Dr. L. (Lemeng) Dong
- Science Park 904
- Kamernummer: C2.219
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Postbus 1210
1000 BE Amsterdam
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Research interests
Plant metabolites not only have very important pharmaceutical activity, but are also involved in crop protection (directly or indirectly) as defense compounds or in the communication with other organisms, which plays an important role in ecology. Soil-borne diseases and other underground stresses are still big threats to our crops and we are just beginning to understand the belowground (rhizosphere) biology and the role of chemical interactions seems much more complicated and important than anticipated. My research interest is to understand the molecular mechanisms underlying the belowground Interkingdom chemical Interactions and the effects on this of (1) evolution, (2) nutrient availability, and (3) biotic stress, and translate this knowledge into applications of biotechnological, medical and environmental interest.
1. Evolution
I study the contribution of microevolution (domestication/genetic variation) and macroevolution (across species/families) in the chemical interactions between plants and other organisms.
Using wild and domesticated cucurbits and genetic variation I look for the effect of artificial and natural selection on root microbiome recruitment under phosphate stress. In addition, I study the macroevolutionary mechanisms driving signaling molecule production and perception. Using comparative transcriptome, metabolome, metagenome and metatranscriptome and molecular biology approaches across families/species, I want to explore widely-conserved and family-specific signaling molecules/microbes in plant-microbe interactions that protect plants against harmful and attract beneficial organisms (Figure 1). To achieve this, I am working with PhD student Sébastien Jaupitre and bioinformatician Fred White in MiCROP to study the signaling molecule biosynthesis and perception under phosphate starvation across 5 plant families.
2. Nutrient availability and biotic stress
a) In MiCROP I will work with PhD student Sebastien to find new signaling molecules and unravel their production, transportation and perception that influence beneficial microbes under phosphate starvation. In addition, we also would like to understand how aboveground herbivore attack influences belowground gene expression, metabolite exudation and microbiome recruitment.
b) In collaboration with Prof. Harro Bouwmeester, I am co-supervising two PhD students (Changsheng Li & Yanting Wang) funded by Chinese Scholarship Council. We study how phosphate starvation influences plant metabolism, and what the role of strigolactones is in these changes. We aim to fully elucidate strigolactone biosynthesis pathways in diverse plant species and explore their functional plasticity.
c) In my Marie Curie project and a ‘Holland Innovative Potato’ project, with two PhD students Alessandra Guerrieri and Davar Abedini, and in collaboration with Aska Goverse and Andre Bertran of the WUR Laboratory of Nematology, we study plant-nematode interaction through plant signaling molecules and the influence of nitrogen and microbes on this (Figure 2).
Figure 1 Across family microbial recruitment by phosphate starvation induced signaling molecules. Figure 2 Plant-cyst nematode interaction through signaling molecules. -
People
Yanting Wang, PhD, biosynthesis and role of strigolactones in the phosphate starvation response in tomato. Alessandra Guerrieri, PhD, chemical communication between tomato and nematodes. Changsheng Li, PhD, strigolactone biosynthesis in Gramineae and functional diversity of strigolactones. Davar Abedini, PhD, signaling molecule mediated plant-nematode-microbe interaction. Sébastien Jaupitre, PhD, macroevolution of plant-microbe interaction. Fred White, bioinformatician, developing/implementing data analysis pipelines. Yuting Yang, technician, developing/implementing molecular biology tools. -
Open positions
Open positions
We will soon open a postdoc position on Microp, please stay tuned.
BSc and MSc projects
We have opportunities for BSc and MSc projects on our research topics. Please ask for more information (l.dong2@uva.nl).
PhD and visiting scholarships
We support talented MSc students to apply for PhD scholarships such as from China Scholarship Council (CSC), EPS Graduate Programme (https://www.graduateschool-eps.info/graduate-programme/) and other scholarships.
We also welcome visiting scholars or exchange students; please don’t hesitate to contact me (l.dong2@uva.nl) for further information.
Postdoc fellowships
If you are interested in one of the topics in the Metabolism LAB and would like to apply for your own postdoc fellowship (e.g. Marie Curie, EMBO, HFSP, FEBS or NWO VENI etc.), it would be my pleasure to host you and discuss these interesting topics with you. Please email me via l.dong2@uva.nl.
