Construction of Microbial Cell Factories by Systems and Synthetic Biotechnology

Wu, Yaokang; Gu, Yang; Tian, Rongzhen; Du, Guocheng; Chen, Jian; Liu, Long

doi:10.1007/978-981-15-0446-4_2

Yaokang Wu^3,4,
Yang Gu^3,4,
Rongzhen Tian^3,4,
Guocheng Du^3,4,
Jian Chen⁴ &
…
Long Liu^3,4

848 Accesses
1 Citations

Abstract

With the growing concern regarding worsening environment, microbial cell factories have been built for the biorefinery of many products including chemicals, biofuel, nutraceuticals, and pharmaceuticals from renewable biomass resources. In this chapter, we introduced the mainly strategies for the design, construction, and optimization of metabolic pathway. In addition, the applications of modular metabolic engineering and dynamic regulation for the further optimization and regulation of metabolic network were discussed. Furthermore, we also highlighted the role of system biology such as omics technology, genomics-based metabolic model, and genome-scale engineering tools. Finally, future perspectives on the design and construction of microbial cell factories were provided.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Chapter: USD 29.95; Price excludes VAT (USA)

eBook: USD 129.00; Price excludes VAT (USA)

Softcover Book: USD 169.99; Price excludes VAT (USA)

Hardcover Book: USD 169.99; Price excludes VAT (USA)

