Publications

Liu, D., Garrigues, S., Culleton, H., McKie, V. A., & de Vries, R. P. (2024). Analysis of the molecular basis for the non-amylolytic and non-proteolytic nature of Aspergillus vadensis CBS 113365. New Biotechnology, 82, 25-32. https://doi.org/10.1016/j.nbt.2024.04.003

Shokrian Hajibehzad, S. (2024). From compact greens to ascending stems: elucidating the role of ATH1 in regulating internode growth dynamics in Arabidopsis thaliana. Utrecht University. https://doi.org/10.33540/2418

Theobald, S., Vesth, T. C., Geib, E., Nybo, J. L., Frisvad, J. C., Larsen, T. O., Kuo, A., LaButti, K., Lyhne, E. K., Kjærbølling, I., Ledsgaard, L., Barry, K., Clum, A., Chen, C., Nolan, M., Sandor, L., Lipzen, A., Mondo, S., Pangilinan, J., ... Andersen, M. R. (2024). Genomic Analysis of Aspergillus Section Terrei Reveals a High Potential in Secondary Metabolite Production and Plant Biomass Degradation. Journal of Fungi, 10(7), Article 507. https://doi.org/10.3390/jof10070507

Coolen, S., Molen, M. A. R. D., Kwakernaak, I., van Pelt, J. A., Postma, J. L., van Alen, T., Jansen, R. S., & Welte, C. U. (2024). Microbiota of pest insect Nezara viridula mediate detoxification and plant defense repression. ISME Journal, 18(1), Article wrae097. https://doi.org/10.1093/ismejo/wrae097

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, 114(5), 1097-1105. 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

Bouzid, O., Allouache, A., de Vries, R. P., Zitouni, D., Benoit-Gelber, I., Houbraken, J., & Aziza, M. A. (2024). High potential low-cost crude enzymes from Algerian fungal strains for plant polysaccharides hydrolysis. Biofuels, 15(7), 767-772. https://doi.org/10.1080/17597269.2023.2295661

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

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