Plant stem cells and regeneration
Key Laboratory of Plant Carbon Capture
Lin Xu
Personal Profile
2005-2008 PhD, Institut de Biologie Moléculaire des Plantes, CNRS, University of Strasbourg, France.
2008-2013 Associate Professor in Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, China.
2013-2020 Professor in Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, China.
2020-present Professor in CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, China.
Research Work
The overall goal of our research is to reveal the molecular basis and evolutionary route of stem cell pluripotency that allows plants to regenerate adventitious roots and shoots. We have three research directions: de novo root regeneration in leaf cuttings, pluripotency of callus in tissue culture, and evolution of plant stem cells and organs.
De novo root regeneration in leaf cuttings. Detached Arabidopsis leaves are cultured on B5 medium without exogenous hormones, and adventitious roots can be regenerated from the wounded site on the detached leaf. Detached leaves sense many early signals (wound signals, environmental signals, and developmental status) to adjust auxin production. Auxin is then transported into regeneration-competent cells in the vasculature and triggers cell fate transition to form roots. We aim to reveal the mechanism from signal sensing to cell fate transition during de novo root regeneration in leaf cuttings.
Pluripotency of callus in tissue culture. We use the in vitro tissue culture system to study callus formation and organ regeneration. Callus is a group of pluripotent cells that can regenerate either shoots or roots. We aim to reveal the mechanism of pluripotency acquisition in callus.
Evolution of plant stem cells and organs. We have collected typical model plants (Marchantia polymorpha, Selaginella kraussiana, Psilotum nudum, Ceratopteris richardii, rice, and etc.) to study the evolution of plant stem cells and organs. Currently we are focusing on analysis of how roots had been originated and evolved in vascular plants.
Main Achievements
Establishment of methods to study de novo organ regeneration
The cellular and molecular mechanisms underlying adventitious rooting and shooting from wounded plants are barely understood because of the lack of efficient research methods. Therefore, we first tried to establish methods to study de novo organ regeneration mimicking natural conditions.
To study de novo shoot regeneration, we established a method in which Arabidopsis (Arabidopsis thaliana) and tomato (Solanum lycopersicum) seedlings are decapitated at the hypocotyl, and then adventitious shoots regenerate from the decapitated hypocotyls. The adventitious shoot can normally develop to replace the decapitated shoot. No exogenous hormones are supplied in this system. Therefore, the shooting process is dependent on endogenous hormones in the plant and mimics adventitious shooting under natural conditions.
To study de novo root regeneration, we established a system in which Arabidopsis leaf explants are cultured on B5 medium without exogenous hormones. This simple method results in adventitious root formation from the wounded site on the leaf explant.
We have also used an in vitro tissue culture system for root and shoot regeneration. By comparing organ regeneration under natural conditions and in in vitro tissue culture, we have explored whether the regenerative abilities in in vitro tissue culture borrow from natural regenerative abilities.
Cell lineage and molecular framework of de novo organ regeneration
The RP establishment is a key step in de novo organ regeneration. Not all cells are able to initiate a RP, and only some regeneration-competent cells (e.g. pericycle, procambium, and some parenchyma cells) within the vasculature are able to undergo fate transition.
In de novo root regeneration, early signals (wound signals, environmental signals, and developmental status) may converge in mesophyll cells, leaf margin cells and some vascular cells (simply referred to as converter cells) to promote auxin production in the leaf explant. Auxin is then transported from converter cells into regeneration-competent cells (e.g. procambium cells) and triggers cell fate transition. The first step of cell fate transition is the priming of the regeneration-competent cell to become the root founder cell with specific expression of WOX11/12. The second step is the initiation of the RP from the root founder cell by cell division. In this step, WOX11/12 expression decreases while WOX5/7 and LBD16 are co-expressed in the RP cells.
