Publications

2024

van Butselaar, T., Silva, S., Lapin, D., Bañales Belaunde, I., Tonn, S., van Schie, C., & Van den Ackerveken, G. (2024). The Role of Salicylic Acid in the Expression of RECEPTOR-LIKE PROTEIN 23 and Other Immunity-Related Genes. Phytopathology, PHYTO10230413KC. Advance online publication. https://doi.org/10.1094/PHYTO-10-23-0413-KC
Duran, K., Kohlstedt, M., van Erven, G., Klostermann, C. E., America, A. H. P., Bakx, E., Baars, J. J. P., Gorissen, A., de Visser, R., de Vries, R. P., Wittmann, C., Comans, R. N. J., Kuyper, T. W., & Kabel, M. A. (2024). From 13C-lignin to 13C-mycelium: Agaricus bisporus uses polymeric lignin as a carbon source. Science advances, 10(16), Article eadl3419. https://doi.org/10.1126/sciadv.adl3419
Xu, L., Li, J., Gonzalez Ramos, V. M., Lyra, C., Wiebenga, A., Grigoriev, I. V., de Vries, R. P., Mäkelä, M. R., & Peng, M. (2024). Genome-wide prediction and transcriptome analysis of sugar transporters in four ascomycete fungi. Bioresource Technology, 391(Pt B), Article 130006. https://doi.org/10.1016/j.biortech.2023.130006

