Computational approach towards understanding structural and functional role of cytokinin oxidase/dehydrogenase 2 (CKX2) in enhancing grain yield in rice plant

Abstract

Cytokinin oxidase/dehydrogenase (CKX) is the only known enzyme associated with irreversible degradation of cytokinins in plants. CKX2 contains flavin adenine dinucleotide (FAD) domain. Earlier studies utilising antisense & hpRNAi suppression techniques in mutant/transgenic rice plants revealed that when CKX2 binds with FAD, CKX2 expression reduces, which in turn causes cytokinin aggregation in inflorescence meristem that subsequently enhances both branches and grain number resulting in increased grain yield. Owing to the non-existence of complete three-dimensional structure of CKX2, insight into the structure and function of CKX2 and its relationship with its cofactor FAD is still a topic of debate. In the present study, computational approach was employed to estimate the three-dimensional structure of CKX2 through comparative modelling approach. Later, CKX2 and FAD interaction study was performed to understand the underlying mechanism involved with reduced expression of CKX2. Molecular dynamic simulation studies of both CKX2 and CKX-FAD complex revealed that after binding with FAD, CKX2 experienced increased pressure and reduced RMSD, potential energy and free energy landscape energy, which in turn lessen anti-correlation between almost all α and β strands and random motion of C-α, subsequently reducing CKX2 expression. In near future, these information can be utilised for increasing rice yield under irrigated field condition by introgression of Gn1a gene through marker assisted back-crossing breeding.

Abbreviations
GROMACS	=	GROningen MAchine for Chemical Simulations
NPT	=	Constant Number of Particles, Volume and Temperature
RMSD	=	Root Mean Square Deviation
RMSF	=	Root Mean Square Fluctuations
QTL	=	quantitative trait loci
FAD	=	flavin adenine dinucleotide
NVT	=	Constant Number of Particles, Pressure and Temperature
LINCS	=	Linear Constraint Solver
CKX2	=	Cytokinin oxidase/dehydrogenase 2
MM/PBSA	=	Molecular Mechanics/Poisson–Boltzmann surface area
SDF	=	Structure Data File

Communicated by Ramaswamy H. Sarma

Keywords:

• CKX2
• protein–ligand interaction
• molecular dynamics simulation
• FAD
• grain yield
• rice

Acknowledgement

The authors thank the Director, ICAR-National Rice Research Institute, Cuttack, India, for providing computational assistance to carry out the work.

Disclosure statement

The authors declare no conflicts of interest.

Additional information

Funding

The authors acknowledge the Department of Science and Technology (DST), Government of India, New Delhi, for providing financial assistance through grant number: DST/INSPIRE Fellowship/2013/992 to Inspire Fellow Miss. Gayatri Gouda.