References
-
Wang, H., Pu, Y., Ragauskas, A. & Yang, B. From lignin to valuable products–strategies, challenges, and prospects. Bioresour Technol. 271, 449–461 (2019).
-
Grgas, D. et al. The bacterial degradation of Lignin—A review. Water 15, 1272 (2023).
-
Davis, R. E. et al. Process design and economics for the conversion of lignocellulosic biomass to hydrocarbon fuels and coproducts: 2018 biochemical design case Update; biochemical Deconstruction and conversion of biomass to fuels and products via integrated biorefinery pathways (2018). National Renewable Energy Laboratory, Golden, CO. NREL/TP-5100-71949.
-
Sale, K. et al. Synthetic Microbial Consortium for Biological Breakdown and Conversion of Lignin Sandia National Laboratories, Albuquerque, NM. SAND2022-131. (2022).
-
Saini, S. & Sharma, K. K. Fungal lignocellulolytic enzymes and lignocellulose: A critical review on their contribution to multiproduct biorefinery and global biofuel research. Int. J. Biol. Macromol. 193, 2304–2319 (2021).
-
Granja-Travez, R. S., Persinoti, G. F., Squina, F. M. & Bugg, T. D. H. Functional genomic analysis of bacterial lignin degraders: diversity in mechanisms of lignin oxidation and metabolism. Appl. Microbiol. Biotechnol. 104, 3305–3320 (2020).
-
Schick Zapanta, L. & Tien, M. The roles of Veratryl alcohol and oxalate in fungal lignin degradation. J. Biotechnol. 53, 93–102 (1997).
-
Shin, S. K., Ko, Y. J., Hyeon, J. E. & Han, S. O. Studies of advanced lignin valorization based on various types of lignolytic enzymes and microbes. Bioresour Technol. 289, 121728 (2019).
-
Janusz, G. et al. Lignin degradation: microorganisms, enzymes involved, genomes analysis and evolution. FEMS Microbiol. Rev. 41, 941–962 (2017).
-
Brink, D. P., Ravi, K., Lidén, G. & Gorwa-Grauslund, M. F. Mapping the diversity of microbial lignin catabolism: experiences from the eLignin database. Appl. Microbiol. Biotechnol. 103, 3979–4002 (2019).
-
Hainal, A. R., Capraru, A. M., Volf, I. & Popa, V. I. Lignin as a carbon source for the cultivation of some Rhodotorula species. Cellul Chem. Technol 87–96 (2012).
-
Sláviková, E. & Košíková, B. Modification of lignin by Geotrichum Klebahnii. World J. Microbiol. Biotechnol. 17, 1–3 (2001).
-
Sláviková, E., Košíková, B. & Mikulášová, M. Biotransformation of waste lignin products by the soil-inhabiting yeast Trichosporon pullulans. Can. J. Microbiol. 48, 200–203 (2002).
-
Broos, W. et al. Evaluation of lignocellulosic wastewater valorization with the oleaginous yeasts R. kratochvilovae EXF7516 and C. oleaginosum ATCC 20509. Fermentation 8, 204 (2022).
-
Wakil, S. et al. Production, characterization and purification of laccase by yeasts isolated from ligninolytic soil. J. Pure Appl. Microbiol. 11, 847–869 (2017).
-
Ali, S. S. et al. Coupling Azo dye degradation and biodiesel production by manganese-dependent peroxidase producing oleaginous yeasts isolated from wood-feeding termite gut symbionts. Biotechnol. Biofuels. 14, 61 (2021).
-
Ali, S. S., Al-Tohamy, R. & Sun, J. Performance of Meyerozyma caribbica as a novel manganese peroxidase-producing yeast inhabiting wood-feeding termite gut symbionts for Azo dye decolorization and detoxification. Sci. Total Environ. 806, 150665 (2022).
-
Ai, M., Zhu, Y. & Jia, X. Recent advances in constructing artificial microbial consortia for the production of medium-chain-length polyhydroxyalkanoates. World J. Microbiol. Biotechnol. 37, 2 (2021).
-
Braun, M. K. et al. Catalytic decomposition of the oleaginous yeast Cutaneotrichosporon oleaginosus and subsequent biocatalytic conversion of liberated free fatty acids. ACS Sustain. Chem. Eng. 7, 6531–6540 (2019).
-
Sawpan, M. A. Polyurethanes from vegetable oils and applications: a review. J. Polym. Res. 25, 184 (2018).
-
Patel, A. et al. An overview of potential oleaginous microorganisms and their role in biodiesel and Omega-3 fatty acid-based industries. Microorganisms 8, (2020).
-
Yaguchi, A., Robinson, A., Mihealsick, E. & Blenner, M. Metabolism of aromatics by Trichosporon oleaginosus while remaining oleaginous. Microb. Cell. Factories. 16, 206 (2017).
-
Bracharz, F., Beukhout, T., Mehlmer, N. & Brück, T. Opportunities and challenges in the development of Cutaneotrichosporon oleaginosus ATCC 20509 as a new cell factory for custom tailored microbial oils. Microb. Cell. Factories. 16, 178 (2017).
-
Yaguchi, A., Rives, D. & Blenner, M. New kids on the block: emerging oleaginous yeast of biotechnological importance. AIMS Microbiol. 3, 227–247 (2017).
-
Yaguchi, A. Development of Cutaneotrichosporon Oleaginosus To Convert Lignin-Derived Phenolics To Oleochemicals (Clemson University, 2020).
