The 5′ untranslated region (UTR) of a carotenoid messenger RNA can sense metabolite accumulation in Arabidopsis

R Aryal1, Y Alagoz1, S Holland2, J Watkins2, M Shashikanth2, B Pogson2 and C Cazzonelli1

  1. Hawkesbury Institute for the Environment, Western Sydney University
  2. Research School of Biology, Australian National University

Many messenger RNAs, in addition to protein coding regions, harbor regulatory domains in their untranslated regions (UTRs). In bacteria, several families of RNA structural switches called riboswitches are found in the UTRs of mRNA that sense metabolite accumulation and regulate gene or protein expression. In eukaryotes however, only the thiamine riboswitch has been identified to date. Metabolic pathways are tightly controlled in plants in order to maintain cellular homeostasis. Arabidopsis epsilon lycopene cyclase (εLCY) expression is responsive to cis-carotenoid feedback regulation (Cazzonelli et al. 2009, Plant Cell 21:39-53). Here we describe the metabolic feedforward regulation by an RNA regulatory switch at the 5′ UTR of the Arabidopsis εLCY gene. The Arabidopsis εLCY harbors two alternative transcription start sites separated by 74bp AT rich segment. The longer transcript can form two alternative secondary structures at the 5′ end. The 74bp additional sequence in the longer transcript is highly conserved across many plant species indicating its importance in gene regulation. Presence of the shorter transcript suggests that the 74bp terminal sequence is dispensable and actively removed in response to specific environmental conditions. The εLCY expression is downregulated in the Arabidopsis and tomato mutants that accumulate cis-carotenoid intermediates. We created a reporter gene construct with εLCY promoter plus 5′ UTR fused with luciferase. The expression of luciferase is downregulated in Arabidopsis etiolated seedlings accumulating cis-carotenoids indicating a role of the 5′ UTR and promoter in sensing carotenoid flux through the pathway. Our findings highlight the importance of the 5′ UTR in sensing metabolic change in plants.