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Volumn 1, Issue 1, 2018, Pages

An automated Design-Build-Test-Learn pipeline for enhanced microbial production of fine chemicals

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EID: 85059806983     PISSN: None     EISSN: 23993642     Source Type: Journal    
DOI: 10.1038/s42003-018-0076-9     Document Type: Article
Times cited : (179)

References (40)
  • 1
    • 84940436063 scopus 로고    scopus 로고
    • Bricks and blueprints: methods and standards for DNA assembly
    • PID: 26081612, COI: 1:CAS:528:DC%2BC2MXhtFWqur7K
    • Casini, A., Storch, M., Baldwin, G. S. & Ellis, T. Bricks and blueprints: methods and standards for DNA assembly. Nat. Rev. Mol. Cell Biol. 16, 568–576 (2015).
    • (2015) Nat. Rev. Mol. Cell Biol. , vol.16 , pp. 568-576
    • Casini, A.1    Storch, M.2    Baldwin, G.S.3    Ellis, T.4
  • 2
    • 84979209149 scopus 로고    scopus 로고
    • System-level genome editing in microbes
    • PID: 27472027, COI: 1:CAS:528:DC%2BC28Xht1aitr7J
    • Csörgő, B., Nyerges, Á., Pósfai, G. & Fehér, T. System-level genome editing in microbes. Curr. Opin. Microbiol. 33, 113–122 (2016).
    • (2016) Curr. Opin. Microbiol. , vol.33 , pp. 113-122
    • Csörgő, B.1    Nyerges, A.2    Pósfai, G.3    Fehér, T.4
  • 3
    • 84921517479 scopus 로고    scopus 로고
    • Functional optimization of gene clusters by combinatorial design and assembly
    • PID: 25419741, COI: 1:CAS:528:DC%2BC2cXhvFKlsrnL
    • Smanski, M. J. et al. Functional optimization of gene clusters by combinatorial design and assembly. Nat. Biotechnol. 32, 1241–1249 (2014).
    • (2014) Nat. Biotechnol. , vol.32 , pp. 1241-1249
    • Smanski, M.J.1
  • 4
    • 84958109894 scopus 로고    scopus 로고
    • Multiplexed engineering in biology
    • PID: 26897356, COI: 1:CAS:528:DC%2BC28Xislejsrs%3D
    • Rogers, J. K. & Church, G. M. Multiplexed engineering in biology. Trends Biotechnol. 34, 198–206 (2016).
    • (2016) Trends Biotechnol. , vol.34 , pp. 198-206
    • Rogers, J.K.1    Church, G.M.2
  • 5
    • 84980022887 scopus 로고    scopus 로고
    • Bioinformatics for the synthetic biology of natural products: integrating across the Design-Build-Test cycle
    • PID: 27185383, COI: 1:CAS:528:DC%2BC28XotF2msLY%3D
    • Carbonell, P. et al. Bioinformatics for the synthetic biology of natural products: integrating across the Design-Build-Test cycle. Nat. Prod. Rep. 33, 925–932 (2016).
    • (2016) Nat. Prod. Rep. , vol.33 , pp. 925-932
    • Carbonell, P.1
  • 6
    • 85021688655 scopus 로고    scopus 로고
    • Recent advances in systems metabolic engineering tools and strategies
    • PID: 28675826, COI: 1:CAS:528:DC%2BC2sXhtVOjurbM
    • Chae, T. U. U., Choi, S. Y. Y., Kim, J. W. W., Ko, Y.-S. S. & Lee, S. Y. Y. Recent advances in systems metabolic engineering tools and strategies. Curr. Opin. Biotechnol. 47, 67–82 (2017).
    • (2017) Curr. Opin. Biotechnol. , vol.47 , pp. 67-82
    • Chae, T.U.U.1    Choi, S.Y.Y.2    Kim, J.W.W.3    Ko, Y.S.S.4    Lee, S.Y.Y.5
  • 7
    • 85020710659 scopus 로고    scopus 로고
    • Engineering biological systems using automated biofoundries
    • PID: 28602523, COI: 1:CAS:528:DC%2BC2sXhtVShtLjK
    • Chao, R., Mishra, S., Si, T. & Zhao, H. Engineering biological systems using automated biofoundries. Metab. Eng. 42, 98–108 (2017).
