Genome-scale and pathway engineering for the sustainable aviation fuel precursor isoprenol production in Pseudomonas putida

Banerjee, Deepanwita; Yunus, Ian S.; Wang, Xi; Kim, Jinho; Srinivasan, Aparajitha; Menchavez, Russel; Chen, Yan; Gin, Jennifer W.; Petzold, Christopher J.; Martin, Hector Garcia; Magnuson, Jon K.; Adams, Paul D.; Simmons, Blake A.; Mukhopadhyay, Aindrila; Kim, Joonhoon; Lee, Taek Soon

doi:10.1016/j.ymben.2024.02.004

Genome-scale and pathway engineering for the sustainable aviation fuel precursor isoprenol production in Pseudomonas putida

Journal Article · 29 February 2024 · Metabolic Engineering

DOI:https://doi.org/10.1016/j.ymben.2024.02.004· OSTI ID:2305760

Banerjee, Deepanwita; Yunus, Ian S.; Wang, Xi; Kim, Jinho; Srinivasan, Aparajitha; Menchavez, Russel; Chen, Yan; Gin, Jennifer W.; Petzold, Christopher J.; Martin, Hector Garcia; Magnuson, Jon K.; Adams, Paul D.; Simmons, Blake A.; Mukhopadhyay, Aindrila; Kim, Joonhoon;

Not Available

View Journal Article

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231; AC05-76RL01830

OSTI ID:: 2305760

Alternate ID(s):: OSTI ID: 2406479; OSTI ID: 2429229

Journal Information:: Metabolic Engineering, Journal Name: Metabolic Engineering Journal Issue: C Vol. 82; ISSN 1096-7176

Publisher:: ElsevierCopyright Statement

Country of Publication:: Belgium

Language:: English

References (67)

