ROOT ORGANOGENESIS, REGENERATION AND ROOTING

Group leader: Miguel Ángel Moreno Risueño - Assistant Professor
This email address is being protected from spambots. You need JavaScript enabled to view it.  910679150 (Office 183 )   910679130 (Lab 185 )

 

 

Personnel:

 

The root system is essential for the survival of terrestrial plants and environmental adaptation, instructing whole plant growth and production. Most plant organs are newly formed after embryogenesis, providing nutrition, anchorage, reproduction, and more. Additionally, plants can regenerate almost any organ. To further understand organ formation and regeneration, we use the root of the plant Arabidopsis thaliana as a model, allowing us to study in vivo morphogenic processes through biomarker imaging, genetics, and RNA-sequencing. We use these data to learn intrinsic system properties through Gene Regulatory Network (GRN) inference and computer simulations.


The development of root traits that increase aerial plant biomass and nutrition has not been systematically exploited. We are translating our knowledge from model species into crops (poplar and tomato) to identify new breeding traits, markers and natural eco-friendly bio-stimulants.

 

 Figure 1: Root formation and development in Arabidopsis (A), Poplar (B) and Tomato (C)

 


Understanding the Root Clock Mechanism and Exploiting it to Develop Novel Root Traits and Biostimulants

In Arabidopsis, the root clock regulates the spacing of lateral organs along the primary root through oscillating gene expression, while the hormone auxin plays an important role in maintaining and generating gene oscillations.

 

 

     

 

Figure 2: The root clock generates periodic gene expression (bright colors in movies) in the oscillation zone (OZ) to create new branching sites (PBS), where lateral roots (LR) are formed along the primary root (PR). The OZ is located above the stem cell niche (SCN). A multilevel computer simulation shows how gene expression oscillation coordinates with cell division and growth

 



Our work has identified the core molecular mechanism driving the root clock and how it is modified by exogenous cues. We identified auxin response factors, auxin-sensitive inhibitors, and auxin forming a negative regulatory loop circuit driving gene expression oscillations. Through multilevel computer modeling fitted to experimental data we explain how gene expression oscillations coordinate with cell division and growth to create the periodic pattern of organ spacing. We also show that external auxin stimuli can lead to entrainment of the root clock.

We are currently investigating

• Novel regulation of periodic auxin signaling and its memorization to generate new root branches.
• Unveiling the root clock in poplar and tomato to improve root vigor.
• Characterizing novel natural molecules targeting root clock components and its potential use as biostimulants.

 

Figure 3: A) Unraveling novel root clock regulators of periodic auxin signaling through analyses of mutants (e.g. OZ#8) with expanded oscillation zone (OZ). B) Conservation of the root clock in crops. C, D) Identification of natural compounds (C.N.) targeting the root clock and characterization of their potential use as biostimulants.

 


Stem Cell Induction and the Effect of Environmental Conditions

Root systems, as observed in Arabidopsis thaliana, undergo lateral root formation, a developmental mechanism requiring the establishment of stem cell lineages.


We have dissected the formative phase of lateral root development through single-cell RNA sequencing (scRNA-seq), computational approaches, and confocal microscopy, defining the associated cell types and developmental trajectories. Our analysis reveals an ontological hierarchy for lateral root formation with an early and sequential split of main root tissues and stem cells. We have also reconstructed an Arabidopsis spatiotemporal cell-type-specific transcriptional map of the root stem cell lineage from precursor to fully developed stem cells through RNA sequencing (RNA-seq) of single and double fluorescent markers.

Figure 4: A) Computed developmental trajectories for early root organogenesis based on single-cell transcriptomic analyses. B) Fluorescent markers used to profile stem cell induction through RNA-sequencing. C) Reconstructed gene regulatory network for early organogensis. D) A cold response regulator is required for stem cell induction.

 


Employing dynamic Bayesian gene regulatory network inference alongside tree-based methods, we are:

• Understanding lineage developmental progression during root organogenesis.
• Unveiling stem cell induction mechanisms and associated core transcriptional signatures.

