Optimizing Metabolic Pathways for the Improved Production of Natural Products

Methods in Enzymology

Volumn 575, Issue , 2016, Pages 179-193

  Jones, J A ^a   Koffas, M A G ^a  

^a RENSSELAER POLYTECHNIC INSTITUTE   (United States)

Author keywords

Coculture; Fermentation optimization; Genetic optimization; Induction timing; Microbial consortium; Pathway optimization; Transcriptional balancing

Indexed keywords

NATURAL PRODUCT; NUTRACEUTICAL; BIOLOGICAL PRODUCT;

COCULTURE; FERMENTATION OPTIMIZATION; GENE; GENE DOSAGE; METABOLIC ENGINEERING; METABOLISM; PLASMID; PROOF OF CONCEPT; TEMPERATURE; ANIMAL; BACTERIUM; COPY NUMBER VARIATION; FERMENTATION; FUNGUS; GENETIC TRANSCRIPTION; GENETICS; MICROBIOLOGY; PROCEDURES;

ANIMALS; BACTERIA; BIOLOGICAL PRODUCTS; COCULTURE TECHNIQUES; DNA COPY NUMBER VARIATIONS; FERMENTATION; FUNGI; INDUSTRIAL MICROBIOLOGY; METABOLIC ENGINEERING; METABOLIC NETWORKS AND PATHWAYS; PLASMIDS; TRANSCRIPTION, GENETIC;

EID: 84959934868     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/bs.mie.2016.02.010     Document Type: Chapter

References (67)

