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Plant Development & (Epi)Genetics

VU-affiliated Publications

Before moving to the UvA at Science Park in 2014, the Koes group was affiliated to the Free University (VU). Below an overview of their previously published work.

Kusters E, Della Pina S, Castel R, Souer E, Koes R. (2015)  Changes in cis-regulatory elements of a key floral regulator are associated with divergence of inflorescence architectures.  Development. 42(16):2822-31.Della Pina, S., E. Souer and R. Koes (2014). "Arguments in the evo-devo debate: say it with flowers!" J Exp Bot 65(9): 2231-2242.

Faraco, M., C. Spelt, M. Bliek, W. Verweij, A. Hoshino, L. Espen, B. Prinsi, R. Jaarsma, E. Tarhan, A. H. de Boer, G. P. Di Sansebastiano, R. Koes and F. M. Quattrocchio (2014). "Hyperacidification of vacuoles by the combined action of two different P-ATPases in the tonoplast determines flower color." Cell Rep 6(1): 32-43.

Provenzano, S., C. Spelt, S. Hosokawa, N. Nakamura, F. Brugliera, L. Demelis, D. P. Geerke, A. Schubert, Y. Tanaka, F. Quattrocchio and R. Koes (2014). "Genetics and evolution of anthocyanin methylation." Plant Physiol 165: 962-977.

Quattrocchio, F. M., C. Spelt and R. Koes (2013). "Transgenes and protein localization: myths and legends." Trends Plant Sci 18(9): 473-476.

Verhoef, N., T. Yokota, K. Shibata, G. J. de Boer, T. Gerats, M. Vandenbussche, R. Koes and E. Souer (2013). "Brassinosteroid biosynthesis and signalling in Petunia hybrida." J Exp Bot 64(8): 2435-2448.

Faraco, M., G. P. Di Sansebastiano, K. Spelt, R. Koes and F. M. Quattrocchio (2011). "One protoplast is not the other." Plant Physiol 156(2): 474-478.

Zenoni, S., N. D’Agostino, G. Tornielli, B., F. Quattrocchio, M. L. Chiusano, R. Koes, J. Zethof, F. Guzzo, M. Delledonne, L. Frusciante, T. Gerats and M. Pezzotti (2011). "Revealing impaired pathways in the an11 mutant by high-throughput characterization of Petunia axillaris and Petunia inflata transcriptomes." Plant Journal 68: 11-27.

Castel, R., E. Kusters and R. Koes (2010). "Inflorescence development in petunia: through the maze of botanical terminology." J Exp Bot 61(9): 2235-2246.

Koes, R., M. Bliek, R. Castel, E. Kusters, A. Procissi, A. Rebocho and I. Roobeek (2009). Development of the petunia inflorescence. Petunia: Evolutionary, Developmental and Physiological Genetics. T. Gerats and J. Strommer. Heidelberg, Springer: 179-198.

Tornielli, G., R. Koes and F. Quattrocchio (2009). The genetics of flower color. Petunia: Evolutionary, Developmental and Physiological Genetics. T. Gerats and J. Strommer. Heidelberg, Springer: 269-300.

Vandenbussche M, H. A., Zethof J, Koes R, Rijpkema AS, Gerats T (2009). "Differential recruitment of WOX transcription factors for lateral development and organ fusion in Petunia and Arabidopsis." Plant Cell 21(8): 2269-2283.

Koes, R. (2008). "Evolution and development of virtual inflorescences." Trends Plant Sci. 13(1): 1-3.

Rebocho, A. B., M. Bliek, E. Kusters, R. Castel, A. Procissi, I. Roobeek, E. Souer and R. Koes (2008). "Role of EVERGREEN in the development of the cymose petunia inflorescence." Dev Cell 15(3): 437-447.

Souer, E., A. B. Rebocho, M. Bliek, E. Kusters, R. A. de Bruin and R. Koes (2008). "Patterning of Inflorescences and Flowers by the F-Box Protein DOUBLE TOP and the LEAFY Homolog ABERRANT LEAF AND FLOWER of Petunia." Plant Cell 20: 2033-2048.

Tornielli, G. B., R. E. Koes and F. M. Quattrocchio (2008). The Genetcis of flower color. Petunia Monography. T. Gerats and J. Strommer, Elsevier..

