|GHANDCHI, FREDERICK - University Of Illinois
|CAETANO-ANOLLES, GUSTAVO - University Of Illinois
Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/22/2016
Publication Date: 9/12/2016
Citation: Ghandchi, F.P., Caetano-Anolles, G., Clough, S.J., Ort, D.R. 2016. Investigating the control of chlorophyll degradation by genomic correlation mining. PLoS One. 11(9):eo162327.
Interpretive Summary: The chlorophyll degradation pathway is relevant to the agricultural sector by modulating postharvest fruit and vegetable color. Disruption of the pathway results in the “green seed problem” of oilseed crops such as canola and soybean, leading to photoactive chlorophyll contaminated oils, which in turn cause rancidness and financial losses. In addition, optimizing chlorophyll levels in crop canopies could improve canopy photosynthetic efficiency, leading to higher crop yields. Finally, delaying the induction of chlorophyll degradation in leaves by installing a “stay-green” trait could improve crop productivity, by taking advantage of the lengthening growing season brought on by global warming. This study identifies upstream regulatory elements of chlorophyll degradation, which can be used to modulate plant response to biotic and abiotic factors and thus address wider issues in agribusiness.
Technical Abstract: Chlorophyll degradation is an intricate process that is critical in a variety of plant tissues at different times during the plant life cycle. Many of the photoactive chlorophyll degradation intermediates are exceptionally cytotoxic necessitating that the pathway be carefully coordinated and regulated. The primary regulatory step in the chlorophyll degradation pathway involves the enzyme pheophorbide a oxygenase (PAO), which oxidizes the chlorophyll intermediate pheophorbide a, that is eventually converted to non-fluorescent chlorophyll catabolites. There is evidence that PAO is differentially regulated across different environmental and developmental conditions with both transcriptional and post-transcriptional components, but the involved regulatory elements are uncertain or unknown. We hypothesized that transcription factors modulate PAO expression across different environmental conditions, such as cold and drought, as well as during developmental transitions to leaf senescence and maturation of green seeds. To test these hypotheses, several sets of Arabidopsis genomic and bioinformatic experiments were investigated and re-analyzed using computational approaches. PAO expression was compared across varied environmental conditions in the three separate datasets using regression modeling and correlation mining to identify gene elements co-expressed with PAO. Their functions were investigated as candidate upstream transcription factors or other regulatory elements that may regulate PAO expression. PAO transcript expression was found to be significantly up-regulated in warm conditions, during leaf senescence, and in drought conditions, and in all three conditions significantly positively correlated with expression of transcription factor Arabidopsis thaliana activating factor 1 (ATAF1), suggesting that ATAF1 is triggered in the plant response to these processes or abiotic stresses and in result up-regulates PAO expression. The proposed regulatory network includes the freezing, senescence, and drought stresses modulating factor ATAF1 and various other transcription factors and pathways, which in turn act to regulate chlorophyll degradation by up-regulating PAO expression.