Liao, Y. et al. A sustainable wood biorefinery for low-carbon footprint chemicals production. Science 367, 1385–1390 (2020).
Meng, Q. et al. Sustainable production of benzene from lignin. Nat. Commun. 12, 4534 (2021).
Subbotina, E. et al. Oxidative cleavage of C–C bonds in lignin. Nat. Chem. 13, 1118–1125 (2021).
Werner, A. Z. et al. Lignin conversion to β-ketoadipic acid by Pseudomonas putida via metabolic engineering and bioprocess development. Sci. Adv. 9, eadj0053 (2023).
Schutyser, W. et al. Chemicals from lignin: an interplay of lignocellulose fractionation, depolymerisation, and upgrading. Chem. Soc. Rev. 47, 852–908 (2018).
Questell-Santiago, Y. M., Galkin, M. V., Barta, K. & Luterbacher, J. S. Stabilization strategies in biomass depolymerization using chemical functionalization. Nat. Rev. Chem. 4, 311–330 (2020).
Gu, N. X. et al. Autoxidation catalysis for carbon–carbon bond cleavage in lignin. ACS Cent. Sci. 9, 2277–2285 (2023).
Palumbo, C. T. et al. Catalytic carbon–carbon bond cleavage in lignin via manganese–zirconium-mediated autoxidation. Nat. Commun. 15, 862 (2024).
Palumbo, C. T. et al. Accessing monomers from lignin through carbon–carbon bond cleavage. Nat. Rev. Chem. 8, 799–816 (2024).
Tomás, R. A. F., Bordado, J. C. M. & Gomes, J. F. P. p-Xylene oxidation to terephthalic acid: a literature review oriented toward process optimization and development. Chem. Rev. 113, 7421–7469 (2013).
Speight, J. Petroleum refinery processes. In Kirk-Othmer Encyclopedia of Chemical Technology (Wiley, 2018); https://doi.org/10.1002/0471238961.1805060919160509.a01.pub3.
Musser, M. T. Cyclohexanol and cyclohexanone. In Ullmann’s Encyclopedia of Industrial Chemistry (Wiley, 2000); https://doi.org/10.1002/14356007.a08_217
Zakzeski, J., Bruijnincx, P. C. A., Jongerius, A. L. & Weckhuysen, B. M. The catalytic valorization of lignin for the production of renewable chemicals. Chem. Rev. 110, 3552–3599 (2010).
Sun, Z., Fridrich, B., de Santi, A., Elangovan, S. & Barta, K. Bright side of lignin depolymerization: toward new platform chemicals. Chem. Rev. 118, 614–678 (2018).
Ralph, J., Lapierre, C. & Boerjan, W. Lignin structure and its engineering. Curr. Opin. Biotechnol. 56, 240–249 (2019).
Lucarini, M. & Pedulli, G. F. Free radical intermediates in the inhibition of the autoxidation reaction. Chem. Soc. Rev. 39, 2106–2119 (2010).
Stone, M. L. et al. Continuous hydrodeoxygenation of lignin to jet-range aromatic hydrocarbons. Joule 6, 2324–2337 (2022).
Webber, M. S. et al. Lignin deoxygenation for the production of sustainable aviation fuel blendstocks. Nat. Mater. 23, 1622–1638 (2024).
Webber, M. S. et al. Drop-in sustainable aviation fuels enabled by feedstock-agnostic lignin deoxygenation. Cell Rep. Phys. Sci. 6, 102687 (2025).
Shanks, B. H. & Keeling, P. L. Bioprivileged molecules: creating value from biomass. Green Chem. 19, 3177–3185 (2017).
Cywar, R. M., Rorrer, N. A., Hoyt, C. B., Beckham, G. T. & Chen, E. Y. X. Bio-based polymers with performance-advantaged properties. Nat. Rev. Mater. 7, 83–103 (2021).
Partenheimer, W. Methodology and scope of metal/bromide autoxidation of hydrocarbons. Catal. Today 23, 69–158 (1995).
Partenheimer, W. The aerobic oxidative cleavage of lignin to produce hydroxyaromatic benzaldehydes and carboxylic acids via metal/bromide catalysts in acetic acid/water mixtures. Adv. Synth. Catal. 351, 456–466 (2009).
Liu, A. et al. Biomanufacturing of value-added chemicals from lignin. Curr. Opin. Biotechnol. 89, 103178 (2024).
Pereyra-Camacho, M. A. & Pardo, I. Biological degradation of phthalates: from bioremediation to plastic waste valorization. ChemSusChem 19, e202501955 (2026).
Weimer, A., Kohlstedt, M., Volke, D. C., Nikel, P. I. & Wittmann, C. Industrial biotechnology of Pseudomonas putida: advances and prospects. Appl. Microbiol. Biotechnol. 104, 7745–7766 (2020).
Martínez-García, E. & de Lorenzo, V. Pseudomonas putida as a synthetic biology chassis and a metabolic engineering platform. Curr. Opin. Biotechnol. 85, 103025 (2024).