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Publicaties
2024
Abegaz, F., Abedini, D., White, F., Guerrieri, A., Zancarini, A., Dong, L., Westerhuis, J. A., van Eeuwijk, F., Bouwmeester, H., & Smilde, A. K. (2024). A strategy for differential abundance analysis of sparse microbiome data with group-wise structured zeros. Scientific Reports, 14, Article 12433. https://doi.org/10.1038/s41598-024-62437-w [details]- Li, C., Haider, I., Wang, J. Y., Quinodoz, P., Suarez Duran, H. G., Méndez, L. R., Horber, R., Fiorilli, V., Votta, C., Lanfranco, L., Correia de Lemos, S. M., Jouffroy, L., Moegle, B., Miesch, L., De Mesmaeker, A., Medema, M. H., Al-Babili, S., Dong, L., & Bouwmeester, H. J. (2024). OsCYP706C2 diverts rice strigolactone biosynthesis to a noncanonical pathway branch. Science Advances, 10(35), Article eadq3942. https://doi.org/10.1126/sciadv.adq3942 [details]
2023
- Almeida, A., Trevenzoli Favero, B., Dong, L., Cárdenas, P. D., Saenz-Mata, J., Lütken, H., & Bak, S. (2023). Lessons learned from metabolic engineering in hairy roots: Transcriptome and metabolic profile changes caused by Rhizobium-mediated plant transformation in Cucurbitaceae species. Plant physiology and biochemistry : PPB, 201, Article 107797. https://doi.org/10.1016/j.plaphy.2023.107797 [details]
- Ezquerro, M., Li, C., Pérez-Pérez, J., Burbano-Erazo, E., Barja, M. V., Wang, Y., Dong, L., Lisón, P., López-Gresa, M. P., Bouwmeester, H. J., & Rodríguez-Concepción, M. (2023). Tomato geranylgeranyl diphosphate synthase isoform 1 is involved in the stress-triggered production of diterpenes in leaves and strigolactones in roots. New Phytologist, 239(6), 2292–2306. https://doi.org/10.1111/nph.19109 [details]
- Guan, J-C., Li, C., Flint-Garcia, S., Suzuki, M., Wu, S., Saunders, J. W., Dong, L., Bouwmeester, H. J., McCarty, D. R., & Koch, K. E. (2023). Maize domestication phenotypes reveal strigolactone networks coordinating grain size evolution with kernel-bearing cupule architecture. The Plant Cell, 35(3), 1013-1037. Advance online publication. https://doi.org/10.1093/plcell/koac370 [details]
- Li, C., Dong, L., Durairaj, J., Guan, J. C., Yoshimura, M., Quinodoz, P., Horber, R., Gaus, K., Li, J., Setotaw, Y. B., Qi, J., De Groote, H., Wang, Y., Thiombiano, B., Floková, K., Walmsley, A., Charnikhova, T. V., Chojnacka, A., Correia de Lemos, S., ... Bouwmeester, H. J. (2023). Maize resistance to witchweed through changes in strigolactone biosynthesis. Science, 379(6627), 94-99. https://doi.org/10.1126/science.abq4775 [details]
2022
- Almeida, A., Dong, L., Thorsen, T. H., Raadam, M. H., Khakimov, B., Carreno-Quintero, N., Kampranis, S. C., & Bak, S. (2022). Metabolic engineering of cucurbitacins in Cucurbita pepo hairy roots. Frontiers in Plant Science, 13, Article 1021907. https://doi.org/10.3389/fpls.2022.1021907 [details]
- Mashiguchi, K., Seto, Y., Onozuka, Y., Suzuki, S., Takemoto, K., Wang, Y., Dong, L., Asami, K., Noda, R., Kisugi, T., Kitaoka, N., Akiyama, K., Bouwmeester, H., & Yamaguchi, S. (2022). A carlactonoic acid methyltransferase that contributes to the inhibition of shoot branching in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 119(14), Article e2111565119. https://doi.org/10.1073/pnas.2111565119 [details]
