REGULATION OF LATERAL ROOT DEVELOPMENT DURING NUTRIENT DEFICIENCIES

Group leader: Juan Carlos del Pozo Benito - Research Professor CSIC-INIA
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Personnel:

 

In the past century, we has witnessed an extraordinary success of plant agronomy and breeding, resulting in the doubling of crop productivity. This increase was to a great extent the result of increasing inputs, water and fertilizers, pesticides and also genetic breeding. Present demographic tendencies, which predict a doubling of the population at 2050, and the growing interest to exploit plants as renewable energy sources are prompting us to augment crop production gains. However, nowadays, the circumstances are rather different: society is demanding an increase of the production but within a more sustainable agricultural system, increasing the yield with less inputs to make it maintainable and adaptable to the future generations. The plant root system, in addition to provide anchor to the soil, is responsible of establishing the symbiotic relations with the rhizosphere, and acquiring nutrients and water from the soil. In addition, root function seems to be important to cope with many abiotic and biotic stresses. In this context, the root system plays an important role in plant development and growth, and therefore, root system improvement, which has not been completely exploited, will be necessary to fulfill the future needs of the increasing human population in terms of food production.

 


Currently, our main research areas in the lab are
  1. Identification of new compounds that increase the root system
  2. Root responses to phosphate starvation
  3. Analysis of the natural variation in the response to phosphate starvation
  4. Identification of novel fungi that improve plant growth with low phosphate in the medium
  5. Unraveling the molecular mechanism behind the heat stress in roots and shoots: from DNA methylation to gene transcription and miRNA movement
  6. Identification of new bacteria and fungi that increase plant tolerance to heat

 

One of the challenges in our lab is to identify new genes and microbes that improve the growth of the root system under low nutrient availability, specifically under low phosphate (Pi) or low nitrate (N), two macronutrients whose shortage severely limits agricultural production. One of the problems/limitations in root biology studies has been that plants were grown with the root system in presence of light, condition that alters plant growth and responses. To identify root variability and novel genes associated with the response to a particular environment, we are designed a new cultivation system called D-Root (Figure 1), which allow us to cultivate plants with the root system in darkness while shoot grows in a normal photoperiodic illumination, simulating natural condition (Silva-Navas et al., 2015).


Figure 1: The Dark-Root (D-Root) device allows to grow Arabidopsis seedlings in vitro with the root system in the darkness while exposing the shoot to the light.



a) Graphic representation of the D-Root device. b) The petri dish is inserted into the methacrylate box. Arrow points to the methacrylate combo used to block partially the light coming from the top. c) D-Root device adaptation to illuminate roots with different light wavelengths using led technology or a UV- lamp.

 

One of the projects in the lab is focused in understanding the role of BiAux, a novel compound that specifically increases the number of lateral roots (LRs) in plants. BiAux treatment increases expression the SKP2B::GUS and DR5::GUS, which are auxin response markers that label the lateral root prebranching site –PBS- (Figure 2).  Our results indicate that BiAux acts as a modulator of the auxin receptor sensitivity through the activity of TIR1, and AFB2 co-receptors. At present, we are exploring the molecular mode of action of BiAux and the specific targets of the TI1/AFB2-auxin-Biaux complex.


Figure 2: BiAux increases the lateral root prebranch sites and modified TIR/AFB activity

 

A) Phenotype of Arabidopsis seedlings treated with mock or BiAux. Arabidopsis SKP2Bp::GUS seedlings grown in MS1/2 medium for 4 days and then transferred to new plates containing mock or 5 µM of BiAux during 6 days. Right panels show the GUS-stained roots labeled in red (1; apical region of primary root) or green (2; shootwards part of the root). Numbers indicate the position of the pictures in the GUS stained roots. Scale bar corresponds to 0.5 cm. B) Yeast-two hybrid interaction between TIR1 and Aux/IAA1, Aux/IAA3, Aux/IAA14 or Aux/IAA7 in presence of auxin (10 µM IAA) with or without 5 µM of BiAux. C) Binding site defined by a neighborhood of 4 Å around BiAux (sticks with carbons in green) in the superposition of crystal (sticks with carbons in dark blue) and optimized (sticks with carbons in light blue) structures. The scale bar on top of this panel indicates the range of PB-EP values (in kT/e units) used in these images.

