Phylogenetic Analysis of Neutral Ceramidase
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10.5120/18923-0271 |
Nirmal Rajah.r and Rufus Auxillia. Article: Phylogenetic Analysis of Neutral Ceramidase. International Journal of Computer Applications 108(7):18-23, December 2014. Full text available. BibTeX
@article{key:article,
author = {Nirmal Rajah.r and Rufus Auxillia},
title = {Article: Phylogenetic Analysis of Neutral Ceramidase},
journal = {International Journal of Computer Applications},
year = {2014},
volume = {108},
number = {7},
pages = {18-23},
month = {December},
note = {Full text available}
}
Abstract
Neutral ceramidase (NCDase) plays an important role in cell regulation, and has been observed in most of the organism across different groups. In this study the molecular evolution of NCDase in different organisms was studied. The phylogenetic tree relationships among the organisms were explored by comparing the sequences of their NCDase. Mulitle sequence alignment of NCDase protein sequence of different source organisms revealed sequence level homology and highly conserved regions level. A conserved hexapeptide sequence GDVSPN within a large conserved domain was observed frequently in the sequences studies, further study of the sequences indicated the presence of Ser/Thr rich mucin like domains in the sequences of vertebrate NCDase enzymes, but was totally absent in invertebrates and bacteria, confirming the specific domain was acquired separately in mammals during the course of evolution. Comparisons of similarity values and inspection of phylogenetic tree was used to better trace the evolutionary history of Neutral ceramidase and resolve relationships between the organisms.
References
- Edgar, Robert C. "MUSCLE: multiple sequence alignment with high accuracy and high throughput. " Nucleic acids research 32. 5 (2004): 1792-1797. ?
- Felsenstein J. Confidence limits on phylogenies: An approach using the bootstrap. Evolution (1985) 39:783-791.
- Galadari, S. , Wu, B. X. , Mao, C. , Roddy, P. , El Bawab, S. , & Hannun, Y. X. (2006). Identification of a novel amidase motif in neutral ceramidase. Biochem. J, 393, 687-695. ?. ?
- Houben, E. , Holleran, W. M. , Yaginuma, T. , Mao, C. , Obeid, L. M. , Rogiers, V. , & Uchida, Y. (2006). Differentiation-associated expression of ceramidase isoforms in cultured keratinocytes and epidermis. Journal of lipid research, 47(5), 1063-1070. ? (2006): 1063-1070. ?
- Ito, Makoto, (2002) Molecular evolution of Neutral Ceramidase : From Bacteria to Mammals In Ceramide Signaling (41-45) Landes Bioscience, Texas, U. S. A
- Maher, D. M. , Gupta, B. K. , Nagata, S. , Jaggi, M. , & Chauhan, S. C. (2011). Mucin 13: structure, function, and potential roles in cancer pathogenesis. Molecular Cancer Research, 9(5), 531-537. ?
- Nakagawa, T. , Tani, M. , Sueyoshi, N. , & Ito, M. (2011). The Mucin Box and Signal/Anchor Sequence of Rat Neutral Ceramidase Recruit Bacterial Sphingomyelinase to the Plasma Membrane. Bioscience, biotechnology, and biochemistry, 75(5), 987-990.
- Penn, O. , Privman, E. , Ashkenazy, H. , Landan, G. , Graur, D. , & Pupko, T. (2010). GUIDANCE: a web server for assessing alignment confidence scores. Nucleic acids research, 38(suppl 2), W23-W28. ?
- Saitou N. and Nei M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution (1987) 4:406-425.
- Shayman, James A. "Sphingolipids. " Kidney international 58. 1 (2000): 11-26.
- Sneath P. H. A. and Sokal R. R. (1973). Numerical Taxonomy. Freeman, San Francisco.
- Steentoft, C. , Vakhrushev, S. Y. , Joshi, H. J. , Kong, Y. , Vester?Christensen, M. B. , Schjoldager, K. T. B. , . . . & Clausen, H. (2013). Precision mapping of the human O?GalNAc glycoproteome through SimpleCell technology. The EMBO journal, 32(10), 1478-1488. ?. ?
- Swofford, D. L. , Olsen, G. J. , Waddell, P. J. , & Hillis, D. M. (1996). {Phylogenetic inference}. ?
- Tamura K. , Stecher G. , Peterson D. , Filipski A. , and Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6. 0. Molecular Biology and Evolution (2013)30: 2725-2729.
- Tani, M. , Okino, N. , Mitsutake, S. , Tanigawa, T. , Izu, H. , & Ito, M. (2000). Purification and Characterization of a Neutral Ceramidase from Mouse Liver a single protein catalyzes the reversible reaction in which ceramide is both hydrolyzed and synthesized. journal of biological chemistry, 275(5), 3462-3468
- Tani, Motohiro, Hiroshi Iida, and Makoto Ito. "O-glycosylation of mucin-like domain retains the neutral ceramidase on the plasma membranes as a type II integral membrane protein. " Journal of Biological Chemistry 278. 12 (2003): 10523-10530.
- Zuckerkandl E. and Pauling L. Evolutionary divergence and convergence in proteins. Edited in Evolving Genes and Proteins by V. Bryson and H. J. Vogel, (1965):97-166. Academic Press, New York.