Transcriptomic and Cell-Specific Translatomic Aanalysis in Early Iron Deficiency Response in Arabidopsis

Iron is an essential micronutrient for plant growth, development and productivity. Although it is abundant in soil, the bio-availability of iron is often low for plants in many areas of the world. The insufficient quantity of usable iron in plants causes reduction in chlorophyll synthesis, reduced photosynthesis rate and decreased growth and yield. Two major strategies, Strategy I and II, have been discovered to be involved in response to low iron and a complex network of biochemical and molecular pathways participate in the processes.

Cellular transcriptional regulation is associated with iron deficiency responses. Multiple genes and pathways involved in iron-deficiency responses have been identified in plants in the past decade. Here, we measured different physiological parameters and used RNA-Seq to elucidate the physiological and molecular responses in early stage of iron deficiency in the whole leaf of model plant species Arabidopsis thaliana. In this study, Arabidopsis showed reduced chlorophyll content, increased ferric reductase activity and reduced antioxidant enzyme activities when stressed by iron deficiency. In addition, we have identified multiple pathways that may play promising roles in the response to iron deficiency, e.g., 1) we found that the auxin biosynthesis under iron deficiency is preferentially depended on the TAA-YUC pathway rather than the CYP79 pathways; 2) TCA cycle is involved in mediating the acclimation process to the stress condition; 3) glucosinolate synthesis could be a limiting factor for iron deficiency response due to its negative relationship with hormone and energy metabolism.

Systemic signals generated from leaves are critical for triggering iron deficiency responses in roots. Due to the physiological characteristic and cellular ultrastructure of companion cells (CCs), we hypothesize that the CCs located in phloem play essential roles in regulating systemic nutrient signaling. In this study, by using a cell-specific TRAP-Seq, we discovered that not only CCs respond more drastically than the other cells in leaf, the altered molecular pathways in the CCs are also more diverse during early iron deficiency response. In particular, we found that auxin and sucrose transport and metabolism in the CCs may be two of the key regulatory processes that plants use to exert the shoot-to-root signaling process. Our discoveries have collectively suggested that CCs may function as the central machinery in the systemic signaling in response to iron deficiency. A comparison between whole leaf transcriptome and translatome also suggested that translatomic analysis is a more sensitive method for gene profiling than conventional transcriptomic analysis.