-
Li, X., Li, M., Pu, Y., Ragauskas, A. J. & Zheng, Y. Black liquor valorization by using marine protist Thraustochytrium striatum and the preliminary metabolic mechanism study. ACS Sustain. Chem. Eng. 8, 1786–1796 (2020).
-
Wang, W., Chen, X., Katahira, R. & Tucker, M. Characterization and Deconstruction of oligosaccharides in black liquor from deacetylation process of corn Stover. Front. Energy Res. 7, 54 (2019).
-
Vilela, N. et al. Integrative omics analyses of the ligninolytic Rhodosporidium fluviale LM-2 disclose catabolic pathways for biobased chemical production. Biotechnol. Biofuels Bioprod. 16, 5 (2023).
-
He, Y., Li, X., Ben, H., Xue, X. & Yang, B. Lipid production from dilute alkali corn Stover lignin by Rhodococcus strains. ACS Sustain. Chem. Eng. 5, 2302–2311 (2017).
-
Vermaas, J. V. et al. Passive membrane transport of lignin-related compounds. Proc. Natl. Acad. Sci. 116, 23117–23123 (2019).
-
Fujita, M. et al. A TonB-dependent receptor constitutes the outer membrane transport system for a lignin-derived aromatic compound. Commun. Biol. 2, 1–10 (2019).
-
Beckham, G. T., Johnson, C. W., Karp, E. M., Salvachúa, D. & Vardon, D. R. Opportunities and challenges in biological lignin valorization. Curr. Opin. Biotechnol. 42, 40–53 (2016).
-
Michalska, K. et al. Characterization of transport proteins for aromatic compounds derived from lignin: benzoate derivative binding proteins. J. Mol. Biol. 423, 555–575 (2012).
-
Ozbek, O. & Ulgen, O. Ileri Ercan, N. The toxicity of Polystyrene-Based nanoparticles in Saccharomyces cerevisiae is associated with nanoparticle charge and uptake mechanism. Chem. Res. Toxicol. 34, 1055–1068 (2021).
-
Baldacci-Cresp, F. et al. A rapid and quantitative safranin-based fluorescent microscopy method to evaluate cell wall lignification. Plant. J. 102, 1074–1089 (2020).
-
Hawkins, S. & Boudet, A. Wound-induced lignin and Suberin deposition in a Woody angiosperm (Eucalyptus Gunnii Hook.): histochemistry of early changes in young plants. Protoplasma 191, 96–104 (1996).
-
Gill, C. O., Hall, M. J. & Ratledge, C. Lipid accumulation in an oleaginous yeast (Candida 107) growing on glucose in single-stage continuous culture. Appl. Environ. Microbiol. 33, 231–239 (1977).
-
Hansson, L. & Dostálek, M. Lipid formation by Cryptococcus albidus in nitrogen-limited and in carbon-limited Chemostat cultures. Appl. Microbiol. Biotechnol. 24, 187–192 (1986).
-
Lankiewicz, T. S. et al. Lignin Deconstruction by anaerobic fungi. Nat. Microbiol. 8, 596–610 (2023).
-
Chua, M. G. S., Chen, C. L., Chang, H. M. & Kirk, T. K. 13 C NMR Spectroscopic Study of Spruce Lignin Degraded Phanerochaete chrysosporium. Holzforschung 36, 165–172 (1982).
-
Yelle, D. J., Wei, D., Ralph, J. & Hammel, K. E. Multidimensional NMR analysis reveals truncated lignin structures in wood decayed by the brown rot basidiomycete Postia placenta. Environ. Microbiol. 13, 1091–1100 (2011).
-
Oates, N. C. et al. A multi-omics approach to lignocellulolytic enzyme discovery reveals a new ligninase activity from Parascedosporium putredinis NO1. Proc. Natl. Acad. Sci. 118, e2008888118 (2021).
-
Awad, D. & Brueck, T. Optimization of protein isolation by proteomic qualification from Cutaneotrichosporon oleaginosus. Anal. Bioanal Chem. 412, 449–462 (2020).
-
Fuchs, T. et al. Identifying carbohydrate-active enzymes of Cutaneotrichosporon oleaginosus using systems biology. Microb. Cell. Factories. 20, 205 (2021).
-
Teufel, F. et al. SignalP 6.0 predicts all five types of signal peptides using protein Language models. Nat. Biotechnol. 40, 1023–1025 (2022).
-
Barrett, K., Hunt, C. J., Lange, L. & Meyer, A. S. Conserved unique peptide patterns (CUPP) online platform: peptide-based functional annotation of carbohydrate active enzymes. Nucleic Acids Res. 48, W110–W115 (2020).
-
Pócsi, I., Prade, R. A., Penninckx, M. J. & Glutathione Altruistic Metabolite in Fungi. in Advances in Microbial Physiology 49 1–76 (Academic Press, 2004).
-
Goodell, B. et al. Low molecular weight chelators and phenolic compounds isolated from wood decay fungi and their role in the fungal biodegradation of wood. J. Biotechnol. 53, 133–162 (1997).
-
Hammel, K. E., Kapich, A. N., Jensen, K. A. & Ryan, Z. C. Reactive oxygen species as agents of wood decay by fungi. Enzyme Microb. Technol. 30, 445–453 (2002).
-
Arantes, V., Milagres, A. M. F., Filley, T. R. & Goodell, B. Lignocellulosic polysaccharides and lignin degradation by wood decay fungi: the relevance of nonenzymatic Fenton-based reactions. J. Ind. Microbiol. Biotechnol. 38, 541–555 (2011).
