Growth and Development of higher plants

Lessa Alvim Kamei, C., Van den Daele, H., Vandepoele, K., Maes, S., Boruc, J., Russinova, E., Inzé, D., and De Veylder, L. (2008). The PRA1 gene family in Arabidopsis. Plant Physiol. 147, 1735-1749.

De Grauwe, L., Chaerle, L., Dugardeyn, J., Decat, J., Rieu, I., Vriezen, W.H., Baghour, M., Moritz, T., Beemster, G.T.S., Phillips, A.L., Harberd, N.P., Hedden, P., and Van Der Straeten, D. (2008). Reduced gibberellin response affects ethylene biosynthesis and responsiveness in the Arabidopsis gai eto2-1 double mutant. New Phytol. 177, 128-141 [Err. 178, 457].

Swarup, K., Benková, E., Swarup, R., Casimiro, I., Péret, B., Yang, Y., Parry, G., Nielsen, E., De Smet, I., Vanneste, S., Levesque, M.P., Carrier, D., James, N., Calvo, V., Ljung, K., Kramer, E., Roberts, R., Graham, N., Marillonnet, S., Patel, K., Jones, J.D.G., Taylor, C.G., Schachtman, D.P., May, S., Sandberg, G., Benfey, P., Friml, J., Kerr, I., Beeckman, T., Laplaze, L., and Bennett, M.J. (2008). The auxin influx carrier LAX3 promotes lateral root emergence. Nat. Cell Biol. 10, 946-954.

Ubeda-Tomás, S., Swarup, R., Coates, J., Swarup, K., Laplaze, L., Beemster, G.T.S., Hedden, P., Bhalerao, R., and Bennett, M.J. (2008). Root growth in Arabidopsis requires gibberellin/DELLA signalling in the endodermis. Nat. Cell Biol. 10, 625-628.

Berckmans, B., and De Veylder, L. (2009). Transcriptional control of the cell cycle. Curr. Opin. Plant Biol. 12, 599-605.

Boudolf, V., Lammens, T., Boruc, J., Van Leene, J., Van Den Daele, H., Maes, S., Van Isterdael, G., Russinova, E., Kondorosi, E., Witters, E., De Jaeger, G., Inzé, D., and De Veylder, L. (2009). CDKB1;1 forms a functional complex with CYCA2;3 to suppress endocycle onset. Plant Physiol. 150, 1482-1493.

de Almeida Engler, J., De Veylder, L., De Groodt, R., Rombauts, S., Boudolf, V., De Meyer, B., Hemerly, A., Ferreira, P., Beeckman, T., Karimi, M., Hilson, P., Inzé, D., and Engler, G. (2009). Systematic analysis of cell-cycle gene expression during Arabidopsis development. Plant J. 59, 645-660.

De Rybel, B., Audenaert, D., Beeckman, T., and Kepinski, S. (2009). The past, present and future of chemical biology in auxin research. ACS Chem. Biol. 4, 987-998.

De Rybel, B., Audenaert, D., Vert, G., Rozhon, W., Mayerhofer, J., Peelman, F., Coutuer, S., Denayer, T., Jansen, L., Nguyen, L., Vanhoutte, I., Beemster, G.T.S., Vleminckx, K., Jonak, C., Chory, J., Inzé, D., Russinova, E., and Beeckman, T. (2009). Chemical inhibition of a subset of Arabidopsis thaliana GSK3-like kinases activates brassinosteroid signaling. Chem. Biol. 16, 594-604.

De Smet, I., Voß, U., Jürgens, G., and Beeckman, T. (2009). Receptor-like kinases shape the plant. Nat. Cell Biol. 11, 1166-1173.

Dissmeyer, N., Weimer, A.K., Pusch, S., De Schutter, K., Lessa Alvim Kamei, C., Nowack, M.K., Novak, B., Duan, G. L., Zhu, Y. G., De Veylder, L., and Schnittger, A. (2009). Control of cell proliferation, organ growth, and DNA damage response operate independently of dephosphorylation of the Arabidopsis Cdk1 homolog CDKA;1. Plant Cell 21, 3641-3654.