1. Ajikumar, P.K., Xiao, W.-H., Tyo, K.E.J., Wang, Y., Simeon, F., Leonard, E., et al. Isoprenoid pathway optimization for Taxol precursor overproduction in Escherichia coli. Science 330 (2010), 70–74, 10.1126/science.1191652.
2. Anderson, J.C., Dueber, J.E., Leguia, M., Wu, G.C., Goler, J.A., Arkin, A.P., et al. BglBricks: A flexible standard for biological part assembly. Journal of Biological Engineering, 4, 2010, 1, 10.1186/1754-1611-4-1.
3. Baek, J.-M., Mazumdar, S., Lee, S.-W., Jung, M.-Y., Lim, J.-H., Seo, S.-W., et al. Butyrate production in engineered Escherichia coli with synthetic scaffolds. Biotechnology and Bioengineering 110 (2013), 2790–2794, 10.1002/bit.24925.
4. Bhan, N., Xu, P., Koffas, M.A.G., Pathway and protein engineering approaches to produce novel and commodity small molecules. Current Opinion in Biotechnology 24 (2013), 1137–1143, 10.1016/j.copbio.2013.02.019.
5. Bizzini, A., Zhao, C., Budin-Verneuil, A., Sauvageot, N., Giard, J.-C., Auffray, Y., et al. Glycerol is metabolized in a complex and strain-dependent manner in Enterococcus faecalis. Journal of Bacteriology 192 (2010), 779–785, 10.1128/JB.00959-09.
6. Blazeck, J., Alper, H.S., Promoter engineering: Recent advances in controlling transcription at the most fundamental level. Biotechnology Journal 8 (2013), 46–58, 10.1002/biot.201200120.
7. Brewster, R.C., Jones, D.L., Phillips, R., Tuning promoter strength through RNA polymerase binding site design in Escherichia coli. PLoS Computational Biology 8 (2012), 1–10, 10.1371/journal.pcbi.1002811.
8. Cress, B.F., Toparlak, Ö.D., Guleria, S., Lebovich, M., Stieglitz, J.T., Englaender, J.A., et al. CRISPathBrick: Modular combinatorial assembly of type II-A CRISPR arrays for dCas9-mediated multiplex transcriptional repression in E. coli. ACS Synthetic Biology 4 (2015), 987–1000, 10.1021/acssynbio.5b00012.
9. Cress, B.F., Trantas, E.A., Ververidis, F., Linhardt, R.J., Koffas, M.A., Sensitive cells: Enabling tools for static and dynamic control of microbial metabolic pathways. Current Opinion in Biotechnology 36 (2015), 205–214, 10.1016/j.copbio.2015.09.007.
10. Da Silva, G.P., Mack, M., Contiero, J., Glycerol: A promising and abundant carbon source for industrial microbiology. Biotechnology Advances 27 (2009), 30–39, 10.1016/j.biotechadv.2008.07.006.
11. De Kok, S., Stanton, L.H., Slaby, T., Durot, M., Holmes, V.F., Patel, K.G., et al. Rapid and reliable DNA assembly via ligase cycling reaction. ACS Synthetic Biology 3 (2014), 97–106, 10.1021/sb4001992.
12. De Mey, M., Maertens, J., Lequeux, G.J., Soetaert, W.K., Vandamme, E.J., Construction and model-based analysis of a promoter library for E. coli: An indispensable tool for metabolic engineering. BMC Biotechnology, 7, 2007, 34, 10.1186/1472-6750-7-34.
13. Donovan, R.S., Robinson, C.W., Glick, B.R., Review: Optimizing inducer and culture conditions for expression of foreign proteins under the control of the lac promoter. Journal of Industrial Microbiology 16 (1996), 145–154, 10.1007/BF01569997.
14. Dueber, J.E., Wu, G.C., Malmirchegini, G.R., Moon, T.S., Petzold, C.J., Ullal, A.V., et al. Synthetic protein scaffolds provide modular control over metabolic flux. Nature Biotechnology 27 (2009), 753–759, 10.1038/nbt.1557.
15. Engler, C., Kandzia, R., Marillonnet, S., A one pot, one step, precision cloning method with high throughput capability. PloS One, 3, 2008, e3647, 10.1371/journal.pone.0003647.
16. Farasat, I., Kushwaha, M., Collens, J., Easterbrook, M., Guido, M., Salis, H.M., Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria. Molecular Systems Biology, 10, 2014, 731, 10.15252/msb.20134955.
17. Feng, J., Jester, B.W., Tinberg, C.E., Mandell, D.J., Antunes, M.S., Chari, R., et al. A general strategy to construct small molecule biosensors in eukaryotes. Elife, 4, 2015, e10606, 10.7554/eLife.10606.
18. Freestone, T.S., Zhao, H., Combinatorial pathway engineering for optimized production of the anti-malarial FR900098. Biotechnology and Bioengineering 113 (2015), 384–392, 10.1002/bit.25719.
19. Gebreselassie, N.A., Antoniewicz, M.R., (13)C-metabolic flux analysis of co-cultures: A novel approach. Metabolic Engineering 31 (2015), 132–139, 10.1016/j.ymben.2015.07.005.
20. Gibson, D.G., Young, L., Chuang, R.-Y., Venter, J.C., Hutchison, C.A., Smith, H.O., Enzymatic assembly of DNA molecules up to several hundred kilobases. Nature Methods 6 (2009), 343–345, 10.1038/nmeth.1318.
21. Hashimoto, T., Yamada, Y., New genes in alkaloid metabolism and transport. Current Opinion in Biotechnology 14 (2003), 163–168, 10.1016/S0958-1669(03)00027-2.
22. He, W., Fu, L., Li, G., Jones, J.A., Linhardt, R.J., Koffas, M., Production of chondroitin in metabolically engineered E. coli. Metabolic Engineering 27 (2015), 92–100, 10.1016/j.ymben.2014.11.003.
23. Ho, S.N., Hunt, H.D., Horton, R.M., Pullen, J.K., Pease, L.R., Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene 77 (1989), 51–59, 10.1016/0378-1119(89)90358-2.