-
Mattila, H., Österman-Udd, J., Mali, T. & Lundell, T. Basidiomycota fungi and ROS: genomic perspective on key enzymes involved in generation and mitigation of reactive oxygen species. Front. Fungal Biol. 3, 837605 (2022).
-
Drula, E. et al. The carbohydrate-active enzyme database: functions and literature. Nucleic Acids Res. 50, D571–D577 (2022).
-
Thurston, C. F. The structure and function of fungal laccases. Microbiology 140, 19–26 (1994).
-
Glumoff, T. et al. Lignin peroxidase from Phanerochaete-chrysosporium. Eur. J. Biochem. 187, 515–520 (1990).
-
Jensen, K. A., Houtman, C. J., Ryan, Z. C. & Hammel, K. E. Pathways for extracellular Fenton chemistry in the brown rot basidiomycete Gloeophyllum trabeum. Appl. Environ. Microbiol. 67, 2705–2711 (2001).
-
Arantes, V. & Goodell, B. Current Understanding of Brown-Rot fungal biodegradation mechanisms: A review in Deterioration and Protection of Sustainable Biomaterials, (eds Schultz, T. P., Goodell, B. & Nicholas, D. D.) (American Chemical Society, 3–21. (2014).
-
Krueger, M. C., Bergmann, M. & Schlosser, D. Widespread ability of fungi to drive Quinone redox cycling for biodegradation. FEMS Microbiol. Lett. 363, fnw105 (2016).
-
Guillén, F., Martı́nez, M. J., Muñoz, C. & Martı́nez, A. T. Quinone redox cycling in the ligninolytic fungus Pleurotus eryngii leading to extracellular production of superoxide anion radical. Arch. Biochem. Biophys. 339, 190–199 (1997).
-
Prousek, J. Fenton chemistry in biology and medicine. Pure Appl. Chem. 79, 2325–2338 (2007).
-
Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinform. 10, 421 (2009).
-
Dancis, A., Roman, D. G., Anderson, G. J., Hinnebusch, A. G. & Klausner, R. D. Ferric reductase of Saccharomyces cerevisiae: molecular characterization, role in iron uptake, and transcriptional control by iron. Proc. Natl. Acad. Sci. U S A. 89, 3869–3873 (1992).
-
Goodell, B., Qian, Y. & Jellison, J. Fungal decay of wood: soft rot—Brown rot—White rot in Development of Commercial Wood Preservatives, (eds Schultz, T. P., Militz, H., Freeman, M. H., Goodell, B. & Nicholas, D. D.) (American Chemical Society, 9–31. (2008).
-
Philpott, C. C. Iron uptake in fungi: A system for every source. Biochim. Biophys. Acta BBA – Mol. Cell. Res. 1763, 636–645 (2006).
-
Zhang, J., Silverstein, K. A. T., Castaño, J. D., Figueroa, M. & Schilling, J. S. Gene regulation shifts shed light on fungal adaption in plant biomass decomposers. mBio 10, e02176–e02119 (2019).
-
Castaño, J. D., Khoury, E., Goering, I. V., Evans, J., Zhang, J. & J. E. & Unlocking the distinctive enzymatic functions of the early plant biomass deconstructive genes in a brown rot fungus by cell-free protein expression. Appl. Environ. Microbiol. 90, e00122–e00124 (2024).
-
Paysan-Lafosse, T. et al. InterPro in 2022. Nucleic Acids Res. 51, D418–D427 (2023).
-
Liu, J. et al. An extracellular Zn-only superoxide dismutase from Puccinia striiformis confers enhanced resistance to host-derived oxidative stress. Environ. Microbiol. 18, 4118–4135 (2016).
-
Jiang, Y. et al. MULocDeep: A deep-learning framework for protein subcellular and suborganellar localization prediction with residue-level interpretation. Comput. Struct. Biotechnol. J. 19, 4825–4839 (2021).
-
Sützl, L., Foley, G., Gillam, E. M. J., Bodén, M. & Haltrich, D. The GMC superfamily of oxidoreductases revisited: analysis and evolution of fungal GMC oxidoreductases. Biotechnol. Biofuels. 12, 118 (2019).
-
Kersten, P. & Cullen, D. Copper radical oxidases and related extracellular oxidoreductases of wood-decay agaricomycetes. Fungal Genet. Biol. 72, 124–130 (2014).
-
Escutia, M. R. et al. Cloning and sequencing of two Ceriporiopsis subvermispora Bicupin oxalate oxidase allelic isoforms: implications for the reaction specificity of oxalate oxidases and decarboxylases. Appl. Environ. Microbiol. 71, 3608–3616 (2005).
-
Presley, G. N., Zhang, J. & Schilling, J. S. A genomics-informed study of oxalate and cellulase regulation by brown rot wood-degrading fungi. Fungal Genet. Biol. 112, 64–70 (2018).
-
Yaropolov, A. I., Skorobogat’ko, O. V., Vartanov, S. S., Varfolomeyev, S. D. & Laccase Appl. Biochem. Biotechnol. 49, 257–280 (1994).
-
Ong, E., Pollock, W. B. R. & Smith, M. Cloning and sequence analysis of two laccase complementary DNAs from the ligninolytic basidiomycete Trametes versicolor. Gene 196, 113–119 (1997).
-
Levasseur, A., Drula, E., Lombard, V., Coutinho, P. M. & Henrissat, B. Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes. Biotechnol. Biofuels. 6, 41 (2013).
