In silico analysis of comparative affinity of phytosiderophore and bacillibactin for iron uptake by YSL15 and YSL18 receptors of Oryza sativa

Abstract

Iron is an important micronutrient for plant growth and development. In the case of Oryza sativa, iron is made available primarily with the help of iron chelators called phytosiderophores i.e. variants of deoxymugineic acid (DMA). They bind with ferric ions and get internalized through Yellow Stripe Like transporters viz. YSL15 and YSL18. However, due to low amount of secretion of phytosiderophores, rice suffers from iron deficiency. Alternatively, siderophores of plant growth promoting rhizobacteria may support iron uptake and make it available to plants via transporting ferric ions possibly through the same transporters. Present study aims to assess comparative binding of DMA and a xenosiderophore (siderophores used by organisms other than the ones producing them) of rhizobacteria i.e. bacillibactin with Fe³⁺ ion and subsequent transporters of rice. Protein–protein interaction and gene expression analysis predicts uptake of Fe³⁺ by YSL15 from the rhizosphere region and further distribution through YSL18 with the help of various predicted functional partners. Docking studies confirm the thermodynamically more favourable structure of bacillibactin-Fe³⁺ complex than DMA-Fe³⁺ complex. Molecular modelling of YSL15 and YSL18 was done through ab initio method and their evaluation by Ramachandran plot, ProSA, ERRAT value and verify 3 D score revealed a good quality models. Comparative binding assessment through docking and molecular dynamics simulation suggests better binding energies of YSL transporters with bacillibactin-Fe³⁺ complex as compared to DMA-Fe³⁺ complex. The current study suggests possible application of xenosiderophores of PGPR origin in supporting plant growth via iron uptake and distribution in rice.

Communicated by Ramaswamy H. Sarma

Keywords:

• Oryza sativa
• phytosiderophore
• bacillibactin
• modelling
• MM/PBSA

Acknowledgement

We thank the University Grants Commission, India for providing non-net fellowship to authors Pratika Singh, and Azmi Khan and research fellowship to Rakesh Kumar under Rajeev Gandhi National Fellowship (RGNF) scheme.

Disclosure statement

The authors declare that they have no conflict of interest.

Additional information

Funding

The study was funded by the University Grants Commission, India in the form of non-net and RGNF fellowships to authors Pratika Singh, Azmi Khan and Rakesh Kumar.