    • (2017) Metab. Eng. , vol.42 , pp. 98-108
    • Chao, R.1    Mishra, S.2    Si, T.3    Zhao, H.4
  • 8
    • 84945276317 scopus 로고    scopus 로고
    • Genome scale engineering techniques for metabolic engineering
    • PID: 26453944, COI: 1:CAS:528:DC%2BC2MXhs1ertLvP
    • Liu, R., Bassalo, M. C., Zeitoun, R. I. & Gill, R. T. Genome scale engineering techniques for metabolic engineering. Metab. Eng. 32, 143–154 (2015).
    • (2015) Metab. Eng. , vol.32 , pp. 143-154
    • Liu, R.1    Bassalo, M.C.2    Zeitoun, R.I.3    Gill, R.T.4
  • 9
    • 85038207858 scopus 로고    scopus 로고
    • RetroPath2.0: a retrosynthesis workflow for metabolic engineers
    • PID: 29233745, COI: 1:CAS:528:DC%2BC2sXitVWgu7bF
    • Delépine, B., Duigou, T., Carbonell, P. & Faulon, J.-L. RetroPath2.0: a retrosynthesis workflow for metabolic engineers. Metab. Eng. 45, 158–170 (2018).
    • (2018) Metab. Eng. , vol.45 , pp. 158-170
    • Delépine, B.1    Duigou, T.2    Carbonell, P.3    Faulon, J.L.4
  • 10
    • 85049059297 scopus 로고    scopus 로고
    • Selenzyme: Enzyme selection tool for pathway design
    • Carbonell, P. et al. Selenzyme: enzyme selection tool for pathway design. Bioinformatics bty065, 10.1093/bioinformatics/bty065 (2018).
    • (2018) Bioinformatics
    • Carbonell, P.1
  • 11
    • 85050807007 scopus 로고    scopus 로고
    • PartsGenie: An integrated tool for optimizing and sharing synthetic biology parts
    • bty105
    • Swainston, N. et al. PartsGenie: an integrated tool for optimizing and sharing synthetic biology parts. Bioinformatics bty105, 10.1093/bioinformatics/bty105 (2018).
    • (2018) Bioinformatics
    • Swainston, N.1
  • 12
    • 85012838041 scopus 로고    scopus 로고
    • Improving metabolic pathway efficiency by statistical model based multivariate regulatory metabolic engineering (MRME)
    • PID: 27490704, COI: 1:CAS:528:DC%2BC28Xht1yht7zI
    • Xu, P., Rizzoni, E. A. A., Sul, S.-Y. Y. & Stephanopoulos, G. Improving metabolic pathway efficiency by statistical model based multivariate regulatory metabolic engineering (MRME). ACS Synth. Biol. 6, 148–158 (2017).
    • (2017) ACS Synth. Biol. , vol.6 , pp. 148-158
    • Xu, P.1    Rizzoni, E.A.A.2    Sul, S.Y.Y.3    Stephanopoulos, G.4
  • 13
    • 84958146942 scopus 로고    scopus 로고
    • Algorithmic co-optimization of genetic constructs and growth conditions: application to 6-ACA, a potential nylon-6 precursor
    • PID: 26519464, COI: 1:CAS:528:DC%2BC28XksVemtbg%3D
    • Zhou, H., Vonk, B., Roubos, J. A., Bovenberg, R. A. L. & Voigt, C. A. Algorithmic co-optimization of genetic constructs and growth conditions: application to 6-ACA, a potential nylon-6 precursor. Nucleic Acids Res. 43, 10560–10570 (2015).
    • (2015) Nucleic Acids Res. , vol.43 , pp. 10560-10570
    • Zhou, H.1    Vonk, B.2    Roubos, J.A.3    Bovenberg, R.A.L.4    Voigt, C.A.5
  • 14
    • 84925348793 scopus 로고    scopus 로고
    • Rational design of a synthetic Entner-Doudoroff pathway for improved and controllable NADPH regeneration
    • PID: 25769287, COI: 1:CAS:528:DC%2BC2MXksF2itbs%3D
    • Ng, C. Y., Farasat, I., Maranas, C. D. & Salis, H. M. Rational design of a synthetic Entner-Doudoroff pathway for improved and controllable NADPH regeneration. Metab. Eng. 29, 86–96 (2015).