Use of ensiled biomass sorghum increases ionic liquid pretreatment efficiency and reduces biofuel production cost and carbon footprint Magurudeniya, Harsha D.; Baral, Nawa Raj; Rodriguez, Alberto Green Chemistry, Vol. 23, Issue 8 https://doi.org/10.1039/D0GC03260C	journal	January 2021
Pseudomonas putida as a functional chassis for industrial biocatalysis: From native biochemistry to trans-metabolism Nikel, Pablo I.; de Lorenzo, Víctor Metabolic Engineering, Vol. 50 https://doi.org/10.1016/j.ymben.2018.05.005	journal	November 2018
Engineering the methylerythritol phosphate pathway in cyanobacteria for photosynthetic isoprene production from CO ₂ Gao, Xiang; Gao, Fang; Liu, Deng Energy & Environmental Science, Vol. 9, Issue 4 https://doi.org/10.1039/C5EE03102H	journal	January 2016
Genetic tools for reliable gene expression and recombineering in Pseudomonas putida Cook, Taylor B.; Rand, Jacqueline M.; Nurani, Wasti Journal of Industrial Microbiology & Biotechnology, Vol. 45, Issue 7 https://doi.org/10.1007/s10295-017-2001-5	journal	January 2018
Response of Pseudomonas putida to Complex, Aromatic‐Rich Fractions from Biomass Park, Mee‐Rye; Chen, Yan; Thompson, Mitchell ChemSusChem, Vol. 13, Issue 17 https://doi.org/10.1002/cssc.202000268	journal	April 2020
Carbon-limited fed-batch production of medium-chain-length polyhydroxyalkanoates by a phaZ-knockout strain of Pseudomonas putida KT2440 Vo, Minh Tri; Ko, Kenton; Ramsay, Bruce Journal of Industrial Microbiology and Biotechnology, Vol. 42, Issue 4 https://doi.org/10.1007/s10295-014-1574-5	journal	April 2015
Techno-economic analysis and life-cycle greenhouse gas mitigation cost of five routes to bio-jet fuel blendstocks Baral, Nawa Raj; Kavvada, Olga; Mendez-Perez, Daniel Energy & Environmental Science, Vol. 12, Issue 3 https://doi.org/10.1039/C8EE03266A	journal	January 2019
Lignin valorization through integrated biological funneling and chemical catalysis Linger, J. G.; Vardon, D. R.; Guarnieri, M. T. Proceedings of the National Academy of Sciences, Vol. 111, Issue 33, p. 12013-12018 https://doi.org/10.1073/pnas.1410657111	journal	August 2014
Large-scale computation of elementary flux modes with bit pattern trees Terzer, Marco; Stelling, Jörg Bioinformatics, Vol. 24, Issue 19 https://doi.org/10.1093/bioinformatics/btn401	journal	August 2008
Biotransformation of toxic lignin and aromatic compounds of lignocellulosic feedstock into eco-friendly biopolymers by Pseudomonas putida KT2440 Mohammad, Saddam Hussain; Bhukya, Bhima Bioresource Technology, Vol. 363 https://doi.org/10.1016/j.biortech.2022.128001	journal	November 2022
Massively Parallel Fitness Profiling Reveals Multiple Novel Enzymes in Pseudomonas putida Lysine Metabolism Thompson, Mitchell G.; Blake-Hedges, Jacquelyn M.; Cruz-Morales, Pablo mBio, Vol. 10, Issue 3 https://doi.org/10.1128/mBio.02577-18	journal	May 2019
Industrial biotechnology of Pseudomonas putida: advances and prospects Weimer, Anna; Kohlstedt, Michael; Volke, Daniel C. Applied Microbiology and Biotechnology, Vol. 104, Issue 18 https://doi.org/10.1007/s00253-020-10811-9	journal	August 2020
Engineering Corynebacterium glutamicum to produce the biogasoline isopentenol from plant biomass hydrolysates Sasaki, Yusuke; Eng, Thomas; Herbert, Robin A. Biotechnology for Biofuels, Vol. 12, Issue 1 https://doi.org/10.1186/s13068-019-1381-3	journal	February 2019
Automated “Cells-To-Peptides” Sample Preparation Workflow for High-Throughput, Quantitative Proteomic Assays of Microbes Chen, Yan; Guenther, Joel M.; Gin, Jennifer W. Journal of Proteome Research, Vol. 18, Issue 10 https://doi.org/10.1021/acs.jproteome.9b00455	journal	August 2019
Development of a broad-host-range sacB-based vector for unmarked allelic exchange Marx, Christopher J. BMC Research Notes, Vol. 1, Article No. 1 https://doi.org/10.1186/1756-0500-1-1	journal	January 2008
Carbon-negative production of acetone and isopropanol by gas fermentation at industrial pilot scale Liew, Fungmin Eric; Nogle, Robert; Abdalla, Tanus Nature Biotechnology https://doi.org/10.1038/s41587-021-01195-w	journal	February 2022
Roles of Cyclic Di-GMP and the Gac System in Transcriptional Control of the Genes Coding for the Pseudomonas putida Adhesins LapA and LapF Martinez-Gil, M.; Ramos-Gonzalez, M. I.; Espinosa-Urgel, M. Journal of Bacteriology, Vol. 196, Issue 8 https://doi.org/10.1128/JB.01287-13	journal	January 2014
