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Nat Plants. 2021 Nov;7(11):1485-1494. doi: 10.1038/s41477-021-01017-6. Epub 2021 Nov 15.

Non-cell autonomous and spatiotemporal signalling from a tissue organizer orchestrates root vascular development.

Nature plants

BaoJun Yang, Max Minne, Federica Brunoni, Lenka Plačková, Ivan Petřík, Yanbiao Sun, Jonah Nolf, Wouter Smet, Kevin Verstaen, Jos R Wendrich, Thomas Eekhout, Klára Hoyerová, Gert Van Isterdael, Jurgen Haustraete, Anthony Bishopp, Etienne Farcot, Ondřej Novák, Yvan Saeys, Bert De Rybel

Affiliations

  1. Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium. [email protected].
  2. VIB Center for Plant Systems Biology, Ghent, Belgium. [email protected].
  3. Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
  4. VIB Center for Plant Systems Biology, Ghent, Belgium.
  5. Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences and Faculty of Science of Palacký University, Olomouc, Czech Republic.
  6. Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium.
  7. VIB Center for Inflammation Research, Data Mining and Modelling for Biomedicine, Ghent, Belgium.
  8. Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czech Republic.
  9. VIB Flow Core, VIB Center for Inflammation Research, Ghent, Belgium.
  10. Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
  11. VIB Protein Service Facility, VIB Center for Inflammation Research, Ghent, Belgium.
  12. School of Biosciences, University of Nottingham, Loughborough, UK.
  13. School of Mathematical Sciences, University of Nottingham, Nottingham, UK.
  14. Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium. [email protected].
  15. VIB Center for Plant Systems Biology, Ghent, Belgium. [email protected].

PMID: 34782768 DOI: 10.1038/s41477-021-01017-6

Abstract

During plant development, a precise balance of cytokinin is crucial for correct growth and patterning, but it remains unclear how this is achieved across different cell types and in the context of a growing organ. Here we show that in the root apical meristem, the TMO5/LHW complex increases active cytokinin levels via two cooperatively acting enzymes. By profiling the transcriptomic changes of increased cytokinin at single-cell level, we further show that this effect is counteracted by a tissue-specific increase in CYTOKININ OXIDASE 3 expression via direct activation of the mobile transcription factor SHORTROOT. In summary, we show that within the root meristem, xylem cells act as a local organizer of vascular development by non-autonomously regulating cytokinin levels in neighbouring procambium cells via sequential induction and repression modules.

© 2021. The Author(s), under exclusive licence to Springer Nature Limited.