    • (2015) Metab. Eng. , vol.29 , pp. 86-96
    • Ng, C.Y.1    Farasat, I.2    Maranas, C.D.3    Salis, H.M.4
  • 15
    • 84962816232 scopus 로고    scopus 로고
    • Rationally reduced libraries for combinatorial pathway optimization minimizing experimental effort
    • PID: 27029461, COI: 1:CAS:528:DC%2BC28Xlt1Kms7c%3D
    • Jeschek, M., Gerngross, D. & Panke, S. Rationally reduced libraries for combinatorial pathway optimization minimizing experimental effort. Nat. Commun. 7, 11163 (2016).
    • (2016) Nat. Commun. , vol.7
    • Jeschek, M.1    Gerngross, D.2    Panke, S.3
  • 16
    • 84896836282 scopus 로고    scopus 로고
    • Rapid and reliable DNA assembly via ligase cycling reaction
    • PID: 24932563, COI: 1:CAS:528:DC%2BC2cXkvFKitQ%3D%3D
    • Kok, S. D. et al. Rapid and reliable DNA assembly via ligase cycling reaction. ACS Synth. Biol. 3, 97–106 (2014).
    • (2014) ACS Synth. Biol. , vol.3 , pp. 97-106
    • Kok, S.D.1
  • 17
    • 84867488931 scopus 로고    scopus 로고
    • Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools
    • PID: 22718978, COI: 1:CAS:528:DC%2BC38XhsFWktL3J
    • Ham, T. S. et al. Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools. Nucleic Acids Res. 40, e141–e141 (2012).
    • (2012) Nucleic Acids Res. , vol.40 , pp. e141
    • Ham, T.S.1
  • 18
    • 85009080868 scopus 로고    scopus 로고
    • Improving synthetic biology communication: recommended practices for visual depiction and digital submission of genetic designs
    • PID: 27267452, COI: 1:CAS:528:DC%2BC28XptFyks78%3D
    • Hillson, N. J., Plahar, H. A., Beal, J. & Prithviraj, R. Improving synthetic biology communication: recommended practices for visual depiction and digital submission of genetic designs. ACS Synth. Biol. 5, 449–451 (2016).
    • (2016) ACS Synth. Biol. , vol.5 , pp. 449-451
    • Hillson, N.J.1    Plahar, H.A.2    Beal, J.3    Prithviraj, R.4
  • 19
    • 84961125909 scopus 로고    scopus 로고
    • Microbial production of natural and non-natural flavonoids: pathway engineering, directed evolution and systems/synthetic biology
    • PID: 26946281, COI: 1:CAS:528:DC%2BC28XksVKmtb0%3D
    • Pandey, R. P., Parajuli, P., Koffas, M. A. G. & Sohng, J. K. Microbial production of natural and non-natural flavonoids: pathway engineering, directed evolution and systems/synthetic biology. Biotechnol. Adv. 34, 634–662 (2016).
    • (2016) Biotechnol. Adv. , vol.34 , pp. 634-662
    • Pandey, R.P.1    Parajuli, P.2    Koffas, M.A.G.3    Sohng, J.K.4
  • 20
    • 84883232076 scopus 로고    scopus 로고
    • Multivariate modular metabolic engineering of Escherichia coli to produce resveratrol from l-tyrosine
    • PID: 23916948, COI: 1:CAS:528:DC%2BC3sXhsVOksbzP
    • Wu, J. et al. Multivariate modular metabolic engineering of Escherichia coli to produce resveratrol from l-tyrosine. J. Biotechnol. 167, 404–411 (2013).
    • (2013) J. Biotechnol. , vol.167 , pp. 404-411
    • Wu, J.1
  • 21
    • 84910130469 scopus 로고    scopus 로고
    • Validation of RetroPath, a computer-aided design tool for metabolic pathway engineering
    • PID: 25224453, COI: 1:CAS:528:DC%2BC2cXhvVGitbfE
    • Fehér, T. et al. Validation of RetroPath, a computer-aided design tool for metabolic pathway engineering. Biotechnol. J. 9, 1446–1457 (2014).
