Yagiz Alagoz


PhD Candidate

Thesis Title

Environmental regulation of RNA, epigenetic and metabolic processes in plants

Research project

Carotenoids are natural pigments synthesized by plants, algae, photosynthetic bacteria and aphids. In plants, carotenoids take role in photosynthesis, photoprotection and production of some phytohormones (Abscisic acid and Strigolactones) and signalling molecules that attract beneficial fungi. In animals, carotenoids help to maintain health and promote reproduction. In humans, there is a daily dietary requirement for ingestion of carotenoids that are used to make vitamin A, which prevents eye diseases and some cancers.

Through the use of genetic engineering, new biofortification strategies have been developed to enhance the access to these health promoting compounds. One of the best known examples is the enrichment of carotenoids in white rice to make golden rice. However, biofortification strategies can be unpredictable due to metabolic feedback regulation that maintains metabolite composition insuring cellular homeostasis. Therefore, a deeper understanding and knowledge of feedback regulatory mechanisms is required to advance genomic engineering approaches for successful biofortication.

In eukaryotic systems, gene transcription occurs when the information in specific segment of DNA copies itself into a messenger RNA (mRNA) which has 5' and 3' untranslated regions (5' & 3' UTR) either side of the protein coding region. The 5'UTR can affect gene transcription and protein translation depending upon developmental and environmental factors. We hypothesise that the 5'UTR is an important regulatory switch sensing metabolite levels and controlling the regulation of carotenogenesis in plants. Similar mechanisms can operate in bacteria to fine-tune metabolic levels in response to environmental stress.

When plant seeds germinate underground in the dark they soon become exposed to light triggering major changes in energy organelle biogenesis and secondary metabolic processes. This transition from dark to light provides an ideal model to investigate the effects of metabolite accumulation on feedback regulatory mechanisms in plants.

My research interests include understanding the genome-wide regulation of transcription start sites (TSS) and role of 5'UTR in the metabolic feedback regulation in carotenoid biosynthesis pathway (see Figures below). An ultimate goal of my research is to discover novel RNA regulatory switches in the 5'UTR of mRNA that control gene expression in response to environmental and developmental cues.

metabolic feedback regulation in carotenoid biosynthesis pathway

Research supervisors

Dr Christopher Cazzonelli, Professor David Tissue, Dr Alexie Papanicolaou


Alagoz Y, Nayak P, Dhami N, Cazzonelli CI, (2018) 'cis-carotene biosynthesis, evolution and regulation in plants: The emergence of novel signaling metabolites', Archives of Biochemistry and Biophysics, vol.654, pp 172-184

Alagoz Y, Gurkok T, Parmaksiz I, Unver T, (2016) 'Identification and Sequence Analysis of Alkaloid Biosynthesis Genes in Papaver Section Oxytona', Turkish Journal of Biology, vol.40, pp 174-183

Alagoz Y, Gurkok T, Zhang B, Unver T, (2016) 'Manipulating the Biosynthesis of Bioactive Compound Alkaloids for Next-Generation Metabolic Engineering in Opium Poppy Using CRISPR-Cas9 Genome Editing Technology', Scientific Reports, vol.6, Article no.30910