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Adaptive laboratory evolution of Pseudomonas putida KT2440 improves p-coumaric and ferulic acid catabolism and tolerance
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A Pseudomonas strain was adapted to metabolize high levels of cytotoxic hydroxycinnamic acids from lignin breakdown.
“In a comparable case, a Pseudomonas strain was adapted to metabolize high levels of cytotoxic hydroxycinnamic acids from lignin breakdown122.”
From The link between ancient microbial fluoride resistance mechanisms and bioengineering organofluorine degradation or synthesis (2024) · cites this paper as [122]
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The Catalytic Valorization of Lignin for the Production of Renewable Chemicals
Zakzeski, J., Bruijnincx, P. C. A., Jongerius, A. L., & Weckhuysen, B. M. (2010) · Chemical Reviews · doi:10.1021/cr900354u · Cited by 4,468
Catalytic Transformation of Lignin for the Production of Chemicals and Fuels
Li, C., Zhao, X., Wang, A., Huber, G. W., & Zhang, T. (2015) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00155 · Cited by 2,951
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Research works printed but not linked: 84
- Abdelaziz, 2016, Biological valorization of low molecular weight lignin, Biotechnol. Adv., 10.1016/j.biotechadv.2016.10.001 · DOI
- Altschul, 1997, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res., 10.1093/nar/25.17.3389 · DOI · Paper page
- Anand, 2020, OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states, Mol. Biol. Evol., 37, 660, 10.1093/molbev/msz251 · DOI
- Baral, 2019, Approaches for more efficient biological conversion of lignocellulosic feedstocks to biofuels and bioproducts, ACS Sustain. Chem. Eng., 10.1021/acssuschemeng.9b01229 · DOI
- Barton, 2018, Enabling the valorization of guaiacol-based lignin: integrated chemical and biochemical production of cis,cis-muconic acid using metabolically engineered Amycolatopsis sp ATCC 39116, Metab. Eng., 45, 200, 10.1016/j.ymben.2017.12.001 · DOI
- Basler, 2018, A Pseudomonas putida efflux pump acts on short-chain alcohols, Biotechnol. Biofuels, 11, 136, 10.1186/s13068-018-1133-9 · DOI
- Becker, 2018, Metabolic engineering of Corynebacterium glutamicum for the production of cis, cis-muconic acid from lignin, Microb. Cell Factories, 17, 10.1186/s12934-018-0963-2 · DOI
- Becker, 2019, A field of dreams: lignin valorization into chemicals, materials, fuels, and health-care products, Biotechnol. Adv., 10.1016/j.biotechadv.2019.02.016 · DOI
- Beckham, 2016, Opportunities and challenges in biological lignin valorization, Curr. Opin. Biotechnol., 10.1016/j.copbio.2016.02.030 · DOI
- Belda, 2016, The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis, Environ. Microbiol., 18, 3403, 10.1111/1462-2920.13230 · DOI · Paper page
- Bentley, 2020, Engineering glucose metabolism for enhanced muconic acid production in Pseudomonas putida KT2440, Metab. Eng., 59, 64, 10.1016/j.ymben.2020.01.001 · DOI
- Black, 2016, Aqueous stream characterization from biomass fast pyrolysis and catalytic fast pyrolysis, ACS Sustain. Chem. Eng., 4, 6815, 10.1021/acssuschemeng.6b01766 · DOI