Abu-Omar, M. M. et al. Guidelines for performing lignin-first biorefining. Energy Environ. Sci. 14, 262–292 (2021).
Dao Thi, H. et al. Identification and quantification of lignin monomers and oligomers from reductive catalytic fractionation of pine wood with GC × GC – FID/MS. Green Chem. 24, 191–206 (2022).
Sullivan, M. M., Chen, C.-J. & Bhan, A. Catalytic deoxygenation on transition metal carbide catalysts. Catal. Sci. Technol. 6, 602–616 (2016).
Gong, W. H. In Industrial Arene Chemistry (ed. Mortier, J.) 1107–1135 (Wiley, 2023).
Weeda, E. P. et al. O2-permeable membrane reactor for continuous oxidative depolymerization of lignin. Joule 8, 3336–3346 (2024).
Jiménez, J. I., Miñambres, B., García, J. L. & Díaz, E. Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440. Environ. Microbiol. 4, 824–841 (2002).
Fuchs, G., Boll, M. & Heider, J. Microbial degradation of aromatic compounds—from one strategy to four. Nat. Rev. Microbiol. 9, 803–816 (2011).
Werner, A. Z. et al. Tandem chemical deconstruction and biological upcycling of poly(ethylene terephthalate) to β-ketoadipic acid by Pseudomonas putida KT2440. Metab. Eng. 67, 250–261 (2021).
Sullivan, K. P. et al. Mixed plastics waste valorization through tandem chemical oxidation and biological funneling. Science 378, 207–211 (2022).
Huenemann, J. D. et al. Combinatorial pathway engineering using multiplex serine recombinase-assisted genome engineering (mSAGE). Preprint at bioRxiv https://doi.org/10.1101/2025.07.11.664204 (2025).
Boll, M., Geiger, R., Junghare, M. & Schink, B. Microbial degradation of phthalates: biochemistry and environmental implications. Environ. Microbiol. Rep. 12, 3–15 (2019).
Elmore, J. R. et al. High-throughput genetic engineering of nonmodel and undomesticated bacteria via iterative site-specific genome integration. Sci. Adv. 9, eade1285 (2023).
Nomura, Y., Harashima, S. & Oshima, Y. PHT, a transmissible plasmid responsible for phthalate utilization in Pseudomonas putida. J. Ferment. Bioeng. 70, 295–300 (1990).
Shimodaira, J. et al. Draft genome sequence of Comamonas sp. strain E6 (NBRC 107749), a degrader of phthalate isomers through the protocatechuate 4,5-cleavage pathway. Genome Announc. 3, e0064315 (2015).
Sandberg, T. E., Salazar, M. J., Weng, L. L., Palsson, B. O. & Feist, A. M. The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology. Metab. Eng. 56, 1–16 (2019).
Johnson, C. W. et al. Innovative chemicals and materials from bacterial aromatic catabolic pathways. Joule 3, 1523–1537 (2019).
Rorrer, N. A. et al. Production of β-ketoadipic acid from glucose in Pseudomonas putida KT2440 for use in performance-advantaged nylons. Cell Rep. Phys. Sci. 3, 100840 (2022).
Vardon, D. R. et al. cis,cis-Muconic acid: separation and catalysis to bio-adipic acid for nylon-6,6 polymerization. Green Chem. 18, 3397–3413 (2016).
Capelli, S. et al. Bio-adipic acid production by catalysed hydrogenation of muconic acid in mild operating conditions. Appl. Catal. B 218, 220–229 (2017).
Capelli, S. et al. Bio adipic acid production from sodium muconate and muconic acid: a comparison of two systems. ChemCatChem 11, 3075–3084 (2019).
Khalil, I., Quintens, G., Junkers, T. & Dusselier, M. Muconic acid isomers as platform chemicals and monomers in the biobased economy. Green Chem. 22, 1517–1541 (2020).
Wilkes, R. A. et al. Comparison of microbial strains as candidate hosts and genetic reservoirs for the valorization of lignin streams. Green Chem. 26, 12053–12069 (2024).
Worsey, M. J. & Williams, P. A. Metabolism of toluene and xylenes by Pseudomonas (putida (arvilla) mt-2: evidence for a new function of the TOL plasmid. J. Bacteriol. 124, 7–13 (1975).
Carraher, J. M., Pfennig, T., Rao, R. G., Shanks, B. H. & Tessonnier, J.-P. cis,cis-Muconic acid isomerization and catalytic conversion to biobased cyclic-C6-1,4-diacid monomers. Green Chem. 19, 3042–3050 (2017).
Ver Elst, C. et al. Synthesis of levulinic acids from muconic acids in hot water. Angew. Chem. Int. Ed. 62, e202309597 (2023).
Bartling, A. W. et al. Techno-economic analysis and life cycle assessment of a biorefinery utilizing reductive catalytic fractionation. Energy Environ. Sci. 14, 4147–4168 (2021).
Arts, W. et al. Stepping away from purified solvents in reductive catalytic fractionation: a step forward towards a disruptive wood biorefinery process. Energy Environ. Sci. 16, 2518–2539 (2023).
