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Pak. J. Bot., 47(3): 1075-1086, 2015. |
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Updated: 23-06-15 | ||||
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IN SILICO ANALYSIS, MAPPING OF REGULATORY ELEMENTS AND CORRESPONDING PROTEIN-DNA INTERACTION IN atpβ GENE PROMOTER FROM DIFFERENT TOMATO VARIETIES
MAHAM HASSAN1, ZABTA KHAN SHINWARI2 AND TARIQ MAHMOOD1*
Abstract: Chloroplast atpB gene encodes the β-subunit of ATP synthase having a function in the synthesis of ATP. ATP synthase is usually present in the mitochondrial and chloroplast membranes as well as in prokaryotes with a highly conserved structure. With the aim to study the functional diversity, atpB gene promoter from Solanum lycopersicum varieties (VCT-1, 127, PETO-86, LBR-16, Continental, LBR-06, CLN-2498D, CLN-2777, LBR-09) was amplified, sequenced and analyzed. BLAST tool analyzed the sequences. Cis acting elements were predicted using Consite tool in the promoter region as these elements have importance in gene regulation and maps of the cis-acting elements were constructed with the help of DOG software for each variety. It was seen from the constructed maps that the distribution pattern of trans-acting elements was quite diverse in the atpB promoter of studied tomato varieties. Various trans-acting elements (HMG-IY, HFH-2, TBP, c-Fos and SOX17) were docked with respective DNA sequence using HADDOCK online software. Main focus was on the analysis of DNA-protein interactions and for this purpose; hydrogen bonds formed with either phosphate backbone or base of DNA were checked. Particularly interactions between amino acid and base pairing were checked. It was revealed that Arginine and Lysine had a greater probability to interact with Thymine and Adenine as compared to other bases and all bonds formed were feasible as their distances were less than 3.5 Ao. During the analysis of interactions, it was also found that Lysine, Arginine, Asparagine and Serine are well capable to bind with Thymine while Glycine and Lysine have made bonds mostly with Adenine.
Key word: Tomato, atpB promoter, Transcriptional factors, DNA-protein interactions.
1Department of Plant Sciences, Quaid-i-Azam University, Islamabad-45320, Pakistan 2Department of Biotechnology, Quaid-i-Azam University, Islamabad-45320, Pakistan *Corresponding author: tmahmood@qau.edu.pk; tmahmood.qau@gmail.com |
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