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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
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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