- Vismans, G., van Bentum, S., Spooren, J., Song, Y., Goossens, P., Valls, J., Snoek, B. L., Thiombiano, B., Schilder, M., Dong, L., Bouwmeester, H. J., Pétriacq, P., Pieterse, C. M. J., Bakker, P. A. H. M., & Berendsen, R. L. (2022). Coumarin biosynthesis genes are required after foliar pathogen infection for the creation of a microbial soil-borne legacy that primes plants for SA-dependent defenses. Scientific Reports, 12(1), Article 22473. https://doi.org/10.1038/s41598-022-26551-x [details]
- Vlaar, L. E., Thiombiano, B., Abedini, D., Schilder, M., Yang, Y., & Dong, L. (2022). A Combination of Metabolomics and Machine Learning Results in the Identification of a New Cyst Nematode Hatching Factor. Metabolites , 12(6), Article 551. https://doi.org/10.3390/metabo12060551 [details]
- Wang, Y., Durairaj, J., Suárez Duran, H. G., van Velzen, R., Flokova, K., Liao, C-Y., Chojnacka, A., MacFarlane, S., Schranz, M. E., Medema, M. H., van Dijk, A. D. J., Dong, L., & Bouwmeester, H. J. (2022). The tomato cytochrome P450 CYP712G1 catalyzes the double oxidation of orobanchol en route to the rhizosphere signaling strigolactone, solanacol. New Phytologist, 235(5), 1884-1899. Advance online publication. https://doi.org/10.1111/nph.18272 [details]
2021
- Abedini, D., Jaupitre, S., Bouwmeester, H., & Dong, L. (2021). Metabolic interactions in beneficial microbe recruitment by plants. Current Opinion in Biotechnology, 70, 241-247. https://doi.org/10.1016/j.copbio.2021.06.015 [details]
- Bouwmeester, H., Li, C., Thiombiano, B., Rahimi, M., & Dong, L. (2021). Adaptation of the parasitic plant lifecycle: germination is controlled by essential host signaling molecules. Plant Physiology, 185(4), 1292–1308. Advance online publication. https://doi.org/10.1093/plphys/kiaa066 [details]
- Dong, L., Almeida, A., Pollier, J., Khakimov, B., Bassard, J-E., Miettinen, K., Stærk, D., Mehran, R., Olsen, C. E., Motawia, M. S., Goossens, A., & Bak, S. (2021). An independent evolutionary origin for insect deterrent cucurbitacins in Iberis amara. Molecular Biology and evolution, 38(11), 4659–4673. https://doi.org/10.1093/molbev/msab213 [details]
- Guerrieri, A., Floková, K., Vlaar, L. E., Schilder, M. L., Kramer, G., Chojnacka, A., van Dijk, Y. R., Bouwmeester, H. J., & Dong, L. (2021). UPLC-MS/MS analysis and biological activity of the potato cyst nematode hatching stimulant, solanoeclepin A, in the root exudate of Solanum spp. Planta, 254(6), Article 112. https://doi.org/10.1007/s00425-021-03766-2 [details]
- Vlaar, L. E., Bertran, A., Rahimi, M., Dong, L., Kammenga, J. E., Helder, J., Goverse, A., & Bouwmeester, H. J. (2021). On the role of dauer in the adaptation of nematodes to a parasitic lifestyle. Parasites & Vectors, 14, Article 554. https://doi.org/10.1186/s13071-021-04953-6 [details]
- Wang, Y., Suárez Duran, H. G., van Haarst, J. C., Schijlen, E. G. W. M., Ruyter-Spira, C., Medema, M. H., Dong, L., & Bouwmeester, H. J. (2021). The role of strigolactones in P deficiency induced transcriptional changes in tomato roots. BMC plant biology, 21, Article 349. https://doi.org/10.1186/s12870-021-03124-0 [details]
- Xu, X., Jibran, R., Wang, Y., Dong, L., Flokova, K., Esfandiari, A., McLachlan, A. R. G., Heiser, A., Sutherland-Smith, A. J., Brummell, D. A., Bouwmeester, H. J., Dijkwel, P. P., & Hunter, D. A. (2021). Strigolactones regulate sepal senescence in Arabidopsis. Journal of Experimental Botany, 72(15), 5462–5477. Advance online publication. https://doi.org/10.1093/jxb/erab199 [details]
2020
- Almeida, A., Dong, L., Appendino, G., & Bak, S. (2020). Plant triterpenoids with bond-missing skeletons: biogenesis, distribution and bioactivity. Natural Product Reports, 37(9), 1207-1228. https://doi.org/10.1039/c9np00030e [details]