-
Kersten, P. & Cullen, D. Extracellular oxidative systems of the lignin-degrading basidiomycete Phanerochaete Chrysosporium. Fungal Genet. Biol. 44, 77–87 (2007).
-
Jönsson, L., Sjöström, K., Häggström, I. & Nyman, P. O. Characterization of a laccase gene from the white-rot fungus Trametes versicolor and structural features of basidiomycete laccases. Biochim. Biophys. Acta BBA – Protein Struct. Mol. Enzymol. 1251, 210–215 (1995).
-
Larrondo, L. F., Canessa, P., Melo, F., Polanco, R. & Vicuña, R. Cloning and characterization of the genes encoding the high-affinity iron-uptake protein complex Fet3/Ftr1 in the basidiomycete Phanerochaete Chrysosporium. Microbiology 153, 1772–1780 (2007).
-
Kües, U. & Rühl, M. Multiple Multi-Copper oxidase gene families in Basidiomycetes – What for? Curr. Genomics. 12, 72–94 (2011).
-
Cantalapiedra, C. P., Hernández-Plaza, A., Letunic, I., Bork, P. & Huerta-Cepas J. eggNOG-mapper v2: functional Annotation, orthology Assignments, and domain prediction at the metagenomic scale. Mol. Biol. Evol. 38, 5825–5829 (2021).
-
Akileswaran, L., Brock, B. J., Cereghino, J. L. & Gold, M. H. 1,4-Benzoquinone reductase from Phanerochaete chrysosporium: cDNA cloning and regulation of expression. Appl. Environ. Microbiol. 65, 415–421 (1999).
-
Brock, B. J., Rieble, S. & Gold, M. H. Purification and characterization of a 1,4-Benzoquinone reductase from the basidiomycete Phanerochaete Chrysosporium. Appl. Environ. Microbiol. 61, 3076–3081 (1995).
-
Brock, B. J. & Gold, M. H. 1,4-Benzoquinone reductase from the basidiomycete Phanerochaete chrysosporium: spectral and kinetic analysis. Arch. Biochem. Biophys. 331, 31–40 (1996).
-
Jensen, K. A., Ryan, Z. C., Wymelenberg, V., Cullen, A., Hammel, K. E. & D. & An nadh:quinone oxidoreductase active during biodegradation by the Brown-Rot basidiomycete Gloeophyllum trabeum. Appl. Environ. Microbiol. 68, 2699–2703 (2002).
-
Wang, J. et al. The conserved domain database in 2023. Nucleic Acids Res. 51, D384–D388 (2023).
-
Kawai, S., Umezawa, T. & Higuchi, T. -Benzoquinone monoketals, novel degradation products of β-O-4 lignin model compounds by Coriolus versicolor and lignin peroxidase of Phanerochaete Chrysosporium. FEBS Lett. 210, 61–65 (1987).
-
Adnan, M. et al. Carbon catabolite repression in filamentous fungi. Int. J. Mol. Sci. 19, 48 (2017).
-
Martínez, M. J., Ruiz-Dueñas, F. J., Guillén, F. & Martínez, Á. T. Purification and catalytic properties of two manganese peroxidase isoenzymes from Pleurotus eryngii. Eur. J. Biochem. 237, 424–432 (1996).
-
Martorell, M. M., Pajot, H. F. & Figueroa, L. I. C. D. Biological degradation of reactive black 5 dye by yeast Trichosporon Akiyoshidainum. J. Environ. Chem. Eng. 5, 5987–5993 (2017).
-
Kobayashi, Y. et al. Chromosome-level genome assemblies of Cutaneotrichosporon spp. (Trichosporonales, Basidiomycota) reveal imbalanced evolution between nucleotide sequences and chromosome synteny. BMC Genom. 24, 609 (2023).
-
Close, D. & Ojumu, J. Draft genome sequence of the oleaginous yeast Cryptococcus curvatus ATCC 20509. Genome Announc. 4, e01235–e01216 (2016).
-
Grigoriev, I. V. et al. The genome portal of the department of energy joint genome Institute. Nucleic Acids Res. 40, D26–D32 (2012).
-
Twala, P. P., Mitema, A., Baburam, C. & Feto, N. A. Breakthroughs in the discovery and use of different peroxidase isoforms of microbial origin. AIMS Microbiol. 6, 330–349 (2020).
-
Paszczynski, A., Crawford, R., Funk, D. & Goodell, B. De Novo synthesis of 4,5-Dimethoxycatechol and 2,5-Dimethoxyhydroquinone by the brown rot fungus Gloeophyllum trabeum. Appl. Environ. Microbiol. 65, 674–679 (1999).
-
Chiang, Y. M., Lin, T. S. & Wang, C. C. C. Total heterologous biosynthesis of fungal natural products in Aspergillus Nidulans. J. Nat. Prod. 85, 2484–2518 (2022).
-
Sha, Y. et al. Adaptive laboratory evolution boosts Yarrowia lipolytica tolerance to vanillic acid. J. Biotechnol. 367, 42–52 (2023).
-
Barnhart-Dailey, M. C. et al. Internalization and accumulation of model lignin breakdown products in bacteria and fungi. Biotechnol. Biofuels. 12, 175 (2019).
-
Shimizu, M., Kobayashi, Y., Tanaka, H. & Wariishi, H. Transportation mechanism for Vanillin uptake through fungal plasma membrane. Appl. Microbiol. Biotechnol. 68, 673–679 (2005).
-
Saier, M. H. Jr et al. The transporter classification database (TCDB): 2021 update. Nucleic Acids Res. 49, D461–D467 (2021).
