Identification and characterization of a grain micronutrient-related OsFRO2 rice gene ortholog from micronutrient-rich little millet (Panicum sumatrense)

Abstract

Minor millets are considered as nutrient-rich cereals having significant effect in improving human health. In this study, a rice ortholog of Ferric Chelate Reductase (FRO2) gene involved in plant metal uptake has been identified in iron-rich Little millet (LM) using PCR and next generation sequencing-based strategy. FRO2 gene-specific primers designed from rice genome amplified 2.7 Kb fragment in LM genotype RLM-37. Computational genomics analyses of the sequenced amplicon showed high level sequence similarity with rice OsFRO2 gene. The predicted gene structure showed the presence of 6 exons and 5 introns and its protein sequence was found to contain ferric reductase and NOX_Duox_Like_FAD_NADP domains. Further, 3D structure analysis of FCR-LM model protein (494 amino acids) shows that it has 18 helices, 10 beta sheets, 10 strands, 41 beta turn and 5 gamma turn with slight deviation from the FCR-Os structure. Besides, the structures of FCR-LM and FCR-Os were modelled followed by molecular dynamics simulations. The overall study revealed both sequence and structural similarity between the identified gene and OsFRO2. Thus, a putative ferric chelate reductase gene has been identified in LM paving the way for using this approach for identification of orthologs of other metal genes from millets. This also facilitates mining of effective alleles of known genes for improvement of staple crops like rice.

Keywords: Ferric Chelate Reductase; Little millet; MD simulation; Metal homeostasis; Sequencing.

Fig. 1

PCR amplification of full length FRO2 gene fragment in different minor millets. M 1 Kb DNA ladder; 1, 4, 7; Little millet (RLM-37); 2, 5, 8 Barnyard millet (Sawa local) 3, 6, 9 Finger millet (GPU67) using different primer sets detailed in Table 2

Fig. 2

a 3D structure of FCR-LM generated through threading-based method with different colored domains and regions. The N-terminal domain (residues 1–51; Orange red), Ferric reductase domain (residues 52–136; Cyan), linker helix (residues 137–165; Violet color), Nox_Duox_Like_FAD domain (165–355; blue) and Helix+ C-Terminal domain (residues 366–494; Forest Green). b Secondary structure representation for FCR-LM model generated via ProFunc Server. c Structural comparison of residues of FCR-LM with respective residues of X-ray and NMR structures made using PROSA web server

Fig. 3

a 3D structure of FCR-Os generated through threading-based method with different colored domains and regions. The N-terminal domain (residues 1–66; Orange red), Ferric reductase domain (residues 67–188; Cyan), linker helix (residues 189–217; Violet color), Nox_Duox_Like_FAD domain (218–406; blue) and Helix+ C-Terminal domain (residues 407–489; Forest Green). b Secondary structure representation for FCR-Os model generated via ProFunc Server. c Structural comparison of residues of FCR-Os with respective residues of X-ray and NMR structures made using PROSA web server

Fig. 4

a Total energy of profile for the FCR-LM (Black) and FCR-Os (Red) with respect to time of simulation. b RMSD plot showing the fluctuation height (nm) versus time (ns) of simulation

Fig. 5

a Calculated RMSF plot for atoms of FCR-LM versus fluctuation height (nm). b The B-factor representation of the FCR-LM protein with highly (red), medium (green) and less flexible (blue) atoms during dynamics simulation

Fig. 6

a Calculated RMSF plot for atoms of FCR-Os versus fluctuation height (nm). b The B-factor representation of the FCR-Os protein with highly (red), medium (green) and less flexible (blue) atoms during dynamics simulation