Sylvia de Pater
Assistant professor
- Name
- Dr. B.S. de Pater
- Telephone
- +31 71 527 4760
- b.s.de.pater@biology.leidenuniv.nl
- ORCID iD
- 0000-0003-2626-3661
I am interested in plant DSB repair and Agrobacterium T-DNA integration with the ultimate aim to improve the rather low frequency of gene-targeting in plants.
More information about Sylvia de Pater
PhD Candidates
Supporting staff
Courses
Research
My research interest is DSB repair and Agrobacterium T-DNA integration in plants, which knowledge will be ultimately applied to optimize site-specific mutagenesis and the rather low frequency of gene-targeting. Several research lines are being followed: 1) inactivation of random integration and 2) enhancing homologous recombination by introducing specific double strand breaks using custom-made endonucleases. To prevent unwanted DNA integrations, nucleases are also being introduced as proteins via the type four secretion system (T4SS) or as T-DNA in plant mutants that fail to integrate T-DNA.
Genome Engineering
I worked on several projects with the aim of improving the rather low frequency of gene-targeting in plants. We follow two approaches: inactivation of random integration and enhancing homologous recombination by introducing specific double strand breaks and increase the number of available repair emplates. For this latter approach we made use of zinc-finger nucleases (ZFN) and Tal Effector nucleases (TALEN). More recently, we focus on the use of CRISPR/Cas nucleases. In addition we try to further enhance gene-targeting by using cells that have a more active homologous recombination machinery.
Furthermore, methods are being explored for targeted mutagenesis (also called “genome editing”) of plant genes via a non-GMO approaches, using site-specific nuclease proteins expressed in Agrobacterium and transported via its T4SS to plant cells or through transformation of plant mutated in the Polθ gene that no longer integrate T-DNA. After transfer, the nucleases will induce double strand breaks (DSBs) at a specific location in the genome, which upon imperfect repair via non-homologous end joining (NHEJ) might result in mutations.
T-DNA integration and DNA Repair.
Closely related to the above subject I study the different DNA repair pathways in plants. In eukaryotic organisms DNA double strand breaks (DSB) are repaired via two mechanisms: homologous recombination (HR) and non-homologous end-joining (NHEJ). I want to identify the different components of these repair pathways in order to manipulate the balance between them. Furthermore repair pathways are being studied responsible for integration of Agrobacterium T-DNA in the host genome. A essential protein is Polymerase θ, which action together with other important factors, leads to the integration of the T-DNA in the plant genome.
Co-promotor
- Gary Strunks (2019) Strategies for improvement of genome editing in Arabidopsis thaliana.
- Daan Schmitz (2018) CRISPR/Cas-induced targeted mutagenesis with Agrobacterium mediated protein delivery.
- Hexi Shen (2017) Role of non-homologous end-joining in T-DNA integration in Arabidopsis thaliana.
- Marijn Knip (2012) DAYSLEEPER: from genomic parasite to indispensable gene.
- Qi Jia (2011) DNA repair and gene-targeting in plant end-joining mutants.
- Sandra Langeveld (2001) Role of reversibly glycosylated polypeptides in starch biosynthesis.
- Flip Hoedemaeker (1995) Structure and stability of legume lectin.
- Ron van Eijsden (1994) Mutational analysis of pea lectin.
Greenpoint
I am manager of the greenpoint facilities at the ground floor and the tissue culture facilities at the fifth floor and I supervise the supporting staff involved (Ward de Winter and Jan Vink).
Teaching
I am teacher at the second year course Molecular Biology.
BSc and MSc students are welcome to do an internship under my supervision on one of the subjects described under research. The subjects can be very divers with many different techniques; therefore, the program will be made just before the start of the internship. Possible subjects concern DNA repair pathways in plants and improvement of gene-targeting by using custom-made nucleases. Techniques may be used like cloning, plant transformation, analysis of transgenic plants and mutants on DNA, RNA and proteins level.
Assistant professor
- Science
- Instituut Biologie Leiden
- IBL Plant Sciences
- Kamoen L., Kralemann L.E.M., Schendel R. van, Tol N. van, Hooykaas P.J.J., Pater B.S. de & Tijsterman M. (2024), Genetic dissection of mutagenic repair and T-DNA capture at CRISPR-induced DNA breaks in Arabidopsis thaliana, PNAS Nexus 3(3): pgae094.
- Pater S. de, Kamoen L., Schendel R. van, Hooykaas P.J.J. & Tijsterman M. (2024), Profiling Cas9- and Cas12a-induced mutagenesis in Arabidopsis thaliana, The Plant Journal : .
- Tol N. van, Schendel R. van, Bos. A, Kregten M. van, Pater B.S. de, Hooykaas P.J.J. & Tijsterman M. (2022), Gene targeting in polymerase theta-deficient arabidopsis thaliana, The Plant Journal 109(1): 112-125.