References

  1. Lucas, W. J. et al. The plant vascular system: evolution, development and functions. J. Integr. Plant Biol. 55, 294–388 (2013). - PubMed
  2. De Rybel, B., Mähönen, A. P., Helariutta, Y. & Weijers, D. Plant vascular development: from early specification to differentiation. Nat. Rev. Mol. Cell Biol. 17, 30–40 (2016). - PubMed
  3. Bishopp, A. et al. A mutually inhibitory interaction between auxin and cytokinin specifies vascular pattern in roots. Curr. Biol. 21, 917–926 (2011). - PubMed
  4. De Rybel, B. et al. Plant development. Integration of growth and patterning during vascular tissue formation in Arabidopsis. Science 345, 1255215 (2014). - PubMed
  5. Ohashi-Ito, K. et al. A bHLH complex activates vascular cell division via cytokinin action in root apical meristem. Curr. Biol. 24, 2053–2058 (2014). - PubMed
  6. De Rybel, B. et al. A bHLH complex controls embryonic vascular tissue establishment and indeterminate growth in Arabidopsis. Dev. Cell 24, 426–437 (2013). - PubMed
  7. Katayama, H. et al. A negative feedback loop controlling bHLH complexes is involved in vascular cell division and differentiation in the root apical meristem. Curr. Biol. 25, 3144–3150 (2015). - PubMed
  8. Ohashi-Ito, K. & Bergmann, D. C. Regulation of the Arabidopsis root vascular initial population by LONESOME HIGHWAY. Development 134, 2959–2968 (2007). - PubMed
  9. Ohashi-Ito, K., Matsukawa, M. & Fukuda, H. An atypical bHLH transcription factor regulates early xylem development downstream of auxin. Plant Cell Physiol. 54, 398–405 (2013). - PubMed
  10. Ohashi-Ito, K., Oguchi, M., Kojima, M., Sakakibara, H. & Fukuda, H. Auxin-associated initiation of vascular cell differentiation by LONESOME HIGHWAY. Development 140, 765–769 (2013). - PubMed
  11. Vera-Sirera, F. et al. A bHLH-based feedback loop restricts vascular cell proliferation in plants. Dev. Cell 35, 432–443 (2015). - PubMed
  12. Miyashima, S. et al. Mobile PEAR transcription factors integrate positional cues to prime cambial growth. Nature 565, 490–494 (2019). - PubMed
  13. Smet, W. et al. DOF2.1 controls cytokinin-dependent vascular cell proliferation downstream of TMO5/LHW. Curr. Biol. 29, 520–529.e6 (2019). - PubMed
  14. Wybouw, B. & De Rybel, B. Cytokinin - a developing story. Trends Plant Sci. 24, 177–185 (2019). - PubMed
  15. Kuroha, T. et al. Functional analyses of LONELY GUY cytokinin-activating enzymes reveal the importance of the direct activation pathway in Arabidopsis. Plant Cell 21, 3152–3169 (2009). - PubMed
  16. Tokunaga, H. et al. Arabidopsis lonely guy (LOG) multiple mutants reveal a central role of the LOG-dependent pathway in cytokinin activation. Plant J. 69, 355–365 (2012). - PubMed
  17. Mähönen, A. P. et al. A novel two-component hybrid molecule regulates vascular morphogenesis of the Arabidopsis root. Genes Dev. 14, 2938–2943 (2000). - PubMed
  18. Wendrich, J. R. et al. Vascular transcription factors guide plant epidermal responses to limiting phosphate conditions. Science 370, eaay4970 (2020). - PubMed
  19. Xu, Z. et al. Functional genomic analysis of Arabidopsis thaliana glycoside hydrolase family 1. Plant Mol. Biol. 55, 343–367 (2004). - PubMed
  20. Leah, R., Kigel, J., Svendsen, I. & Mundy, J. Biochemical and molecular characterization of a barley seed beta-glucosidase. J. Biol. Chem. 270, 15789–15797 (1995). - PubMed
  21. Dharmawardhana, D. P., Ellis, B. E. & Carlson, J. E. A beta-glucosidase from lodgepole pine xylem specific for the lignin precursor coniferin. Plant Physiol. 107, 331–339 (1995). - PubMed
  22. Brzobohatý, B. et al. Release of active cytokinin by a beta-glucosidase localized to the maize root meristem. Science 262, 1051–1054 (1993). - PubMed
  23. Weijers, D. et al. An Arabidopsis Minute-like phenotype caused by a semi-dominant mutation in a RIBOSOMAL PROTEIN S5 gene. Development 128, 4289–4299 (2001). - PubMed
  24. Bartrina, I., Otto, E., Strnad, M., Werner, T. & Schmülling, T. Cytokinin regulates the activity of reproductive meristems, flower organ size, ovule formation, and thus seed yield in Arabidopsis thaliana. Plant Cell 23, 69–80 (2011). - PubMed
  25. Zurcher, E. et al. A robust and sensitive synthetic sensor to monitor the transcriptional output of the cytokinin signaling network in planta. Plant Physiol. 161, 1066–1075 (2013). - PubMed
  26. Werner, T., Motyka, V., Strnad, M. & Schmülling, T. Regulation of plant growth by cytokinin. Proc. Natl Acad. Sci. USA 98, 10487–10492 (2001). - PubMed