Lee, S. Y. et al. A comprehensive metabolic map for production of bio-based chemicals. Nat. Catal. 2, 18–33 (2019).
Sluiter, A. et al. NREL/TP-510-42618: Determination of Structural Carbohydrates and Lignin in Biomass (National Renewable Energy Laboratory, 2008).
Miscall, J., Christensen, E. D., Olstad, J., Deutch, S. & Ferrell, J. R. III NREL/TP-5100-80967: Determination of Carbon, Hydrogen, Nitrogen, and Oxygen in Bio-oils (National Renewable Energy Laboratory, 2021).
Woodworth, S. P., Ramirez, K. J. & Beckham, G. T. Aromatic monomers analysis for reductive catalytic fractionation of lignin by liquid chromatography with diode array detection. protocols.io https://doi.org/10.17504/protocols.io.bp2l6x6jdlqe/v1 (2025).
Haugen, S., Alt, H., Ramirez, K., Michener, W. E. & Beckham, G. T. Analysis of HDO autoxidation products by UHPLC-DAD. protocols.io https://doi.org/10.17504/protocols.io.kqdg31ex1l25/v1 (2026).
Hosseini-Sarvari, M., Ataee-Kachouei, T. & Moeini, F. Preparation, characterization, and catalytic application of nano Ag/ZnO in the oxidation of benzylic C–H bonds in sustainable media. RSC Adv. 5, 9050–9056 (2015).
Gomez, M. V. & de la Hoz, A. NMR reaction monitoring in flow synthesis. Beilstein J. Org. Chem. 13, 285–300 (2017).
Wang, Z. et al. Cooperative interplay between a flexible PNN–Ru(II) complex and a NaBH4 additive in the efficient catalytic hydrogenation of esters. Catal. Sci. Technol. 7, 1297–1304 (2017).
Zhang, Y. et al. Catalyst-free aerobic oxidation of aldehydes into acids in water under mild conditions. Green Chem. 19, 5708–5713 (2017).
Wu, D. H., Chen, A. D. & Johnson, C. S. An improved diffusion-ordered spectroscopy experiment incorporating bipolar-gradient pulses. J. Magn. Reson. A 115, 260–264 (1995).
Stanley, L., Katahira, R. & Beckham, G. T. Molecular weight determination of lignin via gel permeation chromatography. protocols.io https://doi.org/10.17504/protocols.io.n2bvj1r15vk5/v1 (2026).
Wick, R. R. et al. Trycycler: consensus long-read assemblies for bacterial genomes. Genome Biol. 22, 266 (2021).
Kolmogorov, M., Yuan, J., Lin, Y. & Pevzner, P. A. Assembly of long, error-prone reads using repeat graphs. Nat. Biotechnol. 37, 540–546 (2019).
Vaser, R. & Šikić, M. Time- and memory-efficient genome assembly with Raven. Nat. Comput. Sci. 1, 332–336 (2021).
Li, H. Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. Bioinformatics 32, 2103–2110 (2016).
Kasai, D. et al. 2,3-Dihydroxybenzoate meta-cleavage pathway is involved in o-phthalate utilization in Pseudomonas sp. strain PTH10. Sci. Rep. 9, 1253 (2019).
Farasat, I. et al. Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria. Mol. Syst. Biol. 10, 731 (2014).
Halper, S. M., Hossain, A. & Salis, H. M. Synthesis success calculator: predicting the rapid synthesis of DNA fragments with machine learning. ACS Synth. Biol. 9, 1563–1571 (2020).
Reis, A. C. & Salis, H. M. An automated model test system for systematic development and improvement of gene expression models. ACS Synth. Biol. 9, 3145–3156 (2020).
Cetnar, D. P. & Salis, H. M. Systematic quantification of sequence and structural determinants controlling mRNA stability in bacterial operons. ACS Synth. Biol. 10, 318–332 (2021).
Elmore, J. R., Furches, A., Wolff, G. N., Gorday, K. & Guss, A. M. Development of a high efficiency integration system and promoter library for rapid modification of Pseudomonas putida KT2440. Metab. Eng. Commun. 5, 1–8 (2017).
Johnson, C. W. & Beckham, G. T. Aromatic catabolic pathway selection for optimal production of pyruvate and lactate from lignin. Metab. Eng. 28, 240–247 (2015).
Salvachúa, D. et al. Bioprocess development for muconic acid production from aromatic compounds and lignin. Green Chem. 20, 5007–5019 (2018).
Ramirez, K., Ingraham, M., Haugen, S. & Beckham, G. T. Analysis of a lignin derived single product using chemical and biological redox using UHPLC-MS/MS-DAD. protocols.io https://doi.org/10.17504/protocols.io.36wgqprjyvk5/v1 (2026).
Alt, H. M. et al. Analysis of sugars, small organic acids, and alcohols by HPLC-RID. protocols.io https://doi.org/10.17504/protocols.io.5qpvob7y9l4o/v2 (2024).