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

Abdel-Mawgoud AM, Markham KA, Palmer CM, Liu N, Stephanopoulos G, Alper HS. Metabolic engineering in the host Yarrowia lipolytica. Metab Eng. 2018;50:192–208. https://doi.org/10.1016/j.ymben.2018.07.016.
Article CAS PubMed Google Scholar
Ahn JH, Lee JA, Bang J, Lee SY. Membrane engineering via trans-unsaturated fatty acids production improves succinic acid production in Mannheimia succiniciproducens. J Ind Microbiol Biotechnol. 2018;45:555–66. https://doi.org/10.1007/s10295-018-2016-6.
Article CAS PubMed Google Scholar
Ajikumar PK, Xiao W-H, Tyo KEJ, Wang Y, Simeon F, Leonard E, Mucha O, Phon TH, Pfeifer B, Stephanopoulos G. Isoprenoid pathway optimization for taxol precursor overproduction in Escherichia coli. Science. 2010;330:70–4. https://doi.org/10.1126/science.1191652.
Article CAS PubMed PubMed Central Google Scholar
Alper H, Fischer C, Nevoigt E, Stephanopoulos G. Tuning genetic control through promoter engineering. Proc Natl Acad Sci. 2005;102:12678–83. https://doi.org/10.1073/pnas.0504604102.
Article CAS PubMed PubMed Central Google Scholar
Ao X, Yao Y, Li T, Yang T-T, Dong X, Zheng Z-T, Chen G-Q, Wu Q, Guo Y. A multiplex genome editing method for Escherichia coli based on CRISPR-Cas12a. Front Microbiol. 2018;9:1–13. https://doi.org/10.3389/fmicb.2018.02307.
Article Google Scholar
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: tool for the unification of biology. Nat Genet. 2000;25:25–9. https://doi.org/10.1038/75556.
Article CAS PubMed PubMed Central Google Scholar
Bailey J. Toward a science of metabolic engineering. Science. 1991;252:1668–75. https://doi.org/10.1126/science.2047876.
Article CAS PubMed Google Scholar
Bashor CJ, Kondev J, Khalil AS. Complex signal processing in synthetic circuits using cooperative regulatory assemblies. Science. 2019;8287:1–11.
Google Scholar
Becker J, Wittmann C. Systems metabolic engineering of Escherichia coli for the heterologous production of high value molecules. Curr Opin Biotechnol. 2016;42:178–88. https://doi.org/10.1016/j.copbio.2016.05.004.
Article CAS PubMed Google Scholar
Becker J, Rohles CM, Wittmann C. Metabolically engineered Corynebacterium glutamicum for bio-based production of chemicals, fuels, materials, and healthcare products. Metab Eng. 2018:1–20. https://doi.org/10.1016/j.ymben.2018.07.008.
Bervoets I, Charlier D. Diversity, versatility and complexity of bacterial gene regulation mechanisms: opportunities and drawbacks for applications in synthetic biology. FEMS Microbiol Rev. 2019; https://doi.org/10.1093/femsre/fuz001.
Besada-Lombana PB, McTaggart TL, Da Silva NA. Molecular tools for pathway engineering in Saccharomyces cerevisiae. Curr Opin Biotechnol. 2018;53:39–49. https://doi.org/10.1016/j.copbio.2017.12.002.
Article CAS PubMed Google Scholar
Biggs BW, De Paepe B, Santos CNS, De Mey M, Kumaran Ajikumar P. Multivariate modular metabolic engineering for pathway and strain optimization. Curr Opin Biotechnol. 2014;29:156–62. https://doi.org/10.1016/j.copbio.2014.05.005.
Article CAS PubMed Google Scholar
Biz A, Proulx S, Xu Z, Siddartha K, Indrayanti AM, Mahadevan R. Systems biology based metabolic engineering for non-natural chemicals. Biotechnol Adv. 2019; https://doi.org/10.1016/j.biotechadv.2019.04.001.
Bonde MT, Klausen MS, Anderson MV, Wallin AIN, Wang HH, Sommer MOA. MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering. Nucleic Acids Res. 2014;42:W408–15. https://doi.org/10.1093/nar/gku428.
Article CAS PubMed PubMed Central Google Scholar
Bordbar A, Monk JM, King ZA, Palsson BO. Constraint-based models predict metabolic and associated cellular functions. Nat Rev Genet. 2014a;15:107–20. https://doi.org/10.1038/nrg3643.
Article CAS PubMed Google Scholar
Bordbar A, Nagarajan H, Lewis NE, Latif H, Ebrahim A, Federowicz S, Schellenberger J, Palsson BO. Minimal metabolic pathway structure is consistent with associated biomolecular interactions. Mol Syst Biol. 2014b;10:737. https://doi.org/10.15252/msb.20145243.
Article CAS PubMed PubMed Central Google Scholar
Brockman IM, Prather KLJ. Dynamic knockdown of E. coli central metabolism for redirecting fluxes of primary metabolites. Metab Eng. 2015a;28:104–13. https://doi.org/10.1016/j.ymben.2014.12.005.
Article CAS PubMed Google Scholar
Brockman IM, Prather KLJ. Dynamic metabolic engineering: new strategies for developing responsive cell factories. Biotechnol J. 2015b;10:1360–9. https://doi.org/10.1002/biot.201400422.
Article CAS PubMed PubMed Central Google Scholar
Buffing MF, Link H, Christodoulou D, Sauer U. Capacity for instantaneous catabolism of preferred and non-preferred carbon sources in Escherichia coli and Bacillus subtilis. Sci Rep. 2018;8:11760. https://doi.org/10.1038/s41598-018-30266-3.
Article CAS PubMed PubMed Central Google Scholar
Bujara M, Schümperli M, Pellaux R, Heinemann M, Panke S. Optimization of a blueprint for in vitro glycolysis by metabolic real-time analysis. Nat Chem Biol. 2011;7:271–7. https://doi.org/10.1038/nchembio.541.
Article CAS PubMed Google Scholar
Cai Y, Huang CLV, Richardson SM, Stracquadanio G, Mitchell LA, Lee D, DiCarlo JE, Chandrasegaran S, Yang K, Dymond JS, Bader JS, Boeke JD. Design of a synthetic yeast genome. Science. 2017;355:1040–4. https://doi.org/10.1126/science.aaf4557.
Article CAS PubMed Google Scholar
Cameron DE, Collins JJ. Tunable protein degradation in bacteria. Nat Biotechnol. 2014;32:1276–81. https://doi.org/10.1038/nbt.3053.
Article CAS PubMed PubMed Central Google Scholar
Campodonico MA, Andrews BA, Asenjo JA, Palsson BO, Feist AM. Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path. Metab Eng. 2014;25:140–58. https://doi.org/10.1016/j.ymben.2014.07.009.
Article CAS PubMed Google Scholar
Cardoso J, Jensen K, Lieven C, Hansen ASL, Galkina S, Beber ME, Özdemir E, Herrgard M, Redestig H, Sonnenschein N. Cameo: a python library for computer aided metabolic engineering and optimization of cell factories. ACS Synth Biol. 2018:acssynbio.7b00423. https://doi.org/10.1021/acssynbio.7b00423.
Caron M-P, Bastet L, Lussier A, Simoneau-Roy M, Masse E, Lafontaine DA. Dual-acting riboswitch control of translation initiation and mRNA decay. Proc Natl Acad Sci. 2012;109:E3444–53. https://doi.org/10.1073/pnas.1214024109.
Article PubMed PubMed Central Google Scholar
Caspeta L, Chen Y, Ghiaci P, Feizi A, Baskov S, Hallström BM, Petranovic D, Nielsen J. Altered sterol composition renders yeast thermotolerant. Science. 2014;346:75–8. https://doi.org/10.1126/science.1258137.
Article CAS PubMed Google Scholar
Chae TU, Choi SY, Kim JW, Ko Y-S, Lee SY. Recent advances in systems metabolic engineering tools and strategies. Curr Opin Biotechnol. 2017;47:67–82. https://doi.org/10.1016/j.copbio.2017.06.007.
Article CAS PubMed Google Scholar
Chao R, Mishra S, Si T, Zhao H. Engineering biological systems using automated biofoundries. Metab Eng. 2017;42:98–108. https://doi.org/10.1016/j.ymben.2017.06.003.
Article CAS PubMed PubMed Central Google Scholar
Charubin K, Bennett RK, Fast AG, Papoutsakis ET. Engineering clostridium organisms as microbial cell-factories: challenges & opportunities. Metab Eng. 2018; https://doi.org/10.1016/j.ymben.2018.07.012.
Chatterjee N, Walker GC. Mechanisms of DNA damage, repair, and mutagenesis. Environ Mol Mutagen. 2017;58:235–63. https://doi.org/10.1002/em.22087.
Article CAS PubMed PubMed Central Google Scholar
Chen Z, Rappert S, Zeng AP. Rational design of allosteric regulation of homoserine dehydrogenase by a nonnatural inhibitor l -lysine. ACS Synth Biol. 2015;4:126–31. https://doi.org/10.1021/sb400133g.
Article CAS PubMed Google Scholar
Chen X, Gao C, Guo L, Hu G, Luo Q, Liu J, Nielsen J, Chen J, Liu L. DCEO biotechnology: tools to design, construct, evaluate, and optimize the metabolic pathway for biosynthesis of chemicals. Chem Rev. 2017:acs.chemrev.6b00804. https://doi.org/10.1021/acs.chemrev.6b00804.
Chen L, Gu W, Xu H y, Yang GL, Shan XF, Chen G, Kang Y h, Wang CF, Qian AD. Comparative genome analysis of Bacillus velezensis reveals a potential for degrading lignocellulosic biomass. 3 Biotech. 2018;8:253. https://doi.org/10.1007/s13205-018-1270-7.
Article PubMed PubMed Central Google Scholar
Chew YH, Goldberg AP, Sekar JAP, Roth YD, Karr JR, Szigeti B, Chew YH, Sekar JAP, Roth YD, Karr JR. Emerging whole-cell modeling principles and methods. Curr Opin Biotechnol. 2018;51:97–102. https://doi.org/10.1016/j.copbio.2017.12.013.
Article CAS PubMed Google Scholar
Choi HS, Lee SY, Kim TY, Woo HM. In silico identification of gene amplification targets for improvement of lycopene production. Appl Environ Microbiol. 2010;76:3097–105. https://doi.org/10.1128/AEM.00115-10.
