Rediverting carbon flux in Clostridium ljungdahlii using CRISPR interference (CRISPRi)

Woolston, Benjamin M.; Emerson, David F.; Currie, Devin H.; Stephanopoulos, Gregory

doi:10.1016/j.ymben.2018.06.006

Rediverting carbon flux in Clostridium ljungdahlii using CRISPR interference (CRISPRi)

Journal Article · Sun Jul 01 00:00:00 EDT 2018 · Metabolic Engineering

DOI:https://doi.org/10.1016/j.ymben.2018.06.006· OSTI ID:1779368

Woolston, Benjamin M.; Emerson, David F.; Currie, Devin H.; Stephanopoulos, Gregory

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Sponsoring Organization:: USDOE Advanced Research Projects Agency - Energy (ARPA-E)

Grant/Contract Number:: AR0000433

OSTI ID:: 1779368

Journal Information:: Metabolic Engineering, Journal Name: Metabolic Engineering Journal Issue: C Vol. 48; ISSN 1096-7176

Publisher:: ElsevierCopyright Statement

Country of Publication:: Belgium

Language:: English

References (54)

Dynamic metabolic engineering: New strategies for developing responsive cell factories Brockman, Irene M.; Prather, Kristala L. J. Biotechnology Journal, Vol. 10, Issue 9 https://doi.org/10.1002/biot.201400422	journal	April 2015
CRISPR-based genome editing and expression control systems in Clostridium acetobutylicum and Clostridium beijerinckii Li, Qi; Chen, Jun; Minton, Nigel P. Biotechnology Journal, Vol. 11, Issue 7 https://doi.org/10.1002/biot.201600053	journal	June 2016
Gene transcription repression in Clostridium beijerinckii using CRISPR-dCas9 : Gene Transcription in Wang, Yi; Zhang, Zhong-Tian; Seo, Seung-Oh Biotechnology and Bioengineering, Vol. 113, Issue 12 https://doi.org/10.1002/bit.26020	journal	June 2016
Overcoming the energetic limitations of syngas fermentation Molitor, Bastian; Marcellin, Esteban; Angenent, Largus T. Current Opinion in Chemical Biology, Vol. 41 https://doi.org/10.1016/j.cbpa.2017.10.003	journal	December 2017
Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression Qi, Lei S.; Larson, Matthew H.; Gilbert, Luke A. Cell, Vol. 152, Issue 5, p. 1173-1183 https://doi.org/10.1016/j.cell.2013.02.022	journal	February 2013
Maintenance of ATP Homeostasis Triggers Metabolic Shifts in Gas-Fermenting Acetogens Valgepea, Kaspar; de Souza Pinto Lemgruber, Renato; Meaghan, Kieran Cell Systems, Vol. 4, Issue 5 https://doi.org/10.1016/j.cels.2017.04.008	journal	May 2017
Stoichiometric and energetic analyses of non-photosynthetic CO2-fixation pathways to support synthetic biology strategies for production of fuels and chemicals Fast, Alan G.; Papoutsakis, Eleftherios T. Current Opinion in Chemical Engineering, Vol. 1, Issue 4 https://doi.org/10.1016/j.coche.2012.07.005	journal	November 2012
Acetogenic mixotrophy: novel options for yield improvement in biofuels and biochemicals production Fast, Alan G.; Schmidt, Ellinor D.; Jones, Shawn W. Current Opinion in Biotechnology, Vol. 33 https://doi.org/10.1016/j.copbio.2014.11.014	journal	June 2015
Selective enhancement of autotrophic acetate production with genetically modified Acetobacterium woodii Straub, Melanie; Demler, Martin; Weuster-Botz, Dirk Journal of Biotechnology, Vol. 178 https://doi.org/10.1016/j.jbiotec.2014.03.005	journal	May 2014
Bacterial CRISPR: accomplishments and prospects Peters, Jason M.; Silvis, Melanie R.; Zhao, Dehua Current Opinion in Microbiology, Vol. 27 https://doi.org/10.1016/j.mib.2015.08.007	journal	October 2015
A modular system for Clostridium shuttle plasmids Heap, John T.; Pennington, Oliver J.; Cartman, Stephen T. Journal of Microbiological Methods, Vol. 78, Issue 1, p. 79-85 https://doi.org/10.1016/j.mimet.2009.05.004	journal	July 2009
