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OJBTM

Online Journal of Bioinformatics ©

Volume 17(3):180-191, 2016.

In silico chromosomal mapping and functional annotation of TaPHT1;1 a high-affinity

phosphate transporter gene in wheat (Triticum aestivum L.).

 

Anuj Kumar1*, Madhu Rathore2*, KP Singh3, Pankaj Kr Tyagi4, Naveen Sharma5

 

1* Advanced Centre for Computational & Applied Biotechnology, Uttarakhand Council for Biotechnology (UCB), Dehradun 2* Microbial Research Laboratory, Department of Biotechnology, MLS University Udaipur Rajasthan 3Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana, 4Department of Biotechnology, MIET, Meerut, UP, 5Department of Health Research, Second Floor, IRCS Building, New Delhi 1* and 2* shows equal first authorship & Corresponding authors

   

ABSTRACT

 

Kumar A, Rathore M, Singh KP, Tyagi PK, Sharma N., In silico chromosomal mapping and functional annotation of TaPHT1;1 a high-affinity phosphate transporter gene in wheat (Triticum aestivum L.), Onl J Bioinform., 17(3):180-191, 2016. Phosphorus deficiency is a major limiting factor for crop yield worldwide. Phosphorus (P) is also an important limiting macro-inorganic nutrient for wheat and P use efficiency (PUE).  PHT1’1 has high affinity for inorganic P (Pi) from low- and high-Pi environments but structural and functional aspects remain unresolved. Present research describes the location of PHT1;1 on wheat 4AL, 4BL, and 4DL chromosomes and model a 3D structure of TaPHT1;1 by homology modeling refined by Ramachandran plot simulations. The results of BLASTN showed 99% sequence similarity with IWGSC_chr4AL_V2_ab_k71 contig of chromosome 4AL, 96% with IWGSC_chr4BL_ab_k71 contig  of chromosome 4BL and 97% with IWGSC_chr4DL_V3_k71 contig of chromosome 4DL in wheat genome. Predicted gene structure of TaPHT1;1 on 4AL consisted of two exons, 4BL three and 4DL one exon. Secondary structure of TaPHT1;1 had 37.77% α helices, 22.73% extended strand, 8.56% β turns and 31.02% random coils with MW 41287.98 g/mol. PSI-BLAST revealed f 37.76% similarity with chain A crystal structure of eukaryotic phosphate transporter PDB ID: 4J05. The TaPHT1;1 model was submitted to PMDB with ID:PM0080724. Structure based functional annotation of TaPHT1;1 molecular modeling to predict regulatory networks for PHT1;1 in Arabidopsis genome was placed for annotation on  chromosomal map. We find that TaPHT1;1 orthologs are similar to AtDREB1A.

 

Key Words: In Silico, chromosome TaPHT1;1 , affinity, phosphate transporter,  gene, wheat.

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