Analysis of optimality in natural and perturbed metabolic networks Segre, D.; Vitkup, D.; Church, G. M. Proceedings of the National Academy of Sciences, Vol. 99, Issue 23 https://doi.org/10.1073/pnas.232349399	journal	November 2002
Tuning a high performing multiplexed-CRISPRi Pseudomonas putida strain to further enhance indigoidine production Czajka, Jeffrey J.; Banerjee, Deepanwita; Eng, Thomas Metabolic Engineering Communications, Vol. 15 https://doi.org/10.1016/j.mec.2022.e00206	journal	December 2022
Renewable production of high density jet fuel precursor sesquiterpenes from Escherichia coli Liu, Chun-Li; Tian, Tian; Alonso-Gutierrez, Jorge Biotechnology for Biofuels, Vol. 11, Issue 1 https://doi.org/10.1186/s13068-018-1272-z	journal	October 2018
Critical enzyme reactions in aromatic catabolism for microbial lignin conversion Erickson, Erika; Bleem, Alissa; Kuatsjah, Eugene Nature Catalysis, Vol. 5, Issue 2 https://doi.org/10.1038/s41929-022-00747-w	journal	February 2022
Approaches for More Efficient Biological Conversion of Lignocellulosic Feedstocks to Biofuels and Bioproducts Baral, Nawa Raj; Sundstrom, Eric R.; Das, Lalitendu ACS Sustainable Chemistry & Engineering, Vol. 7, Issue 10 https://doi.org/10.1021/acssuschemeng.9b01229	journal	April 2019
Generation of Pseudomonas putida KT2440 Strains with Efficient Utilization of Xylose and Galactose via Adaptive Laboratory Evolution Lim, Hyun Gyu; Eng, Thomas; Banerjee, Deepanwita ACS Sustainable Chemistry & Engineering, Vol. 9, Issue 34 https://doi.org/10.1021/acssuschemeng.1c03765	journal	August 2021
Construction ofpha-Operon-Defined Knockout Mutants ofPseudomonas putida KT2442 and their Applications in Poly(hydroxyalkanoate) Production Ouyang, Shao-Ping; Liu, Qian; Fang, Lei Macromolecular Bioscience, Vol. 7, Issue 2 https://doi.org/10.1002/mabi.200600187	journal	February 2007
Isopentenyl diphosphate (IPP)-bypass mevalonate pathways for isopentenol production Kang, Aram; George, Kevin W.; Wang, George Metabolic Engineering, Vol. 34 https://doi.org/10.1016/j.ymben.2015.12.002	journal	March 2016
Refactoring the upper sugar metabolism of Pseudomonas putida for co-utilization of cellobiose, xylose, and glucose Dvořák, Pavel; de Lorenzo, Víctor Metabolic Engineering, Vol. 48 https://doi.org/10.1016/j.ymben.2018.05.019	journal	July 2018
Generation of ionic liquid tolerant Pseudomonas putida KT2440 strains via adaptive laboratory evolution Lim, Hyun Gyu; Fong, Bonnie; Alarcon, Geovanni Green Chemistry, Vol. 22, Issue 17 https://doi.org/10.1039/D0GC01663B	journal	January 2020
Engineering Pseudomonas putida for isoprenoid production by manipulating endogenous and shunt pathways supplying precursors Hernandez-Arranz, Sofía; Perez-Gil, Jordi; Marshall-Sabey, Dominic Microbial Cell Factories, Vol. 18, Issue 1 https://doi.org/10.1186/s12934-019-1204-z	journal	September 2019
Metabolic engineering of Pseudomonas putida for increased polyhydroxyalkanoate production from lignin Salvachúa, Davinia; Rydzak, Thomas; Auwae, Raquel Microbial Biotechnology, Vol. 13, Issue 1 https://doi.org/10.1111/1751-7915.13481	journal	January 2020
Biofilm formation-defective mutants inPseudomonas putida López-Sánchez, Aroa; Leal-Morales, Antonio; Jiménez-Díaz, Lorena FEMS Microbiology Letters, Vol. 363, Issue 13 https://doi.org/10.1093/femsle/fnw127	journal	May 2016
Pseudomonas putida KT2440 Strain Metabolizes Glucose through a Cycle Formed by Enzymes of the Entner-Doudoroff, Embden-Meyerhof-Parnas, and Pentose Phosphate Pathways Nikel, Pablo I.; Chavarría, Max; Fuhrer, Tobias Journal of Biological Chemistry, Vol. 290, Issue 43 https://doi.org/10.1074/jbc.M115.687749	journal	September 2015
Production Cost and Carbon Footprint of Biomass-Derived Dimethylcyclooctane as a High-Performance Jet Fuel Blendstock Baral, Nawa Raj; Yang, Minliang; Harvey, Benjamin G. ACS Sustainable Chemistry & Engineering, Vol. 9, Issue 35 https://doi.org/10.1021/acssuschemeng.1c03772	journal	August 2021
Microorganisms as bioabatement agents in biomass to bioproducts applications Sodré, Victoria; Vilela, Nathália; Tramontina, Robson Biomass and Bioenergy, Vol. 151 https://doi.org/10.1016/j.biombioe.2021.106161	journal	August 2021
Panorama: A Targeted Proteomics Knowledge Base Sharma, Vagisha; Eckels, Josh; Taylor, Greg K. Journal of Proteome Research, Vol. 13, Issue 9 https://doi.org/10.1021/pr5006636	journal	July 2014
