Dr. P.M. (Petra) Bleeker
- Science Park 904
- Room number: C2.213
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Postbus 1210
1000 BE Amsterdam
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Profile
Research interest
In the department of Plant Physiology we aim to elucidate plant-signal transduction pathways employed in biotic interactions, focussing on the role of plant metabolites. We research perception and signaling mechanisms during plant-insect interactions. In my research we study the defence against pest-insects via the production of specialised metabolites with tomato and whitefly as model species. The lab combines metabolomics, transcriptomics and genome information with phenotypic responses. We make use of the natural variation found in ancestral/ wild tomato accessions to identify metabolites, genes and regulatory elements and try to apply this knowledge to reconstruct defence pathways in cultivated tomato.
Worldwide, insects and viruses cause enormous losses in crop production. Much like what we currently experience, crops are hit with virus infections often transmitted by vector insects such as whiteflies and thrips. Such infestations threaten food production worldwide, a problem only amplified by global warming. Conventional control of vector insects is difficult. Yearly 3.5 million tons of pesticides are applied globally. Theses pesticides are often persistent in the environment and harm off-target organisms, pollution ground- and surface waters. Many (wild) plant species have evolved (chemical) insect defences that can be explored as alternatives to the use of persistant insecticides, mechanisms that can be re-introduced in defenceless cultivars.
wild tomato ancestor anti-insect metabolites
Wild tomatoes produce a wide variety of defence-related metabolites, termed specialised metabolites. Estimates on the divergence of specialised metabolites reach over 200.000 different structures, including flavonoids, acylsugars, alkaloids and a huge variety of terpenoids (isoprenoids). The latter are among the most reported bioactive compounds in relation to insects.
Combining resistance assays with a metabolomics approach we identified the sesquiterpene 7-epizingiberene and its dehydrogenated derivative R-curcumene from the wild tomato Solanum habrochaites to repel the silverleaf whitefly Bemisia tabaci, a potent vector of Geminiviridae (Bleeker et al., 2009, 2011). Transcriptomics of a range of wild accessions next led to the identification and characterisation of the two genes underlying the biosynthesis of 7-epizingiberene (i.e. ShzFPS and ShZIS) in wild tomato which were consequently introgressed in a cultivated background (Bleeker et al., 2012).
We however also observed low survival rates of whiteflies on the leaf surface of S. habrochaites, which led to the hypothesis that the volatile sesquiterpenes must signal the presence of a (related) toxic compound, hence triggering the repellence response. As metabolic profiles are complex mixtures we developed a customised Random Forest learning algorithm to predict specialised metabolites that can explain the resistance phenotype (Kortbeek, Galland et al., 2021). Using this feature selection approach we predicted that in our S. habrochaites, an alcohol derivative of 7-epizingiberene, present on the leaf surface, is causal to the whitefly toxicity phenotype.
Recently, the P450-enzyme involved in oxidation of the volatile 7-epizingiberene to two compounds, 9-hydroxy-zingiberene and 9-hydroxy-10,11-epoxyzingiberene was identified (Zabel et al., 2021) and its activity thoroughly investigated. We showed that especially the latter sesquiterpene-derivative exhibits toxicity against whitefly.
regulation and secretion
Plants often produce and store defence metabolites in specialised structures. In tomato anti-insect metabolites are mostly produced in specialised glandular hairs called trichomes. These are like biochemical factories, present on the surface of green tissues. Type-VI trichomes of tomato consist of a secretory cavity surrounded by four metabolically acitve secretory cells. Within the Plant Physiology department we are interested in investigating these tomato glandular trichomes, their content, the factors that govern their development, the storage ability and the transport of metabolites.
The biosynthesis of defence compounds is costly and therefore under tight regulation. Whereas the biosynthetic genes for the production of terpenes are now largely identified, less is known about the regulation of the terpene biosynthetic pathways in tomato trichomes. Several transcription factors involved in metabolite production and for the presence of glandular trichomes have been identified over recent years. The lab of Robert Schuurink identified keyplayer MYC1, a trancription factor instrumental for the presence of type VI glandular trichomes on tomato (Xu et al., 2018).