-
Chen, J. Y., Kuruparan, A., Zamani-Babgohari, M. & Gonzales-Vigil, E. Dynamic changes to the plant cuticle include the production of volatile cuticular wax–derived compounds. Proc. Natl. Acad. Sci. 120, e2307012120 (2023).
-
Cillingová, A. et al. Eukaryotic transporters for hydroxyderivatives of benzoic acid. Sci. Rep. 7, 8998 (2017).
-
Nomura, T. et al. Exposure of the yeast Saccharomyces cerevisiae to functionalized polystyrene latex nanoparticles: influence of surface charge on toxicity. Environ. Sci. Technol. 47, 3417–3423 (2013).
-
Nomura, T., Kuriyama, Y., Toyoda, S. & Konishi, Y. Direct measurements of colloidal behavior of polystyrene nanoparticles into budding yeast cells using atomic force microscopy and confocal microscopy. Colloids Surf. Physicochem Eng. Asp. 555, 653–659 (2018).
-
Maslanka, R., Kwolek-Mirek, M. & Zadrag-Tecza, R. Autofluorescence of yeast Saccharomyces cerevisiae cells caused by glucose metabolism products and its methodological implications. J. Microbiol. Methods. 146, 55–60 (2018).
-
Bhatta, H. & Goldys, E. M. Characterization of yeast strains by fluorescence lifetime imaging microscopy. FEMS Yeast Res. 8, 81–87 (2008).
-
Stringer, C., Wang, T., Michaelos, M. & Pachitariu, M. Cellpose: a generalist algorithm for cellular segmentation. Nat. Methods. 18, 100–106 (2021).
-
Surre, J. et al. Strong increase in the autofluorescence of cells signals struggle for survival. Sci. Rep. 8, 12088 (2018).
-
Hazan, R., Levine, A. & Abeliovich, H. Benzoic acid, a weak organic acid food Preservative, exerts specific effects on intracellular membrane trafficking pathways in Saccharomyces cerevisiae. Appl. Environ. Microbiol. 70, 4449–4457 (2004).
-
Awashra, M. & Młynarz, P. The toxicity of nanoparticles and their interaction with cells: an in vitro metabolomic perspective. Nanoscale Adv. 5, 2674–2723 (2023).
-
Ali, S. S. et al. Could termites be hiding a goldmine of obscure yet promising yeasts for energy crisis solutions based on aromatic wastes? A critical state-of-the-art review. Biotechnol. Biofuels Bioprod. 15, 35 (2022).
-
Ahuatzi-chacón, D. et al. Kinetic study of phenol hydroxylase and catechol 1,2-dioxygenase biosynthesis by Candida tropicalis cells grown on different phenolic substrates. World J. Microbiol. Biotechnol. 20, 695–702 (2004).
-
Durham, D. R., McNamee, C. G. & Stewart, D. B. Dissimilation of aromatic compounds in Rhodotorula graminis: biochemical characterization of pleiotropically negative mutants. J. Bacteriol. 160, 771–777 (1984).
-
Anderson, E. M. et al. Reductive catalytic fractionation of corn Stover lignin. ACS Sustain. Chem. Eng. 4, 6940–6950 (2016).
-
Broos, W. et al. Rhodotorula Kratochvilovae outperforms Cutaneotrichosporon oleaginosum in the valorisation of lignocellulosic wastewater to microbial oil. Process. Biochem. 137, 229–238 (2024).
-
Yaguchi, A. et al. Identification of oleaginous yeasts that metabolize aromatic compounds. J. Ind. Microbiol. Biotechnol. 47, 801–813 (2020).
-
Nogué, V. S. et al. Integrated diesel production from lignocellulosic sugars via oleaginous yeast. Green. Chem. 20, 4349–4365 (2018).
-
Sachan, A., Ghosh, S. & Mitra, A. Biotransformation of p-coumaric acid by Paecilomyces variotii. Lett. Appl. Microbiol. 42, 35–41 (2006).
-
Sachan, A., Ghosh, S. & Mitra, A. Transforming p-coumaric acid into p-hydroxybenzoic acid by the mycelial culture of a white rot fungus. Afr. J. Microbiol. Res. 4, 267–273 (2009).
-
Lubbers, R. J. M. et al. Discovery of novel p-Hydroxybenzoate-m-hydroxylase, Protocatechuate 3,4 Ring-Cleavage dioxygenase, and hydroxyquinol 1,2 Ring-Cleavage dioxygenase from the filamentous fungus Aspergillus Niger. ACS Sustain. Chem. Eng. 7, 19081–19089 (2019).
-
Lubbers, R. J. M. et al. Evolutionary adaptation of Aspergillus Niger for increased ferulic acid tolerance. J. Appl. Microbiol. 128, 735–746 (2020).
-
Lubbers, R. J. M., Dilokpimol, A., Visser, J. & de Vries, R. P. Aspergillus Niger uses the peroxisomal CoA-dependent β-oxidative genes to degrade the hydroxycinnamic acids caffeic acid, ferulic acid, and p-coumaric acid. Appl. Microbiol. Biotechnol. 105, 4199–4211 (2021).
-
Gallage, N. J. & Møller, B. L. Vanillin–Bioconversion and bioengineering of the most popular plant flavor and its De Novo biosynthesis in the vanilla Orchid. Mol. Plant. 8, 40–57 (2015).