Gonzalez, N., Beemster, G.T.S., and Inzé, D. (2009). David and Goliath: what can the tiny weed Arabidopsis teach us to improve biomass production in crops? Curr. Opin. Plant Biol. 12, 157-164.

Horiguchi, G., Gonzalez, N., Beemster, G.T.S., Inzé, D., and Tsukaya, H. (2009). Impact of segmental chromosomal duplications on leaf size in the grandifolia-D mutants of Arabidopsis thaliana. Plant J. 60, 122-133.

Péret, B., De Rybel, B., Casimiro, I., Benková, E., Swarup, R., Laplaze, L., Beeckman, T., and Bennett, M.J. (2009). Arabidopsis lateral root development: an emerging story. Trends Plant Sci. 14, 399-408.

Rojas, C.A., Barbosa Eloy, N., de Freitas Lima, M., Lopes Rodrigues, R., Ozório Franco, L., Himanen, K., Beemster, G.T.S., Silva Hemerly, A., and Cavalcanti Gomes Ferreira, P. (2009). Overexpression of the Arabidopsis anaphase promoting complex subunit CDC27a increases growth rate and organ size. Plant Mol Biol. 71, 307-318.

Ubeda-Tomás, S., Federici, F., Casimiro, I., Beemster, G.T.S., Bhalerao, R., Swarup, R., Doerner, P., Haseloff, J., and Bennett, M.J. (2009). Gibberellin signalling in the endodermis controls Arabidopsis root meristem size. Curr. Biol. 19, 1194-1199.

Van Der Kelen, K., Beyaert, R., Inzé, D., and De Veylder, L. (2009). Translational control of eukaryotic gene expression. Crit. Rev. Biochem. Mol. Biol. 44, 143-168.

Vandepoele, K., Quimbaya, M., Casneuf, T., De Veylder, L., and Van de Peer, Y. (2009). Unraveling transcriptional control in Arabidopsis using cis-regulatory elements and coexpression networks. Plant Physiol. 150, 535-546.

Boruc, J., Van den Daele, H., Hollunder, J., Rombauts, S., Mylle, E., Hilson, P., Inzé, D., De Veylder, L., and Russinova, E. (2010). Functional modules in the Arabidopsis core cell cycle binary protein-protein interaction network. Plant Cell 22, 1264-1280.

Cools, T., Iantcheva, A., Maes, S., Van Den Daele, H., and De Veylder, L. (2010). A replication stress-induced synchronization method for Arabidopsis thaliana root meristems. Plant J. 64, 705-714.

De Bodt, S., Carvajal, D., Hollunder, J., Van den Cruyce, J., Movahedi, S., and Inzé, D. (2010). CORNET: a user-friendly tool for data mining and integration. Plant Physiol. 152, 1167-1179.

De Rybel, B., Vassileva, V., Parizot, B., Demeulenaere, M., Grunewald, W., Audenaert, D., Van Campenhout, J., Overvoorde, P., Jansen, L., Vanneste, S., Möller, B., Wilson, M., Holman, T., Van Isterdael, G., Brunoud, G., Vuylsteke, M., Vernoux, T., De Veylder, L., Inzé, D., Weijers, D., Bennett, M.J., and Beeckman, T. (2010). A novel Aux/IAA28 signaling cascade activates GATA23-dependent specification of lateral root founder cell identity. Curr. Biol. 20, 1697-1706.

De Smet, I., Lau, S., Voß, U., Vanneste, S., Benjamins, R., Rademacher, E.H., Schlereth, A., De Rybel, B., Vassileva, V., Grunewald, W., Naudts, M., Levesque, M.P., Ehrishmann, J.S., Inzé, D., Luschnig, C., Benfey, P.N., Weijers, D., Van Montagu, M.C.E., Bennett, M.J., Jürgens, G., and Beeckman, T. (2010). Bimodular auxin response controls organogenesis in Arabidopsis. Proc. Natl. Acad. Sci. USA 107, 2705-2710.

Den Herder, G., Van Isterdael, G., Beeckman, T., and De Smet, I. (2010). The roots of a new green revolution. Trends Plant Sci. 15, 600-607.

