@Sprouting from the Root


 

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Publications (Selected Highlights)


Hong, J.H., Savina, M., Du, J., Devendran, A., Kannivadi Ramakanth, K., Tian, X., Sim, W.S., Mironova, V.V. and Xu, J.* (2017) A Sacrifice-for-survival mechanism protects root stem cell niche from chilling stress. Cell 170, 102-113.


Cruz-Ramírez, A., Díaz-Triviño, S., Blilou, I., Grieneisen, V.A., Sozzani, R., Zamioudis, C., Miskolczi, P., Nieuwland, J., Benjamins, R., Dhonukshe, P., Caballero-Pérez, J., Horvath, B., Long, Y.C., Mähonën, A.P., Zhang, H.T., Xu, J., Murray, J.A.H., Benfey, P.N., Bako, L., Marée, A.F.M.*, and Scheres, B.* (2012) A bistable circuit involving SCARECROW-RETINOBLASTOMA integrates cues to inform asymmetric stem cell division. Cell 150, 1002-1015.


Grieneisen, V.A., Xu, J., Maree, A.F.M., Hogeweg, P. and Scheres, B.* (2007) Auxin transport is sufficient to generate a maximum and gradient guiding root growth. Nature (Article) 449, 1008-1013.


Wisniewska, J., Xu, J., Seifertova, D., Brewer, P.B., Ruzicka, K., Blilou, I., Benkova, E., Scheres, B. and Friml, J.* (2006) Polar PIN localization directs auxin flow in plants. Science 312, 883.


Xu, J., Hofhuis, H., Heidstra, R., Sauer, M., Friml, J. and Scheres, B.* (2006) A molecular framework for plant regeneration. Science 311, 385-388. (Featured in Nature Reviews Molecular Cell Biology 7, 154, and Nature Reviews Genetics 7, 157.)


Blilou, I., Xu, J., Wildwater, M., Willemsen, W., Paponov, I., Friml, J., Heidstra, R., Aida, M., Palme, K. and Scheres, B.* (2005) The PIN auxin efflux facilitator network controls growth and patterning in Arabidopsis roots. Nature (Article) 433, 39-44.



Publications (Full List)


2017

Krishnamurthy, P., Mohanty, B., Wijaya, E., Lee, D.-Y., Lim, T.M., Lin, Q.S., Xu, J., Loh, C.S. and Kumar, P. (2017) Transcriptomics analysis of salt stress tolerance in the roots of the mangrove Avicennia officinalis. Sci Rep 7, 10031. DOI:10.1038/s41598-017-10730-2.


Ghosh, D., Lin, Q.Q., Xu, J. and Hellmann, H.A. (2017) Editorial: How plants deal with stress: exploration through proteome investigation. Front Plant Sci. DOI: 10.3389/fpls.2017.01176.


Hong, J.H., Savina, M., Du, J., Devendran, A., Kannivadi Ramakanth, K., Tian, X., Sim, W.S., Mironova, V.V. and Xu, J.* (2017) A Sacrifice-for-survival mechanism protects root stem cell niche from chilling stress. Cell 170, 102-113.


Zhang, Y., Yu, Q.Q., Jian, N., Yan, X., Wang, C., Wang, Q.M., Liu, J.Z., Zhu, M.Y., Bednarek, S.Y., Xu, J. and Pan, J.W. (2017) Clathrin regulates blue light-triggered lateral auxin distribution and hypocotylphototropism in Arabidopsis. Plant Cell Environ 40, 165-176.


2016

Lup, S.D., Tian, X., Xu, J. and Pérez-Pérez, J.M. (2016) Wound signaling of regenerative cell reprogramming. Plant Sci 250, 178-187.

Kareem, A., Radhakrishnan, D., Wang, X., Balamurugan, S., Trivedi, Z.B., Sugimoto, K., Xu, J., Mahonen, A.P. and Prasad, K. (2016) Protocol: a method to study direct reprogramming of lateral root primordia to fertile shoots. Plant Methods 12, 27.

