Probing the structural basis of Citrus phytochrome B using computational modelling and molecular dynamics simulation approaches

Abstract Phytochromes (Phys) are known as red/far-red light photoreceptors and are responsible for directing the photosensory responses across the species, majorly from fungal, bacterial and plant kingdoms. Such responses majorly include photosynthetic potential and pigmentation in bacteria, whereas in a plant, they are involved in chloroplast development and photomorphogenesis. Many prokaryotic Phys have been modelled for their structural and functional analysis, but their plant counterparts have not been explored yet. To date, only the crystal structures of the photo-sensing module (PSM) of PhyB isoform from Arabidopsis thaliana and Glycine max have been resolved experimentally. Thus, in this study, we elucidated the complete 3D structure of Citrus PhyB. Initially, the structure and organization of the Citrus PhyB have been predicted computationally, which were found to have the same domain organization as A. thaliana and G. max PhyBs, yet their considerable distinct structural difference indicated potential divergence in signaling and functioning. Therefore, to evaluate the structural implications of Citrus PhyB, we compared its structure with A. thaliana and G. max PhyBs using molecular dynamics (MD) simulation approaches. The modeling studies revealed that the region of Citrus PhyB-GAF domain possibly contributes to the variations between Citrus, A. thaliana and G. max PhyBs structures. Hence, structural and molecular insights into Citrus PhyB can help to understand better the Phys and thus, an essential framework can be designed for optogenetic reagents and various agricultural/horticulture benefits.