Isopentenyl diphosphate (IPP)-bypass mevalonate pathways for isopentenol production

Kang, Aram; George, Kevin W.; Wang, George; Baidoo, Edward; Keasling, Jay D.; Lee, Taek Soon

doi:10.1016/j.ymben.2015.12.002

Isopentenyl diphosphate (IPP)-bypass mevalonate pathways for isopentenol production

Journal Article · Wed Dec 16 23:00:00 EST 2015 · Metabolic Engineering

DOI:https://doi.org/10.1016/j.ymben.2015.12.002· OSTI ID:1393030

Kang, Aram ^[1]; George, Kevin W. ^[1]; Wang, George ^[1]; Baidoo, Edward ^[1]; Keasling, Jay D. ^[2]; Lee, Taek Soon ^[1]

Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)

Branched C 5 alcohols are promising biofuels with excellent combustion properties. A mevalonate (MVA)-based isoprenoid biosynthetic pathway for C 5 alcohols was constructed in Escherichia coli using genes from several organisms, and the pathway was optimized to achieve over 50% theoretical yield. Although the MVA pathway is energetically less efficient than the native methylerythritol 4-phosphate (MEP) pathway, implementing the MVA pathway in bacterial hosts such as E. coli is advantageous due to its lack of endogenous regulation. The MVA and MEP pathways intersect at isopentenyl diphosphate (IPP), the direct precursor to isoprenoid-derived C 5 alcohols and initial precursor to longer chain terpenes, which makes independent regulation of the pathways difficult. In pursuit of the complete "decoupling" of the MVA pathway from native cellular regulation, we designed novel IPP-bypass MVA pathways for C 5 alcohol production by utilizing promiscuous activities of two enzymes, phosphomevalonate decarboxylase (PMD) and an E. coli-endogenous phosphatase (AphA). These bypass pathways have reduced energetic requirements, are further decoupled from intrinsic regulation, and are free from IPP-related toxicity. In addition to these benefits, we demonstrate that reduced aeration rate has less impact on the bypass pathway than the original MVA pathway. Finally, we showed that performance of the bypass pathway was primarily determined by the activity of PMD. We designed PMD mutants with improved activity and demonstrated titer increases in the mutant strains. These modified pathways would be a good platform for industrial production of isopentenol and related chemicals such as isoprene.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1393030

Alternate ID(s):: OSTI ID: 1400019

Journal Information:: Metabolic Engineering, Journal Name: Metabolic Engineering Vol. 34; ISSN 1096-7176

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

References (34)