Genetic Cell-Surface Modification for Optimized Foam Fractionation Blesken, Christian C.; Bator, Isabel; Eberlein, Christian Frontiers in Bioengineering and Biotechnology, Vol. 8 https://doi.org/10.3389/fbioe.2020.572892	journal	October 2020
Simple fed-batch technique for high cell density cultivation of Escherichia coli Korz, D. J.; Rinas, U.; Hellmuth, K. Journal of Biotechnology, Vol. 39, Issue 1 https://doi.org/10.1016/0168-1656(94)00143-Z	journal	February 1995
In Silico Constraint-Based Strain Optimization Methods: the Quest for Optimal Cell Factories Maia, Paulo; Rocha, Miguel; Rocha, Isabel Microbiology and Molecular Biology Reviews, Vol. 80, Issue 1 https://doi.org/10.1128/MMBR.00014-15	journal	November 2015
Multi-omics analysis unravels a segregated metabolic flux network that tunes co-utilization of sugar and aromatic carbons in Pseudomonas putida Kukurugya, Matthew A.; Mendonca, Caroll M.; Solhtalab, Mina Journal of Biological Chemistry, Vol. 294, Issue 21 https://doi.org/10.1074/jbc.RA119.007885	journal	April 2019
A metabolic pathway for catabolizing levulinic acid in bacteria Rand, Jacqueline M.; Pisithkul, Tippapha; Clark, Ryan L. Nature Microbiology, Vol. 2, Issue 12 https://doi.org/10.1038/s41564-017-0028-z	journal	September 2017
High‐quality genome‐scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities Nogales, Juan; Mueller, Joshua; Gudmundsson, Steinn Environmental Microbiology, Vol. 22, Issue 1 https://doi.org/10.1111/1462-2920.14843	journal	November 2019
Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization Burgard, Anthony P.; Pharkya, Priti; Maranas, Costas D. Biotechnology and Bioengineering, Vol. 84, Issue 6 https://doi.org/10.1002/bit.10803	journal	October 2003
Pseudomonas putida in the quest of programmable chemistry Martínez-García, Esteban; de Lorenzo, Víctor Current Opinion in Biotechnology, Vol. 59 https://doi.org/10.1016/j.copbio.2019.03.012	journal	October 2019
Structural and functional analysis of cellular networks with CellNetAnalyzer Klamt, Steffen; Saez-Rodriguez, Julio; Gilles, Ernst D. BMC Systems Biology, Vol. 1, Issue 1 https://doi.org/10.1186/1752-0509-1-2	journal	January 2007
Growth-coupled overproduction is feasible for almost all metabolites in five major production organisms von Kamp, Axel; Klamt, Steffen Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/ncomms15956	journal	June 2017
Guiding stars to the field of dreams: Metabolically engineered pathways and microbial platforms for a sustainable lignin-based industry Weiland, Fabia; Kohlstedt, Michael; Wittmann, Christoph Metabolic Engineering, Vol. 71 https://doi.org/10.1016/j.ymben.2021.11.011	journal	May 2022
OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions Ranganathan, Sridhar; Suthers, Patrick F.; Maranas, Costas D. PLoS Computational Biology, Vol. 6, Issue 4 https://doi.org/10.1371/journal.pcbi.1000744	journal	April 2010
Engineering isoprenoids production in metabolically versatile microbial host Pseudomonas putida Wang, Xi; Baidoo, Edward E. K.; Kakumanu, Ramu Biotechnology for Biofuels and Bioproducts, Vol. 15, Issue 1 https://doi.org/10.1186/s13068-022-02235-6	journal	December 2022
Engineering Pseudomonas putida for efficient aromatic conversion to bioproduct using high throughput screening in a bioreactor Eng, Thomas; Banerjee, Deepanwita; Lau, Andrew K. Metabolic Engineering, Vol. 66 https://doi.org/10.1016/j.ymben.2021.04.015	journal	July 2021
Optimization of the IPP-bypass mevalonate pathway and fed-batch fermentation for the production of isoprenol in Escherichia coli Kang, Aram; Mendez-Perez, Daniel; Goh, Ee-Been Metabolic Engineering, Vol. 56 https://doi.org/10.1016/j.ymben.2019.09.003	journal	December 2019
Dynamics of benzoate metabolism in Pseudomonas putida KT2440 Sudarsan, Suresh; Blank, Lars M.; Dietrich, Alexander Metabolic Engineering Communications, Vol. 3 https://doi.org/10.1016/j.meteno.2016.03.005	journal	December 2016
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0 Heirendt, Laurent; Arreckx, Sylvain; Pfau, Thomas Nature Protocols, Vol. 14, Issue 3 https://doi.org/10.1038/s41596-018-0098-2	journal	February 2019
COBRApy: COnstraints-Based Reconstruction and Analysis for Python Ebrahim, Ali; Lerman, Joshua A.; Palsson, Bernhard O. BMC Systems Biology, Vol. 7, Issue 1 https://doi.org/10.1186/1752-0509-7-74	journal	January 2013