Zhang, Y.H., Zheng, L.L., Hong, J.H., Gong, X.M., Zhou, C., Pérez-Pérez, J.M. and Xu, J. (2016) TOPOISOMERASE1α acts through two distinct mechanisms to regulate stele and columella stem cell maintenance. Plant Physiol 171, 483-493.


Gong, X., Flores-Vegara, M.A., Hong, J.H., Chu, H.W., Lim, J., Franks, R.G., Liu, Z.C. and Xu, J.* (2016) SEUSS integrates gibberellin signalling with transcriptional inputs from the SHR-SCR-SCL3 module to regulate middle cortex formation in the Arabidopsis root. Plant Physiol 170, 1675-1683.


2015

Seah, Y.F., El Farran, C.A., Warrier, T., Xu, J. and Loh Y.H. (2015) Induced pluripotency and gene editing in disease modelling: perspectives and challenges. Int J Mol Sci 16, 28614-28634.

Yu, Q.Q., Zhang, Y., Wang, J., Yan, X., Wang, C., Xu, J. and Pan, J.W. (2015) Clathrin-mediated auxin efflux and maxima regulate hypocotyl hook formation and light-stimulated hook opening in Arabidopsis. Mol Plant 9, 101-112.

Li, J.T., Zhao, Y.*, Chu, H.W., Wang, L.K., Fu, Y.R., Lu, P., Upadhyaya, N., Chen, C.L., Mou, T.M., Feng, Y.Q., Kumar, P. and Xu, J.* (2015) SHOEBOX modulates root meristem size in rice through dose-dependent effects of gibberellins on cell elongation and proliferation. PLoS Genet 11, e1005464. (Featured on the 
frontpage of the journal's website).


Hong, J.H., Chu, H.W., Zhang, C., Ghosh, D., Gong, X.M. and Xu, J. (2015) A quantitative analysis of stem cell homeostasis in the Arabidopsis columella root cap. Front Plant Sci 6, 206.


2014
Ahmadi, N., Audebert, A., Bennett, M.J., Bishopp, A., Costa de Oliveria, A., Courtois, B., Diedhiou, A., Diévart, A., Gantet, P., Ghesquière, A., Guiderdoni, E., Henry, A., Inukai, Y., Kochian, L., Laplaze, L., Lucas, M., Luu, D.T., Manneh, B., Mo, X., Muthurajan, R., Périn, C., Price, A., Robin, S., Sentenac, H., Sine, B., Uga, Y., Véry, A.,A., Wissuwa, M., Wu, P. and Xu, J. (2014) The roots of future rice harvests. Rice 7, 29.

Huang, J.B., Liu, H.L., Chen, M., Li, X.J., Wang, M.Y., Yang, Y.L., Wang, C.L., Huang, J.Q., Liu, G.L., Liu, Y.T., Xu, J., Cheung, A.Y. and Tao, L.Z. (2014) ROP3 GTPase contributes to polar auxin transport and auxin response and is important for embryogenesis and seedling growth in Arabidopsis. Plant Cell 26, 3501-3518.


Wang, L.K., Chu, H.W., Li, Z.Y., Wang, J., Li, J.T., Qiao, Y., Fu, Y.R., Mou, T.M., Chen, C.L. and Xu, J.(2014) Origin and development of the root cap in rice. Plant Physiol 166, 603-613.


Ghosh, D.* and Xu, J.* (2014) Abiotic stress responses in plant roots: a proteomics perspective. Front Plant Sci 5, 6.

Guo, J.Z., Wei, J., Xu, J. and Sun, M.X. (2014) Inducible knock-down of GNOM during root formation reveals tissue-specific response to auxin transport and its modulation of local auxin biosynthesis. J Exp Bot 65, 1165-1179.


2013
Chu, H.W., Liang, W.Q., Li, J., Hong, F., Wu, Y.F., Wang, L.K., Wang, J., Wu, P., Liu, C.M., Zhang, Q.F.,Xu, J.* and Zhang, D.B.* (2013) A CLE-WOX signaling module regulates root meristem maintenance and vascular tissue development in rice. J Exp Bot 64, 5359-5369.


