Integrated analysis of isopentenyl pyrophosphate (IPP) toxicity in isoprenoid-producing Escherichia coli
Abstract
Isopentenyl pyrophosphate (IPP) toxicity presents a challenge in engineered microbial systems since its formation is unavoidable in terpene biosynthesis. In this work, we develop an experimental platform to study IPP toxicity in isoprenol-producing Escherichia coli. We first characterize the physiological response to IPP accumulation, demonstrating that elevated IPP levels are linked to growth inhibition, reduced cell viability, and plasmid instability. We show that IPP toxicity selects for pathway “breakage” using proteomics to identify a reduction in phosphomevalonate kinase (PMK) as a probable recovery mechanism. Next, using multi-omics data, we demonstrate that endogenous E. coli metabolism is globally impacted by IPP accumulation, which slows nutrient uptake, decreases ATP levels, and perturbs nucleotide metabolism. We also observe the extracellular accumulation of IPP and present preliminary evidence that IPP can be transported by E. coli, findings that might be broadly relevant for the study of isoprenoid biosynthesis. Finally, we discover that IPP accumulation leads to the formation of ApppI, a nucleotide analog of IPP that may contribute to observed toxicity phenotypes. This comprehensive assessment of IPP stress suggests potential strategies for the alleviation of prenyl diphosphate toxicity and highlights possible engineering targets for improved IPP flux and high titer isoprenoid production.
- Authors:
-
- Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Systems & Engineering Division
- Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Systems & Engineering Division; Univ. of California, Berkeley, CA (United States). Dept. of Plant and Microbial Biology
- Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Chemical and Biological Processes Development Group
- Univ. of Eastern Finland, Kuopio (Finland). School of Pharmacy, Biocenter Kuopio
- Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging Division
- Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Systems & Engineering Division; Univ. of California, Berkeley, CA (United States). Dept. of Bioengineering; Univ. of California, Berkeley, CA (United States). Dept. of Chemical and Biomolecular Engineering; Technical Univ. of Denmark, Lyngby (Denmark). Novo Nordisk Foundation Center for Biosustainability
- Publication Date:
- Research Org.:
- Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1427525
- Alternate Identifier(s):
- OSTI ID: 1530358
- Report Number(s):
- PNNL-SA-138198
Journal ID: ISSN 1096-7176; PII: S1096717617303749
- Grant/Contract Number:
- AC05-76RL01830; AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Metabolic Engineering
- Additional Journal Information:
- Journal Volume: 47; Journal ID: ISSN 1096-7176
- Publisher:
- Elsevier
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Isopentenyl pyrophosphate (IPP); IPP toxicity; isoprenol; ApppI; mevalonate pathway; multi-omics
Citation Formats
George, Kevin W., Thompson, Mitchell, Kim, Joonhoon, Baidoo, Edward E. K., Wang, George, Benites, Veronica Teixeira, Petzold, Christopher J., Chan, Leanne Jade G., Yilmaz, Suzan, Turhanen, Petri, Adams, Paul D., Keasling, Jay D., and Lee, Taek Soon. Integrated analysis of isopentenyl pyrophosphate (IPP) toxicity in isoprenoid-producing Escherichia coli. United States: N. p., 2018.
Web. doi:10.1016/J.YMBEN.2018.03.004.
George, Kevin W., Thompson, Mitchell, Kim, Joonhoon, Baidoo, Edward E. K., Wang, George, Benites, Veronica Teixeira, Petzold, Christopher J., Chan, Leanne Jade G., Yilmaz, Suzan, Turhanen, Petri, Adams, Paul D., Keasling, Jay D., & Lee, Taek Soon. Integrated analysis of isopentenyl pyrophosphate (IPP) toxicity in isoprenoid-producing Escherichia coli. United States. https://doi.org/10.1016/J.YMBEN.2018.03.004
George, Kevin W., Thompson, Mitchell, Kim, Joonhoon, Baidoo, Edward E. K., Wang, George, Benites, Veronica Teixeira, Petzold, Christopher J., Chan, Leanne Jade G., Yilmaz, Suzan, Turhanen, Petri, Adams, Paul D., Keasling, Jay D., and Lee, Taek Soon. Fri .
"Integrated analysis of isopentenyl pyrophosphate (IPP) toxicity in isoprenoid-producing Escherichia coli". United States. https://doi.org/10.1016/J.YMBEN.2018.03.004. https://www.osti.gov/servlets/purl/1427525.