Codon Bias as a Means to Fine-Tune Gene Expression Quax, Tessa E. F.; Claassens, Nico J.; Söll, Dieter Molecular Cell, Vol. 59, Issue 2 https://doi.org/10.1016/j.molcel.2015.05.035	journal	July 2015
Development of an anhydrotetracycline-inducible gene expression system for solvent-producing Clostridium acetobutylicum: A useful tool for strain engineering Dong, Hongjun; Tao, Wenwen; Zhang, Yanping Metabolic Engineering, Vol. 14, Issue 1 https://doi.org/10.1016/j.ymben.2011.10.004	journal	January 2012
Metabolic engineering in chemolithoautotrophic hosts for the production of fuels and chemicals Nybo, S. Eric; Khan, Nymul E.; Woolston, Benjamin M. Metabolic Engineering, Vol. 30 https://doi.org/10.1016/j.ymben.2015.04.008	journal	July 2015
Enhanced solvent production by metabolic engineering of a twin-clostridial consortium Wen, Zhiqiang; Minton, Nigel P.; Zhang, Ying Metabolic Engineering, Vol. 39 https://doi.org/10.1016/j.ymben.2016.10.013	journal	January 2017
Metabolic engineering of Clostridium autoethanogenum for selective alcohol production Liew, Fungmin; Henstra, Anne M.; Kӧpke, Michael Metabolic Engineering, Vol. 40 https://doi.org/10.1016/j.ymben.2017.01.007	journal	March 2017
Systematic testing of enzyme perturbation sensitivities via graded dCas9 modulation in Saccharomyces cerevisiae Deaner, Matthew; Alper, Hal S. Metabolic Engineering, Vol. 40 https://doi.org/10.1016/j.ymben.2017.01.012	journal	March 2017
Arginine deiminase pathway provides ATP and boosts growth of the gas-fermenting acetogen Clostridium autoethanogenum Valgepea, Kaspar; Loi, Kim Q.; Behrendorff, James B. Metabolic Engineering, Vol. 41 https://doi.org/10.1016/j.ymben.2017.04.007	journal	May 2017
CRISPathBrick: Modular Combinatorial Assembly of Type II-A CRISPR Arrays for dCas9-Mediated Multiplex Transcriptional Repression in E. coli Cress, Brady F.; Toparlak, Ö. Duhan; Guleria, Sanjay ACS Synthetic Biology, Vol. 4, Issue 9 https://doi.org/10.1021/acssynbio.5b00012	journal	April 2015
Corynebacterium glutamicum Metabolic Engineering with CRISPR Interference (CRISPRi) Cleto, Sara; Jensen, Jaide VK; Wendisch, Volker F. ACS Synthetic Biology, Vol. 5, Issue 5 https://doi.org/10.1021/acssynbio.5b00216	journal	February 2016
CRISPR/Cas9-Based Efficient Genome Editing in Clostridium ljungdahlii , an Autotrophic Gas-Fermenting Bacterium Huang, He; Chai, Changsheng; Li, Ning ACS Synthetic Biology, Vol. 5, Issue 12 https://doi.org/10.1021/acssynbio.6b00044	journal	June 2016
Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs Na, Dokyun; Yoo, Seung Min; Chung, Hannah Nature Biotechnology, Vol. 31, Issue 2 https://doi.org/10.1038/nbt.2461	journal	January 2013
Refinement and standardization of synthetic biological parts and devices Canton, Barry; Labno, Anna; Endy, Drew Nature Biotechnology, Vol. 26, Issue 7, p. 787-793 https://doi.org/10.1038/nbt1413	journal	July 2008
CO2 fixation by anaerobic non-photosynthetic mixotrophy for improved carbon conversion Jones, Shawn W.; Fast, Alan G.; Carlson, Ellinor D. Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms12800	journal	September 2016
CRISPR interference (CRISPRi) for sequence-specific control of gene expression Larson, Matthew H.; Gilbert, Luke A.; Wang, Xiaowo Nature Protocols, Vol. 8, Issue 11 https://doi.org/10.1038/nprot.2013.132	journal	October 2013
Autotrophy at the thermodynamic limit of life: a model for energy conservation in acetogenic bacteria Schuchmann, Kai; Müller, Volker Nature Reviews Microbiology, Vol. 12, Issue 12 https://doi.org/10.1038/nrmicro3365	journal	November 2014
