC is required for production of the thalianol pathway compounds and may influence rhizosphere interactions.

These novel findings have the potential to inform on previously elusive specialised metabolite regulatory mechanisms and could be instrumental in their increased utilisation and discovery. Additionally, they could be useful in understanding the potential specialised metabolites-mediated cross-kingdom temporal communication dynamics.

Item Type:	Thesis (Doctoral)
Faculty \ School:	Faculty of Science > School of Biological Sciences
Depositing User:	Chris White
Date Deposited:	21 May 2026 08:48
Last Modified:	21 May 2026 08:48
URI:	https://ueaeprints.uea.ac.uk/id/eprint/103121
DOI:

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