Environmental cues affect plant development; and although plants are exposed to disparate environmental conditions, how these cues affect stem cell specification during organogenesis is unknown. Intriguingly, we have found that cold response regulators are required for stem cell induction. We are investigating:

• How cold and other environmental cues regulate stem cell induction and specification during root organogenesis.

 

Understanding Stem Cell Regeneration Under Adverse Environmental Conditions

Plant development involves the specification and regeneration of stem cells, and we have observed that moderate cold induces expression of stem biomarkers, while acute cold is detrimental for development. The activity of stem cells involves telomerase, although its role in regeneration is not fully understood. Telomerase is crucial for maintaining telomere length, which protects chromosome ends from degradation.

 

Figure 5: A) Scheme for known identity transitions during root regeneration based on literature. B) Stem cell specification is enhanced upon moderate cold treatment. C) Stem cell regeneration requires cold response regulators and is promoted by moderate cold treatments. D) Telomere measurements through confocal laser microscopy. E) Research approach for understanding cross regulation between telomerase/telomere length and environmental cues during stem cell regeneration.

 


We are investigating

• How ABA-independent and ABA-dependent responses to environmental cues are integrated into regenerative programs and stem cell regeneration.

• Understanding how telomerase and telomere length influence the capacity of stem cells to regenerate and how this impacts overall plant growth and adaptability.

• Cross-regulation between telomerase/telomere length and environmental cues during stem cell regeneration.


Funding

2023-2026 Understanding root stem cell development and performance under changing environmental conditions. Ref: PID2022-140719NB-I00. Financial Entity: Ministerio de Ciencia e Innovación, Spain. 262.500 €.

2022-2026 Boosting atmospheric carbon dioxide sequestration in poplar roots by Root-Clock and low-degradable metabolite biosynthesis engineering. Ref: TED2021-129530B-I00. Financial Entity: Ministerio de Ciencia e Innovación, Spain. 201.250 €.


REGULATORY MECHANISMS AND SIGNALING MOLECULES DURING POSTEMBRYONIC ROOT FORMATION. Ministerio de Ciencia e Innovación. Programa estatal de fomento de la investigación científica y técnica de excelencia. Proyectos I+D+i - Modalidades “Retos Investigación” y “Generación de Conocimiento”. Proyecto PID2019-111523GB-I00 financiado por MCIN/ AEI /10.13039/501100011033. 

NEW MECHANISMS SPECIFYING AND REGENERATING POSTEMBRYONIC ORGANS IN THE ARABIDOPSIS ROOT. Ministry of Economy and Competitiveness –MINECO- Programa estatal de fomento de la investigación científica y técnica de excelencia. BFU2016-80315-P. 2017-2019.

IDENTIFICATION AND CHARACTERIZATION OF THE DETERMINATION CUES OF ADULT PLANT CELL PLURIPOTENCY USING THE ARABIDOPSIS ROOT. Ministry of Economy and Competitiveness –MINECO- Programa estatal de fomento de la investigación científica y técnica de excelencia. BFU2013-41160-P. 2014-2017. Fondo Europeo de Desarrollo Regional (FEDER).

A MOLECULAR, GENOMICS AND GENETIC ANALYSIS OF NEW STEM CELL FORMATION DURING ROOT MORPHOGENESIS. FP7-PEOPLE-2012-CIG- 322082-Curie Integration Grant. UE. 2012-2016.

SPECIFICATION OF NEW STEM CELLS IN THE ARABIDOPSIS THALIANA ROOT. Ministry of Science and Innovation –MICINN- Programa Ramon y Cajal. RYC-2011-09049. 2012-2017.