Article CAS PubMed PubMed Central Google Scholar
Choi KR, Jang WD, Yang D, Cho JS, Park D, Lee SY. Systems metabolic engineering strategies: integrating systems and synthetic biology with metabolic engineering. Trends Biotechnol. 2019:1–21. https://doi.org/10.1016/j.tibtech.2019.01.003.
Clark TA, Olivares EC, Travers KJ, Webster DR, Lee JH, Turner SW, Korlach J, Flusberg BA. Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat Methods. 2010;7:461–5. https://doi.org/10.1038/nmeth.1459.
Article CAS PubMed PubMed Central Google Scholar
Srinivasan S, Cluett WR, Mahadevan R. Constructing kinetic models of metabolism at genome-scales: a review. Biotechnol J. 2015;10:1345–59. https://doi.org/10.1002/biot.201400522.
Article CAS PubMed Google Scholar
Conrado RJ, Wu GC, Boock JT, Xu H, Chen SY, Lebar T, Turnek J, Tomšič N, Avbelj M, Gaber R, Koprivnjak T, Mori J, Glavnik V, Vovk I, Beninča M, Hodnik V, Anderluh G, Dueber JE, Jerala R, Delisa MP. DNA-guided assembly of biosynthetic pathways promotes improved catalytic efficiency. Nucleic Acids Res. 2012;40:1879–89. https://doi.org/10.1093/nar/gkr888.
Article CAS PubMed Google Scholar
Cordova LT, Alper HS. Central metabolic nodes for diverse biochemical production. Curr Opin Chem Biol. 2016;35:37–42. https://doi.org/10.1016/j.cbpa.2016.08.025.
Article CAS PubMed Google Scholar
Costa RS, Hartmann A, Vinga S. Kinetic modeling of cell metabolism for microbial production. J Biotechnol. 2015;219:126–41. https://doi.org/10.1016/j.jbiotec.2015.12.023.
Article CAS PubMed Google Scholar
Cress BF, Trantas E a, Ververidis F, Linhardt RJ, Koffas M a G. Sensitive cells: enabling tools for static and dynamic control of microbial metabolic pathways. Curr Opin Biotechnol. 2015;36:205–14. https://doi.org/10.1016/j.copbio.2015.09.007.
Article CAS PubMed Google Scholar
Crook NC, Schmitz AC, Alper HS. Optimization of a yeast RNA interference system for controlling gene expression and enabling rapid metabolic engineering. ACS Synth Biol. 2014;3:307–13. https://doi.org/10.1021/sb4001432.
Article CAS PubMed Google Scholar
Dahl RH, Zhang F, Alonso-Gutierrez J, Baidoo E, Batth TS, Redding-Johanson AM, Petzold CJ, Mukhopadhyay A, Lee TS, Adams PD, Keasling JD. Engineering dynamic pathway regulation using stress-response promoters. Nat Biotechnol. 2013;31:1039–46. https://doi.org/10.1038/nbt.2689.
Article CAS PubMed Google Scholar
Dai Z, Nielsen J. Advancing metabolic engineering through systems biology of industrial microorganisms. Curr Opin Biotechnol. 2015;36:8–15. https://doi.org/10.1016/j.copbio.2015.08.006.
Article CAS PubMed Google Scholar
Datsenko KA, Wanner BL. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A. 2000;97:6640–5. https://doi.org/10.1073/pnas.120163297.
Article CAS PubMed PubMed Central Google Scholar
Delcher A. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 2002;27:4636–41. https://doi.org/10.1093/nar/27.23.4636.
Article Google Scholar
Delebecque CJ, Lindner AB, Silver PA, Aldaye FA. Organization of intracellular reactions with rationally designed RNA assemblies. Science. 2011;333:470–4. https://doi.org/10.1126/science.1206938.
Article CAS PubMed Google Scholar
Ding Q, Luo Q, Zhou J, Chen X, Liu L. Enhancing L-malate production of Aspergillus oryzae FMME218-37 by improving inorganic nitrogen utilization. Appl Microbiol Biotechnol. 2018;102:8739–51. https://doi.org/10.1007/s00253-018-9272-2.
Article CAS PubMed Google Scholar
Doong SJ, Gupta A, Prather KLJ. Layered dynamic regulation for improving metabolic pathway productivity in Escherichia coli. Proc Natl Acad Sci. 2018:201716920. https://doi.org/10.1073/pnas.1716920115.
Doudna JA, Charpentier E. The new frontier of genome engineering with CRISPR-Cas9. Science. 2014;346:1258096. https://doi.org/10.1126/science.1258096.
Article CAS PubMed Google Scholar
Dueber JE, Wu GC, Malmirchegini GR, Moon TS, Petzold CJ, Ullal AV, Prather KLJ, Keasling JD. Synthetic protein scaffolds provide modular control over metabolic flux. Nat Biotechnol. 2009;27:753–9. https://doi.org/10.1038/nbt.1557.
Article CAS PubMed Google Scholar
Dugar D, Stephanopoulos G. Relative potential of biosynthetic pathways for biofuels and bio-based products. Nat Biotechnol. 2011;29:1074–8. https://doi.org/10.1038/nbt.2055.
Article CAS PubMed Google Scholar
Egbert RG, Rishi HS, Adler BA, McCormick DM, Toro E, Gill RT, Arkin AP. A versatile platform strain for high-fidelity multiplex genome editing. Nucleic Acids Res. 2019;47:3244–56. https://doi.org/10.1093/nar/gkz085.
Article CAS PubMed PubMed Central Google Scholar
Engler C, Kandzia R, Marillonnet S. A one pot, one step, precision cloning method with high throughput capability. PLoS One. 2008;3:e3647. https://doi.org/10.1371/journal.pone.0003647.
Article CAS PubMed PubMed Central Google Scholar
Enyeart PJ, Chirieleison SM, Dao MN, Perutka J, Quandt EM, Yao J, Whitt JT, Keatinge-Clay a T, Lambowitz a M, Ellington a D. Generalized bacterial genome editing using mobile group II introns and Cre-lox. Mol Syst Biol. 2014;9:685. https://doi.org/10.1038/msb.2013.41.
Article CAS Google Scholar
Esvelt KM, Wang HH. Genome-scale engineering for systems and synthetic biology. Mol Syst Biol. 2014;9:641. https://doi.org/10.1038/msb.2012.66.
Article Google Scholar
Farmer WR, Liao JC. Improving lycopene production in Escherichia coli by engineering metabolic control. Nat Biotechnol. 2000;18:533–7. https://doi.org/10.1038/75398.
Article CAS PubMed Google Scholar
Fuhrer T, Zamboni N. ScienceDirect High-throughput discovery metabolomics. Curr Opin Biotechnol. 2015;31:73–8. https://doi.org/10.1016/j.copbio.2014.08.006.
Article CAS PubMed Google Scholar
Gagne SJ, Stout JM, Liu E, Boubakir Z, Clark SM, Page JE. Identification of olivetolic acid cyclase from Cannabis sativa reveals a unique catalytic route to plant polyketides. Proc Natl Acad Sci. 2012;109:12811–6. https://doi.org/10.1073/pnas.1200330109.
Article PubMed PubMed Central Google Scholar
Garst AD, Bassalo MC, Pines G, Lynch SA, Halweg-Edwards AL, Liu R, Liang L, Wang Z, Zeitoun R, Alexander WG, Gill RT. Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering. Nat Biotechnol. 2017;35:48–55. https://doi.org/10.1038/nbt.3718.
Article CAS PubMed Google Scholar
George KW, Chen A, Jain A, Batth TS, Baidoo EEK, Wang G, Adams PD, Petzold CJ, Keasling JD, Lee TS. Correlation analysis of targeted proteins and metabolites to assess and engineer microbial isopentenol production. Biotechnol Bioeng. 2014;111:1648–58. https://doi.org/10.1002/bit.25226.
Article CAS PubMed Google Scholar
Gibson DG, Benders G a, Axelrod KC, Zaveri J, Algire M a, Moodie M, Montague MG, Venter JC, Smith HO, Hutchison C a. One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome. Proc Natl Acad Sci. 2008;105:20404–9. https://doi.org/10.1073/pnas.0811011106.
Article PubMed PubMed Central Google Scholar
Gilbert LA, Larson MH, Morsut L, Liu Z, Brar GA, Torres SE, Stern-Ginossar N, Brandman O, Whitehead EH, Doudna JA, Lim WA, Weissman JS, Qi LS. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell. 2013;154:442. https://doi.org/10.1016/j.cell.2013.06.044.
Article CAS PubMed PubMed Central Google Scholar
Gilbert LA, Horlbeck MA, Adamson B, Villalta JE, Chen Y, Whitehead EH, Guimaraes C, Panning B, Ploegh HL, Bassik MC, Qi LS, Kampmann M, Weissman JS. Genome-scale CRISPR-mediated control of gene repression and activation. Cell. 2014;159:647–61. https://doi.org/10.1016/j.cell.2014.09.029.
Article CAS PubMed PubMed Central Google Scholar
Gottesman S. The small RNA regulators of Escherichia coli : roles and mechanisms. Annu Rev Microbiol. 2004;58:303–28. https://doi.org/10.1146/annurev.micro.58.030603.123841.
Article CAS PubMed Google Scholar
Gu Y, Deng J, Liu Y, Li J, Shin HD, Du G, Chen J, Liu L. Rewiring the glucose transportation and central metabolic pathways for overproduction of N-acetylglucosamine in Bacillus subtilis. Biotechnol J. 2017;12:1700268. https://doi.org/10.1002/biot.201700020.
Article CAS Google Scholar
Gu Y, Xu X, Wu Y, Niu T, Liu Y, Li J, Du G, Liu L. Advances and prospects of Bacillus subtilis cellular factories: from rational design to industrial applications. Metab Eng. 2018;50:109–21. https://doi.org/10.1016/j.ymben.2018.05.006.
Article CAS PubMed Google Scholar
Gu Y, Lv X, Liu Y, Li J, Du G, Chen J, Rodrigo LA, Liu L. Synthetic redesign of central carbon and redox metabolism for high yield production of N-acetylglucosamine in Bacillus subtilis. Metab Eng. 2019;51:59–69. https://doi.org/10.1016/j.ymben.2018.10.002.
Article CAS PubMed Google Scholar
Guan N, Du B, Li J, Shin HD, Chen RR, Du G, Chen J, Liu L. Comparative genomics and transcriptomics analysis-guided metabolic engineering of Propionibacterium acidipropionici for improved propionic acid production. Biotechnol Bioeng. 2018;115:483–94. https://doi.org/10.1002/bit.26478.