- Blanco-Romero, 2018, Genome-wide analysis of the FleQ direct regulon in Pseudomonas fluorescens F113 and Pseudomonas putida KT2440, Sci. Rep., 8, 13145, 10.1038/s41598-018-31371-z · DOI
- Blomfield, 1991, Allelic exchange in Escherichia coli using the Bacillus subtilis sacB gene and a temperature-sensitive pSC101 replicon, Mol. Microbiol., 5, 1447, 10.1111/j.1365-2958.1991.tb00791.x · DOI
- Boerjan, 2003, Lignin biosynthesis, Annu. Rev. Plant Biol., 54, 519, 10.1146/annurev.arplant.54.031902.134938 · DOI · Paper page
- Bugg, 2015, Enzymatic conversion of lignin into renewable chemicals, Curr. Opin. Chem. Biol., 10.1016/j.cbpa.2015.06.009 · DOI
- Calero, 2018, Genome-wide identification of tolerance mechanisms toward p-coumaric acid in Pseudomonas putida, Biotechnol. Bioeng., 115, 762, 10.1002/bit.26495 · DOI
- Calero, 2019, Chasing bacterial chassis for metabolic engineering: a perspective review from classical to non-traditional microorganisms, Microb. Biotechnol., 12, 98, 10.1111/1751-7915.13292 · DOI
- Choi, 2006, A 10-min method for preparation of highly electrocompetent Pseudomonas aeruginosa cells: application for DNA fragment transfer between chromosomes and plasmid transformation, J. Microbiol. Methods, 64, 391, 10.1016/j.mimet.2005.06.001 · DOI
- Clarke, 1982, The metabolic versatility of pseudomonads, Antonie Leeuwenhoek, 48, 105, 10.1007/BF00405197 · DOI
- Corona, 2018, Life cycle assessment of adipic acid production from lignin, Green Chem., 20, 3857, 10.1039/C8GC00868J · DOI
- Dejonghe, 2001, Bioaugmentation of soils by increasing microbial richness: missing links, Environ. Microbiol., 3, 649, 10.1046/j.1462-2920.2001.00236.x · DOI
- dos Santos, 2004, Insights into the genomic basis of niche specificity of Pseudomonas putida KT2440, Environ. Microbiol., 6, 1264, 10.1111/j.1462-2920.2004.00734.x · DOI
- Duque, 2001, Global and cognate regulators control the expression of the organic solvent efflux pumps TtgABC and TtgDEF of Pseudomonas putida, Mol. Microbiol., 39, 1100, 10.1046/j.1365-2958.2001.02310.x · DOI
- Dvořák, 2017, Bioremediation 3.0: engineering pollutant-removing bacteria in the times of systemic biology, Biotechnol. Adv., 35, 845, 10.1016/j.biotechadv.2017.08.001 · DOI
- Fernandez, 2012, Mechanisms of resistance to chloramphenicol in Pseudomonas putida KT2440, Antimicrob. Agents Chemother., 56, 1001, 10.1128/AAC.05398-11 · DOI
- Franden, 2018, Engineering Pseudomonas putida KT2440 for efficient ethylene glycol utilization, Metab. Eng., 48, 197, 10.1016/j.ymben.2018.06.003 · DOI
- Fuchs, 2011, Microbial degradation of aromatic compounds- from one strategy to four, Nat. Rev. Microbiol., 10.1038/nrmicro2652 · DOI
- Gibson, 2009, Enzymatic assembly of DNA molecules up to several hundred kilobases, Nat. Methods, 6, 343, 10.1038/nmeth.1318 · DOI
- Godoy, 2010, Characterization of the RND family of multidrug efflux pumps: in silico to in vivo confirmation of four functionally distinct subgroups, Microb. Biotechnol., 3, 691, 10.1111/j.1751-7915.2010.00189.x · DOI
- Harwood, 1996, The β-KETOADIPATE pathway and the biology OF self-identity, Annu. Rev. Microbiol., 50, 553, 10.1146/annurev.micro.50.1.553 · DOI
- Jayakody, 2018, Thermochemical wastewater valorization via enhanced microbial toxicity tolerance, Energy Environ. Sci., 11, 1625, 10.1039/C8EE00460A · DOI