2023

Ogden, S. C., Nishimura, M. T., & Lapin, D. (2023). Functional diversity of Toll/interleukin-1 receptor domains in flowering plants and its translational potential. Current Opinion in Plant Biology, 76, Article 102481. https://doi.org/10.1016/j.pbi.2023.102481
Goossens, P., Spooren, J., Baremans, K. C. M., Andel, A., Lapin, D., Echobardo, N., Pieterse, C. M. J., Van den Ackerveken, G., & Berendsen, R. L. (2023). Obligate biotroph downy mildew consistently induces near-identical protective microbiomes in Arabidopsis thaliana. Nature Microbiology, 8(12), 2349-2364. https://doi.org/10.1038/s41564-023-01502-y
Li, J. (2023). Fungi use highly diverse approaches for plant biomass conversion as revealed through bioinformatic analysis. [Doctoral thesis 2 (Research NOT UU / Graduation UU), Universiteit Utrecht]. Utrecht University. https://doi.org/10.33540/1940
Garrigues, S., Peng, M., Kun, R. S., & de Vries, R. P. (2023). Non-homologous end-joining-deficient filamentous fungal strains mitigate the impact of off-target mutations during the application of CRISPR/Cas9. mBio, 14(4), 1-15. Article e0066823. https://doi.org/10.1128/mbio.00668-23
Li, J., Wiebenga, A., Lipzen, A., Ng, V., Tejomurthula, S., Zhang, Y., Grigoriev, I. V., Peng, M., & de Vries, R. P. (2023). Comparative Genomics and Transcriptomics Analyses Reveal Divergent Plant Biomass-Degrading Strategies in Fungi. Journal of fungi (Basel, Switzerland), 9(8), 1-15. Article 860. https://doi.org/10.3390/jof9080860
Salazar-Cerezo, S., de Vries, R. P., & Garrigues, S. (2023). Strategies for the Development of Industrial Fungal Producing Strains. Journal of fungi (Basel, Switzerland), 9(8), 1-33. Article 834. https://doi.org/10.3390/jof9080834
Shokrian Hajibehzad, S., Silva, S. S., Peeters, N., Stouten, E., Buijs, G., Smeekens, S., & Proveniers, M. (2023). Arabidopsis thaliana rosette habit is controlled by combined light and energy signaling converging on transcriptional control of the TALE homeobox gene ATH1. New Phytologist, 239(3), 1051-1067. https://doi.org/10.1111/nph.19014
Griebel, T., Lapin, D., Locci, F., Kracher, B., Bautor, J., Concia, L., Benhamed, M., & Parker, J. E. (2023). Arabidopsis Topless-related 1 mitigates physiological damage and growth penalties of induced immunity. New Phytologist, 239(4), 1404-1419. https://doi.org/10.1111/nph.19054
Liu, D., Garrigues, S., & de Vries, R. P. (2023). Heterologous protein production in filamentous fungi. Applied Microbiology and Biotechnology, 107(16), 5019-5033. https://doi.org/10.1007/s00253-023-12660-8
Duran, K., Magnin, J., America, A. H. P., Peng, M., Hilgers, R., de Vries, R. P., Baars, J. J. P., van Berkel, W. J. H., Kuyper, T. W., & Kabel, M. A. (2023). The secretome of Agaricus bisporus: Temporal dynamics of plant polysaccharides and lignin degradation. iScience, 26(7), 1-22. Article 107087. https://doi.org/10.1016/j.isci.2023.107087
Butselaar, T. V., Silva, S., Lapin, D., Banales, I., Tonn, S., Schie, C. V., & Ackerveken, G. V. D. (2023). Basal expression of immune receptor genes requires low levels of the phytohormone salicylic acid. bioRxiv. https://doi.org/10.1101/2023.07.14.548351
Lapin, D. (2023). Plant immune receptors can sequester and protect host proteins from pathogen-promoted degradation. Molecular Plant, 16(6), 966-967. https://doi.org/10.1016/j.molp.2023.05.001
Peng, M., Bervoets, S., Chin-A-Woeng, T., Granchi, Z., Hildén, K., Mäkelä, M. R., & de Vries, R. P. (2023). The transcriptomic response of two basidiomycete fungi to plant biomass is modulated by temperature to a different extent. Microbiological Research, 270, 1-8. Article 127333. https://doi.org/10.1016/j.micres.2023.127333
Kun, R. S., Salazar-Cerezo, S., Peng, M., Zhang, Y., Savage, E., Lipzen, A., Ng, V., Grigoriev, I. V., de Vries, R. P., & Garrigues, S. (2023). The Amylolytic Regulator AmyR of Aspergillus niger Is Involved in Sucrose and Inulin Utilization in a Culture-Condition-Dependent Manner. Journal of fungi (Basel, Switzerland), 9(4), 1-14. Article 438. https://doi.org/10.3390/jof9040438
van Butselaar, T. (2023). The Salicylic Acid-Mediated Growth-Immunity Tradeoff in Arabidopsis. [Doctoral thesis 1 (Research UU / Graduation UU), Universiteit Utrecht]. Universiteit Utrecht. https://doi.org/10.33540/1694
Goossens, P., Spooren, J., Baremans, K. C. M., Andel, A., Lapin, D., Echobardo, N., Pieterse, C. M. J., Ackerveken, G. V. D., & Berendsen, R. L. (2023). Congruent downy mildew-associated microbiomes reduce plant disease and function as transferable resistobiomes. bioRxiv. https://doi.org/10.1101/2023.03.14.532520
Reddy, S. K., & de Vries, R. (2023). Mycoproteins and yeast proteins in food industry. In Our Future Proteins (pp. 179-187). VU University Press.
Kun, R. S., Garrigues, S., Peng, M., Keymanesh, K., Lipzen, A., Ng, V., Tejomurthula, S., Grigoriev, I. V., & de Vries, R. P. (2023). The transcriptional activator ClrB is crucial for the degradation of soybean hulls and guar gum in Aspergillus niger. Fungal Genetics and Biology, 165, 1-11. Article 103781. https://doi.org/10.1016/j.fgb.2023.103781
Meng, J., Mäkelä, M. R., & de Vries, R. P. (2023). Identification of an l-Arabitol Transporter from Aspergillus niger. Biomolecules, 13(2), 1-11. Article 188. https://doi.org/10.3390/biom13020188
Johanndrees, O., Baggs, E. L., Uhlmann, C., Locci, F., Läßle, H. L., Melkonian, K., Käufer, K., Dongus, J. A., Nakagami, H., Krasileva, K. V., Parker, J. E., & Lapin, D. (2023). Variation in plant Toll/Interleukin-1 receptor domain protein dependence on ENHANCED DISEASE SUSCEPTIBILITY 1. Plant Physiology, 191(1), 626-642. https://doi.org/10.1093/plphys/kiac480