 

Remarkably, using the D-Root device, we have found that root responses to phosphate (Pi) starvation is significantly different to previously described by several groups (Figure 3). These differences prompted us to study this response in dark-grown roots. A transcriptomic analyses by RNA-seq identified a large number of genes that were deregulated in response to Pi deficiency that has not been previously identified, likely by the negative influence of light. We are genomic and genetically characterizing some of these genes.


Figure 3: Root illumination potentiates Pi starvation toot growth inhibition.

 

A) Phenotype of  12 day old Arabidopsis seedling grown with root in presence of light (LGR- Light Grown Roots) or in darkness (DGR-Dark Grown Roots). B) Root growth quantification in A. (low Pi corresponds to 5 µM of Pi).

  

In addition, we have found that Pi starvation response in roots is controlled by the balance of different hormones (Figure 4). In this regard, we found that different isomers of cytokinin, especially cis- and trans-zeatin, have specific roles, controlling differentially gene expression, cell division and root growth.


Figure 4: Hormonal treatments alters root/shoot ratio and Pi distribution in dark-grown roots (DGR) in Pi starvation plants.

 

A) Arabidopsis seedlings were grown for 5 days in full medium and then they were transferred to a medium containing IAA, GA, ABA, or Zeatin for 5 more days. B) Weight Root/Shoot ratio from plants treated with different hormones in +Pi or low Pi. C) Pi accumulation in roots or shoots during plant treatment with different hormones in presence of high phosphate or low Pi. Values are the means of five different experiments ±SD.

 

Plants modulate molecular responses to adapt development to surrounding environment. The transcriptional response of specific root cell layers during adaptation to Pi starvation is poorly known, but might involve cellular specialization based on morphological changes. We are analyzing gene expression (transcriptome) during Pi starvation response at the cell type level, reconstruct a functional network of cellular adaptation and identify regulators required to sustain plant growth and Pi uptake. This information will be used to generate a detailed  transcription/translation map of the Pi starvation response in roots. Interestingly, we did not find any gene that were simultaneously deregulated in all cell layers (Figure 5).


Figure 5: Phosphate starvation response is specific in different cell layers in Arabidopsis.

 

Venn diagrams from up- or down-regulated genes in response to Pi starvation showing the overlapping between the different cell layers (epidermis, cortex, pericycle, vasculature or lateral root cap (LR Cap).

 

We are also using the D-Root to analyze the behavior of different Arabidopsis ecotypes to Pi starvation. We have found significant variability in many traits associated to this responses and identified several SNPs associated to root growth, LR number or Pi amount in roots and shoots.


Table 1. Number of SNPs and inferred associated genes for each trait and phosphate condition.

 

In addition, we are screening an entophytic fungi collection (kindly supply by from Dra. Sacristan) to identify new fungi that increase plant growth under low P conditions. We have developed an effective screening method that allow us to screen several isolates in short period.  Using the D-Root system, and in collaboration with Tradecorp company, we have identified two isolates that seems to increase plant growth under low P conditions. The use of both isolates are in the process of being tested in the field and intellectually protected.

 

We are also really interested in understand the effect of heat on plant nutrition and growth. Extreme heat waves reduce plant growth and productivity, generating significant losses for the agricultural companies and affecting food security worldwide. In our analyses, we found a correlation between Pi deficiency and heat stress responses. So, we decided to analyze the effect of high temperature on plant nutrition. Using classical experiments, we realized that the root system were heated to a similar high temperature than the aerial part. However, in natural ecosystems, the soil acts as a temperature buffers, forming a decreasing gradient. Thus, to study heat stress in a “more natural conditions” in the lab or greenhouses, we engineered a novel device (TGRooZ; Utility Patent ES1293470, licensed to Ibercex) that generates a similar soil-temperature gradient for in vitro plates or soil containing pots (Figure 6). Using the TGRooZ we found that the heat response in the root is quite different than the previous published (Figure 7). Figure we identified new genes and pathways involved in such response. Now, we are extending our research to crops (tomato) and analyzing the effects in transcriptomic, small RNA and differential methylation in shoot and roots in response to heat alone or combined with Pi deficiency.