Article CAS PubMed Google Scholar
Guo J, Zhou YJ, Hillwig ML, Shen Y, Yang L, Wang Y, Zhang X, Liu W, Peters RJ, Chen X, Zhao ZK, Huang L. CYP76AH1 catalyzes turnover of miltiradiene in tanshinones biosynthesis and enables heterologous production of ferruginol in yeasts. Proc Natl Acad Sci. 2013;110:12108–13. https://doi.org/10.1073/pnas.1218061110.
Article PubMed PubMed Central Google Scholar
Gupta A, Reizman IMB, Reisch CR, Prather KLJ. Dynamic regulation of metabolic flux in engineered bacteria using a pathway-independent quorum-sensing circuit. Nat Biotechnol Adv. 2017; https://doi.org/10.1038/nbt.3796.
Haft DH. Using comparative genomics to drive new discoveries in microbiology. Curr Opin Microbiol. 2015;23:189–96. https://doi.org/10.1016/j.mib.2014.11.017.
Article CAS PubMed Google Scholar
Hao T, Wu D, Zhao L, Wang Q, Wang E, Sun J. The genome-scale integrated networks in microorganisms. Front Microbiol. 2018;9:296. https://doi.org/10.3389/fmicb.2018.00296.
Article PubMed PubMed Central Google Scholar
Harwood CR, Pohl S, Smith W, Wipat A. Bacillus subtilis. Model Gram-Positive Synthetic Biology Chassis. In: Methods in microbiology. Copyright {©} 2013 Elsevier Ltd. All rights reserved. 1st ed; 2013. https://doi.org/10.1016/B978-0-12-417029-2.00004-2.
Chapter Google Scholar
Hirasawa T, Shimizu H. Recent advances in amino acid production by microbial cells. Curr Opin Biotechnol. 2016;42:133–46. https://doi.org/10.1016/j.copbio.2016.04.017.
Article CAS PubMed Google Scholar
Ho S-H, Nakanishi A, Ye X, Chang J-S, Hara K, Hasunuma T, Kondo A. Optimizing biodiesel production in marine Chlamydomonas sp. JSC4 through metabolic profiling and an innovative salinity-gradient strategy. Biotechnol Biofuels. 2014;7:97. https://doi.org/10.1186/1754-6834-7-97.
Article CAS PubMed PubMed Central Google Scholar
Hong K-K, Vongsangnak W, Vemuri GN, Nielsen J. Unravelling evolutionary strategies of yeast for improving galactose utilization through integrated systems level analysis. Proc Natl Acad Sci. 2011;108:12179–84. https://doi.org/10.1073/pnas.1103219108.
Article PubMed PubMed Central Google Scholar
Hoynes-O’Connor A, Moon TS. Programmable genetic circuits for pathway engineering. Curr Opin Biotechnol. 2015;36:115–21. https://doi.org/10.1016/j.copbio.2015.08.007.
Article CAS PubMed Google Scholar
Isaacs FJ, Carr PA, Wang HH, Lajoie MJ, Sterling B, Kraal L, Tolonen AC, Gianoulis TA, Goodman DB, Reppas NB, Emig CJ, Bang D, Hwang SJ, Jewett MC, Jacobson JM, Church GM. Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science. 2011;333:348–53. https://doi.org/10.1126/science.1205822.
Article CAS PubMed PubMed Central Google Scholar
Jakočiunas T, Jensen MK, Keasling JD. CRISPR/Cas9 advances engineering of microbial cell factories. Metab Eng. 2016;34:44–59. https://doi.org/10.1016/j.ymben.2015.12.003.
Article CAS PubMed Google Scholar
Janssen BD, Hayes CS. The tm RNA ribosome-rescue system. Adv Protein Chem Struct Biol. 2012;86:151–91. https://doi.org/10.1016/B978-0-12-386497-0.00005-0.
Article CAS PubMed PubMed Central Google Scholar
Jiang Y, Chen B, Duan C, Sun B, Yang J, Yang S. Multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system. Appl Environ Microbiol. 2015;81:2506–14. https://doi.org/10.1128/aem.04023-14.
Article CAS PubMed PubMed Central Google Scholar
Jones P, Binns D, Chang H-Y, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, Pesseat S, Quinn AF, Sangrador-Vegas A, Scheremetjew M, Yong S-Y, Lopez R, Hunter S. InterProScan 5: genome-scale protein function classification. Bioinformatics. 2014;30:1236–40. https://doi.org/10.1093/bioinformatics/btu031.
Article CAS PubMed PubMed Central Google Scholar
Jones JA, Vernacchio VR, Lachance DM, Lebovich M, Fu L, Shirke AN, Schultz VL, Cress B, Linhardt RJ, Koffas MAG. EPathOptimize: a combinatorial approach for transcriptional balancing of metabolic pathways. Sci Rep. 2015;5:1–10. https://doi.org/10.1038/srep11301.
Article CAS Google Scholar
Kanehisa M. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 2006;34:D354–7. https://doi.org/10.1093/nar/gkj102.
Article CAS PubMed Google Scholar
Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM, Bolival B, Assad-Garcia N, Glass JI, Covert MW. A whole-cell computational model predicts phenotype from genotype. Cell. 2012;150:389–401. https://doi.org/10.1016/j.cell.2012.05.044.
Article CAS PubMed PubMed Central Google Scholar
Keasling JD, Chubukov V, Mukhopadhyay A, Petzold CJ, Keasling JD, Martín HG. Synthetic and systems biology for microbial production of commodity chemicals. NPJ Syst Biol Appl. 2016;2:16009. https://doi.org/10.1038/npjsba.2016.9.
Article CAS PubMed PubMed Central Google Scholar
Kim HU, Kim TY, Kim WJ, Lee SY, Park HM, Park JM. Flux variability scanning based on enforced objective flux for identifying gene amplification targets. Bmc Syst Biol. 2012a;6:106. https://doi.org/10.1186/1752-0509-6-106.
Article PubMed PubMed Central Google Scholar
Kim TY, Sohn SB, Kim YB, Kim WJ, Lee SY. Recent advances in reconstruction and applications of genome-scale metabolic models. Curr Opin Biotechnol. 2012b;23:617–23. https://doi.org/10.1016/j.copbio.2011.10.007.
Article CAS PubMed Google Scholar
Kim B, Kim WJ, Kim DI, Lee SY. Applications of genome-scale metabolic network model in metabolic engineering. J Ind Microbiol Biotechnol. 2014;42:339–48. https://doi.org/10.1007/s10295-014-1554-9.
Article CAS PubMed Google Scholar
Kim MK, Lane A, Kelley JJ, Lun DS. E-Flux2 and SPOT: validated methods for inferring intracellular metabolic flux distributions from transcriptomic data. PLoS One. 2016;11:e0157101. https://doi.org/10.1371/journal.pone.0157101.
Article CAS PubMed PubMed Central Google Scholar
King ZA, Feist AM. Optimizing cofactor specificity of oxidoreductase enzymes for the generation of microbial production strains—OptSwap. Ind Biotechnol. 2013;9:236–46. https://doi.org/10.1089/ind.2013.0005.
Article CAS Google Scholar
Knott GJ, Doudna JA. CRISPR-Cas guides the future of genetic engineering. Science. 2018; https://doi.org/10.1126/science.aat5011.
Kochanowski K, Sauer U, Chubukov V. Somewhat in control-the role of transcription in regulating microbial metabolic fluxes. Curr Opin Biotechnol. 2013;24:987–93. https://doi.org/10.1016/j.copbio.2013.03.014.
Article CAS PubMed Google Scholar
Korneli C, Bolten CJ, Godard T, Franco-Lara E, Wittmann C. Debottlenecking recombinant protein production in Bacillus megaterium under large-scale conditions-targeted precursor feeding designed from metabolomics. Biotechnol Bioeng. 2012;109:1538–50. https://doi.org/10.1002/bit.24434.
Article CAS PubMed Google Scholar
Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T, Ussery DW. RNAmmer. Nucleic Acids Res. 2007;35:3100–8. https://doi.org/10.1093/nar/gkm160.
Article CAS PubMed PubMed Central Google Scholar
Lalwani MA, Zhao EM, Avalos JL. Current and future modalities of dynamic control in metabolic engineering. Curr Opin Biotechnol. 2018;52:56–65. https://doi.org/10.1016/j.copbio.2018.02.007.
Article CAS PubMed Google Scholar
Lee SY, Kim HU. Systems strategies for developing industrial microbial strains. Nat Biotechnol. 2015;33:1061–72. https://doi.org/10.1038/nbt.3365.
Article CAS PubMed Google Scholar
Lee JW, Kim HU, Choi S, Yi J, Lee SY. Microbial production of building block chemicals and polymers. Curr Opin Biotechnol. 2011;22:758–67. https://doi.org/10.1016/j.copbio.2011.02.011.
Article CAS PubMed Google Scholar
Lee JW, Na D, Park JM, Lee J, Choi S, Lee SY. Systems metabolic engineering for natural and non-natural chemicals. Nat Chem Biol. 2012;8:536–46. https://doi.org/10.1038/nchembio.970.
Article CAS PubMed Google Scholar
Li W, Li HX, Ji SY, Li S, Gong YS, Yang MM, Chen YL. Characterization of two temperature-inducible promoters newly isolated from B. subtilis. Biochem Biophys Res Commun. 2007;358:1148–53. https://doi.org/10.1016/j.bbrc.2007.05.064.
Article CAS PubMed Google Scholar
Li S, Jendresen CB, Grünberger A, Ronda C, Jensen SI, Noack S, Nielsen AT. Enhanced protein and biochemical production using CRISPRi-based growth switches. Metab Eng. 2016;38:274–84. https://doi.org/10.1016/j.ymben.2016.09.003.
Article CAS PubMed Google Scholar
Li L, Liu X, Wei K, Lu Y, Jiang W. Synthetic biology approaches for chromosomal integration of genes and pathways in industrial microbial systems. Biotechnol Adv. 2019; https://doi.org/10.1016/j.biotechadv.2019.04.002.
Lian J, HamediRad M, Hu S, Zhao H. Combinatorial metabolic engineering using an orthogonal tri-functional CRISPR system. Nat Commun. 2017;8:1688. https://doi.org/10.1038/s41467-017-01695-x.