@article{osti_1427525,
title = {Integrated analysis of isopentenyl pyrophosphate (IPP) toxicity in isoprenoid-producing Escherichia coli},
author = {George, Kevin W. and Thompson, Mitchell and Kim, Joonhoon and Baidoo, Edward E. K. and Wang, George and Benites, Veronica Teixeira and Petzold, Christopher J. and Chan, Leanne Jade G. and Yilmaz, Suzan and Turhanen, Petri and Adams, Paul D. and Keasling, Jay D. and Lee, Taek Soon},
abstractNote = {Isopentenyl pyrophosphate (IPP) toxicity presents a challenge in engineered microbial systems since its formation is unavoidable in terpene biosynthesis. In this work, we develop an experimental platform to study IPP toxicity in isoprenol-producing Escherichia coli. We first characterize the physiological response to IPP accumulation, demonstrating that elevated IPP levels are linked to growth inhibition, reduced cell viability, and plasmid instability. We show that IPP toxicity selects for pathway “breakage” using proteomics to identify a reduction in phosphomevalonate kinase (PMK) as a probable recovery mechanism. Next, using multi-omics data, we demonstrate that endogenous E. coli metabolism is globally impacted by IPP accumulation, which slows nutrient uptake, decreases ATP levels, and perturbs nucleotide metabolism. We also observe the extracellular accumulation of IPP and present preliminary evidence that IPP can be transported by E. coli, findings that might be broadly relevant for the study of isoprenoid biosynthesis. Finally, we discover that IPP accumulation leads to the formation of ApppI, a nucleotide analog of IPP that may contribute to observed toxicity phenotypes. This comprehensive assessment of IPP stress suggests potential strategies for the alleviation of prenyl diphosphate toxicity and highlights possible engineering targets for improved IPP flux and high titer isoprenoid production.},
doi = {10.1016/J.YMBEN.2018.03.004},
journal = {Metabolic Engineering},
number = ,
volume = 47,
place = {United States},
year = {Fri Mar 09 00:00:00 EST 2018},
month = {Fri Mar 09 00:00:00 EST 2018}
}
Web of Science
Works referenced in this record:
Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli
journal, January 2010
- Atsumi, Shota; Wu, Tung‐Yun; Machado, Iara M. P.
- Molecular Systems Biology, Vol. 6, Issue 1
Parts plus pipes: Synthetic biology approaches to metabolic engineering
journal, May 2012
- Boyle, Patrick M.; Silver, Pamela A.
- Metabolic Engineering, Vol. 14, Issue 3
Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow
journal, May 2016
- Brunk, Elizabeth; George, Kevin W.; Alonso-Gutierrez, Jorge
- Cell Systems, Vol. 2, Issue 5
An integrated network approach identifies the isobutanol response network of Escherichia coli
journal, January 2009
- Brynildsen, Mark P.; Liao, James C.
- Molecular Systems Biology, Vol. 5, Issue 1
The ATP-binding cassette transporter A1 regulates phosphoantigen release and Vγ9Vδ2 T cell activation by dendritic cells
journal, June 2017
- Castella, Barbara; Kopecka, Joanna; Sciancalepore, Patrizia
- Nature Communications, Vol. 8, Issue 1
Programming adaptive control to evolve increased metabolite production
journal, October 2013
- Chou, Howard H.; Keasling, Jay D.
- Nature Communications, Vol. 4, Issue 1
Acute Limonene Toxicity in Escherichia coli Is Caused by Limonene Hydroperoxide and Alleviated by a Point Mutation in Alkyl Hydroperoxidase AhpC
journal, May 2015
- Chubukov, Victor; Mingardon, Florence; Schackwitz, Wendy
- Applied and Environmental Microbiology, Vol. 81, Issue 14
Synthetic and systems biology for microbial production of commodity chemicals
journal, April 2016
- Chubukov, Victor; Mukhopadhyay, Aindrila; Petzold, Christopher J.
- npj Systems Biology and Applications, Vol. 2, Issue 1
Improving Microbial Biogasoline Production in Escherichia coli Using Tolerance Engineering
journal, November 2014
- Foo, Jee Loon; Jensen, Heather M.; Dahl, Robert H.