- Jimenez, 2002, Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440, Environ. Microbiol., 4, 824, 10.1046/j.1462-2920.2002.00370.x · DOI
- Johnson, 2017, Eliminating a global regulator of carbon catabolite repression enhances the conversion of aromatic lignin monomers to muconate in Pseudomonas putida KT2440, Metab. Eng. Commun., 5, 19, 10.1016/j.meteno.2017.05.002 · DOI
- Johnson, 2015, Aromatic catabolic pathway selection for optimal production of pyruvate and lactate from lignin, Metab. Eng., 28, 240, 10.1016/j.ymben.2015.01.005 · DOI
- Johnson, 2019, Innovative chemicals and materials from bacterial aromatic catabolic pathways, Joule, 3, 1523, 10.1016/j.joule.2019.05.011 · DOI
- Karlen, 2020, Assessing the viability of recovering hydroxycinnamic acids from lignocellulosic biorefinery alkaline pretreatment waste streams, ChemSusChem, 10.1002/cssc.202000820 · DOI
- Karp, 2016, Quantification of acidic compounds in complex biomass-derived streams, Green Chem., 18, 4750, 10.1039/C6GC00868B · DOI
- Kim, 2017, Indole-induced activities of beta-lactamase and efflux pump confer ampicillin resistance in Pseudomonas putida KT2440, Front. Microbiol., 8, 433, 10.3389/fmicb.2017.00433 · DOI
- Kim, 2014, The sensor kinase GacS negatively regulates flagellar formation and motility in a biocontrol bacterium, Pseudomonas chlororaphis O6, Plant Pathol. J., 30, 215, 10.5423/PPJ.NT.11.2013.0109 · DOI
- Kohlstedt, 2018, From lignin to nylon: cascaded chemical and biochemical conversion using metabolically engineered Pseudomonas putida, Metab. Eng., 47, 279, 10.1016/j.ymben.2018.03.003 · DOI
- LaCroix, 2015, Use of adaptive laboratory evolution to discover key mutations enabling rapid growth of Escherichia coli K-12 MG1655 on glucose minimal medium, Appl. Environ. Microbiol., 81, 17, 10.1128/AEM.02246-14 · DOI
- Lee, 2011, Cumulative number of cell divisions as a meaningful timescale for adaptive laboratory evolution of Escherichia coli, PloS One, 6
- Lieder, 2015, Genome reduction boosts heterologous gene expression in Pseudomonas putida, Microb. Cell Factories, 14, 23, 10.1186/s12934-015-0207-7 · DOI
- Lin, 2016, Systems biology-guided biodesign of consolidated lignin conversion, Green Chem., 18, 5536, 10.1039/C6GC01131D · DOI
- Linger, 2014, Lignin valorization through integrated biological funneling and chemical catalysis, Proc. Natl. Acad. Sci. Unit. States Am., 111, 12013 LP, 10.1073/pnas.1410657111 · DOI
- Liu, 2018, Combinatorial pretreatment and fermentation optimization enabled a record yield on lignin bioconversion, Biotechnol. Biofuels, 11, 21, 10.1186/s13068-018-1021-3 · DOI
- Martínez-García, 2016, The quest for the minimal bacterial genome, Curr. Opin. Biotechnol., 42, 216, 10.1016/j.copbio.2016.09.001 · DOI
- Martínez-García, 2015, Freeing Pseudomonas putida KT2440 of its proviral load strengthens endurance to environmental stresses, Environ. Microbiol., 17, 76, 10.1111/1462-2920.12492 · DOI
- Martínez-García, 2014, Pseudomonas 2.0: genetic upgrading of P. putida KT2440 as an enhanced host for heterologous gene expression, Microb. Cell Factories, 13, 159, 10.1186/s12934-014-0159-3 · DOI
- Martínez-García, 2014, The metabolic cost of flagellar motion in Pseudomonas putidaKT2440, Environ. Microbiol., 16, 291, 10.1111/1462-2920.12309 · DOI