Verweij, W., G. Di  Sansebastiano, F. Quattrocchio and G. Dalessandro (2008). "Advanced microscopy techniques as instruments for cell and tissue analysis in plants: Agrobacterium mediated transient expression of vacuolar GFPs in petunia leaves and petals." Plant Biosystems 142: 1-5.

Verweij, W., C. Spelt, G. P. Di Sansebastiano, J. Vermeer, L. Reale, F. Ferranti, R. Koes and F. Quattrocchio (2008). "An H + P-ATPase on the tonoplast determines vacuolar pH and flower colour." Nat Cell Biol 10(12): 1456-1462.

Baumann, K., M. Perez-Rodriguez, D. Bradley, J. Venail, P. Bailey, H. Jin, R. Koes, K. Roberts and C. Martin (2007). "Control of cell and petal morphogenesis by R2R3 MYB transcription factors." Development 134(9): 1691-1701.

Quattrocchio, F., A. Baudry, L. Lepiniec and E. Grotewold (2006). The regulation of flavonoid biosynthesis. The Science of Flavonoids. E. Grotewold. New York, Springer: 97-122.

Quattrocchio, F., W. Verweij, A. Kroon, C. Spelt, J. Mol and R. Koes (2006). "PH4 of petunia is an R2R3-MYB protein that activates vacuolar acidification through interactions with Basic-Helix-Loop-Helix transcription factors of the anthocyanin pathway." Plant Cell 18: 1274-1291.

Angenent, G. C., J. Stuurman, K. C. Snowden and R. Koes (2005). "Use of Petunia to unravel plant meristem functioning." Trends Plant Sci 10(5): 243-250.

Koes, R., C. W. Verweij and F. Quattrocchio (2005). "Flavonoids: a colorful model for the regulation and evolution of biochemical pathways." Trends Plant Sci. 5: 236-242.

Vandenbussche, M., J. Zethof, E. Souer, R. Koes, G. B. Tornielli, M. Pezzotti, S. Ferrario, G. C. Angenent and T. Gerats (2003). "Toward the analysis of the petunia MADS box gene family by reverse and forward transposon insertion mutagenesis approaches: B, C, and D floral organ identity functions require SEPALLATA-like MADS box genes in petunia." Plant Cell 15(11): 2680-2693.

Spelt, C., F. Quattrocchio, J. Mol and R. Koes (2002). " ANTHOCYANIN1 of petunia controls pigment synthesis, vacuolar pH, and seed coat development by genetically distinct mechanisms." Plant Cell 14(9): 2121-2135.

Tobeña-Santamaria, R., M. Bliek, K. Ljung, G. Sandberg, J. Mol, E. Souer and R. Koes (2002). "FLOOZY of petunia is a flavin monooxygenase-like protein required for the specification of leaf and flower architecture." Genes Dev 6(6): 753-763.

Brugliera, F. and R. Koes (2001). Plant anthocyanidin rutinoside aromatic acyl transferases, International Flower Developments.

Spelt, C., F. Quattrocchio, J. Mol and R. Koes (2000). " anthocyanin1 of petunia encodes a basic-Helix Loop Helix protein that directly activates structural anthocyanin genes." Plant Cell 12: 1619-1631.

de Bruin, R., K. Spelt, J. Mol, R. Koes and F. Quattrocchio (1999). "Selection of high-affinity phage antibodies from phage display libraries." Nature Biotechnology 17(April 1999): 397-399.

de Vetten, N., J. ter Horst, H.-P. van Schaik, B. den Boer, J. Mol and R. Koes (1999). "A cytochome b5 is required for full acivity of flavonoid 3'5'-hydroxylase, a cytochrome P450 involved in the formation of blue flower colors." Proc. Natl. Acad. Sci. USA. 96: 778-783.

Mol, J., E. Cornish, J. Mason and R. Koes (1999). "Novel coloured flowers." Curr Opin Biotechnol 10(2): 198-201.

Quattrocchio, F., J. Wing, K. van der Woude, E. Souer, N. de Vetten, J. Mol and R. Koes (1999). "Molecular analysis of the anthocyanin2 gene of Petunia and its role in the evolution of flower color." Plant Cell 11: 1433-1444.

van Houwelingen, A., E. Souer, J. N. M. Mol and R. E. Koes (1999). "Epigenetic interactions between three dTph1 transposons in two homologous chromosomes activates a new excision-repair mechanism in petunia." Plant Cell 11: 1319-1336.