Figure 6: The TGRooZ device generates a temperature gradient similar to the natural soil.

 

Optical (top) and thermal pictures (bottom), taken with a FLIR E96, of 12x12 cm plates containing agar cultivated at 22ºC, or 32ºC homogenously (22SR,  32SR) or 32TGRooZ. In the right side, is shown optical (top) and thermal pictures (bottom) of 3.5L pots containing soil that were cultivated at 24ºC, or 36ºC homogenously (24SR,  36SR) or 36TGRooZ.Colors indicate the different temperatures found along the plate or the pots.


Figure  7: TGRooZ affects the root and shoot growth of Arabidopsis in response to heat.

 

A) Phenotype of Arabidopsis plants that were grown in homogeneous temperature in root and shoot (22SR for 22ºC or 32SR for 32ºC) or at 32TGRooZ; 32ºC in the aerial part and a decreasing gradient in the root system. B) Confocal images of root meristems of 22RS, 32SR or 32TGRooZ seedlings grown for 6 days after transplanting. White arrowheads indicate the QC and arrows indicate the final of the meristem. Scale bar corresponds to 50 µm. C) Confocal images of a z-stack PI-stained root apical meristems from 22SR, 32SR or 32TGRooZ CYCB1;1:CYCB1;1-GFP seedlings grown for 6 days after transplantin White arrows indicate the end of the meristem. Scale bar corresponds to 50 µm.


Figure 8: Effect of TGRooZ in tomato seedlings. Heat also reduced root and shoot growth in tomato plants, reduction that is recovered by the use of TGRooZ.

 

(A) Optical and thermal pictures, taken with a FLIR E96, of tomato seedlings cultivated on germination paper at 26ºC, or 36ºC homogenous in shoot and root (26SR,  36SR) or 36TGRooZ. The thermal picture shows the homogeneous temperature or the gradient formed. Right photographs correspond to representative pictures of tomato seedling grown in those conditions. Tomato seeds were stratified for 4 days at 4ºC and then they were germinated in darkness for 5 days. Afterwards, seedlings were transferred to germination paper into a zip bag for 7 days. The paper was wetted with one-fourth of MS salts plus 1 mM of MES at pH=5.8. Scale bars correspond to 5 cm.

 

(B) Representative pictures of tomato plants grown in the TGRooZ-pots system for 3 weeks. Note that heat on root (36SR) severely reduces shoot growth.

 

Using the TGRooZ we also found that the microbiota composition recruited by tomato plants are affected by the temperature of the soil. Thus, we were able to identify a synthetic community of bacteria that increases the plant tolerance to heat stress (Figure 9). Now, we are trying to reduce the number of this Syncom to identify the bacteria responsible of this beneficial effect.


Figure 9: A bacteria Syncom increases shoot growth and Pi accumulation during heat stress and activate auxin signaling.

 

Arabidopsis seedlings were grown for 4 days in MS1/2 medium at 22ºC. Afterwards, they were transferred to fresh medium containing solvent (mock) or 10 ml of Syncom on the top surface and transferred to 22ºC, 32ºC or 32TGRooZ.  Seedlings were grown for 7 additional days and then fresh weight per plant (A) and total phosphate (B) were quantified. C) DR5::LUC, grown similarly that plants in A-B, were analyzed for LUC activity to visualize auxin signaling and lateral root formation.

 

Currently, we are also interested in understanding the role of DNA methylation and miRNAs in gene transcription during the plant response to Pi starvation, heat stress or combining both stresses. We will integrate all these data to better understand, in a holistic view, the plant response to multiple stresses. Preliminary data suggest that heat stress has a bigger impact on DNA methylation than Pi starvation. However, both stresses alter the expression of a significant number of genes and miRNAs in response of individual or combined stresses.