-
Fleige, C., Hansen, G., Kroll, J. & Steinbüchel, A. Investigation of the Amycolatopsis sp. Strain ATCC 39116 Vanillin dehydrogenase and its impact on the biotechnical production of Vanillin. Appl. Environ. Microbiol. 79, 81–90 (2013).
-
Achterholt, S., Priefert, H. & Steinbüchel, A. Identification of Amycolatopsis sp. strain HR167 genes, involved in the bioconversion of ferulic acid to Vanillin. Appl. Microbiol. Biotechnol. 54, 799–807 (2000).
-
Mitra, A. et al. 4-Hydroxycinnamoyl-CoA Hydratase/lyase (HCHL)—An enzyme of phenylpropanoid chain cleavage from Pseudomonas. Arch. Biochem. Biophys. 365, 10–16 (1999).
-
Neuberger, G., Maurer-Stroh, S., Eisenhaber, B., Hartig, A. & Eisenhaber, F. Prediction of peroxisomal targeting signal 1 containing proteins from amino acid sequence. J. Mol. Biol. 328, 581–592 (2003).
-
Thumuluri, V., Almagro Armenteros, J. J., Johansen, A. R., Nielsen, H. & Winther, O. DeepLoc 2.0: multi-label subcellular localization prediction using protein Language models. Nucleic Acids Res. 50, W228–W234 (2022).
-
Neujahr, H. Y. & Gaal, A. Phenol hydroxylase from yeast: sulfhydryl groups in phenol hydroxylase from Trichosporon cutaneum. Eur. J. Biochem. 58, 351–357 (1975).
-
Kalin, M., Neujahr, H. Y., Weissmahr, R. N., Sejlitz, T. & Reiser, J. Phenol hydroxylase from Trichosporon cutaneum: gene Cloning, sequence Analysis, and functional expression in Eschenichia coli. J. Bacteriol. 174, 7112–7120 (1992).
-
Nordberg, H. et al. The genome portal of the department of energy joint genome institute: 2014 updates. Nucleic Acids Res. 42, D26–D31 (2014).
-
Westphal, A. H., Tischler, D. & van Berkel, W. J. H. Natural diversity of FAD-dependent 4-hydroxybenzoate hydroxylases. Arch. Biochem. Biophys. 702, 108820 (2021).
-
del Cerro, C. et al. Intracellular pathways for lignin catabolism in white-rot fungi. Proc. Natl. Acad. Sci. 118, e2017381118 (2021).
-
Holesova, Z. et al. Gentisate and 3-oxoadipate pathways in the yeast Candida parapsilosis: identification and functional analysis of the genes coding for 3-hydroxybenzoate 6-hydroxylase and 4-hydroxybenzoate 1-hydroxylase. Microbiology 157, 2152–2163 (2011).
-
Degradation of Homocyclic Aromatic Compounds by Fungi in. in Encyclopedia of Mycology. 477–488 (eds Zaragoza, Ó. & Casadevall, A.) (Elsevier, 2021).
-
Semana, P. & Powlowski, J. Four aromatic intradiol ring cleavage dioxygenases from Aspergillus Niger. Appl. Environ. Microbiol. 85, e01786–e01719 (2019).
-
Lubbers, R. J. M. et al. Vanillic acid and methoxyhydroquinone production from guaiacyl units and related aromatic compounds using Aspergillus Niger cell factories. Microb. Cell. Factories. 20, 151 (2021).
-
Cillingová, A. et al. Transcriptome and proteome profiling reveals complex adaptations of Candida parapsilosis cells assimilating hydroxyaromatic carbon sources. PLOS Genet. 18, e1009815 (2022).
-
Skrzypek, M. S. et al. The Candida genome database (CGD): incorporation of assembly 22, systematic identifiers and visualization of high throughput sequencing data. Nucleic Acids Res. 45, D592–D596 (2017).
-
Mazur, P. et al. Cis,cis-Muconate lactonizing enzyme from Trichosporon cutaneum: evidence for a novel class of cycloisomerases in eucaryotes. Biochemistry 33, 1961–1970 (1994).
-
Martins, T. M. et al. The old 3-oxoadipate pathway revisited: new insights in the catabolism of aromatics in the saprophytic fungus Aspergillus Nidulans. Fungal Genet. Biol. 74, 32–44 (2015).
-
Hibi, M., Sonoki, T. & Mori, H. Functional coupling between vanillate-O-demethylase and formaldehyde detoxification pathway. FEMS Microbiol. Lett. 253, 237–242 (2005).
-
Veličković, M. et al. Mapping microhabitats of lignocellulose decomposition by a microbial consortium. Nat. Chem. Biol. 20, 1033–1043 (2024).
-
Perna, V. et al. Laccase-Catalyzed oxidation of lignin induces production of H2O2. ACS Sustain. Chem. Eng. 8, 831–841 (2020).
-
Li, X., Gluth, A., Zhang, T. & Qian, W. J. Thiol redox proteomics: characterization of thiol-based post-translational modifications. PROTEOMICS 23, 2200194 (2023).
-
Li, X., Gluth, A., Feng, S., Qian, W. J. & Yang, B. Harnessing redox proteomics to study metabolic regulation and stress response in lignin-fed Rhodococci. Biotechnol. Biofuels Bioprod. 16, 180 (2023).
-
Kourist, R. et al. Genomics and transcriptomics analyses of the Oil-Accumulating basidiomycete yeast trichosporon oleaginosus: insights into substrate utilization and alternative evolutionary trajectories of fungal mating systems. mBio 6, e00918–e00915 (2015).
