Bacterial Cells as Model Factories

DOI: 10.4236/ajor.2013.31A007   PDF   HTML   XML   4,188 Downloads   6,817 Views   Citations


Bacteria, like industrial engineers, must manage processes that convert low value inputs into high value outputs. Bacteria are not intelligent, so they utilize self-organizing production systems to accelerate life-sustaining chemical processes. Here I explore two questions. First, can businesses apply the principles of self-organization? Second, can operations researchers contribute to our understanding of biological systems? I explain biochemical concepts in plain terms, illustrated with a few informative laboratory evolution experiments, and describe the organizing principles that underlie complex biological systems. I describe the new disciplines of synthetic biology and metabolic engineering, which offer opportunities for interdisciplinary collaboration between life scientists and operations researchers.

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I. Matsumura, "Bacterial Cells as Model Factories," American Journal of Operations Research, Vol. 3 No. 1A, 2013, pp. 81-86. doi: 10.4236/ajor.2013.31A007.

Conflicts of Interest

The authors declare no conflicts of interest.


[1] R. Wolfenden, “Benchmark Reaction Rates, the Stability of Biological Molecules in Water, and the Evolution of Catalytic Power in Enzymes,” Annual Review of Biochemistry, Vol. 80, No. 1, 2011, pp. 645-667. doi:10.1146/annurev-biochem-060409-093051
[2] A. E. Gray and J. Leonard, “Process Fundamentals,” Harvard Business School, Boston 2007.
[3] J. L. Goldstein and M. S. Brown, “Regulation of the Mevalonate Pathway,” Nature, Vol. 343, No. 6257, 1990, pp. 425-430. doi:10.1038/343425a0
[4] A. Koestler, “The Ghost in the Machine,” Arkana Penguin, Canada, 1989.
[5] R. C. Cadwell and G. F. Joyce, “Randomization of Genes by PCR Mutagenesis,” PCR Methods and Applications, Vol. 2, No. 1, 1992, pp. 28-33. doi:10.1101/gr.2.1.28
[6] W. P. Stemmer, “Rapid Evolution of a Protein in Vitro by DNA Shuffling,” Nature, Vol. 370, No. 6488, 1994, pp. 389-391. doi:10.1038/370389a0
[7] J. C. Moore and F. H. Arnold, “Directed Evolution of a Para-Nitrobenzyl Esterase for Aqueous-Organic Solvents,” Nature Biotechnology, Vol. 14, No. 4, 1996, pp. 458-467. doi:10.1038/nbt0496-458
[8] W. Paley and J. Paxton, “Natural Theology: or, Evidences of the Existence and Attributes of the Deity, Collected from the Appearances of Nature,” Gould and Lincoln, Lincoln, 1802.
[9] C. Darwin, “On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life,” John Murray, London, 1859.
[10] P. Vopalensky and Z. Kozmik, “Eye Evolution: Common Use and Independent Recruitment of Genetic Components,” Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 364, No. 1531, 2009, pp. 2819-2832. doi:10.1098/rstb.2009.0079
[11] W. M. Patrick, et al., “Multicopy Suppression Underpins Metabolic Evolvability,” Molecular Biology and Evolution, Vol. 24, No. 12, 2007, pp. 2716-2722. doi:10.1093/molbev/msm204
[12] H. Nam, et al., “Network Context and Selection in the Evolution to Enzyme Specificity,” Science, Vol. 337, No. 6098, 2012, pp. 1101-1104. doi:10.1126/science.1216861
[13] C. Zimmer, “Microcosm: E. coli and the New Science of Life,” Vintage, New York, 2009.
[14] I. Sarkar, et al., “HIV-1 Proviral DNA Excision Using an Evolved Recombinase,” Science, Vol. 316, No. 5833, 2007, pp. 1912-1915. doi:10.1126/science.1141453
[15] A. Aharoni, et al., “The ‘Evolvability’ of Promiscuous Protein Functions,” Nature Genetics, Vol. 37, No. 1, 2005, pp. 73-76.
[16] I. Matsumura and A. D. Ellington, “In Vitro Evolution of Beta-Glucuronidase into a Beta-Galactosidase Proceeds through Non-Specific Intermediates,” Journal of Molecular Biology, Vol. 305, No. 2, 2001, pp. 331-339. doi:10.1006/jmbi.2000.4259