 

Finally, in collaboration with Dra Monica Perna´s group, we are analyzing the effect of Pi or nitrogen deficiencies combined with high temperature. We have identified significant variability in agronomic traits in a set of Brassica napus varieties. Now, we are analyzing the molecular changes in 2 varieties that showed differential behavior to N or Pi deficiency.

 

Selected articles: (For a full list of articles visit ORCID web 0000-0002-4113-457X)

González-García, M.P., Conesa, C.M., Lozano-Enguita, A., Baca-González, V., Simancas, B., Navarro-Neila, S., Sánchez-Bermúdez, M., Salas-González, I., Caro, E., Castrillo, G., del Pozo, J.C. 2022. Temperature changes in the root ecosystem affect plant functionality. Plant Communications 100514. DOI: 10.1016/j.xplc.2022.100514

Sánchez-Bermúdez, M., del Pozo, J.C., Pernas, M. 2022. Effects of Combined Abiotic Stresses Related to Climate Change on Root Growth in Crops. Frontiers in Plant Science 13. DOI: 10.3389/fpls.2022.918537

Muñoz, A., Mangano, S., Toribio, R., Fernández-Calvino, L., del Pozo, J.C., Castellano, M.M. n.d. The co-chaperone HOP participates in TIR1 stabilization and in auxin response in plants. Plant, Cell & Environment n/a. DOI: 10.1111/pce.14366

Cabrera, J., Conesa, C.M., del Pozo, J.C. n.d. May the dark be with roots: A perspective on how root illumination may bias in vitro research on plant–environment interactions. New Phytologist n/a. DOI: 10.1111/nph.17936

Silva-Navas, J., Salvador, N., del Pozo, J.C., Benito, C., Gallego, F.J. 2021. The rye transcription factor ScSTOP1 regulates the tolerance to aluminum by activating the ALMT1 transporter. Plant Science 310, 110951. DOI: 10.1016/j.plantsci.2021.110951

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

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

Conesa, C.M., Saez, A., Navarro-Neila, S., de Lorenzo, L., Hunt, A.G., Sepúlveda, E.B., Baigorri, R., Garcia-Mina, J.M., Zamarreño, A.M., Sacristán, S., del Pozo, J.C. 2020. Alternative Polyadenylation and Salicylic Acid Modulate Root Responses to Low Nitrogen Availability. Plants 9, 251. DOI: 10.3390/plants9020251

Silva‐Navas, J., Conesa, C.M., Saez, A., Navarro‐Neila, S., Garcia‐Mina, J.M., Zamarreño, A.M., Baigorri, R., Swarup, R., del Pozo, J.C. 2019. Role of cis-zeatin in root responses to phosphate starvation. New Phytologist. DOI: 10.1111/nph.16020

Telléz‐Robledo, B., Manzano, C., Saez, A., Navarro‐Neila, S., Silva‐Navas, J., de Lorenzo, L., González‐García, M.-P., Toribio, R., Hunt, A.G., Baigorri, R., Casimiro, I., Brady, S.M., Castellano, M.M., Del Pozo, J.C. 2019. The polyadenylation factor FIP1 is important for plant development and root responses to abiotic stresses. The Plant Journal. DOI: 10.1111/tpj.14416

Sayas, E., Pérez‐Benavente, B., Manzano, C., Farràs, R., Alejandro, S., del Pozo, J.C., Ferrando, A., Serrano, R. 2018. Polyamines interfere with protein ubiquitylation and cause depletion of intracellular amino acids: a possible mechanism for cell growth inhibition. FEBS Letters. DOI: 10.1002/1873-3468.13299

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".

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".

Fernández-Marcos, M; Desvoyes, B; Manzano, C; Liberman, LM; Benfey, PN; del Pozo, JC; Gutierrez, C. 2016. "Control of Arabidopsis lateral root primordium boundaries by MYB36". New Phytologist. DOI: 10.1111/nph.14304".