 
 


Representative Publications

Ebstrup, E., Ansbøl, J., Paez-Garcia, A., Culp, H., Chevalier, J., Clemmens, P., Coll, N.S., Moreno-Risueno, M.A., Rodriguez, E. 2024. NBR1-mediated selective autophagy of ARF7 modulates root branching. EMBO reports 1–21. DOI: 10.1038/s44319-024-00142-5

González-García, M.P., Sáez, A., Lanza, M., Hoyos, P., Bustillo-Avendaño, E., Pacios, L.F., Gradillas, A., Moreno-Risueño, M.A., Hernaiz, M.J., del Pozo, J.C. 2024. Synthetically derived BiAux modulates auxin co-receptor activity to stimulate lateral root formation. Plant Physiology kiae090. DOI: 10.1093/plphys/kiae090

Perez-Garcia, P., Pucciariello, O., Sanchez-Corrionero, A., Cabrera, J., del Barrio, C., Del Pozo, J.C., Perales, M., Wabnik, K., Moreno-Risueno, M.A. 2023. The cold-induced factor CBF3 mediates root stem cell activity, regeneration and developmental responses to cold. Plant Communications 100737. DOI: 10.1016/j.xplc.2023.100737

Abril-Urias, P., Ruiz-Ferrer, V., Cabrera, J., Olmo, R., Silva, A.C., Díaz-Manzano, F.E., Domínguez-Figueroa, J., Martínez-Gómez, Á., Gómez-Rojas, A., Moreno-Risueno, M.Á., Fenoll, C., Escobar, C. 2023. Divergent regulation of auxin responsive genes in root-knot and cyst nematodes feeding sites formed in Arabidopsis. Frontiers in Plant Science 14. DOI: 10.3389/fpls.2023.1024815

Serrano-Ron, L., Cabrera, J., Perez-Garcia, P., Moreno-Risueno, M.A. 2021. Unraveling Root Development Through Single-Cell Omics and Reconstruction of Gene Regulatory Networks. Frontiers in Plant Science 12, 671. DOI: 10.3389/fpls.2021.661361

Serrano-Ron, L., Perez-Garcia, P., Sanchez-Corrionero, A., Gude, I., Cabrera, J., Ip, P.-L., Birnbaum, K.D., Moreno-Risueno, M.A. 2021. RECONSTRUCTION OF LATERAL ROOT FORMATION THROUGH SINGLE-CELL RNA-SEQ REVEALS ORDER OF TISSUE INITIATION. Molecular Plant. DOI: 10.1016/j.molp.2021.05.028

Perianez-Rodriguez, J., Rodriguez, M., Marconi, M., Bustillo-Avendaño, E., Wachsman, G., Sanchez-Corrionero, A., De Gernier, H., Cabrera, J., Perez-Garcia, P., Gude, I., Saez, A., Serrano-Ron, L., Beeckman, T., Benfey, P.N., Rodríguez-Patón, A., del Pozo, J.C., Wabnik, K., Moreno-Risueno, M.A. 2021. An auxin-regulable oscillatory circuit drives the root clock in Arabidopsis. Science Advances 7, eabd4722. DOI: 10.1126/sciadv.abd4722

Wachsman, G., Zhang, J., Moreno-Risueno, M.A., Anderson, C.T., Benfey, P.N. 2020. Cell wall remodeling and vesicle trafficking mediate the root clock in Arabidopsis. Science 370, 819–823. DOI: 10.1126/science.abb7250

Clark, N.M., Fisher, A.P., Berckmans, B., Broeck, L.V. den, Nelson, E.C., Nguyen, T.T., Bustillo-Avendaño, E., Zebell, S.G., Moreno-Risueno, M.A., Simon, R., Gallagher, K.L., Sozzani, R. 2020. Protein complex stoichiometry and expression dynamics of transcription factors modulate stem cell division. Proceedings of the National Academy of Sciences 117, 15332–15342. DOI: 10.1073/pnas.2002166117

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González-García, M.-P., Bustillo-Avendaño, E., Sanchez-Corrionero, A., del Pozo, J.C., Moreno-Risueno, M.A. 2020. Fluorescence-Activated Cell Sorting Using the D-Root Device and Optimization for Scarce and/or Non-Accessible Root Cell Populations. Plants 9, 499. DOI: 10.3390/plants9040499