Close up of a type-VI glandular trichome of tomato (photo Ruy Kortbeek) translation of research
To re-introduce natural resistance, knowledge on the biosynthetic pathways and how these are regulated is essential. Using an -omics approach in combination with the natural variation in metabolite production and insect resistance found in wild ancestors, we aim to identify limiting factors in sustainable natural insect resistance. Through close collaboration with partners in the Agro-industry, we are able to translate our research findings and benefit the development of a novel generation of crops with increased pest-insect resistance and a significantly reduced dependency on chemical application.
plant physiology
the above is part of the research taking place in the department of Plant Physiology, headed by Prof. dr. Michel Haring, together with dr. Robert Schuurink, dr. Silke Allman and Pulu Sun. Our department is member of the research theme Green Life Sciences (GLS) within the Swammerdam Institute for Life Sciences (SILS).
GLS consists of five complementary disciplines: Plant Physiology (PP), Molecular Plant Pathology (MPP), Plant Cell Biology (PCB), Plant Hormone Biology (PHB) and Plant Development & (Epi)Genetics (PDEG). Next to research collaborations, GLS researchers are active in the education program of the MSc track Green Life Sciences (MSc Biological Sciences) of our Faculty of Science. GLS participates in the Dutch graduate school Experimental Plant Sciences (EPS), a training and network platform for the PhD students and postdocs.
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Research Team
Marc Galland, Data Scientist. Founder and Lead of the Science Park Study Group (link).
Lissy-Anne Denkers, PhD candidate. Insight on the inside: exploring natural variation in phloem-based metabolites for insect resistance. NWO-LIFT
Roxane Snijders PhD candidate. Sustainable crop protection: designing a novel tomato variety with genetic insect resistance. Science & Design UvA-FNWI
Marlot Westera PhD candidate. Towards sustainable resistance against the Tospovirus-thrips pathosystem in crops, TKI-U
Siem van de Kraats, MSc internship
Julia Zwaan, MSc internship
Sabine de Graauw , MSc internship
Former group members
dr. Ruy Kortbeek, current position: Postdoctoral Resesarcher Purdue University USA. (Former: PhD candidate NWO-VIDI)
dr. Rodrigo Therezan, current position: Crop team lead (Rijk Zwaan). (Former: Post-Doc. TKI-U)
Michelle van der Gragt, current position: Highschool teacher. (Former: PhD candidate. NWO Green)
Aleksandra Muras, current position technician, junior breeder BASF (Former: research technician, NWO-VIDI)
Maurice Heilijgers, current position: research technician Rijk Zwaan (Former: research technician, NWO-VIDI)
Former Students (MSc, BSc)
Helena Victoria Cotan, UvA MSc (2022)
Sofia Maia Pinto, UvA MSc (2022)
Gian-Carlo Swaen, Hogeschool Utrecht (2022) in collaboration with Gertjan Kramer (Mass Spectrometry of Biomolecules)
Twan Hofland, UvA BSc Biology (2022)
Isa Vlught, UvA BSc Biology (2022)
Michelle Zwart, UvA MSc Biological Sciences track Green Life Science (2021)
Kamiel Blok, UvA BSc Biology (2021)
Jolanta Szkodon, VU-UvA MSc Bioinformatics and Systems Biology (2020)
Sjors Huizinga, UvA BSc Biology (2020)
Wicher Otten, VU-UvA MSc Bioinformatics and Systems Biology (2019-2020)
Lisette van Brakel, UvA MSc Biological Sciences track Green Life Science (2019)
Lennart Lambalk, UvA BSc Biology
Sanne Ypenburg, UvA MSc Biological Sciences (2017)
Lisa Govers, VU, BSc Biology (2017)
Miguel van der Wolf, UvA BSc Biology (2016)
Frederike Klein, UvA BSc Chemistry (2016)
Felix van Leuven, UvA BSc Biology (2015)
Maarten Rouwet, WUR MSc Plant Breeding (2014).