- mBio, Vol. 5, Issue 6
Correlation analysis of targeted proteins and metabolites to assess and engineer microbial isopentenol production: Targeted Proteomics-Based Correlation Analysis
journal, May 2014
- George, Kevin W.; Chen, Amy; Jain, Aakriti
- Biotechnology and Bioengineering, Vol. 111, Issue 8
Metabolic engineering for the high-yield production of isoprenoid-based C5 alcohols in E. coli
journal, June 2015
- George, Kevin W.; Thompson, Mitchell G.; Kang, Aram
- Scientific Reports, Vol. 5, Issue 1
Standard Flow Liquid Chromatography for Shotgun Proteomics in Bioenergy Research
journal, April 2015
- González Fernández-Niño, Susana M.; Smith-Moritz, A. Michelle; Chan, Leanne Jade G.
- Frontiers in Bioengineering and Biotechnology, Vol. 3
ATP Synthase and the Actions of Inhibitors Utilized To Study Its Roles in Human Health, Disease, and Other Scientific Areas
journal, December 2008
- Hong, Sangjin; Pedersen, Peter L.
- Microbiology and Molecular Biology Reviews, Vol. 72, Issue 4
Selective Calcium-Dependent Inhibition of ATP-Gated P2X3 Receptors by Bisphosphonate-Induced Endogenous ATP Analog ApppI
journal, April 2017
- Ishchenko, Yevheniia; Shakirzyanova, Anastasia; Giniatullina, Raisa
- Journal of Pharmacology and Experimental Therapeutics, Vol. 361, Issue 3
Metabolic pathway balancing and its role in the production of biofuels and chemicals
journal, June 2015
- Jones, J. Andrew; Toparlak, Ö Duhan; Koffas, Mattheos AG
- Current Opinion in Biotechnology, Vol. 33
Advances in the development of nucleoside and nucleotide analogues for cancer and viral diseases
journal, May 2013
- Jordheim, Lars Petter; Durantel, David; Zoulim, Fabien
- Nature Reviews Drug Discovery, Vol. 12, Issue 6
Impact of synthetic biology and metabolic engineering on industrial production of fine chemicals
journal, November 2015
- Jullesson, David; David, Florian; Pfleger, Brian
- Biotechnology Advances, Vol. 33, Issue 7
Isopentenyl diphosphate (IPP)-bypass mevalonate pathways for isopentenol production
journal, March 2016
- Kang, Aram; George, Kevin W.; Wang, George
- Metabolic Engineering, Vol. 34
Synthetic biology and the development of tools for metabolic engineering
journal, May 2012
- Keasling, Jay D.
- Metabolic Engineering, Vol. 14, Issue 3
Application of Functional Genomics to Pathway Optimization for Increased Isoprenoid Production
journal, March 2008
- Kizer, L.; Pitera, D. J.; Pfleger, B. F.
- Applied and Environmental Microbiology, Vol. 74, Issue 10
Fast and accurate short read alignment with Burrows-Wheeler transform
journal, May 2009
- Li, H.; Durbin, R.
- Bioinformatics, Vol. 25, Issue 14
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
journal, November 2013
- Liao, Y.; Smyth, G. K.; Shi, W.
- Bioinformatics, Vol. 30, Issue 7
Microbial tolerance engineering toward biochemical production: from lignocellulose to products
journal, October 2014
- Ling, Hua; Teo, Weisuong; Chen, Binbin
- Current Opinion in Biotechnology, Vol. 29
Isoprenoid generating systems in plants — A handy toolbox how to assess contribution of the mevalonate and methylerythritol phosphate pathways to the biosynthetic process
journal, July 2016
- Lipko, Agata; Swiezewska, Ewa
- Progress in Lipid Research, Vol. 63
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
journal, December 2014
- Love, Michael I.; Huber, Wolfgang; Anders, Simon
- Genome Biology, Vol. 15, Issue 12
Engineering a mevalonate pathway in Escherichia coli for production of terpenoids
journal, June 2003
- Martin, Vincent J. J.; Pitera, Douglas J.; Withers, Sydnor T.