Dhondt, S., Coppens, F., De Winter, F., Swarup, K., Merks, R.M.H., Inzé, D., Bennett, M.J., and Beemster, G.T.S. (2010). SHORT-ROOT and SCARECROW regulate leaf growth in Arabidopsis by stimulating S-phase progression of the cell cycle. Plant Physiol. 154, 1183-1195.

Dhondt, S., Vanhaeren, H., Van Loo, D., Cnudde, V., and Inzé, D. (2010). Plant structure visualization by high-resolution X-ray computed tomography. Trends Plant Sci. 15, 419-422.

Gaamouche, T., de O. Manes, C.-L., Kwiatkowska, D., Berckmans, B., Koumproglou, R., Maes, S., Beeckman, T., Vernoux, T., Doonan, J.H., Traas, J., Inzé, D., and De Veylder, L. (2010). Cyclin-dependent kinase activity retains the shoot apical meristem cells in an undifferentiated state. Plant J. 64, 26-37.

Gonzalez, N., De Bodt, S., Sulpice, R., Jikumaru, Y., Chae, E., Dhont, S., Van Daele, T., De Milde, L., Weigel, D., Kamiya, Y., Stitt, M., Beemster, G.T.S., and Inzé, D. (2010). Increased leaf size: different means to an end. Plant Physiol. 153, 1261-1279.

Hermans, C., Vuylsteke, M., Coppens, F., Cristescu, S., Harren, F.M., Inzé, D., and Verbruggen, N. (2010). Systems analysis of the responses to long-term magnesium deficiency and restoration in Arabidopsis thaliana. New Phytol. 187, 132-144.

Hermans, C., Vuylsteke, M., Coppens, F., Craciun, A., Inzé, D., and Verbruggen, N. (2010). Early transcriptomic changes induced by magnesium deficiency in Arabidopsis thaliana reveal the alteration of circadian clock gene expression in roots and the triggering of abscisic acid-responsive genes. New Phytol. 187, 119-131.

Overvoorde, P., Fukaki, H., and Beeckman, T. (2010). Auxin control of root development. Cold Spring Harbor Perspect. Biol. 2, a001537.

Parizot, B., De Rybel, B., and Beeckman, T. (2010). VisuaLRTC: a new view on lateral root initiation by combining specific transcriptome datasets. Plant Physiol. 153, 34-40.

Skirycz, A., and Inzé, D. (2010). More from less: plant growth under limited water. Curr. Opin. Biotechnol. 21, 197-203.

Skirycz, A., De Bodt, S., Obata, T., De Clercq, I., Claeys, H., De Rycke, R., Andriankaja, M., Van Aken, O., Van Breusegem, F., Fernie, A.R., and Inzé, D. (2010). Developmental stage specificity and the role of mitochondrial metabolism in the response of Arabidopsis leaves to prolonged mild osmotic stress. Plant Physiol. 152, 226-244.

Takahashi, N., Quimbaya, M., Schubert, V., Lammens, T., Vandepoele, K., Schubert, I., Matsui, M., Inzé, D., Berx, G., De Veylder, L. (2010). The MCM-binding protein ETG1 aids sister chromatid cohesion required for postreplicative homologous recombination repair. PLoS Genet. 6, e1000817.

Van Leene, J., Hollunder, J., Eeckhout, D., Persiau, G., Van De Slijke, E., Stals, H., Van Isterdael, G., Verkest, A., Neirynck, S., Buffel, Y., De Bodt, S., Maere, S., Laukens, K., Pharazyn, A., Ferreira, P.C.G., Eloy, N., Renne, C., Meyer, C., Faure, J.-D., Steinbrenner, J., Beynon, J., Larkin, J.C., Van de Peer, Y.., Hilson, P., Kuiper, M., De Veylder, L., Van Onckelen, H., Inzé, D., Witters, E., and De Jaeger, G. (2010). Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana. Mol. Syst. Biol. 6, 397.1-397.12.