Expanding the molecular toolkit for the homoacetogen Clostridium ljungdahlii Molitor, Bastian; Kirchner, Kristina; Henrich, Alexander W. Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep31518	journal	August 2016
Low carbon fuels and commodity chemicals from waste gases – systematic approach to understand energy metabolism in a model acetogen Marcellin, Esteban; Behrendorff, James B.; Nagaraju, Shilpa Green Chemistry, Vol. 18, Issue 10 https://doi.org/10.1039/C5GC02708J	journal	January 2016
Ethanol production in syngas-fermenting Clostridium ljungdahlii is controlled by thermodynamics rather than by enzyme expression Richter, H.; Molitor, B.; Wei, H. Energy & Environmental Science, Vol. 9, Issue 7 https://doi.org/10.1039/C6EE01108J	journal	January 2016
RNA-seq-based comparative transcriptome analysis of the syngas-utilizing bacterium Clostridium ljungdahlii DSM 13528 grown autotrophically and heterotrophically Tan, Yang; Liu, Juanjuan; Chen, Xiaohua Molecular BioSystems, Vol. 9, Issue 11 https://doi.org/10.1039/c3mb70232d	journal	January 2013
Clostridium ljungdahlii represents a microbial production platform based on syngas Kopke, M.; Held, C.; Hujer, S. Proceedings of the National Academy of Sciences, Vol. 107, Issue 29, p. 13087-13092 https://doi.org/10.1073/pnas.1004716107	journal	July 2010
Bacterial synthesis gas (syngas) fermentation Bengelsdorf, Frank R.; Straub, Melanie; Dürre, Peter Environmental Technology, Vol. 34, Issue 13-14 https://doi.org/10.1080/09593330.2013.827747	journal	July 2013
Acetate kinase from Clostridium acetobutylicum: a highly specific enzyme that is actively transcribed during acidogenesis and solventogenesis Winzer, Klaus; Lorenz, Karin; DÜrre, Peter Microbiology, Vol. 143, Issue 10 https://doi.org/10.1099/00221287-143-10-3279	journal	October 1997
The application of Tet repressor in prokaryotic gene regulation and expression: Tet regulation in bacteria Bertram, Ralph; Hillen, Wolfgang Microbial Biotechnology, Vol. 1, Issue 1 https://doi.org/10.1111/j.1751-7915.2007.00001.x	journal	August 2007
Efficient Genome Editing in Clostridium cellulolyticum via CRISPR-Cas9 Nickase Xu, Tao; Li, Yongchao; Shi, Zhou Applied and Environmental Microbiology, Vol. 81, Issue 13 https://doi.org/10.1128/AEM.00873-15	journal	April 2015
Construction and Characterization of a Lactose-Inducible Promoter System for Controlled Gene Expression in Clostridium perfringens Hartman, Andrea H.; Liu, Hualan; Melville, Stephen B. Applied and Environmental Microbiology, Vol. 77, Issue 2 https://doi.org/10.1128/AEM.01536-10	journal	November 2010
Metabolic Engineering of Escherichia coli for Enhanced Production of (R)- and (S)-3-Hydroxybutyrate Tseng, H. -C.; Martin, C. H.; Nielsen, D. R. Applied and Environmental Microbiology, Vol. 75, Issue 10 https://doi.org/10.1128/AEM.02667-08	journal	March 2009
A Genetic System for Clostridium ljungdahlii: a Chassis for Autotrophic Production of Biocommodities and a Model Homoacetogen Leang, Ching; Ueki, Toshiyuki; Nevin, Kelly P. Applied and Environmental Microbiology, Vol. 79, Issue 4 https://doi.org/10.1128/AEM.02891-12	journal	November 2012
Lactose-Inducible System for Metabolic Engineering of Clostridium ljungdahlii Banerjee, Areen; Leang, Ching; Ueki, Toshiyuki Applied and Environmental Microbiology, Vol. 80, Issue 8 https://doi.org/10.1128/AEM.03666-13	journal	February 2014
