Biocomputational Characterization and Evolutionary Analysis of Bubaline Dicer1 Enzyme

  • Singh, Jasdeep ;
  • Mukhopadhyay, Chandra Sekhar ;
  • Arora, Jaspreet Singh ;
  • Kaur, Simarjeet
  • Received : 2014.10.01
  • Accepted : 2014.12.19
  • Published : 2015.06.01


Dicer, an ribonuclease type III type endonuclease, is the key enzyme involved in biogenesis of microRNAs (miRNAs) and small interfering RNAs (siRNAs), and thus plays a critical role in RNA interference through post transcriptional regulation of gene expression. This enzyme has not been well studied in the Indian water buffalo, an important species known for disease resistance and high milk production. In this study, the primary coding sequence (5,778 bp) of bubaline dicer (GenBank: AB969677.1) was determined and the bubaline Dicer1 biocomputationally characterized to determine the phylogenetic signature among higher eukaryotes. The evolutionary tree revealed that all the transcript variants of Dicer1 belonging to a specific species were within the same node and the sequences belonging to primates, rodents and lagomorphs, avians and reptiles formed independent clusters. The bubaline dicer1 is closely related to that of cattle and other ruminants and significantly divergent from dicer of lower species such as tapeworm, sea urchin and fruit fly. Evolutionary divergence analysis conducted using MEGA6 software indicated that dicer has undergone purifying selection over the time. Seventeen divergent sequences, representing each of the families/taxa were selected to study the specific regions of positive vis-$\grave{a}$-vis negative selection using different models like single likelihood ancestor counting, fixed effects likelihood, and random effects likelihood of Datamonkey server. Comparative analysis of the domain structure revealed that Dicer1 is conserved across mammalian species while variation both in terms of length of Dicer enzyme and presence or absence of domain is evident in the lower organisms.


Bubaline;Dicer;Phylogeny;Selection Pressure;Ribonuclease III Domain


  1. Gao, Z., M. Wang, D. Blair, Y. Zheng, and Y. Dou. 2014. Phylogenetic analysis of the endoribonuclease dicer family. PLoS ONE 9(4):e95350.
  2. Gasciolli, V., A. C. Mallory, D. P. Bartel, and H. Vaucheret. 2005. Partially redundant functions of Arabidopsis DICER-like enzymes and a role for DCL4 in producing trans-acting siRNAs. Curr. Biol. 15:1494-1500.
  3. Graur, D. 1985. Amino acid composition and the evolutionary rates of protein-coding genes. J. Mol. Evol. 22:53-62.
  4. Heger, A. and C. P. Ponting. 2007. Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes. Genome Res. 17:1837-1849.
  5. Jones, D. T., W. R. Taylor, and J. M. Thornton. 1992. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8:275-282.
  6. Kimura, M. 1983. The neutral theory of molecular evolution. Cambridge University Press, Cambridge, England.
  7. Kolaczkowski, B., D. N. Hupalo, and A. D. Kern. 2011. Recurrent adaptation in RNA interference genes across the Drosophila phylogeny. Mol. Biol. Evol. 28:1033-1042.
  8. Kurihara, Y. and Y. Watanabe. 2004. Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proc. Natl. Acad. Sci. USA. 101:12753-12758.
  9. Le, S. Q. and O. Gascuel. 2008. An improved general amino acid replacement matrix. Mol. Biol. Evol. 25:1307-1320.
  10. Lee, Y. S., K. Nakahara, J. W. Pham, K. Kim, Z. He, E. J. Sontheimer, and R. W. Carthew. 2004. Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell 117:69-81.
  11. Li, W. H. 1997. Molecular Evolution. Sinauer, Sunderland, MA, USA.
  12. Margis, R., A. F. Fusaro, N. A. Smith, S. J. Curtin, J. M. Watson, E. J. Finnegan, and P. M. Waterhouse. 2006. The evolution and diversification of Dicers in plants. FEBS Lett. 580:2442-2450.
  13. Mukherjee, K., H. Campos, and B. Kolaczkowski. 2012. Evolution of animal and plant dicers: Early parallel duplications and recurrent adaptation of antiviral RNA binding in plants. Mol. Biol. Evol. doi:10.1093/molbev/mss263.
  14. Murphy, D., B. Dancis, and J. R. Brown. 2008. The evolution of core proteins involved in microRNA biogenesis. BMC Evol. Biol. 8:92.
  15. Nei, M. 1987. Molecular Evolutionary Genetics. Columbia University Press, New York, NY, USA.
  16. Nei, M. and S. Kumar. 2000. Molecular Evolution and Phylogenetics. Oxford University Press, NY, USA.
  17. Obbard, D. J., F. M. Jiggins, D. L. Halligan, and T. J. Little. 2006. Natural selection drives extremely rapid evolution in antiviral RNAi genes. Curr. Biol. 16:580-585.
  18. Pond, S. L. K., B. Murrell, M. Fourment, S. W. D. Frost, W. Delport, and K. Scheffler. 2011. A random effects branch-site model for detecting episodic diversifying selection. Mol. Biol. Evol. 28:3033-3043.
  19. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
  20. Cerutti, H. and J. A. Casas-Mollano. 2006. On the origin and functions of RNA-mediated silencing: From protists to man. Curr. Genet. 50:81-99.
  21. Stowe, H. M., E. Curry, S. M. Calcatera, R. L. Krisher, M. Paczkowski, and S. L. Pratt. 2012. Cloning and expression of porcine Dicer and the impact of developmental stage and culture conditions on MicroRNA expression in porcine embryos. Gene 501:198-205.
  22. Tamura, K., G. Stecher, D. Peterson, A. Filipski, and S. Kumar. 2013. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol. Biol. Evol. 30:2725-2729.
  23. Tourasse, N. J. and W. H. Li. 2000. Selective constraints, amino acid composition, and the rate of protein evolution. Mol. Biol. Evol. 17:656-664.
  24. Untergrasser, A., I. Cutcutache, T. Koressaar, J. Ye, B. C. Faircloth, M. Remm, and S. G. Rozen. 2012. Primer3 - new capabilities and interfaces. Nucl. Acids Res. 40(15):e115.
  25. Xie, Z., E. Allen, A. Wilken, and J. C. Carrington. 2005. Dicerlike 4 functions in trans-acting small interfering RNA biogenesis and vegetative phase change in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA .102:12984-12989.

Cited by

  1. Characterization of Functional Divergence of Two Cathelicidin Variants in Indian Sheep vol.11, pp.1176-9343, 2015,


Supported by : Science and Engineering Research Board (SERB), Department of Science and Technology (DST)