Garrido-Arandia, M; Silva-Navas, J; Ramírez-Castillejo, C; Cubells-Baeza, N; Gómez-Casado, C; Barber, D; Pozo, JC; Melendi, PG; Pacios, LF; Díaz-Perales, A. 2016. "Characterisation of a flavonoid ligand of the fungal protein Alt a 1". Scientific Reports. DOI: 10.1038/srep33468".

del Pozo, JC. 2016. "Reactive Oxygen Species: from harmful molecules to fine-tuning regulators of stem cell niche maintenance". PLoS Genetics. DOI: 10.1371/journal.pgen.1006251".

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".

del Pozo, JC; Ramirez-Parra, E. 2015. "Whole genome duplications in plants: an overview from Arabidopsis". Journal of Experimental Botany. DOI: 10.1093/jxb/erv432".

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".

del Pozo, JC; Ramirez-Parra, E. 2014. "Deciphering the molecular bases for drought tolerance in Arabidopsis autotetraploids". Plant Cell and Environment. DOI: 10.1111/pce.12344".

Lario, LD; Ramirez-Parra, E; Gutierrez, C; Spampinato, CP; Casati, P. 2013. "ANTI-SILENCING FUNCTION1 proteins are involved in ultraviolet-induced DNA damage repair and are cell cycle regulated by E2F transcription factors in Arabidopsis". Plant Physiology. DOI: pp.112.212837 [pii] 10.1104/pp.112.212837".

Bratzel F, Yang C, Angelova A, López-Torrejón G, Koch M, del Pozo JC, Calonje M. (January 2012) Regulation of the new imprinted gene AtBMI1C during development requires the interplay of different epigenetic mechanisms. Molecular Plant. 5: 260-269.

Rodríguez-Herva, J. J., González-Melendi, P., Cuartas-Lanza, R., Antúnez-Lamas, M., Río-Alvarez, I., Li, Z., López-Torrejón, G., Díaz, I., del Pozo, J. C., Chakravarty, S., Collmer, A., Rodríguez-Palenzuela, P. y López-Solanilla, E. 2012. "A bacterial cysteine protease effector protein interferes with photosynthesis to suppress plant innate immune responses." Cellular Microbiology. 14(5):669-681.

 

Projects:

  1. BIO2014-52091-RIdentificación de nuevos genes y productos bio-activos para la Optimizacion de los recursos naturales dentro una agricultura sostenible. IP y coordinador: Juan Carlos del Pozo. INIA-CBGP. 140.000 €. 2014- 2017.
  2. 655406-ROOT-BARRIERS.H2020-Molecular mechanisms controlling endodermis and exodermis defferentiation in tomato roots. Marie Curie Fellowship (Awarded to Concepcion Manzano, U. of Davis USA). Coordinator at the INIA: Juan C. del Pozo. € 263,000. January 2016-December 2017-at U. California, Davis, USA. January 2018-January 2019 – at INIA, Spain.
  3. BIO2017-82209-RRoot Responses to Phosphate Starvation: New Approaches to improve Plant Growth with reduced Fertilization.. IP y coordinador: Juan Carlos del Pozo. INIA-CBGP. 150.000 €. 2018- 2020.

Patents:

  1. del Pozo, J.C. and Gutierrez, C. Transgenic plants SKP2D: Obtención and applications. Número de aplicación: 200402349. (11-10-04) País de prioridad: España Entidad titular: CSIC
  2. Juan Carlos del Pozo Benito, Javier Gallego Rodríguez, Javier Silva Navas. New device to cultivate roots in in vitro. Número de aplicación:   U201300727. Priority Date: 19-08-2013) País de prioridad: España. Entidad titular: INIA-UCM.
  3. Juan Carlos del Pozo Benito, Concepcion Manzano Fernandez, Pilar Hoyos Vidal, Maria Josefa Hernaiz, Stephan Pollmann Title: Use of natural compounds to regulate vegetal growth. Application Number: P201630412Priority country: Spain Priority Date: 05-04-16 España Entidad titular:  INIA-UCM-UPM