Article CAS PubMed PubMed Central Google Scholar
Lian J, Mishra S, Zhao H. Recent advances in metabolic engineering of Saccharomyces cerevisiae: new tools and their applications. Metab Eng. 2018;50:85–108. https://doi.org/10.1016/j.ymben.2018.04.011.
Article CAS PubMed Google Scholar
Ling H, Teo W, Chen B, Leong SSJ, Chang MW. Microbial tolerance engineering toward biochemical production: from lignocellulose to products. Curr Opin Biotechnol. 2014;29:99–106. https://doi.org/10.1016/j.copbio.2014.03.005.
Article CAS PubMed Google Scholar
Link H, Kochanowski K, Sauer U. Systematic identification of allosteric protein-metabolite interactions that control enzyme activity in vivo. Nat Biotechnol. 2013;31:357–61. https://doi.org/10.1038/nbt.2489.
Article CAS PubMed Google Scholar
Link H, Christodoulou D, Sauer U. Advancing metabolic models with kinetic information. Curr Opin Biotechnol. 2014;29:8–14. https://doi.org/10.1016/j.copbio.2014.01.015.
Article CAS PubMed Google Scholar
Link H, Fuhrer T, Gerosa L, Zamboni N, Sauer U. Real-time metabolome profiling of the metabolic switch between starvation and growth. Nat Methods. 2015;12 https://doi.org/10.1038/nmeth.3584.
Liu D, Zhang F. Metabolic feedback circuits provide rapid control of metabolite dynamics. ACS Synth Biol. 2018;7:347–56. https://doi.org/10.1021/acssynbio.7b00342.
Article CAS PubMed Google Scholar
Liu Y, Zhu Y, Li J, Shin HD, Chen RR, Du G, Liu L, Chen J. Modular pathway engineering of Bacillus subtilis for improved N-acetylglucosamine production. Metab Eng. 2014;23:42–52. https://doi.org/10.1016/j.ymben.2014.02.005.
Article CAS PubMed Google Scholar
Liu Y, Link H, Liu L, Du G, Chen J, Sauer U. A dynamic pathway analysis approach reveals a limiting futile cycle in N-acetylglucosamine overproducing Bacillus subtilis. Nat Commun. 2016;7:11933. https://doi.org/10.1038/ncomms11933.
Article PubMed PubMed Central Google Scholar
Liu L, Guan N, Li J, Shin H, Du G, Chen J. Development of GRAS strains for nutraceutical production using systems and synthetic biology approaches: advances and prospects. Crit Rev Biotechnol. 2017a;37:139–50. https://doi.org/10.3109/07388551.2015.1121461.
Article CAS PubMed Google Scholar
Liu Y, Li J, Du G, Chen J, Liu L. Metabolic engineering of Bacillus subtilis fueled by systems biology: recent advances and future directions. Biotechnol Adv. 2017b;35:20–30. https://doi.org/10.1016/j.biotechadv.2016.11.003.
Article CAS PubMed Google Scholar
Liu D, Mao Z, Guo J, Wei L, Ma H, Tang Y, Chen T, Wang Z, Zhao X. Construction, model-based analysis, and characterization of a promoter library for fine-tuned gene expression in Bacillus subtilis. ACS Synth Biol. 2018;7:1785–97. https://doi.org/10.1021/acssynbio.8b00115.
Article CAS PubMed Google Scholar
López-Fernández L, Sanchis M, Navarro-Rodríguez P, Nicolás FE, Silva-Franco F, Guarro J, Garre V, Navarro-Mendoza MI, Pérez-Arques C, Capilla J. Understanding Mucor circinelloides pathogenesis by comparative genomics and phenotypical studies. Virulence. 2018;9:707–20. https://doi.org/10.1080/21505594.2018.1435249.
Article CAS PubMed PubMed Central Google Scholar
Lu H, Villada JC, Lee PKH. Modular metabolic engineering for biobased chemical production. Trends Biotechnol. 2019;37:152–66. https://doi.org/10.1016/j.tibtech.2018.07.003.
Article CAS PubMed Google Scholar
Magrane M, Consortium U. UniProt Knowledgebase: a hub of integrated protein data. Database. 2011;2011:bar009. https://doi.org/10.1093/database/bar009.
Article CAS PubMed PubMed Central Google Scholar
Man S, Cheng R, Miao C, Gong Q, Gu Y, Lu X, Han F, Yu W. Artificial trans-encoded small non-coding RNAs specifically silence the selected gene expression in bacteria. Nucleic Acids Res. 2011;39:e50. https://doi.org/10.1093/nar/gkr034.
Article CAS PubMed PubMed Central Google Scholar
Mansell TJ, Warner JR, Gill RT. Trackable multiplex recombineering for gene-trait mapping in E. coli. In: Alper HS, editor. Methods in molecular biology. Totowa: Humana Press; 2013. p. 223–46. https://doi.org/10.1007/978-1-62703-299-5_12.
Chapter Google Scholar
Mattozzi M, Zang Y, Gupta M, Wu X, Plassmeier J, Clarkson S, Zha J, Koffas MAG. Metabolic engineering of Corynebacterium glutamicum for anthocyanin production. Microb Cell Fact. 2018;17:1–13. https://doi.org/10.1186/s12934-018-0990-z.
Article CAS Google Scholar
McClymont K, Soyer OS. Metabolic tinker: an online tool for guiding the design of synthetic metabolic pathways. Nucleic Acids Res. 2013;41:e113. https://doi.org/10.1093/nar/gkt234.
Article CAS PubMed PubMed Central Google Scholar
Microarray-derived TU, Church G. Direct mutagenesis of thousands of genomic. ACS Synth Biol. 2014;4:1–10. https://doi.org/10.1021/sb5001565.
Article CAS Google Scholar
Miller MB, Bassler BL. Quorum sensing in bacteria. Annu Rev Microbiol. 2001;55:165–99. https://doi.org/10.1146/annurev.micro.55.1.165.
Article CAS PubMed Google Scholar
Miller JR, Delcher AL, Koren S, Venter E, Walenz BP, Brownley A, Johnson J, Li K, Mobarry C, Sutton G. Aggressive assembly of pyrosequencing reads with mates. Bioinformatics. 2008;24:2818–24. https://doi.org/10.1093/bioinformatics/btn548.
Article CAS PubMed PubMed Central Google Scholar
Motlagh HN, Wrabl JO, Li J, Hilser VJ. The ensemble nature of allostery. Nature. 2014;508:331–9. https://doi.org/10.1038/nature13001.
Article CAS PubMed PubMed Central Google Scholar
Na D, Yoo SM, Chung H, Park H, Park JH, Lee SY. Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs. Nat Biotechnol. 2013;31:170–4. https://doi.org/10.1038/nbt.2461.
Article CAS PubMed Google Scholar
Nielsen J, Jewett MC. Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae. FEMS Yeast Res. 2008;8:122–31. https://doi.org/10.1111/j.1567-1364.2007.00302.x.
Article CAS PubMed Google Scholar
Nielsen J, Keasling JD. Engineering cellular metabolism. Cell. 2016;164:1185–97. https://doi.org/10.1016/j.cell.2016.02.004.
Article CAS PubMed Google Scholar
Nielsen J, Larsson C, van Maris A, Pronk J. Metabolic engineering of yeast for production of fuels and chemicals. Curr Opin Biotechnol. 2013;24:398–404. https://doi.org/10.1016/j.copbio.2013.03.023.
Article CAS PubMed Google Scholar
Nielsen J, Fussenegger M, Keasling J, Lee SY, Liao JC, Prather K, Palsson B. Engineering synergy in biotechnology. Nat Chem Biol. 2014;10:319–22. https://doi.org/10.1038/nchembio.1519.
Article CAS PubMed Google Scholar
Nikel PI, de Lorenzo V. Pseudomonas putida as a functional chassis for industrial biocatalysis: From native biochemistry to trans-metabolism. Metab Eng. 2018;0–1 https://doi.org/10.1016/j.ymben.2018.05.005.
Niu T, Liu Y, Li J, Koffas M, Du G, Alper HS, Liu L. Engineering a glucosamine-6-phosphate responsive glmS Ribozyme switch enables dynamic control of metabolic flux in Bacillus subtilis for overproduction of N-acetylglucosamine. ACS Synth Biol. 2018;7:2423–35. https://doi.org/10.1021/acssynbio.8b00196.
Article CAS PubMed Google Scholar
Nowroozi FF, Baidoo EEK, Ermakov S, Redding-Johanson AM, Batth TS, Petzold CJ, Keasling JD. Metabolic pathway optimization using ribosome binding site variants and combinatorial gene assembly. Appl Microbiol Biotechnol. 2014;98:1567–81. https://doi.org/10.1007/s00253-013-5361-4.
Article CAS PubMed Google Scholar
O’Brien EJ, Monk JM, Palsson BO. Using genome-scale models to predict biological capabilities. Cell. 2015;161:971–87. https://doi.org/10.1016/j.cell.2015.05.019.
Article CAS PubMed PubMed Central Google Scholar
Oliva G, Sahr T, Buchrieser C. Small RNAs, 5’ UTR elements and RNA-binding proteins in intracellular bacteria: Impact on metabolism and virulence. FEMS Microbiol Rev. 2015;39:331–49. https://doi.org/10.1093/femsre/fuv022.
Article CAS PubMed Google Scholar
Panahi R, Vasheghani-Farahani E, Shojaosadati SA, Bambai B. Induction of Bacillus subtilis expression system using environmental stresses and glucose starvation. Ann Microbiol. 2014;64:879–82. https://doi.org/10.1007/s13213-013-0719-5.
Article CAS Google Scholar
Park JH, Lee KH, Kim TY, Lee SY. Metabolic engineering of Escherichia coli for the production of L-valine based on transcriptome analysis and in silico gene knockout simulation. Proc Natl Acad Sci. 2007;104:7797–802. https://doi.org/10.1073/pnas.0702609104.
Article CAS PubMed PubMed Central Google Scholar
Peralta-Yahya PP, Zhang F, Del Cardayre SB, Keasling JD. Microbial engineering for the production of advanced biofuels. Nature. 2012;488:320–8. https://doi.org/10.1038/nature11478.
Article CAS PubMed Google Scholar
Pharkya P. OptStrain: a computational framework for redesign of microbial production systems. Genome Res. 2004;14:2367–76. https://doi.org/10.1101/gr.2872004.
Article CAS PubMed PubMed Central Google Scholar
