Ljung, Karin - Root Development and Shoot-Root Communication

Research

Karin Ljung in an outdoor environmentPhoto: Elisabeth Ohlson Wallin

My research is focused on mechanisms regulating plant growth and development, especially root development, and the roles played by plant growth regulating substances (plant hormones) in the developmental processes that lead to the formation of the root system.

Over the years, my research has continuously been focused on mechanisms that regulate plant growth and development. In particular, I am interested in two key mechanisms: i) The roles played by plant hormones in primary and secondary root development; and ii) The role of plant hormones in the integrative coordination of above and below ground growth. In order to answer fundamental questions, e.g. how lateral roots are initiated, my group is employing Arabidopsis thaliana as a model organism, but we have recently started to translate this research also into trees and crops.

Auxins and cytokinins are plant hormones that are essential throughout the whole life cycle of higher plants. They play pivotal roles in key growth and developmental processes, and they are central to coordinate responses to different environmental variables. Both hormones act in a concentration-dependent manner, and a complex range of regulatory mechanisms act in concert to ensure that the levels of these compounds are optimal for growth and development. We are studying auxin and cytokinin metabolism, transport and signalling, how these processes are regulated by internal and external signals, and how they influence primary and secondary root development. Recently, my team discovered an enzyme responsible for auxin degradation, DIOXYGENASE FOR AUXIN OXIDATION 1 (DAO1), which opens up the possibility to regulate auxin homeostasis in plants via the auxin degradation pathways. Potentially, this can lead to new ways of modifying the root system architecture.

We have recently developed methods for plant hormone profiling in very small amounts of plant tissues, using liquid chromatography coupled to tandem mass spectrometry analysis (LC-MS/MS). We have also developed techniques for using Fluorescent Activated Cell Sorting (FACS) in combination with mass spectrometry analysis to analyse auxin and cytokinin distribution and metabolism within the Arabidopsis root at cellular and sub-cellular resolution. The formation of local hormone gradients and maxima/minima in developing plant tissues has been shown to be very important for organogenesis, through the coordinated regulation of cell division, cell differentiation and cell elongation.


Schematic overview of the procedure to use isolated protoplasts and cell sorting (FACS) as tool to study metabolites and gene and protein networks
“Isolation of cell‐type specific populations from Arabidopsis thaliana root tissues using protoplasting and FACS-sorting for applications in protoplast regeneration and different omics technologies.” Published in: Fluorescence activated cell sorting - A selective tool for plant cell isolation and analysis. Ioanna Antoniadi, Vladimír Skalický, Guiling Sun, Wen Ma, David W. Galbraith, Ondřej Novák, Karin Ljung. (2022). Cytometry Part A, Volume: 101, Issue: 9, Pages: 725-736.