  27. Matsumoto-Kitano, M. et al. Cytokinins are central regulators of cambial activity. Proc. Natl Acad. Sci. USA 105, 20027–20031 (2008). - PubMed
  28. Schmülling, T. et al. Structure and function of cytokinin oxidase/dehydrogenase genes of maize, rice, Arabidopsis and other species. J. Plant Res. 116, 241–252 (2003). - PubMed
  29. Lee, D. J. et al. Genome-wide expression profiling of ARABIDOPSIS RESPONSE REGULATOR 7(ARR7) overexpression in cytokinin response. Mol. Genet. Genomics 277, 115–137 (2007). - PubMed
  30. Rashotte, A. M., Carson, S. D., To, J. P. & Kieber, J. J. Expression profiling of cytokinin action in Arabidopsis. Plant Physiol. 132, 1998–2011 (2003). - PubMed
  31. Cui, H. et al. Genome-wide direct target analysis reveals a role for SHORT-ROOT in root vascular patterning through cytokinin homeostasis. Plant Physiol. 157, 1221–1231 (2011). - PubMed
  32. Marquès-Bueno, M. D. M. et al. A versatile Multisite Gateway-compatible promoter and transgenic line collection for cell type-specific functional genomics in Arabidopsis. Plant J. 85, 320–333 (2016). - PubMed
  33. Levesque, M. P. et al. Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis. PLoS Biol. 4, e143 (2006). - PubMed
  34. Mellor, N. et al. Theoretical approaches to understanding root vascular patterning: a consensus between recent models. J. Exp. Bot. 68, 5–16 (2017). - PubMed
  35. Mähönen, A. P. et al. Cytokinin signaling and its inhibitor AHP6 regulate cell fate during vascular development. Science 311, 94–98 (2006). - PubMed
  36. Help, H., Mahonen, A. P., Helariutta, Y. & Bishopp, A. Bisymmetry in the embryonic root is dependent on cotyledon number and position. Plant Signal. Behav. 6, 1837–1840 (2011). - PubMed
  37. Helariutta, Y. et al. The SHORT-ROOT gene controls radial patterning of the Arabidopsis root through radial signaling. Cell 101, 555–567 (2000). - PubMed
  38. Nakajima, K., Sena, G., Nawy, T. & Benfey, P. N. Intercellular movement of the putative transcription factor SHR in root patterning. Nature 413, 307–311 (2001). - PubMed
  39. Sozzani, R. et al. Spatiotemporal regulation of cell-cycle genes by SHORTROOT links patterning and growth. Nature 466, 128–132 (2010). - PubMed
  40. Möller, B. K. et al. Auxin response cell-autonomously controls ground tissue initiation in the early Arabidopsis embryo. Proc. Natl Acad. Sci. USA 114, E2533–E2539 (2017). - PubMed
  41. Karimi, M., Depicker, A. & Hilson, P. Recombinational cloning with plant gateway vectors. Plant Physiol. 145, 1144–1154 (2007). - PubMed
  42. Lei, Y. et al. CRISPR-P: a web tool for synthetic single-guide RNA design of CRISPR-system in plants. Mol. Plant 7, 1494–1496 (2014). - PubMed
  43. De Rybel, B. et al. A novel Aux/IAA28 signaling cascade activates GATA23-dependent specification of lateral root founder cell identity. Curr. Biol. 20, 1697–1706 (2010). - PubMed
  44. Ursache, R., Andersen, T. G., Marhavý, P. & Geldner, N. A protocol for combining fluorescent proteins with histological stains for diverse cell wall components. Plant J. 93, 399–412 (2018). - PubMed
  45. Hellemans, J., Mortier, G., De Paepe, A., Speleman, F. & Vandesompele, J. qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data. Genome Biol. 8, R19 (2007). - PubMed
  46. Gong, X. et al. SEUSS integrates gibberellin signaling with transcriptional inputs from the SHR-SCR-SCL3 module to regulate middle cortex formation in the Arabidopsis root. Plant Physiol. 170, 1675–1683 (2016). - PubMed
  47. Svačinová, J. et al. A new approach for cytokinin isolation from Arabidopsis tissues using miniaturized purification: pipette tip solid-phase extraction. Plant Methods 8, 17 (2012). - PubMed
  48. Rappsilber, J., Ishihama, Y. & Mann, M. Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. Anal. Chem. 75, 663–670 (2003). - PubMed
  49. Novák, O., Hauserová, E., Amakorová, P., Dolezal, K. & Strnad, M. Cytokinin profiling in plant tissues using ultra-performance liquid chromatography–electrospray tandem mass spectrometry. Phytochemistry 69, 2214–2224 (2008). - PubMed
  50. Lun, A. T., Bach, K. & Marioni, J. C. Pooling across cells to normalize single-cell RNA sequencing data with many zero counts. Genome Biol. 17, 75 (2016). - PubMed
  51. McGinnis, C. S., Murrow, L. M. & Gartner, Z. J. DoubletFinder: doublet detection in single-cell RNA sequencing data using artificial nearest neighbors. Cell Syst. 8, 329–337.e324 (2019). - PubMed
  52. Clough, S. J. & Bent, A. F. Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 16, 735–743 (1998). - PubMed

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