2022

Li, J., Chroumpi, T., Garrigues, S., Kun, R. S., Meng, J., Salazar-Cerezo, S., Aguilar-Pontes, M. V., Zhang, Y., Tejomurthula, S., Lipzen, A., Ng, V., Clendinen, C. S., Tolić, N., Grigoriev, I. V., Tsang, A., Mäkelä, M. R., Snel, B., Peng, M., & de Vries, R. P. (2022). The Sugar Metabolic Model of Aspergillus niger Can Only Be Reliably Transferred to Fungi of Its Phylum. Journal of fungi (Basel, Switzerland), 8(12), Article 1315. https://doi.org/10.3390/jof8121315
Jochems, P. G. M., Heming, B., Lapin, D., Moonen, N. E. L., Van den Ackerveken, G., & Masereeuw, R. (2022). Bioengineered intestinal tubules as a tool to test intestinal biological efficacy of lettuce species. npj Science of Food, 6(1), 1-8. Article 58. https://doi.org/10.1038/s41538-022-00175-x
Schoonbeek, H. J., Yalcin, H. A., Burns, R., Taylor, R. E., Casey, A., Holt, S., Van den Ackerveken, G., Wells, R., & Ridout, C. J. (2022). Necrosis and ethylene-inducing-like peptide patterns from crop pathogens induce differential responses within seven brassicaceous species. Plant Pathology, 71(9), 2004-2016. https://doi.org/10.1111/ppa.13615
Kun, R. S. (2022). Harnessing the CRISPR/Cas9 system to study the regulatory network of plant biomass degradation in Aspergillus niger. [Doctoral thesis 2 (Research NOT UU / Graduation UU), Universiteit Utrecht]. Utrecht University. https://doi.org/10.33540/745
Venegas, F. A., Koutaniemi, S., Langeveld, S. M. J., Bellemare, A., Chong, S. L., Dilokpimol, A., Lowden, M. J., Hilden, K. S., Leyva-Illades, J. F., Mäkelä, M. R., My Pham, T. T., Peng, M., Hancock, M. A., Zheng, Y., Tsang, A., Tenkanen, M., Powlowski, J., & de Vries, R. P. (2022). Carbohydrate esterase family 16 contains fungal hemicellulose acetyl esterases (HAEs) with varying specificity. New Biotechnology, 70, 28-38. https://doi.org/10.1016/j.nbt.2022.04.003
Li, X., Kouzounis, D., Kabel, M. A., & de Vries, R. P. (2022). GH10 and GH11 endoxylanases in Penicillium subrubescens: Comparative characterization and synergy with GH51, GH54, GH62 α-L-arabinofuranosidases from the same fungus. New Biotechnology, 70, 84-92. https://doi.org/10.1016/j.nbt.2022.05.004
Marinovíc, M., Di Falco, M., Aguilar Pontes, M. V., Gorzsás, A., Tsang, A., de Vries, R. P., Mäkelä, M. R., & Hildén, K. (2022). Comparative Analysis of Enzyme Production Patterns of Lignocellulose Degradation of Two White Rot Fungi: Obba rivulosa and Gelatoporia subvermispora. Biomolecules, 12(8), Article 1017. https://doi.org/10.3390/biom12081017
Dilokpimol, A., Verkerk, B., Li, X., Bellemare, A., Lavallee, M., Frommhagen, M., Underlin, E. N., Kabel, M. A., Powlowski, J., Tsang, A., & de Vries, R. P. (2022). Screening of novel fungal Carbohydrate Esterase family 1 enzymes identifies three novel dual feruloyl/acetyl xylan esterases. FEBS Letters, 596(15), 1932-1943. https://doi.org/10.1002/1873-3468.14322