Alfenito, M. R., E. Souer, C. D. Goodman, R. Buell, J. Mol, R. Koes and V. Walbot (1998). "Functional complementation of anthocyanin sequestration in the vacuole by widely divergent glutathione S-transferases." Plant Cell 10(7): 1135-1149.

Mol, J., E. Grotewold and R. Koes (1998). "How genes paint flowers and seeds." Trends Plant Sci. 3(6): 212-217.

Quattrocchio, F., J. F. Wing, K. van der Woude, J. N. M. Mol and R. Koes (1998). "Analysis of bHLH and MYB-domain proteins: species-specific regulatory differences are caused by divergent evolution of target anthocyanin genes." Plant J. 13(4): 475-488.

Souer, E., A. R. van der Krol, D. Kloos, C. Spelt, M. Bliek, J. Mol and R. Koes (1998). "Genetic control of branching pattern and floral identity during Petunia inflorescence development." Development 125: 733-742.

van Houwelingen, A., E. Souer, C. Spelt, D. Kloos, J. Mol and R. Koes (1998). "Analysis of flower pigmentation mutants generated by random transposon mutagenesis in Petunia hybrida." Plant J. 13: 39-50.

de Vetten, N., F. Quattrocchio, J. Mol and R. Koes (1997). "The an11 locus controlling flower pigmentation in petunia encodes a novel WD-repeat protein conserved in yeast, plants and animals." Genes Dev. 11: 1422-1434.

Souer, E., A. van Houwelingen, D. Kloos, J. N. M. Mol and R. Koes (1996). "The no apical meristem gene of petunia is required for pattern formation in embryos and flowers and is expressed at meristem and primordia boundaries." Cell 85: 159-170.

Koes, R., E. Souer, A. van Houwelingen, L. Mur, C. Spelt, F. Quattrocchio, J. F. Wing, B. Oppedijk, S. Ahmed, T. Maes, T. Gerats, P. Hoogeveen, M. Meesters, D. Kloos and J. N. M. Mol (1995). "Targeted gene inactivation in petunia by PCR-based selection of transposon insertion mutants." Proc. Natl. Acad. Sci. USA 81: 8149-8153.

Mol, J. N. M., T. A. Holton and R. E. Koes (1995). "Floriculture: genetic engineering of commercial traits." Tr. in Biotech. 13: 350-355.

Souer, E., F. Quattrocchio, N. de Vetten, J. N. M. Mol and R. E. Koes (1995). "A general method to isolate genes tagged by a high copy number transposable element." Plant J. 7: 677-685.

Huits, H. S. M., A. G. M. Gerats, M. M. Kreike, J. N. M. Mol and R. E. Koes (1994). "Genetic control of dihydroflavonol 4-reductase gene expression in Petunia hybrida." Plant J. 6(3): 295-310.

Huits, H. S. M., R. E. Koes, H. J. W. Wijsman and A. G. M. Gerats (1994). "Genetic characterization of Act1  the activator of a non-autonomous transposable element from Petunia hybrida." Theor. Appl. Genet. 91: 110-117.

Koes, R. E., F. Quattrocchio and J. N. M. Mol (1994). "The flavonoid biosynthetic pathway in plants: function and evolution." BioEssays 16(2): 123-132.

Kroon, J., E. Souer, A. de Graaff, Y. Xue, J. Mol and R. Koes (1994). "Cloning and structural analysis of the anthocyanin pigmentation locus Rt of Petunia hybrida: characterization of insertion sequences in two mutant alleles." Plant J. 5(1): 69-80.

Quattrocchio, F. (1994). Regulatory genes controlling flower pigmentation in Petunia hybrida, Vrije Universiteit, Amsterdam, The Netherlands.

Quattrocchio, F., J. F. Wing, H. T. C. Leppen, J. N. M. Mol and R. E. Koes (1993). "Regulatory genes controlling anthocyanin pigmentation are functionally conserved among plant species and have distinct sets of target genes." Plant Cell 5: 1497-1512.

