Functional prediction of F3’5’H in color alteration in cotton: an in-silico comparative analysis between cotton and viola

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Research Paper 01/09/2018
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Functional prediction of F3’5’H in color alteration in cotton: an in-silico comparative analysis between cotton and viola

Ammara Ahad, Sana Tahir, Muhammad Azam Ali, Adnan Iqbal, Mukhtar Ahmed, Sidra Akhtar, Rabia Nawaz, Abdul Qayyum Rao, Ahmad Ali Shahid, Zia Ur Rahman, Tayyab Husnain
Int. J. Biosci.13( 3), 185-197, September 2018.
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Abstract

Anthocyanins are water-soluble pigments giving the purple, red and blue colors to various flowers and fruits. Anthocyanins are widespread amongst seed plants playing physiological roles such as to attract pollinators, seed dispersers and against UV–B protection. A key enzyme of this flavonoid pathway, Flavonoid 3’, 5’ hydoxylase,F3’5’H is involved in delphinidin production. Molecular level modifications in pigmentation pattern of cotton fiber, is an attractive and innovative area of research. In present study, comparison of F3’5’H in Gossypium hirsutum (Cotton) and Viola × wittrockiana, sequence alignment for homology, protein modeling along their structural validation and molecular docking analysis were computed. Docking studies were carried out using Autodock Vina and the ligands used were Naringenin and Quercetin. Analysis of results showed the best binding energy values of Viola F3’5’H i-e -8.9 & -9.9 with both ligands respectively. Based on these bioinformatics outcomes it was hypothesized that no matter the presence of this gene naturally in cotton, an over expression of Viola F3’5’H had a potency to alter pigmentation pattern in cotton fibers. This predictive screening method may prove to be significant for productive experimental studies and considered as a bypass for commercial scale research in terms of time and cost.

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Ahad A, Ahmad A, Ud Din S, Rao AQ, Shahid AA, Husnain T. 2015 In silico study for diversing the molecular pathway of pigment formation: an alternative to manual coloring in cotton fibers. Frontiers in plant science 6.

Ahmad A, Javed MR, Rao AQ, Khan MA, Ahad, A, Ud Din S, Shahid AA, Husnain T. 2015 In-Silico Determination of Insecticidal Potential of Vip3Aa-Cry1Ac Fusion Protein Against Lepidopteran Targets Using Molecular Docking. Frontiers in plant science 6.

Aleykutty N. 2012. Docking studies on identified constituents of Helicteres isora as antidiabetic agents. International Journal of Computer Applications 45.

Ali MA, Rehman I, Iqbal A, Din S, Rao AQ, Latif A, Samiullah TR, Azam S, Husnain T. 2014. Nanotechnology, a new frontier in Agriculture. Adv. life science 1, 129-138.

Boss PK, Davies C, Robinson SP. 1996 Analysis of the expression of anthocyanin pathway genes in developing Vitis vinifera L. cv Shiraz grape berries and the implications for pathway regulation. Plant physiology 111, 1059-1066.

Fan X, Fan B, Wang Y, Yang W. 2016. Anthocyanin accumulation enhanced in Lc-transgenic cotton under light and increased resistance to bollworm. Plant biotechnology reports 10, 1-11.

Feng H, Tian X, Liu Y, Li Y, Zhang X, Jones BJ, Sun Y, Sun J. 2013. Analysis of flavonoids and the flavonoid structural genes in brown fiber of upland cotton. PloS one 8, e58820.

Gupta CL, Akhtar S, Bajpaib P, Kandpal K, Desai G, Tiwari AK. 2013. Computational modeling and validation studies of 3-D structure of neuraminidase protein of H1N1 influenza A virus and subsequent in silico elucidation of piceid analogues as its potent inhibitors. EXCLI journal 12, 215.

Holton TA. 2000. Transgenic plants exhibiting altered flower color and methods for producing same. Google Patents.

Katsumoto Y, Fukuchi-Mizutani M, Fukui Y, Brugliera F, Holton TA, Karan M, Nakamura N, Yonekura-Sakakibara K, Togami J, Pigeaire A. 2007. Engineering of the rose flavonoid biosynthetic pathway successfully generated blue-hued flowers accumulating delphinidin. Plant and Cell Physiology 48, 1589-1600.

Liu Q, Singh S, Chapman K, Green A. 2009. Bridging traditional and molecular genetics in modifying cottonseed oil. In: Genetics and Genomics of Cotton, p 353-382. Springer.

Noda N, Aida R, Kishimoto S, Ishiguro K, Fukuchi-Mizutani M, Tanaka Y, Ohmiya A. (2013) Genetic engineering of novel bluer-colored chrysanthemums produced by accumulation of delphinidin-based anthocyanins. Plant and Cell Physiology 54, 1684-1695.

Petrussa E, Braidot E, Zancani M, Peresson, C, Bertolini A, Patui S, Vianello A. 2013. Plant flavonoids—biosynthesis, transport and involvement in stress responses. International journal of molecular sciences 14, 14950-14973.

Rauf MA, Zubair S, Azhar A. 2015. Ligand docking and binding site analysis with pymol and autodock/vina. International Journal of Basic and Applied Sciences 4, 168.

Seeliger D, de Groot BL. 2010. Ligand docking and binding site analysis with PyMOL and Autodock/Vina. Journal of computer-aided molecular design 24, 417-422.

Sharma M, Chai C, Morohashi K, Grotewold E, Snook ME, Chopra S. 2012. Expression of flavonoid 3’-hydroxylase is controlled by P1, the regulator of 3-deoxyflavonoid biosynthesis in maize. BMC plant biology 12, 196.

Shen P, Zhang H, Su Z, Wang S, Xu H. 2015. In Silico Analysis of Tumor Necrosis Factor α-Induced Protein 8-Like-1 (TIPE1) Protein. PloS one 10, e0134114.

Tanaka Y, Brugliera F. 2008. Flower colour. Flowering and its manipulation (Ainsworth C, ed.). Annual Plant Reviews 20, 201-239.

Wang H, Wang W, Li H, Zhang P, Zhan J, Huang W. 2011. Expression and tissue and subcellular localization of anthocyanidin synthase (ANS) in grapevine. Protoplasma 248, 267-279.

Wiederstein M, Sippl MJ. 2007. ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic acids research 35, W407-W410.

Yadav BS, Tripathi V, Kumar A, Khan MF. Barate A, Kumar A, Sharma B. 2012 Molecular modeling and docking characterization of Dectin-1 (PAMP) receptor of Bubalus bubalis. Experimental and molecular pathology 92, 7-12.

Zhang Y, Butelli E, Martin C. 2014. Engineering anthocyanin biosynthesis in plants. Current opinion in plant biology 19, 81-90.