- Kralemann L.E.M., Pater B.S. de, Shen H., Kloet S.L., Schendel R. van, Hooykaas P.J.J. & Tijsterman M. (2022), Distinct mechanisms for genomic attachment of the 5' and 3' ends of Agrobacterium T-DNA in plants, Nature Plants 8(5): 526-534.
- Schmitz D.J., Ali Z., Wang C., Aljedaani F., Hooykaas P.J.J., Mahfouz M. & Pater B.S. de (2020), CRISPR/Cas9 mutagenesis by translocation of Cas9 protein into plant cells via the Agrobacterium type IV secretion system, Frontiers in Genome Editing 2: 6.
- Pater B.S. de, Klemann B.J.P.M. & Hooykaas P.J.J. (2018), True gene-targeting events by CRISPR/Cas-induced DSB repair of the PPO locus with an ectopically integrated repair template, Scientific Reports 8: 3338.
- Shen H., Strunks G.D., Klemann B.J.P.M., Hooykaas P.J.J. & Pater B.S. de (2017), CRISPR/Cas9-Induced Double-Strand Break Repair in Arabidopsis Nonhomologous End-Joining Mutants, G3: Genes | Genomes | Genetics 7(1): 193-202.
- Kregten M. van, Pater B.S. de, Romeijn R., Schendel R. van, Hooykaas P.J.J. & Tijsterman M. (2016), T-DNA integration in plants results from polymerase-theta-mediated DNA repair, Nature Plants 2(10): 16164.
- Pater B.S. de, Pinas J.E., Hooykaas P.J.J. & Zaal E.J. van der (2013), ZFN-mediated gene targeting of the Arabidopsis protoporphyrinogen oxidase gene through Agrobacterium-mediated floral dip transformation, Plant Biotechnology Journal 11(4): 510-515.
- Jia Q., Dulk H. den, Shen H., Hooykaas P.J.J. & Pater S. de (2013), Poly(ADP-ribose)polymerases are involved in micro-homology mediated back-up non-homologous end-joining in Arabidopsis thaliana, Plant Molecular Biology 82(4): 339-351.
- Knip M., Hiemstra S.H., Sietsma A., Castelein M., Pater B.S. de & Hooykaas P.J.J. (2013), DAYSLEEPER: a nuclear and vesicular-localized protein that is expressed in proliferating tissues, BMC Plant Biology 13: 211.
- Lieberman-Lazarovich M., Melamed-Bessudo C., Pater S. de & Levy A.A. (2013), Epigenetic Alterations at Genomic Loci Modified by Gene Targeting in Arabidopsis thaliana, PLoS ONE 8(12): e85383.
- Pater S. de & Hooykaas P.J.J. (2013), Gene replacement. In: Lübberstedt T. & Varshney R.K. (Eds.), Diagnostics in Plant Breeding. Netherlands: Springer. 167-183.
- Knip M., Pater B.S. de & Hooykaas P.J.J. (2012), The SLEEPER genes: a transposase-derived angiosperm-specific gene family, BMC Plant Biology 12: 192.
- Jia Q., Bundock P., Hooykaas P.J.J. & Pater B.S. de (2012), Agrobacterium tumefaciens T-DNA integration and gene-targeting in Arabidopsis thaliana non-homologous end-joining mutants, Journal of Botany 2012: 989272.
- Kraaijeveld K., Zwanenburg B., Hubert B., Vieira C., Pater B.S. de, Alphen J.J.M. van, Dunnen J.T. den & Knijff P. de (2012), Transposon proliferation in an asexual parasitiod, Molecular Ecology 21(16): 3898-3906.
- Gaussand G.M.D.J., Jia Q., Graaff E. van der, Lamers G.E.M., Fransz P.F., Hooykaas P.J.J. & Pater B.S. de (2011), Programmed cell death in the leaves of the Arabidopsis spontaneous necrotic spots (sns-D) mutant correlates with increased expression of the eukaryotic translation initiation factor eIF4B2, Frontiers in Plant Science 2: 9.
- Pater B.S. de, Neuteboom L.W., Pinas J.E., Hooykaas P.J.J. & Zaal E.J. van der (2009), ZFN-induced mutagenesis and gene-targeting in Arabidopsis through Agrobacterium-mediated floral dip transformation, Plant Biotechnology Journal 7(8): 821-835.
- Pater B.S. de, Caspers M., Kottenhagen M., Meima M.E., Stege R. ter & Vetten N. (2006), Manipulation of starch granule size distribution in potato tubers by modulation of plastid division, Plant Biotechnology Journal 4(1): 123-134.
- Maraschin S.F., Lamers G.E.M., Pater B.S. de, Spaink H.P. & Wang M. (2003), 14-3-3 isoforms and pattern formation during barley microspore embryogenesis, Journal of Experimental Botany 54(384): 1033-1043.
