Transcriptomic and proteomic analyses of distinct Arabidopsis organs reveal high PSI-NDH complex accumulation in stems

In addition to leaves, the main site of photosynthetic reactions, active photosynthesis also takes place in stems, siliques and tree trunks. Although non-foliar photosynthesis has a marked effect on plant growth and yield, only limited information on the expression patterns of photosynthesis-related genes and the structure of photosynthetic machinery in different plant organs has been available. Here, we report the results of transcriptomic analysis of various organs of Arabidopsis thaliana and compare the gene expression profiles of young and mature leaves with a special focus on photosynthetic genes. Further, we analyzed the composition and organization of the photosynthetic electron transfer machinery in leaves, stems and green siliques at the protein level using BN-PAGE. RNA-Seq analysis revealed unique gene expression profiles in different plant organs and showed major differences in the expression of photosynthesis-related genes in young as compared to mature rosettes. Gel-based proteomic analysis of the thylakoid protein complex organization further showed that all studied plant organs contain the necessary components of the photosynthetic electron transfer chain. Intriguingly, stems accumulate high amounts of PSI-NDH complex, which has previously been implicated in cyclic electron transfer. Arabidopsis thaliana Col-0 plants were grown on a peat:vermiculite mixture (2:1) in 8 h light/16 h darkness for short day conditions (mature (5 weeks) and young (3 weeks) rosette) and 12 h light/12 h darkness for long day conditions (stems, flowers, green siliques) at photosynthetic photon flux density (PPFD) of 120 µmol m−2 s−1 (Osram Powerstar HQI®-BT 400W/D PRO Daylight) , 50% humidity, and 23°C. Different biological replicates were grown on separate trays at different times. To extract RNA from roots, surface sterilized seeds were plated on half-strength Murashige and Skoog (1/2 MS, Duchefa) plates with 0.8 % plant agar. The plants were grown under the light rhythm of 8 h light/16 h darkness at PPFD of 50 μmol m−2 s −1, 50 % humidity, and 23 °C in a vertical position in an incubator for six weeks. Four biological replicates were conducted for each material. RNA was extracted from 100 mg of each plant material using innuPREP Plant RNA kit (Analytik Jena, Germany) according to manufacturer’s protocol.