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).
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.
Ramirez-Parra, E; Perianez-Rodriguez, J; Navarro-Neila, S; Moreno-Risueño, M; del Pozo, JC. 2016. "The transcription factor OBP4 controls root growth and promotes callus formation". Submitted to New Phytologist.
Silva-Navas, J; Moreno-Risueno, 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". Third revision in Plant Cell.
Silva-Navas, J; Moreno-Risueño, M; Manzano, C; Pallero-Baena, M; Navarro-Neila, S; Tellez, B; Pollmann, S; Carrasco-Loba, V; Garciamina, JM; Roberto Bigorri, R; Gallego, FG; del Pozo, JC. 2016. "Flavonols regulate transition from cell proliferation to differentiation". (Submitted, 2015).
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".
Coego, A; Brizuela, E; Castillejo, P; Ruíz, S; Koncz, C; del Pozo, JC; Piñeiro, M; Jarillo, JA; Paz-Ares, J; León, J; Transplanta Consortium, T. 2014. "The TRANSPLANTA collection of Arabidopsis lines: a resource for functional analysis of transcription factors based on their conditional overexpression". Plant Journal. DOI: 10.1111/tpj.12443".
del Pozo, JC; Manzano, C. 2014. "Auxin and the ubiquitin pathway. Two players–one target: the cell cycle in action". Journal of Experimental Botany. DOI: 10.1093/jxb/ert363".
Manzano, C; Pallero-Baena, M; Casimiro, I; De Rybel, B; Orman-Ligeza, B; Van Isterdael, G; Beeckman, T; Draye, X; Casero, P; del Pozo, JC. 2014. "The emerging role of Reactive Oxygen Species signalling during lateral root development". Plant Physiology. DOI: 10.1104/pp.114.238873".
López-Torrejón, G; Guerra, D; Catalá, R; Salinas, J; del Pozo, JC. 2013. "Identification of SUMO targets by a novel proteomic approach in plants". J Integr Plant Biol. DOI: 10.1111/jipb.12012".
Guerra, D; Mastrangelo, AM; López-Torrejón, G; Marzin, S; Schweizer, P; Stanca, AM; del Pozo, JC; Cattivelli, L; Mazzucotelli, E. 2012. "Identification of a protein network interacting with TdRF1, a wheat RING ubiquitin ligase with a protective role against cellular dehydration". Plant Physiology. DOI: 10.1104/pp.111.183988".
Manzano, C; Ramirez-Parra, E; Casimiro, I; Otero, S; Desvoyes, B; De Rybel, B; Beeckman, T; Casero, P; Gutierrez, C; del Pozo, JC. 2012. "Auxin and Epigenetic Regulation of SKP2B, an F-Box That Represses Lateral Root Formation". Plant Physiology. DOI: 10.1104/pp.112.198341".
Rodríguez-Herva, JJ; González-Melendi, P; Cuartas-Lanza, R; Antúnez-Lamas, M; Rio-Alvarez, I; Li, Z; López-Torrejón, G; Diaz, I; del Pozo, JC; Chakravarthy, S; Collmer, A; Rodríguez-Palenzuela, P; López-Solanilla, E. 2012. "A bacterial cysteine protease effector protein interferes with photosynthesis to suppress plant innate immune responses". Cell Microbiol. DOI: 10.1111/j.1462-5822.2012.01749.x".
Abraham, Z; del Pozo, JC. 2011. "Ectopic expression of E2FB, a cell cycle transcription factor, accelerates flowering and increases fruit yield in tomato". Journal of Plant Growth Regulation. DOI: 10.1007/s00344-011-9215-y".
Bratzel, F; López-Torrejón, G; Koch, M; del Pozo, JC; Calonje, M. 2010. "Keeping cell identity in Arabidopsis requires PRC1 RING-Finger homologs that catalyze H2A monoubiquitination". Current Biology. DOI: 10.1016/j.cub.2010.09.046".
Desvoyes, B; Sanchez, MP; Ramirez-Parra, E; Gutierrez, C. 2010. "Impact of nucleosome dynamics and histone modifications on cell proliferation during Arabidopsis development". Heredity. DOI: 10.1038/hdy.2010.50".
Jurado, S; Abraham, Z; Manzano, C; López-Torrejón, G; Pacios, LF; del Pozo, JC. 2010. "The Arabidopsis cell cycle F-box protein SKP2A binds to auxin". Plant Cell. DOI: 10.1105/tpc.110.078972".
Pérez-Pérez, JM; Candela, H; Robles, P; López-Torrejón, G; del Pozo, JC; Micol, JL. 2010. "A role for AUXIN RESISTANT3 in the coordination of leaf growth". Plant and Cell Physiology. DOI: 10.1093/pcp/pcq123".
Jurado, S; Díaz-Triviño, S; Abraham, Z; Manzano, C; Gutierrez, C; Pozo, Cd. 2008. "SKP2A, an F-box protein that regulates cell division, is degraded via the ubiquitin pathway". Plant Journal. DOI: 10.1111/j.1365-313X.2007.03378.x".
Jurado, S; Trivino, SD; Abraham, Z; Manzano, C; Gutierrez, C; del Pozo, C. 2008. "SKP2A protein, an F-box that regulates cell division, is degraded via the ubiquitin pathway". Plant Signaling & Behavior. DOI: 10.4161/psb.3.10.5888".
Manzano, C; Abraham, Z; López-Torrejón, G; del Pozo, JC. 2008. "Identification of ubiquitinated proteins in Arabidopsis". Plant Molecular Biology. DOI: 10.1007/s11103-008-9358-9".
Ren, H; Santner, A; Pozo, JCd; Murray, JAH; Estelle, M. 2008. "Degradation of the cyclin-dependent kinase inhibitor KRP1 is regulated by two different ubiquitin E3 ligases". Plant Journal. DOI: 10.1111/j.1365-313X.2007.03370.x".
Barrero, JM; Gonzalez-Bayon, R; del Pozo, JC; Ponce, MR; Micol, JL. 2007. "INCURVATA2 encodes the catalytic subunit of DNA Polymerase alpha and interacts with genes involved in chromatin-mediated cellular memory in Arabidopsis thaliana". Plant Cell. DOI: 10.1105/tpc.107.054130".
del Pozo, JC; Diaz-Trivino, S; Cisneros, N; Gutierrez, C. 2007. "The E2FC-DPB transcription factor controls cell division, endoreplication and lateral root formation in a SCF(SKP2A)-dependent manner". Plant Signaling & Behavior. DOI: 10.4161/psb.2.4.3897".
Ramirez-Parra, E; del Pozo, JC; Desvoyes, B; de la Paz Sanchez, M; Gutierrez, C. 2007. "E2F–DP transcription factors", p. 138-163, Annual Plant Reviews Volume 32: Cell Cycle Control and Plant Development. Blackwell Publishing Ltd. DOI: 10.1002/9780470988923.ch6".
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