In in vitro tissue culture, callus formation also requires two steps of cell fate transition. The first step is the priming of the regeneration-competent cell to become the callus founder cell through activation of WOX11/12 by exogenous auxin. The second step is initiation of the callus cells from the callus founder cell with cell division. The cellular nature of the newly formed callus is a group of RP-like cells that co-express WOX5/7 and LBD16.
Overall, establishment of the RP or RP-like callus requires two steps of cell fate transition guided by auxin. Expression of WOX11/12 marks founder cell formation, and co-expression of WOX5/7 and LBD16 marks the identity of the RP or RP-like callus.
Molecular evolution of RP
The appearance of vascular plants was a great step in the colonization of land by plants during evolution (Pires and Dolan, 2012, Phil. Trans. R. Soc. B 367:508-518). The vascular plants evolved into several lineages, two of which survive today: lycophytes and euphyllophytes. The euphyllophytes include ferns and seed plants. We have collected typical model plants to study the initiation and evolution of different types of roots.
Early vascular plants on earth formed only the shoot without roots and leaves. Based on the fossil evidence and the root anatomy of extant vascular plants, there were separate root-evolution events that resulted in different types of roots in extant vascular plants. In the lycophyte lineage, Selaginella kraussiana has only one type of root, i.e. the bifurcating root, in which the division of the root apical meristem gives rise to independent autonomous twin root meristems. In the euphyllophyte lineage, the fern Ceratopteris richardii has adventitious roots and endodermis-derived lateral roots; and the seed plant Arabidopsis thaliana has a primary root, adventitious roots, and pericycle-derived lateral roots. Using these model plants, we have attempted to analyze the evolutionary route of RP initiation and reveal how pluripotent RP stem cells evolved in plants.
Publications
(#, Co-first author; *, corresponding author)
1. Zhai N.#, Sun B.#, Wu S., Zhou F., Jiao Y., Xu L.* (2024) Cytokinin facilitates the patterning of the adventitious root apical meristem from leaf cuttings. Molecular Horticulture 4(1):11. DOI: 10.1186/s43897-024-00091-6
2. Liu W.#, Cai G.#, Zhai N.#, Wang. H., Tang T., Zhang Y., Zhang Z., Sun L., Zhang Y., Beeckman T., Xu L.* (2023) Genome and transcriptome of Selaginella kraussiana reveal evolution of root apical meristems in vascular plants. Curr. Biol. 33(19):4085-4097.e5. DOI:10.1016/j.cub.2023.08.061
3. Zhang T.#, Ge Y.#, Cai G., Pan X., Xu L.* (2023) WOX-ARF modules initiate different types of roots. Cell Rep. 42(8):112966
4. Zhai N.#, Pan X.#, Zeng M., Xu L.* (2023) Developmental trajectory of pluripotent stem cell establishment in Arabidopsis callus guided by a quiescent center-related gene network. Development 150(5):dev200879. DOI:10.1242/dev.200879
5. Liu W.#, Zhang Y.#, Fang X.#, Tran S.#, Zhai N.#, Yang Z., Guo F., Chen L., Yu J., Ison M.S., Zhang T., Sun L., Bian H., Zhang Y.*, Yang L.*, and Xu L.* (2022) Transcriptional landscapes of de novo root regeneration from detached Arabidopsis leaves revealed by time-lapse and single-cell RNA sequencing analyses. Plant Comm. 3:100306. DOI: 10.1016/j.xplc.2022.100306
6. Zhai N., Xu L.* (2021) Pluripotency acquisition in the middle cell layer of callus is required for organ regeneration. Nat. Plants 7:1453-1460 [Cover story]