Farnesol production from Escherichia coli by harnessing the exogenous mevalonate pathway Wang, Chonglong; Yoon, Sang-Hwal; Shah, Asad Ali Biotechnology and Bioengineering, Vol. 107, Issue 3 https://doi.org/10.1002/bit.22831	journal	June 2010
In vitro reconstitution of mevalonate pathway and targeted engineering of farnesene overproduction in Escherichia coli : In Vitro Reconstitution of Mevalonate Pathway Zhu, Fayin; Zhong, Xiaofang; Hu, Mengzhu Biotechnology and Bioengineering, Vol. 111, Issue 7 https://doi.org/10.1002/bit.25198	journal	February 2014
Correlation analysis of targeted proteins and metabolites to assess and engineer microbial isopentenol production: Targeted Proteomics-Based Correlation Analysis George, Kevin W.; Chen, Amy; Jain, Aakriti Biotechnology and Bioengineering, Vol. 111, Issue 8 https://doi.org/10.1002/bit.25226	journal	May 2014
The Two-Component Network and the General Stress Sigma Factor RpoS (??S) in Escherichia coli Hengge, Regine Advances in Experimental Medicine and Biology https://doi.org/10.1007/978-0-387-78885-2_4	book	January 2008
3-Methyl-1-butanol production in Escherichia coli: random mutagenesis and two-phase fermentation Connor, Michael R.; Cann, Anthony F.; Liao, James C. Applied Microbiology and Biotechnology, Vol. 86, Issue 4 https://doi.org/10.1007/s00253-009-2401-1	journal	January 2010
Monoterpene and sesquiterpene synthases and the origin of terpene skeletal diversity in plants Degenhardt, Jörg; Köllner, Tobias G.; Gershenzon, Jonathan Phytochemistry, Vol. 70, Issue 15-16 https://doi.org/10.1016/j.phytochem.2009.07.030	journal	October 2009
Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli Pitera, Douglas J.; Paddon, Chris J.; Newman, Jack D. Metabolic Engineering, Vol. 9, Issue 2 https://doi.org/10.1016/j.ymben.2006.11.002	journal	March 2007
Optimization of the mevalonate-based isoprenoid biosynthetic pathway in Escherichia coli for production of the anti-malarial drug precursor amorpha-4,11-diene Anthony, Jennifer R.; Anthony, Larry C.; Nowroozi, Farnaz Metabolic Engineering, Vol. 11, Issue 1 https://doi.org/10.1016/j.ymben.2008.07.007	journal	January 2009
Targeted proteomics for metabolic pathway optimization: Application to terpene production Redding-Johanson, Alyssa M.; Batth, Tanveer S.; Chan, Rossana Metabolic Engineering, Vol. 13, Issue 2 https://doi.org/10.1016/j.ymben.2010.12.005	journal	March 2011
Optimization of a heterologous mevalonate pathway through the use of variant HMG-CoA reductases Ma, Suzanne M.; Garcia, David E.; Redding-Johanson, Alyssa M. Metabolic Engineering, Vol. 13, Issue 5 https://doi.org/10.1016/j.ymben.2011.07.001	journal	September 2011
Metabolic engineering of Escherichia coli for limonene and perillyl alcohol production Alonso-Gutierrez, Jorge; Chan, Rossana; Batth, Tanveer S. Metabolic Engineering, Vol. 19 https://doi.org/10.1016/j.ymben.2013.05.004	journal	September 2013
Futile cycling increases sensitivity toward oxidative stress in Escherichia coli Adolfsen, Kristin J.; Brynildsen, Mark P. Metabolic Engineering, Vol. 29 https://doi.org/10.1016/j.ymben.2015.02.006	journal	May 2015
Microbial Synthesis of Myrcene by Metabolically Engineered Escherichia coli Kim, Eun-Mi; Eom, Jin-Hee; Um, Youngsoon Journal of Agricultural and Food Chemistry, Vol. 63, Issue 18 https://doi.org/10.1021/acs.jafc.5b01334	journal	May 2015
Structural Basis for Nucleotide Binding and Reaction Catalysis in Mevalonate Diphosphate Decarboxylase Barta, Michael L.; McWhorter, William J.; Miziorko, Henry M. Biochemistry, Vol. 51, Issue 28 https://doi.org/10.1021/bi300591x	journal	July 2012
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants the Keio collection Baba, Tomoya; Ara, Takeshi; Hasegawa, Miki Molecular Systems Biology, Vol. 2, Article No. 2006.0008 https://doi.org/10.1038/msb4100050	journal	February 2006
Microbial engineering for the production of advanced biofuels Peralta-Yahya, Pamela P.; Zhang, Fuzhong; del Cardayre, Stephen B. Nature, Vol. 488, Issue 7411 https://doi.org/10.1038/nature11478	journal	August 2012
Synthetic protein scaffolds provide modular control over metabolic flux Dueber, John E.; Wu, Gabriel C.; Malmirchegini, G. Reza Nature Biotechnology, Vol. 27, Issue 8, p. 753-759 https://doi.org/10.1038/nbt.1557	journal	August 2009
Engineering dynamic pathway regulation using stress-response promoters Dahl, Robert H.; Zhang, Fuzhong; Alonso-Gutierrez, Jorge Nature Biotechnology, Vol. 31, Issue 11 https://doi.org/10.1038/nbt.2689	journal	October 2013
Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes Pfleger, Brian F.; Pitera, Douglas J.; Smolke, Christina D. Nature Biotechnology, Vol. 24, Issue 8 https://doi.org/10.1038/nbt1226	journal	July 2006