Random Forest - How to reach us
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Publications
2023
Kortbeek, R. W. J., Galland, M. D., Muras, A., Therezan, R., Maia, S., Haring, M. A., Schuurink, R. C., & Bleeker, P. M. (2023). Genetic and physiological requirements for high-level sesquiterpene-production in tomato glandular trichomes. Frontiers in Plant Science, 14, Article 1139274. https://doi.org/10.3389/fpls.2023.1139274 [details]
2021
- Kortbeek, R. W. J., Galland, M. D., Muras, A., van der Kloet, F. M., André, B., Heilijgers, M., van Hijum, S. A. F. T., Haring, M. A., Schuurink, R. C., & Bleeker, P. M. (2021). Natural variation in wild tomato trichomes; selecting metabolites that contribute to insect resistance using a random forest approach. BMC plant biology, 21, Article 315. https://doi.org/10.1186/s12870-021-03070-x [details]
- Therezan, R., Kortbeek, R., Vendemiatti, E., Legarrea, S., de Alencar, S. M., Schuurink, R. C., Bleeker, P., & Peres, L. E. P. (2021). Introgression of the sesquiterpene biosynthesis from Solanum habrochaites to cultivated tomato offers insights into trichome morphology and arthropod resistance. Planta, 254(1), Article 11. https://doi.org/10.1007/s00425-021-03651-y [details]
- Zabel, S., Brandt, W., Porzel, A., Athmer, B., Bennewitz, S., Schäfer, P., Kortbeek, R., Bleeker, P., & Tissier, A. (2021). A single cytochrome P450 oxidase from Solanum habrochaites sequentially oxidizes 7-epi-zingiberene to derivatives toxic to whiteflies and various microorganisms. Plant Journal, 105(5), 1309-1325. https://doi.org/10.1111/tpj.15113 [details]
2019
- Bouwmeester, H., Schuurink, R. C., Bleeker, P. M., & Schiestl, F. (2019). The role of volatiles in plant communication. Plant Journal, 100(5), 892-907. https://doi.org/10.1111/tpj.14496 [details]
- Kortbeek, R. W. J., van der Gragt, M., & Bleeker, P. M. (2019). Endogenous plant metabolites against insects. European Journal of Plant Pathology, 154(1), 67–90. Advance online publication. https://doi.org/10.1007/s10658-018-1540-6 [details]
- Visschers, I. G. S., Peters, J. L., Timmermans, L. L. H., Edwards, E., Ferrater, J. B., Balatero, C. H., Stratongjun, M., Bleeker, P. M., van Herwijnen, Z., Glawe, G. A., Bruin, J., van Dam, N. M., & Macel, M. (2019). Resistance to three thrips species in Capsicum spp. depends on site conditions and geographic regions. Journal of Applied Entomology, 143(9), 929-941. https://doi.org/10.1111/jen.12677 [details]
2018
- Steenbergen, M., Abd-El-Haliem, A., Bleeker, P., Dicke, M., Escobar-Bravo, R., Cheng, G., Haring, M. A., Kant, M. R., Kappers, I., Klinkhamer, P. G. L., Leiss, K. A., Legarrea, S., Macel, M., Mouden, S., Pieterse, C. M. J., Sarde, S. J., Schuurink, R. C., De Vos, M., Van Wees, S. C. M., & Broekgaarden, C. (2018). Thrips advisor: exploiting thrips-induced defences to combat pests on crops. Journal of Experimental Botany, 69(8), 1837-1848. https://doi.org/10.1093/jxb/ery060 [details]
- Stevens, S. L. R., Kuzak, M., Martinez, C., Moser, A., Bleeker, P., & Galland, M. (2018). Building a local community of practice in scientific programming for life scientists. PLoS Biology, 16(11), Article e2005561. https://doi.org/10.1371/journal.pbio.2005561 [details]
2016
- Kortbeek, R. W. J., Xu, J., Ramirez, A., Spyropoulou, E., Diergaarde, P., Otten-Bruggeman, I., de Both, M., Nagel, R., Schmidt, A., Schuurink, R. C., & Bleeker, P. M. (2016). Engineering of Tomato Glandular Trichomes for the Production of Specialized Metabolites. In S. E. O'Connor (Ed.), Synthetic Biology and Metabolic Engineering in Plants and Microbes (pp. 305-331). (Methods in Enzymology; Vol. 576). Academic Press. https://doi.org/10.1016/bs.mie.2016.02.014 [details]
