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Molecular modeling and in silico characterization of GmABCC5: a phytate transporter and potential target for low-phytate crops

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Abstract

Designing low-phytate crops without affecting the developmental process in plants had led to the identification of ABCC5 gene in soybean. The GmABCC5 gene was identified and a partial gene sequence was cloned from popular Indian soybean genotype Pusa16. Conserved domains and motifs unique to ABC transporters were identified in the 30 homologous sequences retrieved by BLASTP analysis. The homologs were analyzed for their evolutionary relationship and physiochemical properties. Conserved domains, transmembrane architecture and secondary structure of GmABCC5 were predicted with the aid of computational tools. Analysis identified 53 alpha helices and 31 beta strands, predicting 60% residues in alpha conformation. A three-dimensional (3D) model for GmABCC5 was developed based on 5twv.1.B (Homo sapiens) template homology to gain better insight into its molecular mechanism of transport and sequestration. Spatio-temporal real-time PCR analysis identified mid-to-late seed developmental stages as the time window for the maximum GmABCC5 gene expression, a potential target stage for phytate reduction. Results of this study provide valuable insights into the structural and functional characteristics of GmABCC5, which may be further utilized for the development of nutritionally enriched low-phytate soybean with improved mineral bioavailability.

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Abbreviations

ATP:

Adenosine triphosphate

ABC:

ATP-binding cassette transporter

ABCC5 :

ABC transporter subfamily C member 5

Gm :

Glycine max

PEPCo:

PEP carboxylase

PDB:

Protein Data Bank

NJ:

Neighbor joining

MW:

Molecular weight

pI:

Isoelectric pH

EC:

Extinction coefficient

Ai:

Aliphatic index

Ii:

Instability index

GRAVY:

Grand average hydropathy

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Acknowledgements

Financial support was provided by the Department of Science and Technology, Government of India, in the form of INSPIRE fellowship (IF120064). Funding by the National Fund for Basic, Strategic and Frontier Application Research in Agriculture (RNAi 20-11), Indian Council of Agricultural Research, is duly acknowledged.

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Authors and Affiliations

  1. Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India

    Vanita Pandey, Veda Krishnan, Nabaneeta Basak, Ashish Marathe, Vinutha Thimmegowda, Anil Dahuja, Monica Jolly & Archana Sachdev

  2. Quality and Basic Sciences, ICAR-Indian Institute of Wheat and Barley Research, Karnal, New Delhi, 132 001, India

    Vanita Pandey

  3. Crop Physiology and Biochemistry, ICAR-National Rice Research Institute, Cuttack, 753006, India

    Nabaneeta Basak

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  1. Vanita Pandey
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Correspondence to Archana Sachdev.

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Pandey, V., Krishnan, V., Basak, N. et al. Molecular modeling and in silico characterization of GmABCC5: a phytate transporter and potential target for low-phytate crops. 3 Biotech 8, 54 (2018). https://doi.org/10.1007/s13205-017-1053-6

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