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Pak. J. Bot., 47(6): 2321-2327, 2015.

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IN SILICO ANALYSIS, MAPPING OF REGULATORY ELEMENTS AND CORRESPONDING DNA-PROTEIN INTERACTION IN POLYPHENOL OXIDASE GENE PROMOTER FROM DIFFERENT RICE VARIETIES

TARIQ MAHMOOD¹*, MUJEEB UR REHMAN¹, EJAZ AZIZ¹, IFTIKHAR ALI¹ AND ZABTA KHAN SHINWARI²

¹Department of Plant Sciences, Quaid-i-Azam University, Islamabad-45320, Pakistan

²Department of Biotechnology, Quaid-i-Azam University, Islamabad-45320, Pakistan

^*Corresponding author e-mail: tmahmood.qau@gmail.com; tmahmood@qau.edu.pk

Abstract: Polyphenol oxidase (PPO) is an important enzyme that has positive impact regarding plant resistance against different biotic and abiotic stresses. In the present study PPO promoter from six different rice varieties was amplified and then analyzed for cis- and trans-acting elements. The study revealed a total of 79 different cis-acting regulatory elements including 11 elements restricted to only one or other variety. Among six varieties Pakhal-Basmati had highest number (5) of these elements, whereas C-622 and Rachna-Basmati have no such sequences. Rachna-Basmati, IR-36-Basmati and Kashmir-Basmati had 1, 2 and 3 unique elements, respectively. Different elementsrelated to pathogen, salt and water stresses were found, which may be helpful in controlling PPO activity according to changing environment. Moreover, HADDOCK was used to understand molecular mechanism of PPO regulation and it was found that DNA-protein interactions are stabilized by many potential hydrogen bonds. Adenine and arginine were the most reactive residues in DNA and proteins respectively.Structural comparison of different protein-DNA complexes show that even a highly conserved transcriptional factor can adopt different conformations when they contact a different DNA binding sequence, however their stable interactions depend on the number of hydrogen bonds formed and distance.

Key words: Polyphenol oxidase, Promoter, DNA-protein interaction, Regulatory elements.