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Role of Proteus mirabilis in Caffeine Degradation–A Preliminary Bioinformatics Study

Author Affiliations

  • 1 School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, INDIA

Res. J. Recent Sci., Volume 2, Issue (ISC-2012), Pages 33-40, February,2 (2013)

Abstract

An attempt to find the role of Proteus mirabilis in caffeine degradation using bioinformatics tools has been made here. Soils from coffee industries were taken and the bacterium was isolated and found to degrade caffeine. Identification of the bacterium through Sangers dideoxy sequencing of 16S rDNA was done and its genome taken from online database was used for homology modeling of the enzyme to identify regions of similarity and enzyme structure prediction. Also attempts to secondary structure prediction and protein threading has been done to study the enzyme and compare the enzymes of Proteus mirabilis with that of other reported caffeine degrading organisms.

References

  1. Hiroshi A. and Alan C., Caffeine: a well known but little mentioned compound in plant science, Trends Plant Sci., 6 (9), 407- 413 (2001)
  2. Hiroshi A., Hiroshi S., and Alan C., Caffeine and related purine alkaloids: Biosynthesis, catabolism, function and genetic engineering, Phytochemistry, 69, 841-856 (2008)
  3. Sarath B.V.R., Patra S., Thankur M.S., Karanth N.G. and Varadaraj M.C., Degradation of caffeine by Pseudomonas alcaligenes CFR 1708, Enzyme Microb Tech, 37, 617-624 (2005)
  4. Gokulakrishnan S., Chandraraj K. and Gummadi S.N., Microbial and enzymatic methods for the removal of caffeine, Enzyme Microb Tech, 37, 225-232 (2005)
  5. Siddharth S., Renuka J.E., Abhiroop A., Rounaq N.S., Vrinda G., Bishwambhar M. and Suneetha V., A Preliminary Study and First Report on Caffeine Degrading Bacteria Isolated from the Soils of Chittoor and Vellore, Int Res J Pharm, 3(3), 305-309 (2012)
  6. Walter P., Mario R.M., Roberto G.B. and Ricardo B., Solid-State Fermentation: an Alternative to Improve the Nutritive Value of Coffee Pulp, Appl Environ Microb, 49, 388-393 (1985)
  7. Swati Sucharita Dash and Sathyanarayana N. Gummadi. Enhanced biodegradation of caffeine by Pseudomonas sp. using response surface methodology, Biochem Eng J, 36, 288-293 (2007)
  8. Hakil M., Denis S., Viniegra-Gonzalez and Augur C., Degradation and product analysis of caffeine and related dimethylxanthines by filamentous fungi, Enzyme Microb Techn, 22, 355-359 (1998)
  9. Abebe B., Kassahun T., Mesfin R. and Araya A., Measurement of caffeine in coffee beans with UV/vis spectrometer, Food Chemistry, 108, 310-315 (2008)
  10. Stoica Costin, Sorescu Ionut, ABIS online - Bacterial identification software, http:// www.tgw1916.net/bacteria _logare.html (2007-2012)
  11. Yu C.L., Kale Y., Gopishetty S., Louie T.N. and Subramanian M., A Novel Caffeine Dehydrogenase in Pseudomonas sp. Strain CBB1 Oxidizes Caffeine to Trimethyluric Acid, J. Bacteriol, 190, 772–776 (2008)
  12. Sussman J.L., Lin. D., Jiang. J., Manning. N.O., Prilusky. J., Ritter O. and Abola. E.E., Protein Data Bank (PDB): Database of Three-Dimensional Structural Information of Biological Macromolecules Acta Cryst, 54, 1078-1084 (1998)
  13. Rodriguez. R., Chinea. G., Lopez. N., Pons. T. and Vriend. G., Homology modeling, model and software evaluation: three related resources, Oxford Univ Press, 14, 523-528 (1998)
  14. Dale. J.W. and Smith. J.T., The Purification and Properties of the p-Lactamase Specified by the Resistance Factor R- 1818 in Escherichia coli and Proteus mirabilis, Biochem. J, 123, 493-500 (1971)
  15. Julie D. Thompson., Toby J. Gibson., Frdric Plewniak., Franois Jeanmougin., Desmond G. Higgins., The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by qualityanalysis tools Nucleic Acids Res, 25, 4876–4882 (1997)
  16. Fischer D. and Eisenberg D., Protein fold recognition using sequence-derived predictions, Protein Sci, 5, 947-955 (1996)
  17. Narayanan E., Ben W., Marc A., Madhusudhan M.S., David E., Shen M., Pieper U., Andrej S., Comparative Protein Structure Modeling UNIT 5.6: Using Modeller, Current Protocols in Bioinformatics 5.6.1-5.6.30 (2006)
  18. Vriend G., WHAT IF: a molecular modeling and drug design program, J Mol Graphics, 8, 52-6, 29 (1990)
  19. James U. Bowie., Roland L., David E., A Method to Identify Protein Sequences that Fold into a Known Three Dimensional Structure Science, 253, 164-170 (1991)
  20. Hooft. R.W.W., Sander. C., Scharf. M., Vriend. G., The PDBFINDER database: a summary of PDB, DSSP and HSSP information with added value, Oxford Univ Press ,12, 525-529 (1996)
  21. Jones D.T., Protein secondary structure prediction based on position-specific scoring matrices, J. Mol Biol., 292, 195-202 (1999)
  22. Simossis. V.A. and Heringa. J., PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information, Nucleic Acids Res, W289–W294 (2005)
  23. Eisenberg D., Weiss R.M. and Terwilliger. T.C., The hydrophobic moment detects periodicity in protein hydrophobicity, J PNAS, 81, 140-144 (1984)