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In-silico studies of CBL-CIPK signaling in rice: response against hypoxia is triggered by interaction of CBL10 with CIPK15

Irfan Sadiq, Mahnoor Zulfiqar, Arooma Maryam, Khoula Rehman, Salma Noreen, Muhammad Mursalin, Sadaf Abdul Rauf, Shehreen Amjad and Abdul Rauf Siddiqi

In rice, Oryza sativa, Calcineurin B-Like (OsCBL) protein mediated activation of CBL-Interacting Protein Kinase15 (OsCIPK15) is extremely crucial for plants’ ability to cope up with hypoxic stress. Ten various types of OsCBLs and OsCIPK15 have been implicated in hypoxia, but little is known about the CBL partner that activates CIPK15 signaling. In-silico sequence, structural and functional analyses of OsCBLs and CIPK family members were conducted to explore the OsCBL which binds with and activates OsCIPK15, thus serving as regulatory factor for plant’s response to hypoxia. Sequence analysis revealed four characteristic conserved EF motifs in OsCBL family, whereas OsCIPK15 was found to contain a conserved 128 residue long NAF domain with a highly conserved 18 residue long helical fragment at its N-terminus. Structures of 10 OsCBL proteins and CIPK15 were modeled and protein-protein docking was undertaken to explore binding affinity of each of the ten OsCBL proteins for OsCIPK15. Several binding conformations of OsCBL-CIPK complexes were analyzed estimating their binding affinities on the basis of hydrogen bonding, electrostatic and hydrophobic interactions. OsCBL10 has been found to be the partner in establishing the most stable interaction with OsCIPK15’s NAF domain thereby activating down the stream cascade of molecular events and configuring the plant’s response to hypoxia.

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