-
Zhu, X. & Williamson, P. R. Role of laccase in the biology and virulence of Cryptococcus neoformans. FEMS Yeast Res. 5, 1–10 (2004).
-
Chen, X. et al. The impacts of deacetylation prior to dilute acid pretreatment on the bioethanol process. Biotechnol. Biofuels. 5, 8 (2012).
-
Chen, X. et al. A highly efficient dilute alkali deacetylation and mechanical (disc) refining process for the conversion of renewable biomass to lower cost sugars. Biotechnol. Biofuels. 7, 98 (2014).
-
Sluiter, A. et al. Determination of Structural Carbohydrates and Lignin in Biomass National Renewable Energy Laboratory, Bolder, CO. NREL/TP-510-42618. (2012).
-
Li, X., Li, M., Pu, Y., Ragauskas, A. J. & Zheng, Y. Simultaneous depolymerization and fermentation of lignin into value-added products by the marine protist, Thraustochytrium striatum. Algal Res. 46, 101773 (2020).
-
Li, X. et al. Inhibitory effects of lignin on enzymatic hydrolysis: the role of lignin chemistry and molecular weight. Renew. Energy. 123, 664–674 (2018).
-
Gluth, A. et al. Nitrogen limitation causes a seismic shift in redox state and phosphorylation of proteins implicated in carbon flux and lipidome remodeling in Rhodotorula toruloides. Biotechnol. Biofuels Bioprod. 18, 80 (2025).
-
Hughes, C. S. et al. Single-pot, solid-phase-enhanced sample Preparation for proteomics experiments. Nat. Protoc. 14, 68–85 (2019).
-
Hughes, C. S. et al. Ultrasensitive proteome analysis using paramagnetic bead technology. Mol. Syst. Biol. 10, 757 (2014).
-
Cox, J. et al. Accurate Proteome-wide Label-free quantification by delayed normalization and maximal peptide ratio Extraction, termed MaxLFQ. Mol. Cell. Proteom. MCP. 13, 2513–2526 (2014).
-
Zhu, Y. et al. DEqMS: A method for accurate variance Estimation in differential protein expression Analysis *. Mol. Cell. Proteom. 19, 1047–1057 (2020).
-
Zhang, X. et al. Proteome-wide identification of ubiquitin interactions using UbIA-MS. Nat. Protoc. 13, 530–550 (2018).
-
Huber, W. et al. Orchestrating high-throughput genomic analysis with bioconductor. Nat. Methods. 12, 115–121 (2015).
-
Smeekens, J. M., Xiao, H. & Wu, R. Global analysis of secreted proteins and glycoproteins in Saccharomyces cerevisiae. J. Proteome Res. 16, 1039–1049 (2017).
-
Müller, T. et al. Automated sample Preparation with SP3 for low-input clinical proteomics. Mol. Syst. Biol. 16, e9111 (2020).
-
Sielaff, M. et al. Evaluation of FASP, SP3, and iST protocols for proteomic sample Preparation in the low microgram range. J. Proteome Res. 16, 4060–4072 (2017).
-
Moggridge, S., Sorensen, P. H., Morin, G. B. & Hughes, C. S. Extending the compatibility of the SP3 paramagnetic bead processing approach for proteomics. J. Proteome Res. 17, 1730–1740 (2018).
-
Lampaki, D., Diepold, A., Glatter, T. A. & Serial Sample Processing strategy with improved performance for in-Depth quantitative analysis of type III secretion events in Pseudomonas aeruginosa. J. Proteome Res. 19, 543–553 (2020).
-
Knecht, S., Eberl, H. C. & Bantscheff, M. Interval-Based secretomics unravels Acute-Phase response in hepatocyte model systems. Mol. Cell. Proteom. 21, 100241 (2022).
-
HaileMariam, M. et al. S-Trap, an ultrafast Sample-Preparation approach for shotgun proteomics. J. Proteome Res. 17, 2917–2924 (2018).
-
Laskar, D. D., Tucker, M. P., Chen, X., Helms, G. L. & Yang, B. Noble-metal catalyzed hydrodeoxygenation of biomass-derived lignin to aromatic hydrocarbons. Green. Chem. 16, 897–910 (2014).
-
Nakamura, H. & Watano, S. Direct permeation of nanoparticles across cell membrane: A review. KONA Powder Part. J. 35, 49–65 (2018).
-
Lipke, P. N. & Ovalle, R. Cell wall architecture in yeast: new structure and new challenges. J. Bacteriol. 180, 3735–3740 (1998).
-
Lu, X., Zheng, X., Li, X. & Zhao, J. Adsorption and mechanism of cellulase enzymes onto lignin isolated from corn Stover pretreated with liquid hot water. Biotechnol. Biofuels. 9, 118 (2016).
-
Ashengroph, M. & Amini, J. Bioconversion of isoeugenol to Vanillin and vanillic acid using the resting cells of Trichosporon Asahii. 3 Biotech. 7, 358 (2017).
-
Casey, J. & Dobb, R. Microbial routes to aromatic aldehydes. Enzyme Microb. Technol. 14, 739–747 (1992).
-
Jia, S. R., Cui, J. D., Li, Y. & Sun, A. Y. Production of L-phenylalanine from trans-cinnamic acids by high-level expression of phenylalanine ammonia lyase gene from Rhodosporidium toruloides in Escherichia coli. Biochem. Eng. J. 42, 193–197 (2008).
-
Adeboye, P. T., Bettiga, M. & Olsson, L. ALD5, PAD1, ATF1 and ATF2 facilitate the catabolism of coniferyl aldehyde, ferulic acid and p-coumaric acid in Saccharomyces cerevisiae. Sci. Rep. 7, 42635 (2017).
