Development of petri net-based dynamic model for improved production of farnesyl pyrophosphate by integrating mevalonate and methylerythritol phosphate pathways in yeast

Applied Biochemistry and Biotechnology

Volumn 167, Issue 5, 2012, Pages 1172-1182

  Baadhe, Rama Raju ^a   Mekala, Naveen Kumar ^a   Palagiri, Satwik Reddy ^b   Parcha, Sreenivasa Rao ^a  

^a NATIONAL INSTITUTE OF TECHNOLOGY   (India)

^b Arkabio Research Technologies   (India)

Author keywords

Amorpha diene; Artemisinin; Farnesyl pyrophosphate; Hybrid functional Petri net with extensions; Methylerythritol phosphate pathway; Mevalonate Pathway

Indexed keywords

AMORPHA DIENE; ARTEMISININ; FARNESYL PYROPHOSPHATES; HYBRID FUNCTIONAL PETRI NET WITH EXTENSIONS; METHYLERYTHRITOL PHOSPHATE PATHWAYS; MEVALONATE PATHWAY;

COMPUTER SIMULATION; GENES; OLEFINS; PETRI NETS;

YEAST;

AMORPHADIENE; ARTEMISININ; ARTEMISININ DERIVATIVE; CYTOCHROME P450; FARNESYL DIPHOSPHATE; METHYLERYTHRITOL PHOSPHATE; MEVALONIC ACID; PHOSPHATE; SESQUITERPENE; STEROL; TRITERPENE; UNCLASSIFIED DRUG;

BACTERIUM; BIOSYNTHESIS; CHEMICAL MODEL; CONFERENCE PAPER; CYTOSOL; ENZYME DEGRADATION; ENZYME LOCALIZATION; ENZYME MECHANISM; ENZYME SYNTHESIS; HUMAN; HYBRID FUNCTIONAL PETRI NET WITH EXTENSION; ISOMER; PLASTID; SIGNAL TRANSDUCTION; SIMULATION; STOICHIOMETRY; VALIDATION PROCESS; YEAST;

ERYTHRITOL; MEVALONIC ACID; MODELS, BIOLOGICAL; POLYISOPRENYL PHOSPHATES; SESQUITERPENES; SUGAR PHOSPHATES; YEASTS;

AMORPHA; BACTERIA (MICROORGANISMS); EMBRYOPHYTA; MINK ENTERITIS VIRUS;

EID: 84866376251     PISSN: 02732289     EISSN: 15590291     Source Type: Journal    
DOI: 10.1007/s12010-012-9583-1     Document Type: Conference Paper

References (24)

1. Dubey, V. S., Bhalla, R., & Luthra, R. (2003). Journal of Biosciences, 28, 637-646.
2. Michelle, C. Y., Chang, J., & Keasling, D. (2006). Nature Chemical Biology, 2, 674-681.
3. Kitano, H. (2002). Science, 295, 1662-1664.
4. Sweetlove, L. J., Last, R. L., & Fernie, A. R. (2003). Plant Physiology, 132, 420-425.
5. Sweetlove, L. J., & Fernie, A. R. (2005). New Phytologist, 168, 9-24.
6. Hawari, A. H., & Mohamed-Hussein, Z. A. (2010). BMC Bioinformatics, 11, 83.
7. Teaching Metabolic Control Analysis and Kinetic Modeling 1999. Available from: www.gepasi.org/TeachingMCA.pdf. Accessed February 14, 2011.
8. Koch, I., Heiner, M. (2008) Petri nets, 1st edition: Analysis of Biological Networks (Junker, B, H., Schreiber, F) Wiley, Hoboken, NJ, USA.
9. Gilbert, D., FuB, H., Gu, X., Orton, R., & Robinson, S. (2006). Briefings in Bioinformatics, 7(4), 339-353.
10. Goryanin, I., Hodgman, T. C., & Selkov, E. (1999). Bioinformatics, 15(9), 749-758.
11. Rohdich, F., Hecht, S., Gartner, K., & Adam, P. (2002). Proceedings of the National Academy of Science of the U.S.A, 99(3), 1158-1163.
12. Voynova, N. E., Rios, S. E., & Miziorko, H. M. (2004). Journal of Bacteriology, 186(1), 61-67.
13. Schulte, A. E., Heijden, V. D. R., & Verpoorte, R. (1999). Phytochemistry, 52(6), 975-983.
14. Petri, C. A. (1962). Technical Report RADC-TR-65-377, 2. New York, US: Griffiss Air Force Base.
15. Hiroshi, M., Yukiko, T., Hitoshi, A., & Satoru, M. (2003). In Silico Biology, 3, 389-404.
16. Ina, K., Bjorn, H. J., & Monika, H. (2005). Bioinformatics, 21, 1219-1226.
17. Kanehisa, M., Araki, M., Goto, S., Hattori, M., & Yamanishi, Y. (2008). Nucleic Acids Research, 36, D480-D484.
18. Kanehisa, M., & Goto, S. (2000). Nucleic Acids Research, 28(1), 27-30.
19. Kanehisa, M., Goto, S., Hattori, M., Aoki-Kinoshita, K. F., & Hirakawa, M. (2006). Nucleic Acids Research, 34, D354-D357.
20. Chang, A., Scheer, M., Grote, A., & Schomburg, D. (2009). Nucleic Acids Research, 37, D588-D592.
21. Caspi, R., Foerster, H., Fulcher, C. A., Kaipa, P., Krummenacker, M., & Tissier, C. (2008). Nucleic Acids Research, 36, D623-D631.
22. Nagasaki, M. (2004), PhD Thesis, University of Tokyo, Japan.
23. Miyano, S. 2004.25th International Conference on Application and Theory of Petri nets Bologna, Italy. Available from: http://genome.ib.sci.yamaguchi-u. ac.jp/gon/presentation/ICATPN2004.pdf. Accessed February16, 2011.
24. Newman, J. D., & Chappel, J. (1999). Critical Reviews in Biochemistry and Molecular Biology, 34, 95-106.