    • (2014) Biotechnol. J. , vol.9 , pp. 1446-1457
    • Fehér, T.1
  • 22
    • 80053175916 scopus 로고    scopus 로고
    • BglBrick vectors and datasheets; a synthetic biology platform for gene expression
    • PID: 21933410, COI: 1:CAS:528:DC%2BC3MXhs1OqtbnI
    • Lee, T. S. et al. BglBrick vectors and datasheets; a synthetic biology platform for gene expression. J. Biol. Eng. 5, 12 (2011).
    • (2011) J. Biol. Eng. , vol.5
    • Lee, T.S.1
  • 23
    • 84986208749 scopus 로고    scopus 로고
    • Enhanced pinocembrin production in Escherichia coli by regulating cinnamic acid metabolism
    • PID: 27586788, COI: 1:CAS:528:DC%2BC28XhsVOru7jL
    • Cao, W. et al. Enhanced pinocembrin production in Escherichia coli by regulating cinnamic acid metabolism. Sci. Rep. 6, 32640 (2016).
    • (2016) Sci. Rep. , vol.6
    • Cao, W.1
  • 24
    • 84872221971 scopus 로고    scopus 로고
    • Metabolic engineering of Escherichia coli for (2S)-pinocembrin production from glucose by a modular metabolic strategy
    • PID: 23246524, COI: 1:CAS:528:DC%2BC3sXktFWqt7c%3D
    • 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. 16, 48–55 (2013).
    • (2013) Metab. Eng. , vol.16 , pp. 48-55
    • Wu, J.1    Du, G.2    Zhou, J.3    Chen, J.4
  • 25
    • 84922803616 scopus 로고    scopus 로고
    • (R,S)-Tetrahydropapaveroline production by stepwise fermentation using engineered Escherichia coli
    • COI: 1:CAS:528:DC%2BC2MXksVyrt74%3D
    • Nakagawa, A. et al. (R,S)-Tetrahydropapaveroline production by stepwise fermentation using engineered Escherichia coli. Sci. Rep. 4, 6695 (2015).
    • (2015) Sci. Rep. , vol.4
    • Nakagawa, A.1
  • 26
    • 85026997585 scopus 로고    scopus 로고
    • biochem4j: integrated and extensible biochemical knowledge through graph databases
    • PID: 28708831, COI: 1:CAS:528:DC%2BC2sXitVajsLjL
    • Swainston, N. et al. biochem4j: integrated and extensible biochemical knowledge through graph databases. PLoS ONE 12, e0179130 (2017).
    • (2017) PLoS ONE , vol.12
    • Swainston, N.1
  • 27
    • 44949247292 scopus 로고    scopus 로고
    • Microbial production of plant benzylisoquinoline alkaloids
    • PID: 18492807
    • Minami, H. et al. Microbial production of plant benzylisoquinoline alkaloids. Proc. Natl. Acad. Sci. USA 105, 7393–7398 (2008).
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 7393-7398
    • Minami, H.1
  • 28
    • 79957534528 scopus 로고    scopus 로고
    • The ribosome binding site calculator
    • PID: 21601672, COI: 1:CAS:528:DC%2BC3MXpsVKntb8%3D
    • Salis, H. M. The ribosome binding site calculator. Methods Enzymol. 498, 19–42 (2011).
    • (2011) Methods Enzymol. , vol.498 , pp. 19-42
    • Salis, H.M.1
  • 29
    • 56649114274 scopus 로고    scopus 로고
    • A one pot, one step, precision cloning method with high throughput capability
    • PID: 18985154, COI: 1:CAS:528:DC%2BD1cXhtlKhsbrN
    • Engler, C., Kandzia, R. & Marillonnet, S. A one pot, one step, precision cloning method with high throughput capability. PLoS ONE 3, e3647 (2008).