Pontrelli S, Chiu TY, Lan EI, Chen FYH, Chang P, Liao JC. Escherichia coli as a host for metabolic engineering. Metab Eng. 2018;0–1 https://doi.org/10.1016/j.ymben.2018.04.008.
Qi L, Lucks JB, Liu CC, Mutalik VK, Arkin AP. Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals. Nucleic Acids Res. 2012;40:5775–86. https://doi.org/10.1093/nar/gks168.
Article CAS PubMed PubMed Central Google Scholar
Qiao K, Wasylenko TM, Zhou K, Xu P, Stephanopoulos G. Lipid production in Yarrowia lipolytica is maximized by engineering cytosolic redox metabolism. Nat Biotechnol. 2017;35:173–7. https://doi.org/10.1038/nbt.3763.
Article CAS PubMed Google Scholar
Rahimi T, Niazi A, Deihimi T, Taghavi SM, Ayatollahi S, Ebrahimie E. Genome annotation and comparative genomic analysis of Bacillus subtilis MJ01, a new bio-degradation strain isolated from oil-contaminated soil. Funct Integr Genomics. 2018;18:533–43. https://doi.org/10.1007/s10142-018-0604-1.
Article CAS PubMed Google Scholar
Redden H, Alper HS. The development and characterization of synthetic minimal yeast promoters. Nat Commun. 2015;6:7810.
Article CAS PubMed Google Scholar
Richter F, Fonfara I, Gelfert R, Nack J, Charpentier E. Switchable Cas9. Curr Opin Biotechnol. 2017;48:119–26. https://doi.org/10.1016/j.copbio.2017.03.025.
Article CAS PubMed Google Scholar
Ronda C, Pedersen LE, Sommer MOA, Nielsen AT. CRMAGE: CRISPR optimized MAGE recombineering. Sci Rep. 2016;6:19452. https://doi.org/10.1038/srep19452.
Article CAS PubMed PubMed Central Google Scholar
Rozkov A, Avignone-Rossa CA, Ertl PF, Jones P, O’Kennedy RD, Smith JJ, Dale JW, Bushell ME. Characterization of the metabolic burden on Escherichia coli DH1 cells imposed by the presence of a plasmid containing a gene therapy sequence. Biotechnol Bioeng. 2004;88:909–15. https://doi.org/10.1002/bit.20327.
Article CAS PubMed Google Scholar
Salis HM, Mirsky E a, Voigt C a. Automated design of synthetic ribosome binding sites to control protein expression. Nat Biotechnol. 2009;27:946–50. https://doi.org/10.1038/nbt.1568.
Article CAS PubMed PubMed Central Google Scholar
Sandoval NR, Kim JYH, Glebes TY, Reeder PJ, Aucoin HR, Warner JR, Gill RT. Strategy for directing combinatorial genome engineering in Escherichia coli. Proc Natl Acad Sci. 2012;109:10540–5. https://doi.org/10.1073/pnas.1206299109.
Article PubMed PubMed Central Google Scholar
Serganov A, Patel DJ. Ribozymes, riboswitches and beyond: regulation of gene expression without proteins. Nat Rev Genet. 2007;8:776–90. https://doi.org/10.1038/nrg2172.
Article CAS PubMed PubMed Central Google Scholar
Sévin DC, Kuehne A, Zamboni N, Sauer U. Biological insights through nontargeted metabolomics. Curr Opin Biotechnol. 2015;34:1–8. https://doi.org/10.1016/j.copbio.2014.10.001.
Article CAS PubMed Google Scholar
Sharan SK, Thomason LC, Kuznetsov SG, Court DL. Recombineering: A homologous recombination-based method of genetic engineering. Nat Protoc. 2009;4:206–23. https://doi.org/10.1038/nprot.2008.227.
Article CAS PubMed PubMed Central Google Scholar
Shi S, Chen T, Zhang Z, Chen X, Zhao X. Transcriptome analysis guided metabolic engineering of Bacillus subtilis for riboflavin production. Metab Eng. 2009;11:243–52. https://doi.org/10.1016/j.ymben.2009.05.002.
Article CAS PubMed Google Scholar
Si T, Li B, Comi TJ, Wu Y, Hu P, Wu Y, Min Y, Mitchell DA, Zhao H, Sweedler JV. Profiling of microbial colonies for high-throughput engineering of multistep enzymatic reactions via optically guided matrix-assisted laser desorption/ionization mass spectrometry. J Am Chem Soc. 2017;139:12466–73. https://doi.org/10.1021/jacs.7b04641.
Article CAS PubMed PubMed Central Google Scholar
Singh V, Braddick D. Recent advances and versatility of MAGE towards industrial applications. Syst Synth Biol. 2015;9:1–9. https://doi.org/10.1007/s11693-015-9184-8.
Article CAS PubMed PubMed Central Google Scholar
Smanski MJ, Bhatia S, Zhao D, Park Y, B A Woodruff L, Giannoukos G, Ciulla D, Busby M, Calderon J, Nicol R, Gordon DB, Densmore D, Voigt C a. Functional optimization of gene clusters by combinatorial design and assembly. Nat Biotechnol. 2014;32:1241–9. https://doi.org/10.1038/nbt.3063.
Article CAS PubMed Google Scholar
Snoek T, Chaberski EK, Ambri F, Kol S, Bjørn SP, Pang B, Barajas JF, Welner DH, Jensen MK, Keasling JD. Evolution-guided engineering of small-molecule biosensors. Biorxiv. 2019; https://doi.org/10.1101/601823.
Solomon KV, Sanders TM, Prather KLJ. A dynamic metabolite valve for the control of central carbon metabolism. Metab Eng. 2012;14:661–71. https://doi.org/10.1016/j.ymben.2012.08.006.
Article CAS PubMed Google Scholar
Soma Y, Hanai T. Self-induced metabolic state switching by a tunable cell density sensor for microbial isopropanol production. Metab Eng. 2015;30:7–15. https://doi.org/10.1016/j.ymben.2015.04.005.
Article CAS PubMed Google Scholar
Soma Y, Tsuruno K, Wada M, Yokota A, Hanai T. Metabolic flux redirection from a central metabolic pathway toward a synthetic pathway using a metabolic toggle switch. Metab Eng. 2014;23:175–84. https://doi.org/10.1016/j.ymben.2014.02.008.
Article CAS PubMed Google Scholar
Song CW, Kim DI, Choi S, Jang JW, Lee SY. Metabolic engineering of Escherichia coli for the production of fumaric acid. Biotechnol Bioeng. 2013;110:2025–34. https://doi.org/10.1002/bit.24868.
Article CAS PubMed Google Scholar
Stalidzans E, Seiman A, Peebo K, Komasilovs V, Pentjuss A. Model-based metabolism design: constraints for kinetic and stoichiometric models. Biochem Soc Trans. 2018;46:261–7. https://doi.org/10.1042/BST20170263.
Article CAS PubMed PubMed Central Google Scholar
Stephanopoulos G. Synthetic biology and metabolic engineering. ACS Synth Biol. 2012;1:514–25. https://doi.org/10.1021/sb300094q.
Article CAS PubMed Google Scholar
Stephanopoulos G, Vallino J. Network rigidity and metabolic engineering in metabolite overproduction. Science. 1991;252:1675–81. https://doi.org/10.1126/science.1904627.
Article CAS PubMed Google Scholar
Sukhija K, Pyne M, Ali S, Orr V, Abedi D, Moo-Young M, Chou CP. Developing an extended genomic engineering approach based on recombineering to knock-in heterologous genes to Escherichia coli genome. Mol Biotechnol. 2012;51:109–18. https://doi.org/10.1007/s12033-011-9442-2.
Article CAS PubMed Google Scholar
Sun Z, Meng H, Li J, Wang J, Li Q, Wang Y, Zhang Y. Identification of novel knockout targets for improving terpenoids biosynthesis in saccharomyces cerevisiae. PLoS One. 2014;9:e112615. https://doi.org/10.1371/journal.pone.0112615.
Article CAS PubMed PubMed Central Google Scholar
Tang SY, Cirino PC. Design and application of a mevalonate-responsive regulatory protein. Angew Chemie Int Ed. 2011;50:1084–6. https://doi.org/10.1002/anie.201006083.
Article CAS Google Scholar
Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV. The COG database. Nucleic Acids Res. 2000;29:22–8.
Article Google Scholar
Tietz JI, Schwalen CJ, Patel PS, Maxson T, Blair PM, Tai HC, Zakai UI, Mitchell DA. A new genome-mining tool redefines the lasso peptide biosynthetic landscape. Nat Chem Biol. 2017;13:470–8. https://doi.org/10.1038/nchembio.2319.
Article CAS PubMed PubMed Central Google Scholar
Tomari Y, Zamore PD. Machines for RNAi. Genes Dev. 2005;19:517–29. https://doi.org/10.1101/gad.1284105.Box.
Article CAS PubMed Google Scholar
Tong Z, Zheng X, Tong Y, Shi YC, Sun J. Systems metabolic engineering for citric acid production by Aspergillus niger in the post-genomic era. Microb Cell Fact. 2019;18:28. https://doi.org/10.1186/s12934-019-1064-6.
Article PubMed PubMed Central Google Scholar
Torella JP, Ford TJ, Kim SN, Chen AM, Way JC, Silver PA. Tailored fatty acid synthesis via dynamic control of fatty acid elongation. Proc Natl Acad Sci. 2013;110:11290–5. https://doi.org/10.1073/pnas.1307129110.
Article PubMed PubMed Central Google Scholar
van Dijk EL, Jaszczyszyn Y, Naquin D, Thermes C. The third revolution in sequencing technology. Trends Genet. 2018;34:666–81. https://doi.org/10.1016/j.tig.2018.05.008.
Article CAS PubMed Google Scholar
van Tilburg AY, Cao H, van der Meulen SB, Solopova A, Kuipers OP. Metabolic engineering and synthetic biology employing Lactococcus lactis and Bacillus subtilis cell factories. Curr Opin Biotechnol. 2019;59:1–7. https://doi.org/10.1016/j.copbio.2019.01.007.
Article CAS PubMed Google Scholar
Wang HH, Isaacs FJ, Carr P a, Sun ZZ, Xu G, Forest CR, Church GM. Programming cells by multiplex genome engineering and accelerated evolution. Nature. 2009;460:894–8. https://doi.org/10.1038/nature08187.
Article CAS PubMed PubMed Central Google Scholar
Wang HH, Kim H, Cong L, Jeong J, Bang D, Church GM. Genome-scale promoter engineering by coselection MAGE. Nat Methods. 2012;9:591–3. https://doi.org/10.1038/nmeth.1971.