Biosynthesis of polycyclopropanated high energy biofuels Cruz-Morales, Pablo; Yin, Kevin; Landera, Alexander Joule, Vol. 6, Issue 7 https://doi.org/10.1016/j.joule.2022.05.011	journal	July 2022
Comparison of Three Xylose Pathways in Pseudomonas putida KT2440 for the Synthesis of Valuable Products Bator, Isabel; Wittgens, Andreas; Rosenau, Frank Frontiers in Bioengineering and Biotechnology, Vol. 7 https://doi.org/10.3389/fbioe.2019.00480	journal	January 2020
Reconfiguration of metabolic fluxes in Pseudomonas putida as a response to sub-lethal oxidative stress Nikel, Pablo I.; Fuhrer, Tobias; Chavarría, Max The ISME Journal, Vol. 15, Issue 6 https://doi.org/10.1038/s41396-020-00884-9	journal	January 2021
Microbial production of advanced biofuels Keasling, Jay; Garcia Martin, Hector; Lee, Taek Soon Nature Reviews Microbiology, Vol. 19, Issue 11 https://doi.org/10.1038/s41579-021-00577-w	journal	June 2021
Conversion of poplar biomass into high-energy density tricyclic sesquiterpene jet fuel blendstocks Geiselman, Gina M.; Kirby, James; Landera, Alexander Microbial Cell Factories, Vol. 19, Issue 1 https://doi.org/10.1186/s12934-020-01456-4	journal	November 2020
Redirecting Metabolic Flux via Combinatorial Multiplex CRISPRi-Mediated Repression for Isopentenol Production in Escherichia coli Tian, Tian; Kang, Jing Wei; Kang, Aram ACS Synthetic Biology, Vol. 8, Issue 2 https://doi.org/10.1021/acssynbio.8b00429	journal	January 2019
Model-guided dynamic control of essential metabolic nodes boosts acetyl-coenzyme A–dependent bioproduction in rewired Pseudomonas putida Kozaeva, Ekaterina; Volkova, Svetlana; Matos, Marta R. A. Metabolic Engineering, Vol. 67 https://doi.org/10.1016/j.ymben.2021.07.014	journal	September 2021
Fatty Acid and Alcohol Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing Thompson, Mitchell G.; Incha, Matthew R.; Pearson, Allison N. Applied and Environmental Microbiology, Vol. 86, Issue 21 https://doi.org/10.1128/AEM.01665-20	journal	October 2020
The Pseudomonas putida Crc global regulator controls the hierarchical assimilation of amino acids in a complete medium: Evidence from proteomic and genomic analyses Moreno, Renata; Martínez-Gomariz, Montserrat; Yuste, Luis PROTEOMICS, Vol. 9, Issue 11, p. 2910-2928 https://doi.org/10.1002/pmic.200800918	journal	June 2009
Methyl ketone production by Pseudomonas putida is enhanced by plant‐derived amino acids Dong, Jie; Chen, Yan; Benites, Veronica Teixeira Biotechnology and Bioengineering, Vol. 116, Issue 8 https://doi.org/10.1002/bit.26995	journal	April 2019
Engineered Pseudomonas putida simultaneously catabolizes five major components of corn stover lignocellulose: Glucose, xylose, arabinose, p-coumaric acid, and acetic acid Elmore, Joshua R.; Dexter, Gara N.; Salvachúa, Davinia Metabolic Engineering, Vol. 62 https://doi.org/10.1016/j.ymben.2020.08.001	journal	November 2020
Influence of the Crc global regulator on substrate uptake rates and the distribution of metabolic fluxes in Pseudomonas putida KT2440 growing in a complete medium Molina, Lázaro; La Rosa, Ruggero; Nogales, Juan Environmental Microbiology, Vol. 21, Issue 11 https://doi.org/10.1111/1462-2920.14812	journal	October 2019
Engineering of Pseudomonas putida for accelerated co-utilization of glucose and cellobiose yields aerobic overproduction of pyruvate explained by an upgraded metabolic model Bujdoš, Dalimil; Popelářová, Barbora; Volke, Daniel C. Metabolic Engineering, Vol. 75 https://doi.org/10.1016/j.ymben.2022.10.011	journal	January 2023
Computational prediction of the Crc regulon identifies genus-wide and species-specific targets of catabolite repression control in Pseudomonas bacteria Browne, Patrick; Barret, Matthieu; O'Gara, Fergal BMC Microbiology, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2180-10-300	journal	January 2010
Engineering Saccharomyces cerevisiae for isoprenol production Kim, Jinho; Baidoo, Edward E. K.; Amer, Bashar Metabolic Engineering, Vol. 64 https://doi.org/10.1016/j.ymben.2021.02.002	journal	March 2021

Similar Records

Evolution-guided tolerance engineering of Pseudomonas putida KT2440 for production of the aviation fuel precursor isoprenol

Journal Article · 2025 · Metabolic Engineering · OSTI ID:2566901

Lim, Hyun Gyu; Srinivasan, Aparajitha; Menchavez, Russel; +11 more

Genome-scale and pathway engineering for the sustainable aviation fuel precursor isoprenol production in Pseudomonas putida

Citation Formats

References (67)

Similar Records

Related Subjects