    • (2008) PLoS ONE , vol.3
    • Engler, C.1    Kandzia, R.2    Marillonnet, S.3
  • 30
    • 84902159136 scopus 로고    scopus 로고
    • The synthetic biology open language (SBOL) provides a community standard for communicating designs in synthetic biology
    • PID: 24911500, COI: 1:CAS:528:DC%2BC2cXpsVGqurk%3D
    • Galdzicki, M. et al. The synthetic biology open language (SBOL) provides a community standard for communicating designs in synthetic biology. Nat. Biotechnol. 32, 545–550 (2014).
    • (2014) Nat. Biotechnol. , vol.32 , pp. 545-550
    • Galdzicki, M.1
  • 31
    • 85008616133 scopus 로고    scopus 로고
    • Automatic generation of generalised regular factorial designs
    • Kobilinsky, A., Monod, H. & Bailey, R. A. Automatic generation of generalised regular factorial designs. Comput. Stat. Data Anal. 113, 311–329 (2017).
    • (2017) Comput. Stat. Data Anal. , vol.113 , pp. 311-329
    • Kobilinsky, A.1    Monod, H.2    Bailey, R.A.3
  • 33
    • 0034612342 scopus 로고    scopus 로고
    • One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products
    • PID: 10829079, COI: 1:CAS:528:DC%2BD3cXktFais7c%3D
    • Datsenko, K. A. & Wanner, B. L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. USA 97, 6640–6645 (2000).
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 6640-6645
    • Datsenko, K.A.1    Wanner, B.L.2
  • 34
    • 31544450286 scopus 로고    scopus 로고
    • Construction of Escherichia coli K‐12 in‐frame, single‐gene knockout mutants: the Keio collection
    • Baba, T. et al. Construction of Escherichia coli K‐12 in‐frame, single‐gene knockout mutants: the Keio collection. Mol. Sys. Biol. 2, 2006.0008 (2006).
    • (2006) Mol. Sys. Biol. , vol.2 , pp. 2006.0008
    • Baba, T.1
  • 35
    • 33747333128 scopus 로고    scopus 로고
    • A set of recombineering plasmids for gram-negative bacteria
    • PID: 16750601, COI: 1:CAS:528:DC%2BD28Xos12ktb8%3D
    • Datta, S., Costantino, N. & Court, D. L. A set of recombineering plasmids for gram-negative bacteria. Gene 379, 109–115 (2006).
    • (2006) Gene , vol.379 , pp. 109-115
    • Datta, S.1    Costantino, N.2    Court, D.L.3
  • 36
    • 84988940329 scopus 로고    scopus 로고
    • Efficient assembly of DNA using yeast homologous recombination (YHR)
    • Chandran, S. Efficient assembly of DNA using yeast homologous recombination (YHR). Methods Mol. Biol. 1472, 105–110 (2017).
    • (2017) Methods Mol. Biol. , vol.1472 , pp. 105-110
    • Chandran, S.1
  • 38
    • 84867345063 scopus 로고    scopus 로고
    • A cross-platform toolkit for mass spectrometry and proteomics
    • PID: 23051804, COI: 1:CAS:528:DC%2BC38XhsVyjs7fO
    • Chambers, M. C. et al. A cross-platform toolkit for mass spectrometry and proteomics. Nat. Biotechnol. 30, 918–920 (2012).
    • (2012) Nat. Biotechnol. , vol.30 , pp. 918-920
    • Chambers, M.C.1
  • 39
    • 84936886011 scopus 로고    scopus 로고
    • SEEK: a systems biology data and model management platform
    • PID: 26160520, COI: 1:CAS:528:DC%2BC2MXhs1ajtLbI
    • Wolstencroft, K. et al. SEEK: a systems biology data and model management platform. Bmc. Syst. Biol. 9, 33 (2015).
    • (2015) Bmc. Syst. Biol. , vol.9
    • Wolstencroft, K.1
  • 40
    • 85071192910 scopus 로고    scopus 로고
    • SYNBIOCHEM Design-Build-Test-Learn pipeline
    • v1
    • Carbonell, P. et al. SYNBIOCHEM Design-Build-Test-Learn pipeline. Mendeley Data, v1. 10.17632/8g4wfwtd43 (2018).
    • (2018) Mendeley Data
    • Carbonell, P.1


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