- van Kleeff, P. J. M., Galland, M., Schuurink, R. C., & Bleeker, P. M. (2016). Small RNAs from Bemisia tabaci Are Transferred to Solanum lycopersicum Phloem during Feeding. Frontiers in Plant Science, 7, Article 1759. https://doi.org/10.3389/fpls.2016.01759 [details]
2012
- Alba, J. M., Bleeker, P. M., Glas, J. J., Schimmel, B. C. J., van Wijk, M., Sabelis, M. W., Schuurink, R. C., & Kant, M. R. (2012). The impact of induced plant volatiles on lant-arthropod interactions. In G. Smagghe, & I. Diaz (Eds.), Arthropod-plant interactions: novel insights and approaches for IPM (pp. 15-73). (Progress in biological control; No. 14). Springer. https://doi.org/10.1007/978-94-007-3873-7_2 [details]
- Bleeker, P. M., Mirabella, R., Diergaarde, P. J., Vandoorn, A., Tissier, A., Kant, M. R., Prins, M., de Vos, M., Haring, M. A., & Schuurink, R. C. (2012). Improved herbivore resistance in cultivated tomato with the sesquiterpene biosynthetic pathway from a wild relative. Proceedings of the National Academy of Sciences of the United States of America, 109(49), 20124-20129. https://doi.org/10.1073/pnas.1208756109 [details]
2011
- Almeida Sarmento, R., Lemos, F., Bleeker, P. M., Schuurink, R. C., Pallini, A., Oliveira, M. G. A., Lima, E. R., Kant, M., Sabelis, M. W., & Janssen, A. (2011). A herbivore that manipulates plant defence. Ecology Letters, 14(3), 229-236. https://doi.org/10.1111/j.1461-0248.2010.01575.x [details]
- Bleeker, P. M., Diergaarde, P. J., Ament, K., Schütz, S., Johne, B., Dijkink, J., Hiemstra, H., de Gelder, R., de Both, M. T. J., Sabelis, M. W., Haring, M. A., & Schuurink, R. C. (2011). Tomato-produced 7-epizingiberene and R-curcumene act as repellents to whiteflies. Phytochemistry, 72(1), 68-73. https://doi.org/10.1016/j.phytochem.2010.10.014 [details]
- Bleeker, P. M., Spyropoulou, E. A., Diergaarde, P. J., Volpin, P., de Both, M. T. J., Zerbe, P., Bohlmann, J., Falara, V., Matsuba, Y., Pichersky, E., Haring, M. A., & Schuurink, R. C. (2011). RNA-seq discovery, functional characterization, and comparison of sesquiterpene synthases from Solanum lycopersicum and Solanum habrochaites trichomes. Plant Molecular Biology, 77(4-5), 323-336. https://doi.org/10.1007/s11103-011-9813-x [details]
- Falara, V., Akhtar, T. A., Nguyen, T. T. H., Spyropoulou, E. A., Bleeker, P. M., Schauvinhold, I., Matsuba, Y., Bonini, M. E., Schilmiller, A. L., Last, R. L., Schuurink, R. C., & Pichersky, E. (2011). The tomato terpene synthase gene family. Plant Physiology, 157(2), 770-789. https://doi.org/10.1104/pp.111.179648 [details]
2009
- Bleeker, P. M., Diergaarde, P. J., Ament, K., Guerra, J., Weidner, M., Schütz, S., de Both, M. T. J., Haring, M. A., & Schuurink, R. C. (2009). The role of specific tomato volatiles in tomato-whitefly interaction. Plant Physiology, 151(2), 925-935. https://doi.org/10.1104/pp.109.142661 [details]
- Kant, M. R., Bleeker, P. M., van Wijk, M., Schuurink, R. C., & Haring, M. A. (2009). Plant Volatiles in Defence. In L. C. van Loon (Ed.), Plant innate immunity (pp. 613-666). (ADVANCES IN BOTANICAL RESEARCH; No. 51). Academic Press. https://doi.org/10.1016/S0065-2296(09)51014-2 [details]
2007
- Bleeker, P. M., Ament, K., Diergaarde, P. J., de Both, M., & Schuurink, R. C. (2007). Plant volatiles.
- Bleeker, P. M., Diergaarde, P. J., Haring, M. A., van Schie, C. C. N., Schuurink, R. C., & de Both, M. (2007). Trichome specific promoters.