24. Huang, Q., Lin, Y., Yan, Y., Caffeic acid production enhancement by engineering a phenylalanine over-producing Escherichia coli strain. Biotechnology and Bioengineering 110 (2013), 3188–3196, 10.1002/bit.24988.
25. Jakočiūnas, T., Jensen, M.K., Keasling, J.D., CRISPR/Cas9 advances engineering of microbial cell factories. Metabolic Engineering 34 (2015), 44–59, 10.1016/j.ymben.2015.12.003.
26. Jones, J.A., Collins, S.M., Lachance, D.M., Vernacchio, V.R., Koffas, M.A.G., Optimization of naringenin and p-coumaric acid hydroxylation using the native E. coli hydroxylase complex, HpaBC. Biotechnology Progress 32:1 (2016), 21–25, 10.1002/btpr.2185.
27. Jones, K.L., Kim, S.W., Keasling, J.D., Low-copy plasmids can perform as well as or better than high-copy plasmids for metabolic engineering of bacteria. Metabolic Engineering 2 (2000), 328–338, 10.1006/mben.2000.0161.
28. Jones, J.A., Toparlak, Ö.D., Koffas, M.A., Metabolic pathway balancing and its role in the production of biofuels and chemicals. Current Opinion in Biotechnology 33 (2015), 52–59, 10.1016/j.copbio.2014.11.013.
29. Jones, J.A., Vernacchio, V.R., Lachance, D.M., Lebovich, M., Fu, L., Shirke, A.N., et al. ePathOptimize: A combinatorial approach for transcriptional balancing of metabolic pathways. Scientific Reports, 5, 2015, 11301, 10.1038/srep11301.
30. Jones, J.A., Vernacchio, V.R., Sinkoe, A.L., Collins, S.M., Ibrahim, M.H.A., Lachance, D.M., et al. Experimental and computational optimization of an Escherichia coli co-culture for the efficient production of flavonoids. Metabolic Engineering 35 (2016), 55–63.
31. Kim, E., Moore, B.S., Yoon, Y.J., Reinvigorating natural product combinatorial biosynthesis with synthetic biology. Nature Chemical Biology 11 (2015), 649–659.
32. Lee, T.S., Krupa, R.A., Zhang, F., Hajimorad, M., Holtz, W.J., Prasad, N., et al. BglBrick vectors and datasheets: A synthetic biology platform for gene expression. Journal of Biological Engineering, 5, 2011, 12, 10.1186/1754-1611-5-12.
33. Lee, J.W., Na, D., Park, J.M., Lee, J., Choi, S., Lee, S.Y., Systems metabolic engineering of microorganisms for natural and non-natural chemicals. Nature Chemical Biology 8 (2012), 536–546, 10.1038/nchembio.970.
34. Leonard, E., Yan, Y., Lim, K.H., Koffas, M.A.G., Investigation of two distinct flavone synthases for plant-specific flavone biosynthesis in Saccharomyces cerevisiae. Applied and Environmental Microbiology 71 (2005), 8241–8248, 10.1128/AEM.71.12.8241-8248.2005.
35. Lim, C.G., Wong, L., Bhan, N., Dvora, H., Xu, P., Venkiteswaran, S., et al. Development of a recombinant Escherichia coli strain for overproduction of plant pigment, anthocyanin. Applied and Environmental Microbiology 81 (2015), 6276–6284, 10.1128/AEM.01448-15.
36. Mairhofer, J., Scharl, T., Marisch, K., Cserjan-Puschmann, M., Striedner, G., Comparative transcription profiling and in-depth characterization of plasmid-based and plasmid-free Escherichia coli expression systems under production conditions. Applied and Environmental Microbiology 79 (2013), 3802–3812, 10.1128/AEM.00365-13.
37. Moon, T.S., Dueber, J.E., Shiue, E., Prather, K.L.J., Use of modular, synthetic scaffolds for improved production of glucaric acid in engineered E. coli. Metabolic Engineering 12 (2010), 298–305, 10.1016/j.ymben.2010.01.003.
38. Mutalik, V.K., Guimaraes, J.C., Cambray, G., Lam, C., Christoffersen, M.J., Mai, Q.-A., et al. Precise and reliable gene expression via standard transcription and translation initiation elements. Nature Methods 10 (2013), 354–360, 10.1038/nmeth.2404.
39. Na, D., Lee, D., RBSDesigner: Software for designing synthetic ribosome binding sites that yields a desired level of protein expression. Bioinformatics 26 (2010), 2633–2634, 10.1093/bioinformatics/btq458.
40. Neidhardt, F.C., Bloch, P.L., Smith, D.F., Culture medium for Enterobacteria. Journal of Bacteriology 119 (1974), 736–747.
41. Pham, V.D., Lee, S.H., Park, S.J., Hong, S.H., Production of gamma-aminobutyric acid from glucose by introduction of synthetic scaffolds between isocitrate dehydrogenase, glutamate synthase and glutamate decarboxylase in recombinant Escherichia coli. Journal of Biotechnology 207 (2015), 52–57, 10.1016/j.jbiotec.2015.04.028.
42. Reizman, I.M.B., Stenger, A.R., Reisch, C.R., Gupta, A., Connors, N.C., Prather, K.L.J., Improvement of glucaric acid production in E. coli via dynamic control of metabolic fluxes. Metabolic Engineering Communications 2 (2015), 109–116, 10.1016/j.meteno.2015.09.002.
43. Saini, M., Hong Chen, M., Chiang, C.-J., Chao, Y.-P., Potential production platform of n-butanol in Escherichia coli. Metabolic Engineering 27 (2015), 76–82, 10.1016/j.ymben.2014.11.001.
44. Salis, H.M., Mirsky, E.A., Voigt, C.A., Automated design of synthetic ribosome binding sites to control protein expression. Nature Biotechnology 27 (2009), 946–950, 10.1038/nbt.1568.