Olmo, R., Cabrera, J., Díaz‐Manzano, F.E., Ruiz‐Ferrer, V., Barcala, M., Ishida, T., García, A., Andrés, M.F., Ruiz‐Lara, S., Verdugo, I., Ochoa, M.P., Fukaki, H., del Pozo, J.C., Moreno‐Risueno, M.Á., Kyndt, T., Gheysen, G., Fenoll, C., Sawa, S., Escobar, C. 2020. Root-knot nematodes induce gall formation by recruiting developmental pathways of post-embryonic organogenesis and regeneration to promote transient pluripotency. New Phytologist. DOI: 10.1111/nph.16521

Bustillo-Avendaño, E; Ibáñez, S; Sanz, O; Sousa Barros, JA; Gude, I; Perianez-Rodriguez, J; Micol, JL; Del Pozo, JC; Moreno-Risueno, MA; Pérez-Pérez, JM. 2018. "Regulation of Hormonal Control, Cell Reprogramming, and Patterning during De Novo Root Organogenesis". Plant Physiology. DOI: 10.1104/pp.17.00980".

Manzano, C; Pallero-Baena, M; Silva-Navas, J; Navarro Neila, S; Casimiro, I; Casero, P; Garcia-Mina, JM; Baigorri, R; Rubio, L; Fernandez, JA; Norris, M; Ding, Y; Moreno-Risueno, MA; del Pozo, JC. 2017. "A light-sensitive mutation in Arabidopsis LEW3 reveals the important role of N-glycosylation in root growth and development". Journal of Experimental Botany. DOI: 10.1093/jxb/erx324".

Olmo, R; Cabrera, J; Moreno-Risueno, MA; Fukaki, H; Fenoll, C; Escobar, C. 2017. "Molecular transducers from roots are triggered in Arabidopsis leaves by root-knot nematodes for successful feeding site formation: A conserved post-embryogenic de novo organogenesis program?". Frontiers in Plant Science. DOI: 10.3389/fpls.2017.00875".

Ramirez-Parra, E; Perianez-Rodriguez, J; Navarro-Neila, S; Gude, I; Moreno-Risueno, MA; del Pozo, JC. 2016. "The transcription factor OBP4 controls root growth and promotes callus formation". New Phytologist. DOI: 10.1111/nph.14315".

Silva-Navas, J; Moreno-Risueño, MA; Manzano, C; Téllez-Robledo, B; Navarro-Neila, S; Carrasco, V; Pollmann, S; Gallego, FJ; del Pozo, JC. 2016. "Flavonols mediate root phototropism and growth through regulation of proliferation-to-differentiation transition". Plant Cell. DOI: 10.1105/tpc.15.00857".

Moreno-Risueno, MA; Sozzani, R; Yardımcı, GG; Petricka, JJ; Vernoux, T; Blilou, I; Alonso, J; Winter, CM; Ohler, U; Scheres, B; Benfey, PN. 2015. "Transcriptional control of tissue formation throughout root development". Science. DOI: 10.1126/science.aad1171".

Moreno-Risueno, MA; Sozzani, R; Yardımcı, GG; Petricka, JJ; Vernoux, T; Blilou, I; Alonso, J; Winter, CM; Ohler, U; Scheres, B; Benfey, PN. 2015. "Transcriptional control of tissue formation throughout root development". Science. DOI: 10.1126/science.aad1171".

Liberman, LM; Sparks, EE; Moreno-Risueno, MA; Petricka, JJ; Benfey, PN. 2015. "MYB36 regulates the transition from proliferation to differentiation in the Arabidopsis root". Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1515576112".

Silva-Navas, J; Moreno-Risueno, MA; Manzano, C; Pallero-Baena, M; Navarro-Neila, S; Téllez-Robledo, B; Garcia-Mina, JM; Baigorri, R; Javier Gallego, F; del Pozo, JC. 2015. "D-Root: a system to cultivate plants with the root in darkness or under different light conditions". Plant Journal. DOI: 10.1111/tpj.12998".

Perianez-Rodriguez, J; Manzano, C; Moreno-Risueno, MA. 2014. "Postembryonic organogenesis and plant regeneration from tissues: two sides of the same coin?". Frontiers in Plant Science. DOI: 10.3389/fpls.2014.00219".