Hong, J.H., Seah, S.W. and Xu, J. (2013) The root of ABA action in environmental stress response. Plant Cell Rep 32, 971-983.

Sassi, M.*, Wang, J., Ruberti, I., Vernoux, T.* and Xu, J.* (2013) Shedding light on auxin movement: light-regulation of polar auxin transport in the photocontrol of plant development. Plant Signal Behav 8, e23355.


2012
Sassi, M., Lu, Y., Zhang, Y.H., Wang, J., Dhonukshe, P., Blilou, I., Dai, M.Q., Li, J., Gong, X.M., Jaillais, Y., Yu, X.H., Traas, J., Ruberti, I., Wang, H.Y., Scheres, B., Vernoux, T.* and Xu, J.* (2012) COP1 mediates the coordination of root and shoot growth by light through modulation of PIN1 and PIN2-dependent auxin transport in Arabidopsis. Development 139, 3402-3412. (Featured in “in this issue” of the journal).

Cruz-Ramírez, A., Díaz-Triviño, S., Blilou, I., Grieneisen, V.A., Sozzani, R., Zamioudis, C., Miskolczi, P., Nieuwland, J., Benjamins, R., Dhonukshe, P., Caballero-Pérez, J., Horvath, B., Long, Y.C., Mähonën, A.P., Zhang, H.T., Xu, J., Murray, J.A.H., Benfey, P.N., Bako, L., Marée, A.F.M., and Scheres, B. (2012) A bistable circuit involving SCARECROW-RETINOBLASTOMA integrates cues to inform asymmetric stem cell division. Cell 150, 1002-1015.


Dai, M.Q., Zhang, C., Kania, U., Chen, F., Xue, Q., Mccray, T., Li, G., Qin, G.J., Wakeley, M., Terzaghi, W., Wan, J.M., Zhao, Y.D., Xu, J., Friml, J., Deng, X.W. and Wang, H.Y. (2012) A PP6-type phosphatase holoenzyme directly regulates PIN phosphorylation and auxin efflux in Arabidopsis. Plant Cell 24, 2497-2514.


Li, J., Chu, H.W., Zhang, Y.H., Mou, T.M., Wu, C.Y., Zhang, Q.F. and Xu, J. (2012) HGW encodes a ubiquitin-associated (UBA) domain protein regulating heading date and grain weight in rice. PLoS ONE 7, e34231.

2011
Zhou, X.J., Li, Q., Chen, X., Liu, J.P., Zhang, Q.H., Liu, Y.J., Liu, K.D.* and Xu, J.* (2011) The Arabidopsis RETARDED ROOT GROWTH gene encodes a mitochondria-localized protein that is required for normal cell division in the root meristem. Plant Physiol 157, 1793-1804.


2010
Zhou, W., Wei, L., Xu, J., Zhai, Q., Jiang, H., Chen, R., Chen, Q., Sun, J., Chu, J., Zhu, L., Liu, C.M., Li, C. (2010) Arabidopsis tyrosylprotein sulfotransferase acts in the auxin/PLETHORA pathway in regulating postembryonic maintenance of the root stem cell niche. Plant Cell 22, 3692-3709.


Dhonukshe, P., Huangm F., Galvan-Ampudia, C.S., Mähönen, A.P., Kleine-Vehn, J., Xu, J., Quint, A., Prasad, K., Friml, J., Scheres, B. and Offringa, R. (2010) Plasma membrane-bound AGC3 kinases phosphorylate PIN auxin carriers at TPRXS(N/S) motifs to direct apical PIN recycling. Development 137, 3245-3255.


2008
Willemsen, V., Bauch, M., Bennett, T., Campilho, A., Wolkenfelt, H., Xu, J., Haseloff, J. and Scheres, B. (2008) The NAC domain transcription factors FEZ and SOMBRERO control the orientation of the cell division plane in Arabidopsis root stem cells. Dev Cell 15, 913-922.


Dhonukshe, P., Tanaka, H., Goh, T., Ebine, K., Mahonen, A. P., Prasad, K., Blilou, I., Geldner, N., Xu, J., Uemura, T., Chory, J., Ueda, T., Nakano, A., Scheres, B. and Friml, J. (2008) Generation of cell polarity in plants links endocytosis, auxin distribution and cell fate decisions. Nature 456, 962-966.