7. Yu J.#, Zhang Y.#, Liu W., Wang H., Wen S., Zhang Y., Xu L.* (2020) Molecular evolution of auxin-mediated root initiation in plants. Mol. Biol. Evol. 37(5):1387-1393
8. Zhang G.#, Zhao F.#, Chen L#, Pan Y., Sun L., Bao N., Zhang T., Cui C.-X., Qiu Z., Zhang Y., Yang L., Xu L.* (2019) Jasmonate-mediated wound signaling promotes plant regeneration. Nat. Plants 5:491-497 [Cover story]
9. Liu W.#, Yu J.#, Ge Y., Qin P., Xu L.* (2018) Pivotal role of LBD16 in root and root-like organ initiation. Cell. Mol. Life Sci. 75(18): 3329-3338 [Invited review]
10. Liu J., Hu X., Qin P., Prasad K., Hu Y., Xu L.* (2018) The WOX11-LBD16 pathway promotes pluripotency acquisition in callus cells during de novo shoot regeneration in tissue culture. Plant Cell Physiol. 59(4): 739-748 [Cover story]
11. Liu W., Xu L.* (2018) Recruitment of IC-WOX genes in root evolution. Trends Plant Sci. 23(6): 490-496 [Opinion]
Xu L.* (2018) De novo root regeneration from leaf explants: wounding, auxin, and cell fate transition. Curr. Opin. Plant Biol. 41:39-45 [Invited review]
12. Sheng L.#, Hu X.#, Du Y., Zhang G., Huang H., Scheres B., Xu L.* (2017) Non-canonical WOX11-mediated root branching contributes to plasticity in Arabidopsis root system architecture. Development 144(17): 3126-3133
13. Hu B.#, Zhang G.#, Liu W.#, Shi J.#, Wang H.#, Qi M., Li J., Qin P., Ruan Y., Huang H., Zhang Y., Xu L.* (2017) Divergent regeneration-competent cells adopt a common mechanism for callus initiation in angiosperms. Regeneration 4(3):132–139. [Cover story]
14. Sun B.#, Chen L.#, Liu J., Zhang X., Yang Z., Liu W.*, Xu L.* (2016) TAA family contributes to auxin production during de novo regeneration of adventitious roots from Arabidopsis leaf explants. Sci. Bull. 61(22):1728–1731
Hu X., Xu L.* (2016) Transcription factors WOX11/12 directly activate WOX5/7 to promote root primordia initiation and organogenesis. Plant Physiol. 172(4):2363-2373
15. Chen L., Tong J., Xiao L., Ruan Y., Liu J., Zeng M., Huang H., Wang J.-W., Xu L.* (2016) YUCCA-mediated auxin biogenesis is required for cell fate transition occurring during de novo root organogenesis in Arabidopsis. J. Exp. Bot. 67(14):4273-4284
16. Chen X., Cheng J., Chen L., Zhang G., Huang H., Zhang, Y., Xu L.* (2016) Auxin-independent NAC pathway acts in response to explant-specific wounding and promotes root tip emergence during de novo root organogenesis in Arabidopsis. Plant Physiol. 170(4):2136-2145
17. Zeng M.#, Hu B.#, Li J.#, Zhang G., Ruan Y., Huang H., Wang H.* and Xu L.* (2016) Stem cell lineage in body layer specialization and vascular patterning of rice root and leaf. Sci. Bull. 61(11):847–858
18. Liu J.#, Sheng L.#, Xu Y.#, Li J., Yang Z., Huang H. and Xu L.* (2014) WOX11 and 12 are involved the first-step cell fate transition during de novo root organogenesis in Arabidopsis. Plant Cell. 26(3):1081-1093
19. Xu L.* and Huang H. (2014) Genetic and epigenetic controls of plant regeneration. Curr. Top. Dev. Biol. 108: 1-33 [Invited review]
20. Li G.#, Liu S.#, Wang J., He J., Huang H., Zhang Y.* and Xu L.* (2014) ISWI proteins participate in the genome-wide nucleosome distribution in Arabidopsis. Plant J. 78(4):706-714
21. He C., Chen X., Huang H. and Xu L.* (2012) Reprogramming of H3K27me3 is critical for acquisition of pluripotency from cultured Arabidopsis tissues. PLoS Genet. 8(8): e1002911
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