- Martinez-Gil, 2014, Roles of cyclic Di-GMP and the Gac system in transcriptional control of the genes coding for the Pseudomonas putida adhesins LapA and LapF, J. Bacteriol., 196, 1484, 10.1128/JB.01287-13 · DOI
- Mohamed, 2019, Generation of an E. coli platform strain for improved sucrose utilization using adaptive laboratory evolution, Microb. Cell Factories, 18, 116, 10.1186/s12934-019-1165-2 · DOI
- Mohamed, 2017, Generation of a platform strain for ionic liquid tolerance using adaptive laboratory evolution, Microb. Cell Factories, 16, 1, 10.1186/s12934-017-0819-1 · DOI
- Munson, 2016, Gradient elution moving boundary electrophoresis enables rapid analysis of acids in complex biomass-derived streams, ACS Sustain. Chem. Eng., 4, 7175, 10.1021/acssuschemeng.6b02076 · DOI
- Mycroft, 2015, Biocatalytic conversion of lignin to aromatic dicarboxylic acids in Rhodococcus jostii RHA1 by re-routing aromatic degradation pathways, Green Chem., 17, 4974, 10.1039/C5GC01347J · DOI
- Nikel, 2014, Biotechnological domestication of pseudomonads using synthetic biology, Nat. Rev. Microbiol., 12, 368, 10.1038/nrmicro3253 · DOI
- Okamura-Abe, 2016, Beta-ketoadipic acid and muconolactone production from a lignin-related aromatic compound through the protocatechuate 3,4-metabolic pathway, J. Biosci. Bioeng., 121, 652, 10.1016/j.jbiosc.2015.11.007 · DOI
- Phaneuf, 2019, ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation, Nucleic Acids Res., 47, 10.1093/nar/gky983 · DOI
- Poblete-Castro, 2012, Industrial biotechnology of Pseudomonas putida and related species, Appl. Microbiol. Biotechnol., 93, 2279, 10.1007/s00253-012-3928-0 · DOI
- Ragauskas, 2014, Lignin valorization: improving lignin processing in the biorefinery, Science, 80–
- Ralph, 2010, Hydroxycinnamates in lignification, Phytochemistry Rev., 10.1007/s11101-009-9141-9 · DOI
- Ralph, 1994, Pathway of p-coumaric acid incorporation into maize lignin as revealed by NMR, J. Am. Chem. Soc., 116, 9448, 10.1021/ja00100a006 · DOI
- Ramos, 1998, Efflux pumps involved in toluene tolerance in Pseudomonas putida DOT-T1E, J. Bacteriol., 180, 3323, 10.1128/JB.180.13.3323-3329.1998 · DOI
- Ravi, 2017, Conversion of lignin model compounds by Pseudomonas putida KT2440 and isolates from compost, Appl. Microbiol. Biotechnol., 101, 5059, 10.1007/s00253-017-8211-y · DOI
- Regenhardt, 2002, Pedigree and taxonomic credentials of Pseudomonas putida strain KT2440, Environ. Microbiol., 4, 912, 10.1046/j.1462-2920.2002.00368.x · DOI
- Sainsbury, 2013, Breaking down lignin to high-value chemicals: the conversion of lignocellulose to vanillin in a gene deletion mutant of rhodococcus jostii RHA1, ACS Chem. Biol., 8, 2151, 10.1021/cb400505a · DOI
- Salvachúa, 2018, Bioprocess development for muconic acid production from aromatic compounds and lignin, Green Chem., 20, 5007, 10.1039/C8GC02519C · DOI
- Salvachúa, 2015, Towards lignin consolidated bioprocessing: simultaneous lignin depolymerization and product generation by bacteria, Green Chem., 17, 4951, 10.1039/C5GC01165E · DOI
- Salvachúa, 2020, Metabolic engineering of Pseudomonas putida for increased polyhydroxyalkanoate production from lignin, Microb. Biotechnol., 13, 290, 10.1111/1751-7915.13481 · DOI