- Nature Biotechnology, Vol. 21, Issue 7
A new endogenous ATP analog (ApppI) inhibits the mitochondrial adenine nucleotide translocase (ANT) and is responsible for the apoptosis induced by nitrogen-containing bisphosphonates: A new endogenous ATP analog induced by N-BPs
journal, February 2006
- Mönkkönen, Hannu; Auriola, Seppo; Lehenkari, Petri
- British Journal of Pharmacology, Vol. 147, Issue 4
F 1 -Adenosine Triphosphatase Displays Properties Characteristic of an Antigen Presentation Molecule for Vγ9Vδ2 T Cells
journal, May 2010
- Mookerjee-Basu, Jayati; Vantourout, Pierre; Martinez, Laurent O.
- The Journal of Immunology, Vol. 184, Issue 12
Tolerance engineering in bacteria for the production of advanced biofuels and chemicals
journal, August 2015
- Mukhopadhyay, Aindrila
- Trends in Microbiology, Vol. 23, Issue 8
A comparative view of metabolite and substrate stress and tolerance in microbial bioprocessing: From biofuels and chemicals, to biocatalysis and bioremediation
journal, July 2010
- Nicolaou, Sergios A.; Gaida, Stefan M.; Papoutsakis, Eleftherios T.
- Metabolic Engineering, Vol. 12, Issue 4
Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development
journal, April 2014
- Paddon, Chris J.; Keasling, Jay D.
- Nature Reviews Microbiology, Vol. 12, Issue 5
Structural Diversity and Protein Engineering of the Aminoacyl-tRNA Synthetases
journal, October 2012
- Perona, John J.; Hadd, Andrew
- Biochemistry, Vol. 51, Issue 44
RCytoscape: tools for exploratory network analysis
journal, July 2013
- Shannon, Paul T.; Grimes, Mark; Kutlu, Burak
- BMC Bioinformatics, Vol. 14, Issue 1
Synthesis of ATP derivatives of compounds of the mevalonate pathway (isopentenyl di- and triphosphate; geranyl di- and triphosphate, farnesyl di- and triphosphate, and dimethylallyl diphosphate) catalyzed by T4 RNA ligase, T4 DNA ligase and other ligases
journal, August 2009
- Sillero, Maria A. Günther; de Diego, Anabel; Tavares, Janeth E. F.
- Biochemical Pharmacology, Vol. 78, Issue 4
My Way: Noncanonical Biosynthesis Pathways for Plant Volatiles
journal, October 2016
- Sun, Pulu; Schuurink, Robert C.; Caissard, Jean-Claude
- Trends in Plant Science, Vol. 21, Issue 10
Two strategies for the synthesis of the biologically important ATP analogue ApppI, at a multi-milligram scale
journal, January 2015
- Weisell, Janne; Vepsäläinen, Jouko; Turhanen, Petri A.
- Beilstein Journal of Organic Chemistry, Vol. 11
Metabolic Burden: Cornerstones in Synthetic Biology and Metabolic Engineering Applications
journal, August 2016
- Wu, Gang; Yan, Qiang; Jones, J. Andrew
- Trends in Biotechnology, Vol. 34, Issue 8
clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters
journal, May 2012
- Yu, Guangchuang; Wang, Li-Gen; Han, Yanyan
- OMICS: A Journal of Integrative Biology, Vol. 16, Issue 5
Metabolic engineering of Escherichia coli for high-specificity production of isoprenol and prenol as next generation of biofuels
journal, January 2013
- Zheng, Yanning; Liu, Qiang; Li, Lingling
- Biotechnology for Biofuels, Vol. 6, Article No. 57
Works referencing / citing this record:
Engineering Pseudomonas putida for isoprenoid production by manipulating endogenous and shunt pathways supplying precursors
journal, September 2019
- Hernandez-Arranz, Sofía; Perez-Gil, Jordi; Marshall-Sabey, Dominic
- Microbial Cell Factories, Vol. 18, Issue 1
Orthogonal monoterpenoid biosynthesis in yeast constructed on an isomeric substrate
journal, August 2019
- Ignea, Codruta; Raadam, Morten H.; Motawia, Mohammed S.