Vandenbussche, F., Petrášek, J., Žadníková, P., Hoyerová, K. Pešek, B., Raz, V., Swarup, R., Bennett, M., Zažimalová, Z., Benková, E., and Van Der Straeten, D. (2010). The auxin influx carriers AUX1 and LAX3 are involved in auxin-ethylene interactions during apical hook development in Arabidopsis thaliana seedlings. Development 137, 597-606.

Vanhaeren, H., Gonzalez, N., and Inzé, D. (2010). Hide and seek: uncloaking the vegetative shoot apex of Arabidopsis thaliana. Plant J. 63, 541-548.

Žadníková, P., Petrášek, J., Marhavý, P., Raz, V., Vandenbussche, F., Ding, Z., Schwarzerová, K., Morita, M.T., Tasaka, M., Hejátko, J., Van Der Straeten, D., Friml, J., and Benková, E. (2010). Role of PIN-mediated auxin efflux in apical hook development of Arabidopsis thaliana. Development 137, 607-617.

De Smet, I., and Beeckman, T. (2011). Asymmetric cell division in land plants and algae: the driving force for differentiation. Nat. Rev. Mol. Cell Biol. 12, 177-188.

Roppolo, D., De Rybel, B., Dénervaud Tendon, V., Pfister, A., Alassimone, J., Vermeer, J.E.M., Yamazaki, M., Stierhof, Y.-D., Beeckman, T., and Geldner, N. (2011). A novel protein family mediates Casparian strip formation in the endodermis. Nature 473, 380-383.

Skirycz, A., Vandenbroucke, K., Clauw, P., Maleux, K., De Meyer, B., Dhondt, S., Pucci, A., Gonzalez, N., Hoeberichts, F., Tognetti, V.B., Galbiati, M., Tonelli, C., Van Breusegem, F., Vuylsteke, M., and Inzé, D. (2011). Survival and growth of Arabidopsis plants given limited water are not equal. Nat. Biotechnol. 29, 212-214.

Skirycz, A., Claeys, H., De Bodt, S., Oikawa, A., Shinoda, S., Andriankaja, M., Maleux, K., Barbosa Eloy, N., Coppens, F., Yoo, S.-D., Saito, K., and Inzé, D. (2011). Pause-and-stop: the effects of osmotic stress on cell proliferation during early leaf development in Arabidopsis and a role for ethylene signaling in cell cycle arrest. Plant Cell 23, 1876-1888.

Cools, T., Iantcheva, A., Weimer, A.K., Boens, S., Takahashi, N., Maes, S., Van den Daele, H., Van Isterdael, G., Schnittger, A., and De Veylder, L. (2011). The Arabidopsis thaliana checkpoint kinase WEE1 protects against premature vascular differentiation during replication stress. Plant Cell 23, 1435-1448.

Hermans, C., Chen, J., Coppens, F., Inzé, D., and Verbruggen, N. (2011). Low magnesium status in plants enhances tolerance to cadmium exposure. New Phytol. 192, 428-436.

Radziejwoski, A., Vlieghe, K., Lammens, T., Berckmans, B., Maes, S., Jansen, M.A.K., Knappe, C., Albert, A., Seidlitz, H.K., Bahnweg, G., Inzé, D., and De Veylder, L. (2011). Atypical E2F activity coordinates PHR1 photolyase gene transcription with endoreduplication onset. EMBO J. 30, 355-363.

Vanneste, S., Coppens, F., Lee, E., Donner, T.J., Xie, Z., Van Isterdael, G., Dhondt, S., De Winter, F., De Rybel, B., Vuylsteke, M., De Veylder, L., Friml, J., Inzé, D., Grotewold, E., Scarpella, E., Sack, F., Beemster, G.T.S., and Beeckman, T. (2011). Developmental regulation of CYCA2s contributes to tissue-specific proliferation in Arabidopsis. EMBO J. 30, 3430-3441.

De Smet, I., Voß, U., Lau, S., Wilson, M., Shao, N., Timme, R.E., Swarup, R., Kerr, I., Hodgman, C., Bock, R., Bennett, M., Jürgens, G., and Beeckman, T. (2011). Unraveling the evolution of auxin signaling. Plant Physiol. 155, 209-221.

