Structure Based Computational Analysis and Molecular Phylogeny of C- Phycocyanin Gene from the Selected Cyanobacteria

Authors: N. Reehana, A. Parveez Ahamed, D. Mubarak Ali, A. Suresh, R. Arvind Kumar, N. Thajuddin

Abstract:

Cyanobacteria play a vital role in the production of phycobiliproteins that includes phycocyanin and phycoerythrin pigments. Phycocyanin and related phycobiliproteins have wide variety of application that is used in the food, biotechnology and cosmetic industry because of their color, fluorescent and antioxidant properties. The present study is focused to understand the pigment at molecular level in the Cyanobacteria Oscillatoria terebriformis NTRI05 and Oscillatoria foreaui NTRI06. After extraction of genomic DNA, the amplification of C-Phycocyanin gene was done with the suitable primer PCβF and PCαR and the sequencing was performed. Structural and Phylogenetic analysis was attained using the sequence to develop a molecular model.

Keywords: Cyanobacteria, C-Phycocyanin gene, Phylogenetic analysis, Structural analysis.

Digital Object Identifier (DOI): doi.org/10.5281/zenodo.1088072

References:

[1] N.T. Eriksen, “Production of phycocyanin – a pigment with applications in biology biotechnology foods and medicine,” Applied Microbiology and Biotechnology, 2008, Vol. 80, pp. 1-14.
[2] W. Mount David, “Bioinformatics: Sequence and Genome Analysis,” Spring Harbor Press, 2002, ISBN 0-87969-608-7.
[3] N. Thajuddin, and G. Subramanian, “Cyanobacterial Biodiversity and potential application in Biotechnology,” Current Science., 2005, Vol. 89(1), pp. 47-57.
[4] N. Thajuddin, A. Sandra, Nierzwicki-Bauer, and G. Subramanian, “Cyanobacterial biodiversity and recent trends in their taxonomy,” BDU J. Sci. & Tech., 2007, Vol. 1, pp. 1-14. (in Tamil), 15-28 (in English).
[5] N. Thajuddin, G. Muralitharan, G. Sundaramoorthy, R. Ramamoorthy, S. Ramachandran, M. A. Akbarsha and M. Gunasekaran, “Morphological and genetic diversity of symbiotic Cyanobacteria from cycads,” J. Basic Microbiol., 2010, Vol. 50, pp. 254-265.
[6] N. Thajuddin, and G. Muralitharan, “Applications of PCR based fingerprinting in the phylogeny of marine Cyanobacteria,” Indian Hydrobiol., 2008, Vol. 11(1), pp. 25-41.
[7] G. Muralitharan, and N. Thajuddin, “Evidence on the presence of tRNAfmet group I introns in the marine cyanobacterium Synechococcus elongatus,” Journal of Microbiology and Biotechnology., 2008, Vol.18 (1), pp. 23-27.
[8] G. Muralitharan and N. Thajuddin, “M13 based genotyping of marine cyanobacterial strains from the Indian Subcontinent and maintained in the NFMC germplasm collection,” Journal of Applied Phycology., 2010, Vol.22, pp. 709-716.
[9] G. Muralitharan, and N. Thajuddin, “Rapid differentiation of phenotypically and genotypically similar Synechococcus elongatus strains by PCR fingerprinting,” Biologia, 2011, Vol. 66/2, pp. 238-243.
[10] D. Pandiaraj, D. Mubarak ali. R. Praveenkumar, S. Ravikumar and N. Thajuddin, “Molecular characterization and phylogeny of marine Cyanobacteria from Palk Bay Region of Tamil Nadu, India,” Ecologia, 2012, Vol.2, pp. 23-30.
[11] D. Mubarak ali, J. Arunkumar, K. R. Suriya, K. A. Sheik syed ishack and N. Thajuddin, “Molecular modeling and Phylogenetic analysis of cphycocyanin gene sequence from marine cyanobacterium Phormidium tenue NTDM05,” Seaweed Res. Utiln., 2012, Vol. 34(1&2) pp.35-44.
[12] N. Kumari, A. K. Srivastava, P. Bhargava, and L. Rai, “Molecular approaches towards assessment of cyanobacterial biodiversity,” African Journal of Biotechnology., 2009, Vol. 8(18), pp. 4284-4298.
[13] J.C. Kendrew, R.E. Dickerson, B.E. Strandberg, R.G. Hart, and D.R. Davies, “Structure of Myoglobin,” Nature, 1960, Vol. 185, pp.422-427.
[14] M.J. Foster, “Molecular Modelling on Structural Biology,” Micron, 2002, Vol. 33, pp.365 -384.
[15] J.A. Smoker, and S.R. Barnum, “Rapid small-scale DNA isolation from filamentous cyanobacteria,” FEMS Microbiology Letters., 1988, Vol. 56(1), pp.119 – 122.
[16] B.A. Neilan, “The Molecular Evolution and DNA Profiling of Toxic Cyanobacteria,” Curr. Issues Mol. Biol., 2002, Vol. 4, pp.1-11.
[17] J. Garnier, J. F. Gibrat, and B. Robson, “GOR Secondary structure prediction method version IV,” 1996, Vol. 266, pp. 540-553.
[18] T. V. Desikachary, “Cyanophyta Indian Council of Agricultural Research New Delhi, India,” 1959.
[19] N. Saitou, and M. Nei, “The Neighbor-joining method: A new method for reconstructing phylogenetic trees,” Molecular Biology and Evolution, 1987, Vol.4, pp. 406-425.
[20] K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei, and S. Kumar, “MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods,” Molecular Biology and Evolution., 2011, Vol. 28(10), pp.2731-2739.
[21] K. Guruprasad, B.V. Reddy, M.W. Pandit, “Correlation Between Stability of a Protein and its Dipeptide Composition: A Novel Approach For Predicting In Vivo Stability of a Protein From Its Primary Sequence,” Protein Eng., 1990, Vol. 4(2), pp.155-61.