2007
Grieneisen, V.A., Xu, J., Maree, A.F.M., Hogeweg, P. and Scheres, B. (2007) Auxin transport is sufficient to generate a maximum and gradient guiding root growth. Nature (Article) 449, 1008-1013.


2006
Scheres, B. and Xu, J. (2006) Polar auxin transport and patterning: grow with the flow. Genes Dev 20, 922-926.


Wisniewska, J., Xu, J., Seifertova, D., Brewer, P.B., Ruzicka, K., Blilou, I., Benkova, E., Scheres, B. and Friml, J. (2006) Polar PIN localization directs auxin flow in plants. Science 312, 883.


Xu, J., Hofhuis, H., Heidstra, R., Sauer, M., Friml, J. and Scheres, B. (2006) A molecular framework for plant regeneration. Science 311, 385-388. (Featured in Nature Reviews Molecular Cell Biology 7, 154, and Nature Reviews Genetics 7, 157.)


2005
Xu, J. 
and Scheres, B. (2005) Cell Polarity: ROPing the ends together. Curr Opin Plant Biol 8, 613-618.


Li, L., Xu, J., Xu, Z.H. and Xue, H.W. (2005) Brassinosteroids stimulate plant tropisms through modulation of polar auxin transport in Brassica and Arabidopsis. Plant Cell 17, 2738-2753.


Fiers, M., Golemiec, E., Xu, J., van der Geest, L., Heidstra, R., Stiekema, W. and Liu, C.M. (2005) The 14-Amino Acid CLV3, CLE19, and CLE40 peptides trigger consumption of the root meristem in Arabidopsis through a CLAVATA2-dependent pathway. Plant Cell 17, 2542-2553.


Xu, J. and Scheres, B. (2005) Dissection of Arabidopsis ADP-RIBOSYLATION FACTOR 1 function in epidermal cell polarity. Plant Cell 17, 525-536.


Blilou, I., Xu, J., Wildwater, M., Willemsen, W., Paponov, I., Friml, J., Heidstra, R., Aida, M., Palme, K. and Scheres, B. (2005) The PIN auxin efflux facilitator network controls growth and patterning in Arabidopsis roots. Nature (Article) 433, 39-44.


2003

Casamitjana-Martinez, E., Hofhuis, H.F., Xu, J., Liu, C.M., Heidstra, R. and Scheres, B. (2003) Root-specific CLE19 overexpression and the sol1/2 suppressors implicate a CLV-like pathway in the control of Arabidopsis root meristem maintenance. Curr Biol 13, 1435-1441.


Grebe, M., Xu, J., Mobius, W., Ueda, T., Nakano, A., Geuze, H.J., Rook, M.B. and Scheres, B. (2003) Arabidopsis sterolendocytosis involves actin-mediated trafficking via ARA6-positive early endosomes. Curr Biol 13, 1378-1387.


2001
Grebe, M., Xu, J. and Scheres, B. (2001) Cell axiality and polarity in plants–adding pieces to the puzzle. Curr Opin Plant Biol 4, 520-526.


1999
Yang, W.C., Ye, D., Xu, J. and Sundaresan, V. (1999) The SPOROCYTELESS gene of Arabidopsis is required for initiation of sporogenesis and encodes a novel nuclear protein. Genes Dev 13, 2108-2117.


Book chapters
Xu, J. and Hong, J.H. (2013) Root Development. In Genetics and Genomics of Rice (Zhang, Q. and Wing, R.A. eds). Springer Science.


Xu, J. (2012) Plant root: structure, development, and physiological function. In Plant Physiology and Molecular Biology (4th ed., Chen, X.Y. and Xue, H.W. eds). Higher Education Press. (in Chinese).


Xu, J. (2012) Hormonal control of root development. In Plant Hormones: Function and Molecular Mechanism (Xu, Z.H. and Xue, H.W. eds). Shanghai Scientific & Technical Publishers. (in Chinese).


* Co-correspondence authors