Article CAS PubMed PubMed Central Google Scholar
Wang C, Pfleger BF, Kim SW. Reassessing Escherichia coli as a cell factory for biofuel production. Curr Opin Biotechnol. 2017a;45:92–103. https://doi.org/10.1016/j.copbio.2017.02.010.
Article CAS PubMed Google Scholar
Wang L, Dash S, Ng CY, Maranas CD. A review of computational tools for design and reconstruction of metabolic pathways. Synth Syst Biotechnol. 2017b;2:243–52. https://doi.org/10.1016/j.synbio.2017.11.002.
Article PubMed PubMed Central Google Scholar
Wang X, He Q, Yang Y, Wang J, Haning K, Hu Y, Wu B, He M, Zhang Y, Bao J, Contreras LM, Yang S. Advances and prospects in metabolic engineering of Zymomonas mobilis. Metab Eng. 2018;50:57–73. https://doi.org/10.1016/j.ymben.2018.04.001.
Article CAS PubMed Google Scholar
Waters LS, Storz G. Regulatory RNAs in bacteria. Cell. 2009;136:615–28. https://doi.org/10.1016/j.cell.2009.01.043.
Article CAS PubMed PubMed Central Google Scholar
Williams TC, Averesch NJ, Plan M, Winter G, Vickers CE, Nielsen LK, Krömer JO, Lekieffre N, Winter G, Vickers CE, Nielsen LK, Krömer JO. Quorum-sensing linked RNAi for dynamic pathway control in Saccharomyces cerevisiae. Metab Eng. 2015a;29:124–34. https://doi.org/10.1016/j.ymben.2015.03.008.
Article CAS PubMed Google Scholar
Williams TC, Espinosa MI, Nielsen LK, Vickers CE. Dynamic regulation of gene expression using sucrose responsive promoters and RNA interference in Saccharomyces cerevisiae. Microb Cell Fact. 2015b;14:43. https://doi.org/10.1186/s12934-015-0223-7.
Article CAS PubMed PubMed Central Google Scholar
Winkler WC, Breaker RR. Regulation of bacterial gene expression by riboswitches. Annu Rev Microbiol. 2005;59:487–517. https://doi.org/10.1146/annurev.micro.59.030804.121336.
Article CAS PubMed Google Scholar
Woolston BM, Edgar S, Stephanopoulos G. Metabolic engineering: past and future. Annu Rev Chem Biomol Eng. 2013;4:259–88. https://doi.org/10.1146/annurev-chembioeng-061312-103312.
Article CAS PubMed Google Scholar
Wu J, Du G, Zhou J, Chen J. Metabolic engineering of Escherichia coli for (2S)-pinocembrin production from glucose by a modular metabolic strategy. Metab Eng. 2013;16:48–55. https://doi.org/10.1016/j.ymben.2012.11.009.
Article CAS PubMed Google Scholar
Wu Y, Chen T, Liu Y, Lv X, Li J, Du G, Ledesma-Amaro R, Liu L. CRISPRi allows optimal temporal control of N-acetylglucosamine bioproduction by a dynamic coordination of glucose and xylose metabolism in Bacillus subtilis. Metab Eng. 2018;49:232–41. https://doi.org/10.1016/j.ymben.2018.08.012.
Article CAS PubMed Google Scholar
Xu P. Production of chemicals using dynamic control of metabolic fluxes. Curr Opin Biotechnol. 2018;53:12–9. https://doi.org/10.1016/j.copbio.2017.10.009.
Article CAS PubMed Google Scholar
Xu P, Gu Q, Wang W, Wong L, Bower AG, Collins CH, Koffas MA. Modular optimization of multi-gene pathways for fatty acids production in E. coli. Nat Commun. 2013;4:1409. https://doi.org/10.1038/ncomms2425.
Article CAS PubMed Google Scholar
Xu P, Li L, Zhang F, Stephanopoulos G, Koffas M. Improving fatty acids production by engineering dynamic pathway regulation and metabolic control. Proc Natl Acad Sci. 2014;111:11299–304. https://doi.org/10.1073/pnas.1406401111.
Article CAS PubMed PubMed Central Google Scholar
Yang Y, Lin Y, Li L, Linhardt RJ, Yan Y. Regulating malonyl-CoA metabolism via synthetic antisense RNAs for enhanced biosynthesis of natural products. Metab Eng. 2015;29:217–26. https://doi.org/10.1016/j.ymben.2015.03.018.
Article CAS PubMed Google Scholar
Yang Y, Lin Y, Wang J, Wu Y, Zhang R, Cheng M, Shen X, Wang J, Chen Z, Li C, Yuan Q, Yan Y. Sensor-regulator and RNAi based bifunctional dynamic control network for engineered microbial synthesis. Nat Commun. 2018;9:1–10. https://doi.org/10.1038/s41467-018-05466-0.
Article CAS Google Scholar
Yang D, Yoo SM, Gu C, Ryu JY, Lee JE, Lee SY. Expanded synthetic small regulatory RNA expression platforms for rapid and multiplex gene expression knockdown. Metab Eng. 2019; https://doi.org/10.1016/j.ymben.2019.04.003.
Yim H, Haselbeck R, Niu W, Pujol-Baxley C, Burgard A, Boldt J, Khandurina J, Trawick JD, Osterhout RE, Stephen R, Estadilla J, Teisan S, Schreyer HB, Andrae S, Yang TH, Lee SY, Burk MJ, Van Dien S. Metabolic engineering of Escherichia coli for direct production of 1, 4-butanediol. Nat Chem Biol. 2011;7:445–52. https://doi.org/10.1038/nchembio.580.
Article CAS PubMed Google Scholar
Yim SS, An SJ, Kang M, Lee J, Jeong KJ. Isolation of fully synthetic promoters for high-level gene expression in corynebacterium glutamicum. Biotechnol Bioeng. 2013;110:2959–69. https://doi.org/10.1002/bit.24954.
Article CAS PubMed Google Scholar
Yu D, Ellis HM, Lee E-C, Jenkins NA, Copeland NG, Court DL. An efficient recombination system for chromosome engineering in Escherichia coli. Proc Natl Acad Sci. 2002;97:5978–83. https://doi.org/10.1073/pnas.100127597.
Article Google Scholar
Yu B, Zhang X, Sun W, Xi X, Zhao N, Huang Z, Ying Z, Liu L, Liu D, Niu H, Wu J, Zhuang W, Zhu C, Chen Y, Ying H. Continuous citric acid production in repeated-fed batch fermentation by Aspergillus niger immobilized on a new porous foam. J Biotechnol. 2018;276–277:1–9. https://doi.org/10.1016/j.jbiotec.2018.03.015.
Article CAS PubMed Google Scholar
Zalatan JG, Lee ME, Almeida R, Gilbert LA, Whitehead EH, La Russa M, Tsai JC, Weissman JS, Dueber JE, Qi LS, Lim WA. Engineering complex synthetic transcriptional programs with CRISPR RNA Scaffolds. Cell. 2015;160:339–50. https://doi.org/10.1016/j.cell.2014.11.052.
Article CAS PubMed Google Scholar
Zampieri M, Sekar K, Zamboni N, Sauer U. Frontiers of high-throughput metabolomics. Curr Opin Chem Biol. 2017;36:15–23. https://doi.org/10.1016/j.cbpa.2016.12.006.
Article CAS PubMed Google Scholar
Zelcbuch L, Antonovsky N, Bar-Even A, Levin-Karp A, Barenholz U, Dayagi M, Liebermeister W, Flamholz A, Noor E, Amram S, Brandis A, Bareia T, Yofe I, Jubran H, Milo R. Spanning high-dimensional expression space using ribosome-binding site combinatorics. Nucleic Acids Res. 2013;41 https://doi.org/10.1093/nar/gkt151.
Zhang Y, Buchholz F, Muyrers JPP, Francis Stewart A. A new logic for DNA engineering using recombination in Escherichia coli. Nat Genet. 1998;20:123–8. https://doi.org/10.1038/2417.
Article CAS PubMed Google Scholar
Zhang F, Carothers JM, Keasling JD. Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids. Nat Biotechnol. 2012;30:354–9. https://doi.org/10.1038/nbt.2149.
Article CAS PubMed Google Scholar
Zhang F, Wen Y, Guo X. CRISPR/Cas9 for genome editing: progress, implications and challenges. Hum Mol Genet. 2014;23:R40–6. https://doi.org/10.1093/hmg/ddu125.
Article CAS PubMed Google Scholar
Zhang X, Tervo CJ, Reed JL. Metabolic assessment of E. coli as a Biofactory for commercial products. Metab Eng. 2016;35:64–74. https://doi.org/10.1016/j.ymben.2016.01.007.
Article CAS PubMed Google Scholar
Zhou LB, Zeng AP. Exploring Lysine Riboswitch For Metabolic Flux Control And Improvement of l -lysine synthesis in Corynebacterium glutamicum. ACS Synth Biol. 2015a;4:729–34. https://doi.org/10.1021/sb500332c.
Article CAS PubMed Google Scholar
Zhou LB, Zeng AP. Engineering a lysine-ON riboswitch for metabolic control of lysine production in Corynebacterium glutamicum. ACS Synth Biol. 2015b;4:1335–40. https://doi.org/10.1021/acssynbio.5b00075.
Article CAS PubMed Google Scholar
Zhou L, Niu DD, Tian KM, Chen XZ, Prior BA, Shen W, Shi GY, Singh S, Wang ZX. Genetically switched d-lactate production in Escherichia coli. Metab Eng. 2012;14:560–8. https://doi.org/10.1016/j.ymben.2012.05.004.
Article CAS PubMed Google Scholar
Zhou YJ, Kerkhoven EJ, Nielsen J. Barriers and opportunities in bio-based production of hydrocarbons. Nat Energy. 2018; https://doi.org/10.1038/s41560-018-0197-x.
Zhu L, Zhu Y, Zhang Y, Li Y. Engineering the robustness of industrial microbes through synthetic biology. Trends Microbiol. 2012;20:94–101. https://doi.org/10.1016/j.tim.2011.12.003.
Article CAS PubMed Google Scholar
Zhu X, Zhao D, Qiu H, Fan F, Man S, Bi C, Zhang X. The CRISPR/Cas9-facilitated multiplex pathway optimization (CFPO) technique and its application to improve the Escherichia coli xylose utilization pathway. Metab Eng. 2017;43:37–45. https://doi.org/10.1016/j.ymben.2017.08.003.
Article CAS PubMed Google Scholar
Zuo E, Huo X, Yao X, Hu X, Sun Y, Yin J, He B, Wang X, Shi L, Ping J, Wei Y, Ying W, Wei W, Liu W, Tang C, Li Y, Hu J, Yang H. CRISPR/Cas9-mediated targeted chromosome elimination. Genome Biol. 2017;18:224. https://doi.org/10.1186/s13059-017-1354-4.
Article CAS PubMed PubMed Central Google Scholar