[17] U. Bergthorsson, D. I. Andersson and J. R. Roth, “Ohno’s Dilemma: Evolution of New Genes under Continuous Selection,” Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 43, 2007, pp. 17004-17009. doi:10.1073/pnas.0707158104
[18] D. G. Gibson, et al., “Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome,” Science, Vol. 329, No. 5987, 2010, pp. 52-56. doi:10.1126/science.1190719
[19] R. P. Shetty, D. Endy and T. F. Knight, Jr., “Engineering BioBrick Vectors from BioBrick Parts,” Journal of Biological Engineering, Vol. 2, No. 1, 2008: pp. 5-12 doi:10.1186/1754-1611-2-5
[20] A. Levskaya, et al., “Synthetic Biology: Engineering Escherichia coli to See Light,” Nature, Vol. 438, No. 7067, 2005, pp. 441-442. doi:10.1038/nature04405
[21] S. Topp and J. P. Gallivan, “Guiding Bacteria with Small Molecules and RNA,” Journal of the American Chemical Society, Vol. 129, No. 21, 2007, pp. 6807-6811. doi:10.1021/ja0692480
[22] A. M. Feist, et al., “Reconstruction of Biochemical Networks in Microorganisms,” Nature Reviews Microbiology, Vol. 7, No. 2, 2009, pp. 129-143.
[23] S. K. Lee, et al., “Metabolic Engineering of Microorganisms for Biofuels Production: From Bugs to Synthetic Biology to Fuels,” Current Opinion in Biotechnology, Vol. 19, No. 6, 2008, pp. 556-563. doi:10.1016/j.copbio.2008.10.014
[24] S. Y. McLoughlin and S. D. Copley, “A Compromise Required by Gene Sharing Enables Survival: Implications for Evolution of New Enzyme Activities,” Proceedings of the National Academy of Sciences of the United States of America, Vol. 105, No. 36, 2008, pp. 13497-13502. doi:10.1073/pnas.0804804105
[25] W. M. Patrick and I. Matsumura, “A Study in Molecular Contingency: Glutamine Phosphoribosyl Pyrophosphate Amidotransferase is a Promiscuous and Evolvable Phosphoribosyl Anthranilate Isomerase,” Journal of Molecular Biology, Vol. 377, No. 2, 2008, pp. 323-336. doi:10.1016/j.jmb.2008.01.043
[26] N. D. Price, J. L. Reed and B. O. Palsson, “Genome-Scale Models of Microbial Cells: Evaluating the Consequences of Constraints,” Nature Reviews Microbiology, Vol. 2, No. 11, 2004, pp. 886-897. doi:10.1038/nrmicro1023
[27] H. U. Kim, T. Y. Kim and S. Y. Lee, “Metabolic Flux Analysis and Metabolic Engineering of Microorganisms,” Molecular BioSystems, Vol. 4, No. 2, 2008, pp. 113-120. doi:10.1039/b712395g
[28] H. Mori, et al., “Functional Genomics of Escherichia coli in Japan,” Research in Microbiology, Vol. 151, No. 2, 2000, pp. 121-128. doi:10.1016/S0923-2508(00)00119-4
[29] P. J. Gerrish and R. E. Lenski, “The Fate of Competing Beneficial Mutations in an Asexual Population,” Genetica, Vol. 102-103, No. 1-6, 1998, pp. 127-144.
[30] H. H. Wang, et al., “Programming Cells by Multiplex Genome Engineering and Accelerated Evolution,” Nature, Vol. 460, No. 7257, 2009, pp. 894-898. doi:10.1038/nature08187
[31] J. R. Warner, et al., “Rapid Profiling of a Microbial Genome Using Mixtures of Barcoded Oligonucleotides,” Nature Biotechnology, Vol. 28, No. 8, 2010, pp. 856-862. doi:10.1038/nbt.1653
[32] H. Alper, et al., “Identifying Gene Targets for the Metabolic Engineering of Lycopene Biosynthesis in Escherichia coli,” Metabolic Engineering, Vol. 7, No. 3, 2005, pp. 155-164. doi:10.1016/j.ymben.2004.12.003
[33] L. Kizer, et al., “Application of Functional Genomics to Pathway Optimization for Increased Isoprenoid Production,” Applied and Environmental Microbiology, Vol. 74, No. 10, 2008, pp. 3229-3241. doi:10.1128/AEM.02750-07
[34] F. G. Vital-Lopez, et al., “A Computational Procedure for Optimal Engineering Interventions Using Kinetic Models of Metabolism,” Biotechnology Progress, Vol. 22, No. 6, 2006, pp. 1507-1517.

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