Citation: George H McArthur IV, Pooja P Nanjannavar, Emily H Miller, Stephen S Fong. Integrative metabolic engineering[J]. AIMS Bioengineering, 2015, 2(3): 93-103. doi: 10.3934/bioeng.2015.3.93
[1] |
Stephanopoulos G (2012) Synthetic Biology and Metabolic Engineering. ACS Synth Biol 1: 514-525. doi: 10.1021/sb300094q
![]() |
[2] | Klein-Marcuschamer D, Yadav VG, Ghaderi A, et al. (2010) De novo metabolic engineering and the promise of synthetic DNA. Adv Biochem Eng Biotechnol 120: 101-131. |
[3] | Yadav VG, Stephanopoulos G (2010) Reevaluating synthesis by biology. Curr Opin Microbiol 1-6. |
[4] | Nielsen J, Fussenegger M, Keasling J, et al. (2014) Engineering synergy in biotechnology. Nature Publishing Group 10: 319-322. |
[5] |
Church GM, Elowitz MB, Smolke CD, et al. (2014) Realizing the potential of synthetic biology. Nat Rev Mol Cell Biol 15: 289-294. doi: 10.1038/nrm3767
![]() |
[6] |
Bayer TS (2010) Transforming biosynthesis into an information science. Nat Chem Biol 6: 859-861. doi: 10.1038/nchembio.487
![]() |
[7] |
Yeh BJ, Lim WA (2007) Synthetic biology: lessons from the history of synthetic organic chemistry. Nat Chem Biol 3: 521-525. doi: 10.1038/nchembio0907-521
![]() |
[8] |
Keasling JD (2010) Manufacturing Molecules Through Metabolic Engineering. Science 330: 1355-1358. doi: 10.1126/science.1193990
![]() |
[9] | McArthur IV GH, Fong SS (2010) Toward Engineering Synthetic Microbial Metabolism. J Biomed Biotechnol 2010: 1-10. |
[10] |
Lee JW, Na D, Park JM, et al. (2012) Systems metabolic engineering of microorganisms for natural and non-natural chemicals. Nat Chem Biol 8: 536-546. doi: 10.1038/nchembio.970
![]() |
[11] |
Fong SS (2014) Computational approaches to metabolic engineering utilizing systems biology and synthetic biology. CSBJ 11: 28-34. doi: 10.1016/j.csbj.2014.08.005
![]() |
[12] |
Smolke CD (2009) Building outside of the box: iGEM and the BioBricks Foundation. Nat Biotechnol 27: 1099-1102. doi: 10.1038/nbt1209-1099
![]() |
[13] |
Ham TS, Dmytriv Z, Plahar H, et al. (2012) Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools. Nucleic Acids Res 40: e141-e141. doi: 10.1093/nar/gks531
![]() |
[14] | Mutalik VK, Guimaraes JC, Cambray G, et al. (2013) Precise and reliable gene expression via standard transcription and translation initiation elements. Nat Methods 1-15. |
[15] | Adames NR, Wilson ML, Fang G, et al. (2015) GenoLIB: a database of biological parts derived from a library of common plasmid features. Nucleic Acids Res. |
[16] | Weber T, Blin K, Duddela S, et al. (2015) antiSMASH 3.0--a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res. |
[17] |
Hsiau TH-C, Anderson JC (2014) Engineered DNA Sequence Syntax Inspector. ACS Synth Biol 3: 91-96. doi: 10.1021/sb400176e
![]() |
[18] |
Salis HM, Mirsky EA, Voigt CA (2009) Automated design of synthetic ribosome binding sites to control protein expression. Nat Biotechnol 27: 946-950. doi: 10.1038/nbt.1568
![]() |
[19] |
Casini A, Christodoulou G, Freemont PS, et al. (2014) R2oDNA Designer: Computational Design of Biologically Neutral Synthetic DNA Sequences. ACS Synth Biol 3: 525-528. doi: 10.1021/sb4001323
![]() |
[20] | Siegel JB, Smith AL, Poust S, et al. (2015) Computational protein design enables a novel one-carbon assimilation pathway. Proc Natl Acad Sci USA 112: 3704-3709. |
[21] |
Chappell J, Takahashi MK, Lucks JB (2015) Creating small transcription activating RNAs. Nat Chem Biol 11: 214-220. doi: 10.1038/nchembio.1737
![]() |
[22] |
Stevens JT, Carothers JM (2015) Designing RNA-Based Genetic Control Systems for Efficient Production from Engineered Metabolic Pathways. ACS Synth Biol 4: 107-115. doi: 10.1021/sb400201u
![]() |
[23] |
Carothers JM, Goler JA, Juminaga D, et al. (2011) Model-Driven Engineering of RNA Devices to Quantitatively Program Gene Expression. Science 334: 1716-1719. doi: 10.1126/science.1212209
![]() |
[24] | Oberortner E, Densmore D (2014) Web-Based Software Tool for Constraint-Based Design Specification of Synthetic Biological Systems. ACS Synth Biol 141216122616002. |
[25] |
Czar MJ, Cai Y, Peccoud J (2009) Writing DNA with GenoCAD. Nucleic Acids Res 37: W40-W47. doi: 10.1093/nar/gkp361
![]() |
[26] |
Smanski MJ, Bhatia S, Zhao D, et al. (2014) Functional optimization of gene clusters by combinatorial design and assembly. Nat Biotechnol 32: 1241-1249. doi: 10.1038/nbt.3063