-
Konzock, O., Zaghen, S. & Norbeck, J. Tolerance of Yarrowia lipolytica to inhibitors commonly found in lignocellulosic hydrolysates. BMC Microbiol. 21, 77 (2021).
-
Iwasaki, Y. et al. Novel metabolic pathway for salicylate biodegradation via phenol in yeast trichosporon moniliiforme. Biodegradation 21, 557–564 (2010).
-
Bartsch, S. & Bornscheuer, U. T. Mutational analysis of phenylalanine ammonia lyase to improve reactions rates for various substrates. Protein Eng. Des. Sel. 23, 929–933 (2010).
-
Konzock, O., Tous-Mohedano, M., Cibin, I., Chen, Y. & Norbeck, J. Cinnamic acid and p-coumaric acid are metabolized to 4-hydroxybenzoic acid by Yarrowia lipolytica. AMB Express. 13, 84 (2023).
-
Lubbers, R. J. M. et al. A comparison between the homocyclic aromatic metabolic pathways from plant-derived compounds by bacteria and fungi. Biotechnol. Adv. 37, 107396 (2019).
-
Mikkilä, J. et al. Fungal treatment modifies kraft lignin for lignin- and Cellulose-Based carbon fiber precursors. ACS Omega. 5, 6130–6140 (2020).
-
Ravi, K., García-Hidalgo, J., Gorwa-Grauslund, M. F. & Lidén, G. Conversion of lignin model compounds by Pseudomonas Putida KT2440 and isolates from compost. Appl. Microbiol. Biotechnol. 101, 5059–5070 (2017).
-
Falconnier, B. et al. Vanillin as a product of ferulic acid biotransformation by the white-rot fungus Pycnoporus cinnabarinus I-937: identification of metabolic pathways. J. Biotechnol. 37, 123–132 (1994).
-
Guiraud, P., Steiman, R., Seigle-Murandi, F. & Benoit-Guyod, J. L. Metabolism of vanillic acid by micromycetes. World J. Microbiol. Biotechnol. 8, 270–275 (1992).
-
Ander, P., Hatakka, A. & Eriksson, K. E. Vanillic acid metabolism by the White-Rot fungus Sporotriehum pulverulentum. Arch. Microbiol. 125, 189–202 (1980).
-
Lubbers, R. J. M. et al. Discovery and functional analysis of a Salicylic acid hydroxylase from Aspergillus Niger. Appl. Environ. Microbiol. 87, e02701–e02720 (2021).
-
The UniProt Consortium. UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Res. 49, D480–D489 (2021).
-
Yang, R. Y. et al. Genome sequence of the Trichosporon Asahii environmental strain CBS 8904. Eukaryot. Cell. 11, 1586–1587 (2012).
-
Nordlund, I. & Shingler, V. Nucleotide sequences of the meta-cleavage pathway enzymes 2-hydroxymuconic semialdehyde dehydrogenase and 2-hydroxymuconic semialdehyde hydrolase from Pseudomonas CF600. Biochim. Biophys. Acta BBA – Gene Struct. Expr. 1049, 227–230 (1990).
-
Inoue, J., Shaw, J. P., Rekik, M. & Harayama, S. Overlapping substrate specificities of benzaldehyde dehydrogenase (the XylC gene product) and 2-hydroxymuconic semialdehyde dehydrogenase (the XylG gene product) encoded by TOL plasmid pWW0 of Pseudomonas Putida. J. Bacteriol. 177, 1196–1201 (1995).
-
Kato, H. et al. Identification and characterization of methoxy- and dimethoxyhydroquinone 1,2-dioxygenase from Phanerochaete Chrysosporium. Appl. Environ. Microbiol. 90, e01753–e01723 (2024).
-
O’Fallon, J. V., Busboom, J. R., Nelson, M. L. & Gaskins, C. T. A direct method for fatty acid Methyl ester synthesis: application to wet meat tissues, oils, and feedstuffs. J. Anim. Sci. 85, 1511–1521 (2007).
-
Xie, S., Sun, S. & Dai, S. Y. Efficient coagulation of microalgae in cultures with filamentous fungi. Algal Res. 2, 28–33 (2013).
-
Li, X. et al. Discovery of potential pathways for biological conversion of Poplar wood into lipids by co-fermentation of Rhodococci strains. Biotechnol. Biofuels. 12, 60 (2019).
-
Schneider, C. A., Rasband, W. S. & Eliceiri, K. W. NIH image to imageJ: 25 years of image analysis. Nat. Methods. 9, 671–675 (2012).
-
Gluth, A. et al. Integrative Multi-PTM proteomics reveals dynamic Global, Redox, Phosphorylation, and acetylation regulation in Cytokine-Treated pancreatic beta cells. Mol. Cell. Proteom. 23, 100881 (2024).
-
Xu, Z. et al. Understanding of bacterial lignin extracellular degradation mechanisms by Pseudomonas Putida KT2440 via secretomic analysis. Biotechnol. Biofuels Bioprod. 15, 117 (2022).
-
Ritchie, M. E. et al. Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 43, e47 (2015).
-
Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M. & Tanabe, M. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 44, D457–D462 (2016).
-
Kanehisa, M. & Goto, S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27–30 (2000).
-
Wu, T. et al. ClusterProfiler 4.0: A universal enrichment tool for interpreting omics data. The Innovation 2, 100141 (2021).
-
Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer-, 2016).