Merks, R.M.H., Guravage, M., Inzé, D., and Beemster, G.T.S. (2011). VirtualLeaf: an open source framework for cell-based modeling of plant tissue growth and development. Plant Physiol. 155, 656-666.

Vercruyssen, L., Gonzalez, N., Werner, T., Schmülling, T., and Inzé, D. (2011). Combining enhanced root and shoot growth reveals crosstalk between pathways that control plant organ size in Arabidopsis. Plant Physiol. 155, 1339-1352.

Stes, E., Biondi, S., Holsters, M., and Vereecke, D. (2011). Bacterial and plant signal integration via D3-type cyclins enhances symptom development in the Arabidopsis–Rhodococcus fascians interaction. Plant Physiol. 156, 712-725.

Kheibarshekan Asl, L., Dhondt, S., Boudolf, V., Beemster, G.T.S., Beeckman, T., Inzé, D., Govaerts, W., and De Veylder, L. (2010). Model-based analysis of Arabidopsis leaf epidermal cells reveals distinct division and expansion patterns for pavement and guard cells. Plant Physiol. 156, 2172-2183.

Skirycz, A., Memmi, S., De Bodt, S., Maleux, K., Obata, T., Fernie, A.R., Devreese, B., and Inzé, D. (2011). A reciprocal 15N-labeling proteomic analysis of expanding Arabidopsis leaves subjected to osmotic stress indicates importance of mitochondria in preserving plastid functions. J. Proteome Res. 10, 1018-1027.

In press

Berckmans, B., Vassileva, V., Schmid, S.P.C., Maes, S., Parizot, B., Naramoto, S., Magyar, Z., Lessa Alvim Kamei, C., Bögre, L., Koncz, C., Persiau, G., De Jaeger, G., Friml, J., Simon, R., Beeckman, T, and De Veylder, L. (2011). Auxin-dependent cell cycle reactivation through transcriptional control of E2Fa by LATERAL ORGAN BOUNDARY proteins. Plant Cell, in press.

De Veylder, L., Larkin, J., and Schnittger, A. (2011). Molecular control of endoreduplication in development and physiology. Trends Plant Sci., in press.

Sasabe, M., Boudolf, V., De Veylder, L., Inzé, D., Genschik, P., and Machida, Y. (2011). Phosphorylation of a mitotic kinesin-like protein and a MAPKKK by CDKs is involved in the transition to cytokinesis in plants. Proc. Natl. Acad. Sci. USA, in press.

Eloy, N.B., de Freitas Lima, M., Van Damme, D., Vanhaeren, H., Gonzalez, N., De Milde, L., Hemerly, A.S., Beemster, G.T.S., Inzé, D., and Ferreira, P.C.G. (2011). The APC/C subunit 10 plays an essential role in cell proliferation during leaf development. Plant J., in press.

Heckmann, S., Lermontova, I., Berckmans, B., De Veylder, L., Bäumlein, H., and Schubert, I. (2011). The E2F transcription factor family regulates CENH3 expression in Arabidopsis thaliana. Plant J., in press.

Dhondt, S., Van Haerenborgh, D., Van Cauwenbergh, C., Merks, R.M.H., Philips, W., Beemster, G.T.S., and Inzé, D. (2011). Quantitative analysis of venation patterns of Arabidopsis leaves by supervised image analysis. Plant J., in press.

Berckmans, B., Lammens, T., Van Den Daele, H., Magyar, Z., Bögre, L., and De Veylder, L. (2011). Light-dependent regulation of DEL1 is determined by the antagonistic action of E2Fb and E2Fc. Plant Physiol., in press.

Vannerum, K., Huysman, M.J.J., De Rycke, R., Vuylsteke, M., Leliaert, F., Pollier, J., Lütz-Meindl, U., Gillard, J., De Veylder, L., Goossens, A., Inzé, D., and Vyverman, W. (2011). Transcriptional analysis of cell growth and morphogenesis in Micrasterias (Streptophyta) provides insight into the evolution of expansins in the green algal progenitors of land plants. BMC Plant Biol., in press.