- Langeveld S.M.J., Vennik M., Kottenhage M., Wijk R. van, Buijk A., Kijne J.W. & Pater S. de (2002), Glucosylation activity and complex formation of two classes of reversibly glycosylated polypeptides, Plant Physiology 129(1): 278-289.
- Langeveld S.M.J., Wijk R. van, Stuurman N., Kijne J.W. & Pater B.S. de (2000), B-type granule containing protrusions and interconnection between amyloplasts in developing wheat endosperm revealed by transmission electron microscopy and GFP expression, Journal of Experimental Botany 51(349): 1357-1361.
- Pater B.S. de, Pham K., Memelink J. & Kijne J.W. (1997), RAP-1 is an Arabidopsis myc-like R protein homologue, that binds to G-box sequence motifs, Plant Molecular Biology 34(1): 169-174.
- Booij P., Demel R.A., Pater B.S. de & Kijne J.W. (1996), Insertion of pea lectin into phospholipid monolayer, Plant Molecular Biology 31(1): 169-173.
- Pater B.S. de, Pham K., Klitsie I. & Kijne J.W. (1996), The 22 bp W1 element in the pea lectin promoter is necessary and, as a multimer, sufficient for high gene expression in tobacco seeds, Plant Molecular Biology 32(3): 515-523.
- Pater B.S. de, Greco V., Pham K., Memelink J. & Kijne J. (1996), Characterization of a zinc-dependent transcriptional activator from Arabidopsos, Nucleic Acids Research 24(23): 4624-4631.
- Pater B.S. de, Pham K., Memelink J. & Kijne J.W. (1996), Binding specificity and tissue-specific expression pattern of the Arabdidopsis bZIP transcription factor TGA2, Molecular and General Genetics 250(2): 237-239.
- Eijsden R.R. van, Diaz C.L., Pater B.S. de & Kijne J.W. (1995), Sugar binding activity of pea (pisum sativum) lectin is essential for heterologous infection of transgenic white clover hairy roots by Rhizobium leguminosarum bivar viciae, Plant Molecular Biology 29(3): 431-439.
- Pater B.S. de, Katagiri F., Kijne J.W. & Chua N.H. (1994), bZIP proteins bind to a palindromic sequence without an ACGT core located in a seed‐specific element of the pea lectin promoter, The Plant Journal 6(2): 133-140.
- Pater B.S. de, Pham K., Chua N.H., Memelink J. & Kijne J.W. (1993), A 22-bp fragment of the pea lectin promoter containing essential TGAC-like motifs confers seed-specific gene expression, The Plant Cell 5(8): 877-886.
- Kijne J.W., Bakhuizen R., Brussel A.A.N. van, Canter Cremers H.C.J., Diaz C.L., Pater B.S. de, Smit G., Spaink H.P., Swart S., Wijffelman C.A. & Lugtenberg E.J.J. (1992), The Rhizobium trap: root hair curling in root-nodule symbiosis. In: Callow J.A. & Green J.R. (Eds.), Perspectives in Plant Cell Recognition: Cambridge University Press. 267-284.
- Eijsden R.R. van, Hoedemaeker F.J., Diaz C.L., Lugtenberg E.J.J., Pater B.S. de & Kijne J.W. (1992), Mutational analysis of pea lectin: substitution of Asn125 for Asp in the monosaccharide-binding site eliminates mannose/glucose-binding activity, Plant Molecular Biology 20(6): 1049-1058.
- Lugtenberg E.J.J., Diaz C., Smit G., Pater B.S. de & Kijne J.W. (1991), Roles of Lectin in the Rhizobium-legume symbiosis. In: Hennecke H. & Verma D.P.S. (Eds.), Advances in Molecular Genetics of Plant-Microbe Interactions. Current Plant Science and Biotechnology in Agriculture no. 10. Netherlands: Springer. 174-181.
- Pater B.S. de, Hensgens L.A.M. & Schilperoort R.A. (1990), Structure and expression of a light-inducible shoot-specific rice gene, Plant Molecular Biology 15(3): 399-406.
- Kijne J.W., Diaz C.L., Pater B.S. de, Smit G., Bakhuizen R. & Lugtenberg E.J.J. (1990), Surface interactions between rhizobia and legume root hairs. In: Gresshoff P.M., Roth L.E., Stacey G. & Newton W.E. (Eds.), Nitrogen fixation: achievements and objectives. New York: Chapman & Hall, Inc.. 187-192.
- Hoekema A., Pater B.S. de, Fellinger A.J., Hooykaas P.J.J. & Schilperoort R.A. (1984), The limited host range of an Agrobacterium tumefaciens strain extended by a cytokinin gene from a wide host range T-region, The EMBO Journal 3(13): 3043-3047.