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

[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.