- Sandberg, 2017, Laboratory evolution to alternating substrate environments yields distinct phenotypic and genetic adaptive strategies, Appl. Environ. Microbiol., 83, 10.1128/AEM.00410-17 · DOI
- Schmid, 2001, Industrial biocatalysis today and tomorrow, Nature, 409, 258, 10.1038/35051736 · DOI
- Schutyser, 2018, Chemicals from lignin: an interplay of lignocellulose fractionation, depolymerisation, and upgrading, Chem. Soc. Rev., 10.1039/C7CS00566K · DOI
- Sonoki, 2018, Glucose-free cis , cis -muconic acid production via new metabolic designs corresponding to the heterogeneity of lignin, ACS Sustain. Chem. Eng., 6, 1256, 10.1021/acssuschemeng.7b03597 · DOI
- Sun, 2018, Bright side of lignin depolymerization: toward new platform chemicals, Chem. Rev., 118, 614, 10.1021/acs.chemrev.7b00588 · DOI
- Teran, 2003, Antibiotic-dependent induction of Pseudomonas putida DOT-T1E TtgABC efflux pump is mediated by the drug binding repressor TtgR, Antimicrob. Agents Chemother., 47, 3067, 10.1128/AAC.47.10.3067-3072.2003 · DOI
- Timmis, 1994, Designing microorganisms for the treatment of toxic wastes, Annu. Rev. Microbiol., 48, 525, 10.1146/annurev.mi.48.100194.002521 · DOI
- Tomizawa, 2014, Understanding the limitations in the biosynthesis of polyhydroxyalkanoate (PHA) from lignin derivatives, ACS Sustain. Chem. Eng., 2, 1106, 10.1021/sc500066f · DOI
- Tuck, 2012, Valorization of biomass: deriving more value from waste, Science, 10.1126/science.1218930 · DOI
- Utrilla, 2016, Global rebalancing of cellular resources by pleiotropic point mutations illustrates a multi-scale mechanism of adaptive evolution, Cell Syst, 2, 260, 10.1016/j.cels.2016.04.003 · DOI
- van Duuren, 2011, A limited LCA of bio-adipic acid: manufacturing the nylon-6,6 precursor adipic acid using the benzoic acid degradation pathway from different feedstocks, Biotechnol. Bioeng., 108, 1298, 10.1002/bit.23074 · DOI
- Vardon, 2015, Adipic acid production from lignin, Energy Environ. Sci., 8, 617, 10.1039/C4EE03230F · DOI
- von Graevenitz, 1976, Genetics and biochemistry of Pseudomonas, Yale J. Biol. Med., 49, 308
- Zhao, 2016, Synergistic enzymatic and microbial lignin conversion, Green Chem., 18, 1306, 10.1039/C5GC01955A · DOI
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Stockbridge, R. B., & Wackett, L. P. (2024) · Nature Communications · doi:10.1038/s41467-024-49018-1 · Cited by 80
Metadata
- Authors
- Mohamed, E. T., Werner, A. Z., Salvachúa, D., Singer, C. A., Szostkiewicz, K., Rafael Jiménez-Díaz, M., Eng, T., Radi, M. S., Simmons, B. A., Mukhopadhyay, A., Herrgård, M. J., Singer, S. W., Beckham, G. T., & Feist, A. M.
- Venue
- Metabolic Engineering Communications
- Publisher
- Elsevier BV
- Published
- 2020-12
- Volume
- 11
- Pages
- e00143
- ISSN
- 2214-0301
- PMC
- PMC7490845
- Cited by
- 136
- References
- 2
- Language
- en
- Licence
- Funders
- Center for Bioenergy Innovation
- U.S. Department of Energy (DE-AC36-08GO28308)
- Chinese Academy of Sciences
- Office of Science (DE-AC02-05CH11231)
- Novo Nordisk Fonden (NNF10CC1016517, NNF14OC0011269)
- Biological and Environmental Research
- National Renewable Energy Laboratory
- Lawrence Berkeley National Laboratory
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