2019
- Guerrieri, A., Dong, L., & Bouwmeester, H. J. (2019). Role and exploitation of underground chemical signaling in plants. Pest Management Science, 75(9), 2455-2463. https://doi.org/10.1002/ps.5507 [details]
2018
- Almeida, A., Dong, L., Khakimov, B., Bassard, J. E., Moses, T., Lota, F., Goossens, A., Appendino, G., & Bak, S. (2018). A single oxidosqualene cyclase produces the seco-triterpenoid α-onocerin. Plant Physiology, 176(2), 1469-1484. https://doi.org/10.1104/pp.17.01369
- Dong, L., Pollier, J., Bassard, J. E., Ntallas, G., Almeida, A., Lazaridi, E., Khakimov, B., Arendt, P., de Oliveira, L. S., Lota, F., Goossens, A., Michoux, F., & Bak, S. (2018). Co-expression of squalene epoxidases with triterpene cyclases boosts production of triterpenoids in plants and yeast. Metabolic Engineering, 49, 1-12. https://doi.org/10.1016/j.ymben.2018.07.002
2016
- Dong, L., Jongedijk, E., Bouwmeester, H., & Van Der Krol, A. (2016). Monoterpene biosynthesis potential of plant subcellular compartments. New Phytologist, 209(2), 679-690. Advance online publication. https://doi.org/10.1111/nph.13629
2014
- Masakapalli, S. K., Ritala, A., Dong, L., Van Der Krol, A. R., Oksman-Caldentey, K. M., Ratcliffe, R. G., & Sweetlove, L. J. (2014). Metabolic flux phenotype of tobacco hairy roots engineered for increased geraniol production. Phytochemistry, 99, 73-85. https://doi.org/10.1016/j.phytochem.2013.12.007
- Miettinen, K., Dong, L., Navrot, N., Schneider, T., Burlat, V., Pollier, J., Woittiez, L., Van Der Krol, S., Lugan, R., Ilc, T., Verpoorte, R., Oksman-Caldentey, K. M., Martinoia, E., Bouwmeester, H., Goossens, A., Memelink, J., & Werck-Reichhart, D. (2014). The seco-iridoid pathway from Catharanthus roseus. Nature Communications, 5, Article 3606. https://doi.org/10.1038/ncomms4606
- Miettinen, K., Dong, L., Navrot, N., Schneider, T., Burlat, V., Pollier, J., Woittiez, L., van der Krol, S., Lugan, R., Ilc, T., Verpoorte, R., Oksman-Caldentey, K.-M., Martinoia, E., Bouwmeester, H., Goossens, A., Memelink, J., & Werck-Reichhart, D. (2014). Corrigendum: The seco-iridoid pathway from Catharanthus roseus. Nature Communications, 5, Article 4175. https://doi.org/10.1038/ncomms5175
- Ritala, A., Dong, L., Imseng, N., Seppänen-Laakso, T., Vasilev, N., Van der Krol, S., Rischer, H., Maaheimo, H., Virkki, A., Brändli, J., Schillberg, S., Eibl, R., Bouwmeester, H., & Oksman-Caldentey, K. M. (2014). Evaluation of tobacco (Nicotiana tabacum L. cv. Petit Havana SR1) hairy roots for the production of geraniol, the first committed step in terpenoid indole alkaloid pathway. Journal of Biotechnology, 176(1), 20-28. https://doi.org/10.1016/j.jbiotec.2014.01.031
- Vasilev, N., Schmitz, C., Dong, L., Ritala, A., Imseng, N., Häkkinen, S. T., van der Krol, S., Eibl, R., Oksman-Caldentey, K. M., Bouwmeester, H., Fischer, R., & Schillberg, S. (2014). Comparison of plant-based expression platforms for the heterologous production of geraniol. Plant Cell, Tissue and Organ Culture, 117(3), 373-380. https://doi.org/10.1007/s11240-014-0446-z
2013
- Dong, L., Miettinen, K., Goedbloed, M., Verstappen, F. W. A., Voster, A., Jongsma, M. A., Memelink, J., Krol, S. V. D., & Bouwmeester, H. J. (2013). Characterization of two geraniol synthases from Valeriana officinalis and Lippia dulcis: Similar activity but difference in subcellular localization. Metabolic Engineering, 20, 198-211. https://doi.org/10.1016/j.ymben.2013.09.002
