Plants are sessile organisms that have to adapt their growth to the surrender environment. They have evolved a post-embryonic development to modulate their growth depending on internal (genetic) or external signals and environmental conditions.

The root system, in addition to provide anchor to the soil and to establish the symbiotic relations with the rizosphere, is also responsible of acquiring the nutrients and water from the soil. 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 maintainable agricultural system, increasing the yield with less inputs to make it sustainable and adaptable to the future generations. In this context, the root system improvement has not been completely exploited.

One of the chalanges in our lab is to identify new genes and natural compounds that improve the root system. We are carrying out a systematic study of the root system aimed to obtain more productive plants in low nutrient environments, specifically under low phosphate (Pi) or nitrate (N), two macronutrients whose shortage severely limits agricultural production. On the other hand, excess fertilization, in addition of the high cost to farmers, causes severe groundwater contamination, damaging the enviroment. To identify root variability and novel genes associated with the response to a particular environment, we are using a new cultivation system called D-ROOT (Figure 1), which allow us to grow Arabidopsis plants with the root system in darkness while the shoot grows in a normal photoperiodic illumination, what is a more natural condition that those used until now (Silva-Navas et al., 2015). Using this system we have shown that root light avoidance is mediated by flavonols. This compounds also acts as integrating molecules in the root meristem to balance the proliferating and differentiating pathway (auxin/cytokinin and H2O2/O2-) and to stablish a correct zonation in the root tip (Silva-Navas et al., 2016; under revision).

Figure 1: D-ROOT system. a, b) This system is composed of a black methacrylate box in which a squared petri dish is perfectly inserted and a black methacrylate insert that is incrustated into the agar to block the light coming from the top fluorescents. C) Adaptation of the D-ROOT system to illuminate roots with specific light waves using leds.

Figure 2: Root illumination incites several morphological and molecular changes. We compared plants growing with the root in darkness with plants growing with the root system under illumination.

Figure 3: Arabidopsis seedlings were grown with the root illuminated or in the R-DAR system (root in darkness) and treated with different hormones. AS shown in these panel, the effect of root illumination is additive to the phenotype caused by hormone treatment.


Using the D-ROOT system, we are carrying out a screening of the TRNSPLANTA collection (transcription factors; TF, Coego et al., 2014) to identify new regulators of the nutritional starvation responses non-discovered until now. We also are phenotyping the root architecture of a collection of Arabidopsis natural varieties in response to Pi deficiency. In both approaches we have identified new TF and natural accession that accumulate Pi differentially. In addition, using comparative transcriptomic analyses, we are identifying a large number of genes that respond specifically to phosphate starvation in dark grown roots, which are not influenced by the effect of the light. At present, we have identified more than 500 genes that respond to Pi-deficiency that were not previously described in other Pi-deficiency experiments.

In the last few years, our group has been working on the characterization of the root system formation. We recently identified SKP2B as a new early marker for lateral root development (Manzano et al., 2012).We took advantage of its specific expression pattern combined with a cell sorting and transcriptomic analyses to generate a lateral root specific cs-SKP2B dataset, containing more than 600 genes. Our studies point that this set contains a large number of genes involved in the control of the lateral root primordia (Manzano et al., 2014). We have also carried out a genetic screening to isolate novel mutants with altered root development. Recently, we have cloned and characterized srol1 (Manzano et al., submitted). SROL1 encodes LEW3, an enzyme required for the N-linked glycosylation of proteins, that plays vital roles in cell-wall biosynthesis and the abiotic stress response in Arabidopsis thaliana. Remarkably, the short root phenotype of srol1 is highly conditioned by light, since when the srol1-root grows without light; it almost recovers the normal growth of the root. Preliminary analyses indicate that this conditionally is caused by a light-mediated differential splicing. Other mutant isolated in the screening was sbrel52, which lacks of lateral roots. Recently we have identified that the sbrel52 mutation affects to a component of the polyadenylation machinery, FIP1. FIP1 forms part ofthe CPSF complex: Cleavage and Polyadenylation Specificity Factor and interacts with the Poly(A) polymerase. Recently, in mammals, it has been shown that Fip1 regulates mRNA alternative polyadenylation (APA) to promote stem cell self-renewal and somatic cell reprogramming. APA plays a critical role in post-transcriptional gene control, regulating alternative splicing, RNA stability or protein translation. This APA is highly regulated during development and disease o stress responses We have preliminary data showing that Arabidopsis FIP1 functions in the nitrogen starvation responses as well as in responses to different abiotic and biotic stresses. In collaboration with Dr. A. Hunt we are undertaking genome wide analyses to identify new alternative polyadenylation site dependent on FIP1 function, growing plants in standard conditions or different abiotic stresses.

Figure 4: Identification of new viable alleles of lew3 (srol1) and fip1 (sbrel52).



Representative Publications

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.


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