Koes, R. E., R. Van Blokland, F. Quattrocchio, A. J. Van Tunen and J. N. M. Mol (1990). "Chalcone synthase promoters in petunia are active in pigmented and unpigmented cell types." Plant Cell 2: 379-392.

Quattrocchio, F., M. Tolk, I. Coraggio, J. N. M. Mol, A. Viotti and R. E. Koes (1990). "The maize zein gene zE19 contains two distinct promoters, which are independently activated in endosperm and anthers of transgenic Petunia plants." Plant Mol. Biol. 15: 81-93.

van Tunen, A. J., L. Mur, G. S. Brouns, J.-D. Rienstra, R. E. Koes and J. N. M. Mol (1990). "Pollen- and anther-specific chi  promoters from petunia: Tandem promoter regulation of the chiA gene." Plant Cell 2: 393-401.

Koes, R. E., C. E. Spelt and J. N. M. Mol (1989). "The chalcone synthase multigene family of Petunia hybrida (V30): Differential, light-regulated expression during flower development and UV light induction." Plant Mol. Biol. 12: 213-225.

Koes, R. E., C. E. Spelt, P. J. M. Van den Elzen and J. N. M. Mol (1989). "Cloning and molecular characterization of the chalcone synthase multigene family of Petunia hybrida." Gene. 81: 245-257.

Mol, J., R. Koes, R. van Blokland, A. van Tunen, A. van der Krol and A. Stuitje (1989). The potential use of the glucuronidase reporter gene and antisense technologies to unravel biological functions of flavonoids. Signal molecules in plants and plant-microbe interactions. B. Lugtenberg, Springer Verlag: 65-69.

Koes, R. E. (1988). Genes involved in flavonoid biosynthesis in Petunia hybrida: the chalcone synthase multigene family, Vrije Universiteit, Amsterdam, The Netherlands.

Mol, J. N. M., R. Koes and A. R. Stuitje (1988). Development of inducible gene expression systems for higher plants and cell cultures. Biomolecular Engineering in the EC. E. Magnien. 3: 441-446.

Mol, J. N. M., R. E. Koes, A. G. M. Gerats and A. R. Stuitje (1988). "Cloned genes of phenylpropanoid metabolism." Plant Mol. Biol. Rep. 6: 274-279.

van der Krol, A. R., P. E. Lenting, J. Veenstra, I. M. Van der Meer, R. E. Koes, A. G. M. Gerats, J. N. M. Mol and A. R. Stuitje (1988). "An anti-sense chalcone synthase gene in transgenic plants inhibits flower pigmentation." Nature 333: 866-869.

van Tunen, A. J., R. E. Koes, C. E. Spelt, A. R. Van der Krol, A. R. Stuitje and J. N. M. Mol (1988). "Cloning of the two chalcone flavanone isomerase genes from Petunia hybrida: Coordinate, light-regulated and differential expression of flavonoid genes." EMBO J. 7: 1257-1263.

Koes, R. E., C. E. Spelt, J. N. M. Mol and A. G. M. Gerats (1987). "The chalcone synthase multigene family of Petunia hybrida (V30): Sequence homology, chromosomal localization and evolutionary aspects." Plant Mol. Biol. 10: 375-385.

Mol, J. N. M., R. Koes and A. R. Stuitje (1987). Development of inducible gene expression systems for higher plants and cell cultures. Biomolecular Engineering in the EC. E. Magnien. 2: 741-746.

Koes, R. E., C. E. Spelt, H. J. Reif, P. J. van den Elzen, E. Veltkamp and J. N. Mol (1986). "Floral tissue of Petunia hybrida (V30) expresses only one member of the chalcone synthase multigene family." Nucleic Acids Res 14(13): 5229-5239.

Quattrocchio, F., E. Benvenuto, R. Tavazza, L. Cuozzo and G. Ancora (1986). "A study on the possible role of auxin in potato "hairy root" tissues." J. Plant Physiol. 123: 143-149.

Bovenberg, W. A., R. E. Koes, H. J. J. Nijkamp and A. J. Kool (1984). "Physical mapping nucleotide sequencing and expression in E. coli minicells of the gene for the large subunit of ribulose bisphosphate carboxylase from Petunia hybrida." Curr Genet 8: 231-241.