Key publications

  • Antoniadi I, Mateo-Bonmatí E, Pernisová M, Brunoni F, Antoniadi M, Villalonga M, Ament A, Karády M, Turnbull C, Doležal K, Pěnčík A, Ljung K, Novák O. (2022). IPT9, a cis-zeatin cytokinin biosynthesis gene, promotes root growth. Frontiers in Plant Science, 13
  • Casanova-Sáez, R., Mateo-Bonmatí, E., Šimura, J., Pěnčík, A., Novák, O., & Ljung, K. (2022). Inactivation of the entire Arabidopsis group II GH3s confers tolerance to salinity and water deficit. New Phytologist, 235(1): 263–275
  • Pařízková, B., Antoniadi, I., Poxson, D. J., Karady, M., Simon, D. T., Zatloukal, M., Strnad, M., Doležal, K., Novák, O., & Ljung, K. (2022) iP & OEIP – Cytokinin Micro Application Modulates Root Development with High Spatial Resolution. Adv. Mat. Techn., 7 (10), 2101664
  • Antoniadi, I., Skalický, V., Sun, G., Ma, W., Galbraith, D. W., Novák, O., & Ljung, K. (2022). Fluorescence activated cell sorting - A selective tool for plant cell isolation and analysis. Cytometry Part A, 101(9): 725–736.
  • Mateo-Bonmatí, E., Casanova-Sáez, R., Šimura, J., & Ljung, K. (2021). Broadening the roles of UDP-glycosyltransferases in auxin homeostasis and plant development. The New Phytologist, 232 (2): 642-654.
  • Brunoni F, Collani S, Casanova-Sáez R, Šimura J, Karady M, Schmid M, Ljung K, Bellini C. (2020). Conifers exhibit a characteristic inactivation of auxin to maintain tissue homeostasis. New Phytol., 226(6):1753-1765
  • Antoniadi I, Novák O, Gelová Z, Johnson A, Plíha O, Simerský R, Mik V, Vain T, Mateo-Bonmatí E, Karady M, Pernisová M, Plačková L, Opassathian K, Hejátko J, Robert S, Frim J, Doležal K, Ljung K, Turnbull C. (2020). Cell-surface receptors enable perception of extracellular cytokinins. Nat Commun, 11(1):4284
  • Pencík A, Casanova-Sáez R, Pilarová V, Žukauskaite A, Pinto R, Luis Micol J, Ljung K, Novák O. (2018). Ultra-Rapid Auxin Metabolite Profiling for High-Throughput Arabidopsis Mutant Screening. J Exp Bot., 69 (10):2569-2579
  • Šimura J, Antoniadi I, Široká J, Tarkowská D, Strnad M, Ljung K, Novák O. (2018). Plant Hormonomics: Multiple Phytohormone Profiling by Targeted Metabolomics. Plant Physiol. 177: 476-489.
  • Poxson D J, Karady M, Gabrielsson R, Alkattan A Y, Gustavsson A, Doyle S M, Robert S, Ljung K, Grebe M, Simon D T, Berggren M. (2017). Regulating plant physiology with organic electronics. PNAS, 114(18):4597-4602
  • Novák O, Antoniadi I, Ljung K. (2017). High-Resolution Cell-Type Specific Analysis of Cytokinins in Sorted Root Cell Populations of Arabidopsis thaliana. Methods Mol Biol 1497: 231-248.
  • Novák O, Napier R, Ljung K. (2017). Zooming In on Plant Hormone Analysis: Tissue- and Cell-Specific Approaches. Annu Rev Plant Biol 68: 323-348.
  • Porco S, Pěnčík A, Rashed A, Voß U, Casanova-Sáez R, Bishopp A, Golebiowska A, Bhosale R, Swarup R, Swarup K, Peňáková P, Novák O, Staswick P, Hedden P, Phillips AL, Vissenberg K, Bennett MJ, Ljung K. (2016). Dioxygenase-encoding AtDAO1 gene controls IAA oxidation and homeostasis in Arabidopsis. Proc Natl Acad Sci U S A 113: 11016-21.
  • Petersson SV, Lindén P, Moritz T, Ljung K. (2015) Cell-type specific metabolic profiling of Arabidopsis thaliana protoplasts as a tool for plant systems biology. Metabolomics 11: 1679-1689.
  • Antoniadi I, Plačková L, Simonovik B, Doležal K, Turnbull C, Ljung K*, Novák O* (2015). Cell-Type-Specific Cytokinin Distribution within the Arabidopsis Primary Root Apex. Plant Cell 27:1955-67.
  • Pencík A, Simonovik B, Petersson SV, Henyková E, Simon S, Greenham K, Zhang Y, Kowalczyk M, Estelle M, Zazímalová E, Novák O, Sandberg G and Ljung K (2013). Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid. Plant Cell 25: 3858-3870
  • Sairanen I, Novák O, Pencík A, Ikeda Y, Jones B, Sandberg G and Ljung K (2012). Soluble carbohydrates regulate auxin biosynthesis via PIF proteins in Arabidopsis. Plant Cell 24: 4907-4916.
  • Novák O, Hényková E, Sairanen I, Kowalczyk M, Pospíšil T and Ljung K (2012). Tissue-specific profiling of the Arabidopsis thaliana auxin metabolome. Plant J. 72: 523-536.
  • Jones B, Andersson Gunnerås S, Petersson SV, Tarkowski P, Graham N, May S, Dolezal K, Sandberg G and Ljung K (2010). Cytokinin regulation of auxin synthesis in Arabidopsis involves a homeostatic feedback loop regulated via auxin and cytokinin signal transduction. Plant Cell 22: 2956-2969.
  • Petersson SV, Johansson AI, Kowalczyk K, Makoveychuk A, Wang JY, Moritz T, Grebe M, Benfey PN, Sandberg G and Ljung K (2009). An auxin gradient and maximum in the Arabidopsis root apex shown by high-resolution cell-specific analysis of IAA distribution and synthesis. Plant Cell 21:1659-1668.