- Nature Communications, Vol. 10, Issue 1
Homology-dependent recombination of large synthetic pathways into E. coli genome via λ-Red and CRISPR/Cas9 dependent selection methodology
journal, May 2020
- Su, Buli; Song, Dandan; Zhu, Honghui
- Microbial Cell Factories, Vol. 19, Issue 1
Metabolic engineering for the production of isoprene and isopentenol by Escherichia coli
journal, July 2018
- Li, Meijie; Nian, Rui; Xian, Mo
- Applied Microbiology and Biotechnology, Vol. 102, Issue 18
Cell free biosynthesis of isoprenoids from isopentenol
journal, September 2019
- Ward, Valerie C. A.; Chatzivasileiou, Alkiviadis Orfefs; Stephanopoulos, Gregory
- Biotechnology and Bioengineering, Vol. 116, Issue 12
Modular enzyme assembly for enhanced cascade biocatalysis and metabolic flux
journal, September 2019
- Kang, Wei; Ma, Tian; Liu, Min
- Nature Communications, Vol. 10, Issue 1
Light-based control of metabolic flux through assembly of synthetic organelles
journal, May 2019
- Zhao, Evan M.; Suek, Nathan; Wilson, Maxwell Z.
- Nature Chemical Biology, Vol. 15, Issue 6
Microbial Platform for Terpenoid Production: Escherichia coli and Yeast
journal, October 2018
- Wang, Chonglong; Liwei, Mudanguli; Park, Ji-Bin
- Frontiers in Microbiology, Vol. 9
Towards efficient terpenoid biosynthesis: manipulating IPP and DMAPP supply
journal, February 2019
- Wang, Qin; Quan, Shu; Xiao, Han
- Bioresources and Bioprocessing, Vol. 6, Issue 1
Production of sesterterpene ophiobolin by a bifunctional terpene synthase in Escherichia coli
journal, September 2019
- Yuan, Wei; Lv, Shuang; Chen, Linyue
- Applied Microbiology and Biotechnology, Vol. 103, Issue 21-22
Modular Engineering of Biomass Degradation Pathways
journal, April 2019
- Chaves, Julie E.; Presley, Gerald N.; Michener, Joshua K.
- Processes, Vol. 7, Issue 4
Terpenoid Metabolic Engineering in Photosynthetic Microorganisms
journal, October 2018
- Vavitsas, Konstantinos; Fabris, Michele; Vickers, Claudia
- Genes, Vol. 9, Issue 11
Recent advances of metabolic engineering strategies in natural isoprenoid production using cell factories
journal, January 2020
- Li, Meijie; Hou, Feifei; Wu, Tong
- Natural Product Reports, Vol. 37, Issue 1
Modular engineering for microbial production of carotenoids
journal, June 2020
- Li, Cheng; Swofford, Charles A.; Sinskey, Anthony J.
- Metabolic Engineering Communications, Vol. 10
Modular enzyme assembly for enhanced cascade biocatalysis and metabolic flux
journal, September 2019
- Kang, Wei; Ma, Tian; Liu, Min
- Nature Communications, Vol. 10, Issue 1
Light-based control of metabolic flux through assembly of synthetic organelles
journal, May 2019
- Zhao, Evan M.; Suek, Nathan; Wilson, Maxwell Z.
- Nature Chemical Biology, Vol. 15, Issue 6
Cell-free biosynthesis of limonene using enzyme-enriched Escherichia coli lysates
journal, January 2019
- Dudley, Quentin M.; Nash, Connor J.; Jewett, Michael C.
- Synthetic Biology, Vol. 4, Issue 1
Bacterial microcompartments: catalysis-enhancing metabolic modules for next generation metabolic and biomedical engineering
journal, October 2019
- Kirst, Henning; Kerfeld, Cheryl A.
- BMC Biology, Vol. 17, Issue 1
Engineering Pseudomonas putida for isoprenoid production by manipulating endogenous and shunt pathways supplying precursors
journal, September 2019
- Hernandez-Arranz, Sofía; Perez-Gil, Jordi; Marshall-Sabey, Dominic
- Microbial Cell Factories, Vol. 18, Issue 1
Microbial Platform for Terpenoid Production: Escherichia coli and Yeast
journal, October 2018
- Wang, Chonglong; Liwei, Mudanguli; Park, Ji-Bin
- Frontiers in Microbiology, Vol. 9
Terpenoid Metabolic Engineering in Photosynthetic Microorganisms
journal, October 2018
- Vavitsas, Konstantinos; Fabris, Michele; Vickers, Claudia
- Genes, Vol. 9, Issue 11
Adaptation of hydroxymethylbutenyl diphosphate reductase enables volatile isoprenoid production
journal, March 2020
- Bongers, Mareike; Perez-Gil, Jordi; Hodson, Mark P.
- eLife, Vol. 9