- Höfer, R., Dong, L., André, F., Ginglinger, J. F., Lugan, R., Gavira, C., Grec, S., Lang, G., Memelink, J., Van Der Krol, S., Bouwmeester, H., & Werck-Reichhart, D. (2013). Geraniol hydroxylase and hydroxygeraniol oxidase activities of the CYP76 family of cytochrome P450 enzymes and potential for engineering the early steps of the (seco)iridoid pathway. Metabolic Engineering, 20, 221-232. https://doi.org/10.1016/j.ymben.2013.08.001
2011
- Dong, L., Sui, C., Liu, Y., Yang, Y., Wei, J., & Yang, Y. (2011). Validation and application of reference genes for quantitative gene expression analyses in various tissues of Bupleurum chinense. Molecular Biology Reports, 38(8), 5017-5023. https://doi.org/10.1007/s11033-010-0648-3
2010
- Sui, C., Wei, J. H., Chen, S. L., Chen, H. Q., Dong, L. M., & Yang, C. M. (2010). Construction of a full-length enriched cDNA library and analysis of 3111 ESTs from roots of Bupleurum Chinense DC. Botanical Studies, 51(1), 7-16. https://ejournal.sinica.edu.tw/bbas/content/2010/1/Bot511-02/Bot511-02.html
2009
- Dong, L. M., Wei, J. H., Liu, Y. J., & Yang, C. M. (2009). Advances in studies on spatial-specific distributions of secondary metabolites and related enzymes in plants. Chinese Traditional and Herbal Drugs, 40(1), 153-155.
2020
- Dong, L., & Bouwmeester, H. (2020). Biosynthesis and Regulation of Belowground Signaling Molecules. In E. Pichersky, & N. Dudareva (Eds.), Biology of Plant Volatiles (2nd ed., pp. 203-215). CRC Press. Advance online publication. https://doi.org/10.1201/9780429455612-13 [details]
2022
- Guerrieri, A. (2022). Solanoeclepin A: Characterization of a rhizosphere communication molecule in tomato and potato. [Thesis, fully internal, Universiteit van Amsterdam]. [details]
- Li, C. (2022). Elucidation of the biosynthetic pathway and biological roles of strigolactones in maize and rice. [Thesis, fully internal, Universiteit van Amsterdam]. [details]
2022
- Wang, Y., Durairaj, J., Suárez Duran, H. G., van Velzen, R., Flokova, K., Liao, C.-Y., Chojnacka, A., MacFarlane, S., Schranz, M. ., Medema, M. H., van Dijk, A. D. J., Dong, L. & Bouwmeester, H. J. (2022). Data underlying the publication: The tomato cytochrome P450 CYP712G1 catalyzes the double oxidation of orobanchol en route to the rhizosphere signaling strigolactone, solanacol. 4TU.ResearchData. https://doi.org/10.4121/14891094
2021
- Dong, L. (2021). Independent evolutionary origin for insect deterrent cucurbitacins. Zenodo. https://doi.org/10.5281/zenodo.4943411
- Wang, Y., Duran, H. G. ., van Haarst, J. C., Schijlen, E. G. W. M., Ruyter-Spira, C., Medema, M. H., Dong, L. & Bouwmeester, H. J. (2021). Additional file 1 of The role of strigolactones in P deficiency induced transcriptional changes in tomato roots. Figshare. https://doi.org/10.6084/m9.figshare.15047799.v1
- Vlaar, L., Bertran, A., Rahimi, M., Dong, L., Kammenga, J. E., Helder, J., Goverse, A. & Bouwmeester, H. J. (2021). Additional file 1 of On the role of dauer in the adaptation of nematodes to a parasitic lifestyle. Figshare. https://doi.org/10.6084/m9.figshare.16893285.v1
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Nevenwerkzaamheden
- Geen nevenwerkzaamheden
Abegaz, F., Abedini, D., White, F., Guerrieri, A., Zancarini, A., Dong, L., Westerhuis, J. A., van Eeuwijk, F., Bouwmeester, H., & Smilde, A. K. (2024). A strategy for differential abundance analysis of sparse microbiome data with group-wise structured zeros. Scientific Reports, 14, Article 12433.