45. Santos, C.N.S., Koffas, M., Stephanopoulos, G., Optimization of a heterologous pathway for the production of flavonoids from glucose. Metabolic Engineering 13 (2011), 392–400, 10.1016/j.ymben.2011.02.002.
46. Seo, S.W., Yang, J.-S., Kim, I., Yang, J., Min, B.E., Kim, S., et al. Predictive design of mRNA translation initiation region to control prokaryotic translation efficiency. Metabolic Engineering 15 (2013), 67–74, 10.1016/j.ymben.2012.10.006.
47. Shao, Z., Zhao, H., Zhao, H., DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways. Nucleic Acids Research, 37, 2009, e16, 10.1093/nar/gkn991.
48. Shetty, R.P., Endy, D., Knight, T.F., Engineering BioBrick vectors from BioBrick parts. Journal of Biological Engineering, 2, 2008, 5, 10.1186/1754-1611-2-5.
49. Shiloach, J., Fass, R., Growing E. coli to high cell density—A historical perspective on method development. Biotechnology Advances 23 (2005), 345–357, 10.1016/j.biotechadv.2005.04.004.
50. Siedler, S., Stahlhut, S.G., Malla, S., Maury, J., Neves, A.R., Novel biosensors based on flavonoid-responsive transcriptional regulators introduced into Escherichia coli. Metabolic Engineering 21 (2014), 2–8, 10.1016/j.ymben.2013.10.011.
51. Solomon, K.V., Sanders, T.M., Prather, K.L.J., A dynamic metabolite valve for the control of central carbon metabolism. Metabolic Engineering 14 (2012), 661–671, 10.1016/j.ymben.2012.08.006.
52. Temme, K., Hill, R., Segall-Shapiro, T.H., Moser, F., Voigt, C.A., Modular control of multiple pathways using engineered orthogonal T7 polymerases. Nucleic Acids Research 40 (2012), 8773–8781, 10.1093/nar/gks597.
53. Thodey, K., Galanie, S., Smolke, C.D., A microbial biomanufacturing platform for natural and semisynthetic opioids. Nature Chemical Biology 10 (2014), 837–844, 10.1038/nchembio.1613.
54. Tyo, K.E.J., Ajikumar, P.K., Stephanopoulos, G., Stabilized gene duplication enables long-term selection-free heterologous pathway expression. Nature Biotechnology 27 (2009), 760–765, 10.1038/nbt.1555.
55. Wang, J., Guleria, S., Koffas, M.A., Yan, Y., Microbial production of value-added nutraceuticals. Current Opinion in Biotechnology 37 (2015), 97–104, 10.1016/j.copbio.2015.11.003.
56. Wu, J., Du, G., Chen, J., Zhou, J., Enhancing flavonoid production by systematically tuning the central metabolic pathways based on a CRISPR interference system in Escherichia coli. Scientific Reports, 5, 2015, 13477, 10.1038/srep13477.
57. Xu, P., Gu, Q., Wang, W., Wong, L., Bower, A.G.W., Collins, C.H., et al. Modular optimization of multi-gene pathways for fatty acids production in E. coli. Nature Communications, 4, 2013, 1409, 10.1038/ncomms2425.
58. Xu, P., Li, L., Zhang, F., Stephanopoulos, G., Koffas, M., Improving fatty acids production by engineering dynamic pathway regulation and metabolic control. Proceedings of the National Academy of Sciences of the United States of America 111 (2014), 11299–11304, 10.1073/pnas.1406401111.
59. Xu, P., Vansiri, A., Bhan, N., Koffas, M.A.G., ePathBrick: A synthetic biology platform for engineering metabolic pathways in E. coli. ACS Synthetic Biology 1 (2012), 256–266, 10.1021/sb300016b.
60. Yan, Y., Huang, L., Koffas, M.A.G., Biosynthesis of 5-deoxyflavanones in microorganisms. Biotechnology Journal 2 (2007), 1250–1262, 10.1002/biot.200700119.
61. Yan, Y., Li, Z., Koffas, M.A.G., High-yield anthocyanin biosynthesis in engineered Escherichia coli. Biotechnology and Bioengineering 100 (2008), 126–140, 10.1002/bit.21721.
62. Zhang, F., Carothers, J.M., Keasling, J.D., Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids. Nature Biotechnology 30 (2012), 354–359, 10.1038/nbt.2149.
63. Zhang, J., Jensen, M.K., Keasling, J.D., Development of biosensors and their application in metabolic engineering. Current Opinion in Chemical Biology 28 (2015), 1–8, 10.1016/j.cbpa.2015.05.013.
64. Zhang, H., Li, Z., Pereira, B., Stephanopoulos, G., Engineering E. coli-E. coli cocultures for production of muconic acid from glycerol. Microbial Cell Factories, 14, 2015, 134, 10.1186/s12934-015-0319-0.
65. Zhang, H., Pereira, B., Li, Z., Stephanopoulos, G., Engineering Escherichia coli coculture systems for the production of biochemical products. Proceedings of the National Academy of Sciences of the United States of America 112 (2015), 8266–8271, 10.1073/pnas.1506781112.
66. Zhao, S., Jones, J.A., Lachance, D.M., Bhan, N., Khalidi, O., Venkataraman, S., et al. Improvement of catechin production in Escherichia coli through combinatorial metabolic engineering. Metabolic Engineering 28 (2015), 43–53, 10.1016/j.ymben.2014.12.002.
67. Zhou, K., Qiao, K., Edgar, S., Stephanopoulos, G., Distributing a metabolic pathway among a microbial consortium enhances production of natural products. Nature Biotechnology 33 (2015), 377–383, 10.1038/nbt.3095.