Engineering a mevalonate pathway in Escherichia coli for production of terpenoids Martin, Vincent J. J.; Pitera, Douglas J.; Withers, Sydnor T. Nature Biotechnology, Vol. 21, Issue 7 https://doi.org/10.1038/nbt833	journal	June 2003
Metabolic engineering for the high-yield production of isoprenoid-based C5 alcohols in E. coli George, Kevin W.; Thompson, Mitchell G.; Kang, Aram Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep11128	journal	June 2015
Tuning Escherichia coli for membrane protein overexpression Wagner, S.; Klepsch, M. M.; Schlegel, S. Proceedings of the National Academy of Sciences, Vol. 105, Issue 38 https://doi.org/10.1073/pnas.0804090105	journal	September 2008
Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis Bonanno, J. B.; Edo, C.; Eswar, N. Proceedings of the National Academy of Sciences, Vol. 98, Issue 23, p. 12896-12901 https://doi.org/10.1073/pnas.181466998	journal	November 2001
Identification of active site residues in mevalonate diphosphate decarboxylase: Implications for a family of phosphotransferases Krepkiy, Dmitriy; Miziorko, Henry M. Protein Science, Vol. 13, Issue 7 https://doi.org/10.1110/ps.04725204	journal	July 2004
Functional Linkage between Genes That Regulate Osmotic Stress Responses and Multidrug Resistance Transporters: Challenges and Opportunities for Antibiotic Discovery Cohen, B. Eleazar Antimicrobial Agents and Chemotherapy, Vol. 58, Issue 2 https://doi.org/10.1128/AAC.02095-13	journal	December 2013
Engineering of an Escherichia coli Strain for the Production of 3-Methyl-1-Butanol Connor, Michael R.; Liao, James C. Applied and Environmental Microbiology, Vol. 74, Issue 18 https://doi.org/10.1128/AEM.00468-08	journal	August 2008
Identification of Isopentenol Biosynthetic Genes from Bacillus subtilis by a Screening Method Based on Isoprenoid Precursor Toxicity Withers, S. T.; Gottlieb, S. S.; Lieu, B. Applied and Environmental Microbiology, Vol. 73, Issue 19, p. 6277-6283 https://doi.org/10.1128/AEM.00861-07	journal	August 2007
Synthetic Pathway for Production of Five-Carbon Alcohols from Isopentenyl Diphosphate Chou, Howard H.; Keasling, Jay D. Applied and Environmental Microbiology, Vol. 78, Issue 22 https://doi.org/10.1128/AEM.01175-12	journal	August 2012
Formation of Isobutene from 3-Hydroxy-3-Methylbutyrate by Diphosphomevalonate Decarboxylase Gogerty, D. S.; Bobik, T. A. Applied and Environmental Microbiology, Vol. 76, Issue 24 https://doi.org/10.1128/AEM.01917-10	journal	October 2010
ATP Requirement for Acidic Resistance in Escherichia coli Sun, Y.; Fukamachi, T.; Saito, H. Journal of Bacteriology, Vol. 193, Issue 12 https://doi.org/10.1128/JB.00091-11	journal	April 2011
Identification in Haloferax volcanii of Phosphomevalonate Decarboxylase and Isopentenyl Phosphate Kinase as Catalysts of the Terminal Enzyme Reactions in an Archaeal Alternate Mevalonate Pathway VanNice, J. C.; Skaff, D. A.; Keightley, A. Journal of Bacteriology, Vol. 196, Issue 5 https://doi.org/10.1128/JB.01230-13	journal	December 2013
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 engineering of Escherichia coli for high-specificity production of isoprenol and prenol as next generation of biofuels Zheng, Yanning; Liu, Qiang; Li, Lingling Biotechnology for Biofuels, Vol. 6, Article No. 57 https://doi.org/10.1186/1754-6834-6-57	journal	January 2013
Combination of Entner-Doudoroff Pathway with MEP Increases Isoprene Production in Engineered Escherichia coli Liu, Huaiwei; Sun, Yuanzhang; Ramos, Kristine Rose M. PLoS ONE, Vol. 8, Issue 12 https://doi.org/10.1371/journal.pone.0083290	journal	December 2013

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A mevalonate bypass system facilitates elucidation of plastid biology in malaria parasites Swift, Russell P.; Rajaram, Krithika; Liu, Hans B. PLOS Pathogens, Vol. 16, Issue 2 https://doi.org/10.1371/journal.ppat.1008316	journal	February 2020
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Recent advances of metabolic engineering strategies in natural isoprenoid production using cell factories Li, Meijie; Hou, Feifei; Wu, Tong Natural Product Reports, Vol. 37, Issue 1 https://doi.org/10.1039/c9np00016j	journal	January 2020
Two-step pathway for isoprenoid synthesis Chatzivasileiou, Alkiviadis Orfefs; Ward, Valerie; Edgar, Steven McBride Proceedings of the National Academy of Sciences, Vol. 116, Issue 2 https://doi.org/10.1073/pnas.1812935116	journal	December 2018
Metabolic engineering of Escherichia coli for the production of isoprenoids Ward, Valerie C. A.; Chatzivasileiou, Alkiviadis O.; Stephanopoulos, Gregory FEMS Microbiology Letters, Vol. 365, Issue 10 https://doi.org/10.1093/femsle/fny079	journal	March 2018
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