![]() |
[27] |
Purcell O, Peccoud J, Lu TK (2014) Rule-Based Design of Synthetic Transcription Factors in Eukaryotes. ACS Synth Biol 3: 737-744. doi: 10.1021/sb400134k
![]() |
[28] | Kaznessis YN (2011) SynBioSS-Aided Design of Synthetic Biological Constructs, 1st ed., vol. 498. Elsevier Inc. 137-152. |
[29] |
Myers CJ, Barker N, Jones K, et al. (2009) iBioSim: a tool for the analysis and design of genetic circuits. Bioinformatics 25: 2848-2849. doi: 10.1093/bioinformatics/btp457
![]() |
[30] |
Hillson NJ, Rosengarten RD, Keasling JD (2012) j5 DNA Assembly Design Automation Software. ACS Synth Biol 1: 14-21. doi: 10.1021/sb2000116
![]() |
[31] |
Gibson DG, Young L, Chuang R-Y, et al. (2009) Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods 6: 343-345. doi: 10.1038/nmeth.1318
![]() |
[32] |
Gibson DG, Smith HO, Hutchison CA, et al. (2010) Chemical synthesis of the mouse mitochondrial genome. Nat Methods 7: 901-903. doi: 10.1038/nmeth.1515
![]() |
[33] | Richardson SM, Nunley PW, Yarrington RM, et al. (2010) GeneDesign 3.0 is an updated synthetic biology toolkit. Nucleic Acids Res 38: 2603-2606. |
[34] |
Jakočiūnas T, Bonde I, Herrgård M, et al. (2015) Multiplex metabolic pathway engineering using CRISPR/Cas9 in Saccharomyces cerevisiae. Metab Eng 28: 213-222. doi: 10.1016/j.ymben.2015.01.008
![]() |
[35] | Wang HH, Isaacs FJ, Carr PA, et al. (2009) Programming cells by multiplex genome engineering and accelerated evolution. Nature 1-6. |
[36] |
Wang HH, Kim H, Cong L, et al. (2012) Genome-scale promoter engineering by coselection MAGE. Nat Methods 9: 591-593. doi: 10.1038/nmeth.1971
![]() |
[37] |
Hsu PD, Scott DA, Weinstein JA, et al. (2013) DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol 31: 827-832. doi: 10.1038/nbt.2647
![]() |
[38] |
Montague TG, Cruz JM, Gagnon JA, et al. (2014) CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing. Nucleic Acids Res 42: W401-W407. doi: 10.1093/nar/gku410
![]() |
[39] | Doench JG, Hartenian E, Graham DB, et al. (2014) Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation. Nat Biotechnol 1-8. |
[40] |
Bonde MT, Klausen MS, Anderson MV, et al. (2014) MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering. Nucleic Acids Res 42: W408-W415. doi: 10.1093/nar/gku428
![]() |
[41] |
Untergasser A, Nijveen H, Rao X, et al. (2007) Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res 35: W71-W74. doi: 10.1093/nar/gkm306
![]() |
[42] | Wilson ML, Cai Y, Hanlon R, et al. (2012) Sequence verification of synthetic DNA by assembly of sequencing reads. Nucleic Acids Res 41: e25-e25. |
[43] | O'Brien EJ, Lerman JA, Chang RL, et al. (2013) Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction. Mol Syst Biol 9: 1-13. |
[44] |
Ball DA, Lux MW, Adames NR, et al. (2014) Adaptive Imaging Cytometry to Estimate Parameters of Gene Networks Models in Systems and Synthetic Biology. PLoS ONE 9: e107087. doi: 10.1371/journal.pone.0107087
![]() |
[45] |
Beal J, Weiss R, Densmore D, et al. (2012) An End-to-End Workflow for Engineering of Biological Networks from High-Level Specifications. ACS Synth Biol 1: 317-331. doi: 10.1021/sb300030d
![]() |
[46] |
Canton B, Labno A, Endy D (2008) Refinement and standardization of synthetic biological parts and devices. Nat Biotechnol 26: 787-793. doi: 10.1038/nbt1413
![]() |
[47] |
Endy D (2005) Foundations for engineering biology. Nature 438: 449-453. doi: 10.1038/nature04342
![]() |
[48] | Fisher AB, Canfield ZB, Hayward LC, et al. (2013) Ex vivo DNA assembly. Front Bioeng Biotechnol 1: 1-7. |
[49] |
Galdzicki M, Clancy KP, Oberortner E, et al. (2014) The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology. Nat Biotechnol 32: 545-550. doi: 10.1038/nbt.2891
![]() |
[50] | Chan LY, Kosuri S, Endy D, et al. (2005) Refactoring bacteriophage T7. Mol Syst Biol 1: 0018. |
[51] |
Temme K, Zhao D, Voigt CA (2012) Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca. P Natl Acad Sci U S A 109: 7085-7090. doi: 10.1073/pnas.1120788109
![]() |
[52] |
Yadav VG, De May M, Lim CG, et al. (2012) The Future of Metabolic Engineering and Synthetic Biology: Towards a Systematic Practice. Metab Eng 14: 233-241. doi: 10.1016/j.ymben.2012.02.001
![]() |