Evidence of Plastid Influence on Epigenetic Reprogramming in Arabidopsis and Crop Plants

In plants, plastids serve as sensors of developmental and environmental stimuli, allowing cells to modulate gene expression and likely to reprogram the epigenome in a heritable fashion. MSH1 is an organellar DNA binding and thylakoid protein with profound roles in development, stress responses and redox balance. Current evidence supports MSH1 as important for influencing transgenerational epigenetic inheritance. MSH1, together with its interacting partner PPD3, localize to small, distinctive plastids that display low autofluorescence and reside within the epidermis and vascular parenchyma. We have termed these organelles ‘sensory plastids’. Our observations imply proteome heterogeneity in different plastid types across discrete cell populations. To gain insight into the role of sensory plastids, we combined Fluorescence-Activated Cell Sorting (FACS) and proteomics to characterize their proteomes in Arabidopsis floral stems. We used Translating Ribosome Affinity Purification (TRAP) analysis followed by RNA sequencing technology (TRAP-SEQ) to assess both MSH1-containing and MSH1-depleted, cell-specific translating RNAs. Early results suggest that protein counts for oxidation-reduction processes and responders to abiotic stimulus are more prominent in rank in sensory plastids than in chloroplasts, which suggests plastid specialized function. TRAP-SEQ experiments revealed that cells depleted of MSH1 actively translate proteins for oxidation-reduction processes, cell redox homeostasis and auxin response, which suggest a role of MSH1 in triggering retrograde signaling in specific cell types. Finding correlations between cell-specific translatomes and the plastid proteome profiles within these cells would help to understand the underpinnings of organellar functional specialization.