Antisense RNA Strategies for Metabolic Engineering of Clostridium acetobutylicum Desai, Ruchir P.; Papoutsakis, Eleftherios T. Applied and Environmental Microbiology, Vol. 65, Issue 3 https://doi.org/10.1128/AEM.65.3.936-945.1999	journal	March 1999
Energy Conservation Associated with Ethanol Formation from H ₂ and CO ₂ in Clostridium autoethanogenum Involving Electron Bifurcation Mock, Johanna; Zheng, Yanning; Mueller, Alexander P. Journal of Bacteriology, Vol. 197, Issue 18 https://doi.org/10.1128/JB.00399-15	journal	July 2015
NADP-Specific Electron-Bifurcating [FeFe]-Hydrogenase in a Functional Complex with Formate Dehydrogenase in Clostridium autoethanogenum Grown on CO Wang, S.; Huang, H.; Kahnt, J. Journal of Bacteriology, Vol. 195, Issue 19 https://doi.org/10.1128/JB.00678-13	journal	July 2013
Evidence for a Hexaheteromeric Methylenetetrahydrofolate Reductase in Moorella thermoacetica Mock, J.; Wang, S.; Huang, H. Journal of Bacteriology, Vol. 196, Issue 18 https://doi.org/10.1128/JB.01839-14	journal	July 2014
Design of Antisense RNA Constructs for Downregulation of the Acetone Formation Pathway of Clostridium acetobutylicum Tummala, S. B.; Welker, N. E.; Papoutsakis, E. T. Journal of Bacteriology, Vol. 185, Issue 6 https://doi.org/10.1128/JB.185.6.1923-1934.2003	journal	March 2003
Insights into CO ₂ Fixation Pathway of Clostridium autoethanogenum by Targeted Mutagenesis Liew, Fungmin; Henstra, Anne M.; Winzer, Klaus mBio, Vol. 7, Issue 3 https://doi.org/10.1128/mBio.00427-16	journal	May 2016
Converting Carbon Dioxide to Butyrate with an Engineered Strain of Clostridium ljungdahlii Ueki, Toshiyuki; Nevin, Kelly P.; Woodard, Trevor L. mBio, Vol. 5, Issue 5 https://doi.org/10.1128/mBio.01636-14	journal	October 2014
Metabolic Engineering: Past and Future Woolston, Benjamin M.; Edgar, Steven; Stephanopoulos, Gregory Annual Review of Chemical and Biomolecular Engineering, Vol. 4, Issue 1 https://doi.org/10.1146/annurev-chembioeng-061312-103312	journal	June 2013
Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii Nagarajan, Harish; Sahin, Merve; Nogales, Juan Microbial Cell Factories, Vol. 12, Issue 1 https://doi.org/10.1186/1475-2859-12-118	journal	January 2013
An insight into the role of phosphotransacetylase (pta) and the acetate/acetyl-CoA node in Escherichia coli Castaño-Cerezo, Sara; Pastor, José M.; Renilla, Sergio Microbial Cell Factories, Vol. 8, Issue 1 https://doi.org/10.1186/1475-2859-8-54	journal	January 2009
BglBrick vectors and datasheets: A synthetic biology platform for gene expression Lee, Taek; Krupa, Rachel A.; Zhang, Fuzhong Journal of Biological Engineering, Vol. 5, Issue 1 https://doi.org/10.1186/1754-1611-5-12	journal	January 2011
Metabolic modeling of synthesis gas fermentation in bubble column reactors Chen, Jin; Gomez, Jose A.; Höffner, Kai Biotechnology for Biofuels, Vol. 8, Issue 1 https://doi.org/10.1186/s13068-015-0272-5	journal	June 2015
Genome editing of Clostridium autoethanogenum using CRISPR/Cas9 Nagaraju, Shilpa; Davies, Naomi Kathleen; Walker, David Jeffrey Fraser Biotechnology for Biofuels, Vol. 9, Issue 1 https://doi.org/10.1186/s13068-016-0638-3	journal	October 2016
Commercial Biomass Syngas Fermentation Daniell, James; Köpke, Michael; Simpson, Séan Energies, Vol. 5, Issue 12 https://doi.org/10.3390/en5125372	journal	December 2012
Antisense-RNA-Mediated Gene Downregulation in Clostridium pasteurianum Pyne, Michael; Moo-Young, Murray; Chung, Duane Fermentation, Vol. 1, Issue 1 https://doi.org/10.3390/fermentation1010113	journal	December 2015

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