A systems biology-oriented investigation of Arabidopsis retrograde-signaling-defective mutant gun1 reveals the co-expression-based HUBs at the center of plastid development and homeostasis

In the present study we investigated at the system level the proteome obtained from seedlings of Arabidopsis thaliana wild-type Col-0 and gun1-101 and gun1-102 mutant plants treated or not with lincomycin (Lin), a chloroplast translation inhibitor widely used to inhibit chloroplast biogenesis and to trigger the plastid-to-nucleus retrograde communication. Specifically, we attempted a description of cellular responses to Lincomycin in wild-type genetic background and in retrograde signaling-defective mutant gun1. Hypotheses and key players emerged by our holistic view were validated at the experimental level. Our findings suggest that, in the presence of Lincomycin, cell responses rely on the plastid compartment in a GUN1-dependent manner, while in the gun1-mutant background, the activity of extra-plastid compartments prevails. Moreover, results obtained by complementary approaches depict the Oxygen Evolving Complex subunit PsbO as an atypical Photosynthesis-related protein by accumulating in non-photosynthetic plastids and having a superhub role in modulating chloroplast dismantling upon impairment of plastid functions.