Download references

Author information

Authors and Affiliations

Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
Yaokang Wu, Yang Gu, Rongzhen Tian, Guocheng Du & Long Liu
Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
Yaokang Wu, Yang Gu, Rongzhen Tian, Guocheng Du, Jian Chen & Long Liu

Authors

Yaokang Wu
View author publications
You can also search for this author in PubMed Google Scholar
Yang Gu
View author publications
You can also search for this author in PubMed Google Scholar
Rongzhen Tian
View author publications
You can also search for this author in PubMed Google Scholar
Guocheng Du
View author publications
You can also search for this author in PubMed Google Scholar
Jian Chen
View author publications
You can also search for this author in PubMed Google Scholar
Long Liu
View author publications
You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Long Liu .

Editor information

Editors and Affiliations

School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
Long Liu
School of Biotechnology, Jiangnan University, Wuxi, China
Jian Chen

Rights and permissions

Reprints and permissions

Copyright information

About this chapter

Cite this chapter

Wu, Y., Gu, Y., Tian, R., Du, G., Chen, J., Liu, L. (2019). Construction of Microbial Cell Factories by Systems and Synthetic Biotechnology. In: Liu, L., Chen, J. (eds) Systems and Synthetic Biotechnology for Production of Nutraceuticals . Springer, Singapore. https://doi.org/10.1007/978-981-15-0446-4_2

Download citation

DOI: https://doi.org/10.1007/978-981-15-0446-4_2
Published: 03 January 2020
Publisher Name: Springer, Singapore
Print ISBN: 978-981-15-0445-7
Online ISBN: 978-981-15-0446-4
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)

Publish with us

Policies and ethics