Talk / presentation
- Bleeker, P. M. (speaker) & van der Does, H. C. (speaker) (23-11-2016). Tussen Plant en Plaag, UvA/Spui 25. http://www.spui25.nl/gedeelde-content/evenementen/evenementen/2016/11/beta-in-de-binnenstad-tussen-plant-en-plaag.html
2021
- Galland, M., Bleeker, P. & Gragt, M. (2-2-2021). Small RNA-seq and messenger RNA-seq of F1 cross between different species of tomato (lycopersicum, habrochaites). Zenodo. https://doi.org/10.5281/zenodo.4494409
- Galland, M., Therezan, R., Kortbeek, R. & Bleeker, P. (2-2-2021). LTP2 related material. Zenodo. https://doi.org/10.5281/zenodo.4687875
- Kortbeek, R. W. J., Galland, M., Muras, A., van der Kloet, F., André, B., Heilijgers, M., van Hijum, S. A. F. T., Haring, M. A., Schuurink, R. C. & Bleeker, P. (2021). Additional file 9 of Natural variation in wild tomato trichomes; selecting metabolites that contribute to insect resistance using a random forest approach. Figshare. https://doi.org/10.6084/m9.figshare.14903849.v1
- Kortbeek, R. W. J., Galland, M., Muras, A., van der Kloet, F., André, B., Heilijgers, M., van Hijum, S. A. F. T., Haring, M. A., Schuurink, R. C. & Bleeker, P. (2021). Additional file 10 of Natural variation in wild tomato trichomes; selecting metabolites that contribute to insect resistance using a random forest approach. Figshare. https://doi.org/10.6084/m9.figshare.14903819.v1
- Kortbeek, R. W. J., Galland, M., Muras, A., van der Kloet, F., André, B., Heilijgers, M., van Hijum, S. A. F. T., Haring, M. A., Schuurink, R. C. & Bleeker, P. (2021). Additional file 11 of Natural variation in wild tomato trichomes; selecting metabolites that contribute to insect resistance using a random forest approach. Figshare. https://doi.org/10.6084/m9.figshare.14903822.v1
2020
- Galland, M., Gragt, M. & Bleeker, P. (17-11-2020). Processed data for the sRNA landscape chapter. Zenodo. https://doi.org/10.5281/zenodo.5564147
- Bleeker, P. & Galland, M. (17-9-2020). DNA-seq of Solanum habrochaites PI127826 and LA1777 DNA (part II). Zenodo. https://doi.org/10.5281/zenodo.4268097
- Galland, M. & Bleeker, P. (17-8-2020). DNA-seq of Solanum habrochaites PI127826 and LA1777 DNA (part I). Zenodo. https://doi.org/10.5281/zenodo.4618196
- Galland, M. & Bleeker, P. (7-4-2020). Stem trichome small RNA-Seq from the 20 accessions. Zenodo. https://doi.org/10.5281/zenodo.3742788
- Galland, M. & Bleeker, P. (24-1-2020). Scaled counts of trichome mRNA-seq from the 20 accessions. Zenodo. https://doi.org/10.5281/zenodo.3627091
2019
- Castillo, A., Bleeker, P. & Schuurink, R. (19-12-2019). Small RNA dataset whitefly - tomato. Zenodo. https://doi.org/10.5281/zenodo.4680850
- Galland, M. & Bleeker, P. (12-12-2019). Stem trichome PARE-Seq (degradome) data from the 20 accessions. Zenodo. https://doi.org/10.5281/zenodo.4034262
- Galland, M. & Bleeker, P. (18-10-2019). Genomic sequences and annotations for Solanum lycopersicum, Solanum pennellii and Solanum habrochaites. Zenodo. https://doi.org/10.5281/zenodo.5761962
- Galland, M., Bleeker, P. & Kortbeek, R. (25-3-2019). Stem trichome mRNA-Seq from S. lycopersicum x S. habrochaites PI127826 crosses (F2 lines). Zenodo. https://doi.org/10.5281/zenodo.4491747
2017
- Galland, M., Kortbeek, R. & Bleeker, P. (23-11-2017). Stem trichome mRNA-Seq from lycopersicum x habrochaites crosses (Parents and F1). Zenodo. https://doi.org/10.5281/zenodo.4322913
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Ancillary activities
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Enza Zaden Research & Development B.V.
Sr. Researcher Fytopathologie
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Enza Zaden Research & Development B.V.
Kortbeek, R. W. J., Galland, M. D., Muras, A., Therezan, R., Maia, S., Haring, M. A., Schuurink, R. C., & Bleeker, P. M. (2023). Genetic and physiological requirements for high-level sesquiterpene-production in tomato glandular trichomes. Frontiers in Plant Science, 14, Article 1139274.