MOLECULAR BASES OF PLANT DEVELOPMENTAL PHASE TRANSITIONS

Group leader: Jose Antonio Jarillo Quiroga - Research Professor INIA
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Group leader: Manuel Angel Piñeiro Galvín - Research Professor INIA
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Personnel:


During their life cycle plants undergo a number of developmental phases, including embryonic, vegetative and reproductive development. These developmental stages are characterised by specific patterns of cellular differentiation. The switch from a developmental phase to the next is under the control of spatial and temporal patterns of gene expression, so that selective activation or silencing of genes directs plant development through different phase changes. Our group is focused on understanding the molecular mechanisms involved in the regulation of plant developmental transitions. In particular we are interested in phase transitions such as flowering and germination with adaptive value for plant species as well as a significant impact on crop yield.


The floral transition marks the opening of the reproductive development and the timing of this developmental switch is essential to determine the reproductive success of plant species. For that reason plants tune very precisely the time of flowering initiation in response to both endogenous and environmental factors, ensuring that the production of flowers and fruits take place under optimal conditions. Using the model plant species Arabidopsis thaliana, and related Brassicaceae species, we are focused on studying the mechanisms that work to repress flowering until plants reach a particular developmental stage or are under optimal environmental conditions.


In addition, we are interested in the molecular basis of germination repression during seed dormancy in Arabidopsis. As for the floral transition, germination is also under the control of both endogenous and environmental factors, ensuring that seed growth is restarted under optimal conditions for the survival of the organism. Dormancy, or the transitory inability of viable seeds to germinate under favourable conditions, is from that point of view a trait with a high adaptive value and relevance in cultivated species.

Relevant results

Plant specific proteins EBS and SHL mediate chromatin-dependent repression of Arabidopsis master genes of flowering, reproductive development and dormancy.

We have characterized two Arabidopsis homologous genes, SHL and EBS, which encode effector proteins with functional domains specifically recognizing histone modifications (Mouriz et al., 2015) essential for gene expression control in eukaryotic organisms. Both proteins are involved in the chromatin-mediated repression of flowering and have independent roles in controlling master genes of flowering time. The proteins SHL and EBS are necessary to maintain an inactive chromatin conformation of the genes that act in Arabidopsis as switches of flowering initiation such as FT and SOC1. Both proteins interact with histone deacetylases, contributing to the silencing of flowering genes during vegetative growth (López-González et al., 2014). EBS is involved in additional processes occurring during reproductive growth such as inflorescence architecture, flower initiation and floral organ identity. We are following transcriptomics and Chromatin Immunoprecipitation (ChIP) approaches (Komar et al., 2016; Jarillo et al., 2018) to identify genes that mediate the function of EBS in the regulation of these developmental processes. Furthermore, we have revealed an additional role for this chromatin protein in the control of seed dormancy, emphasizing the relevance of crosstalk between histone modifications for the tight regulation of the period of quiescence in seeds (Narro-Diego et al., 2017).


EBS and SHL belong to a family of plant specific chromatin remodelling factors, and play partially redundant roles in the control of flowering time in Arabidopsis..
 

 

The PHYB-HOS1-CO module integrates red-light signals into Arabidopsis flowering regulation.

In Arabidopsis, the ability to distinguish day-length is largely the result of the complex regulation of the CO gene, both at the transcriptional and post-translational level. The coincidence of CO expression with light in long-day conditions is essential for the promotion of flowering. Besides, different light qualities play specific roles in the photoperiodic response, and while blue and far-red light promote flowering, red light delays it through phyB function. It was already known that CO protein stability is controlled by various light signals during the day, but the molecular mechanism mediating the red light-induced degradation of CO that regulates photoperiodic flowering in Arabidopsis remains to be elucidated. We have revealed a key role for the E3 Ubiquitin Ligase protein HOS1/ESD6 in this mechanism (Lázaro et al, 2012). We have demonstrated that the degradation of CO under red light is prevented in the hos1 and the phyB mutants and thus HOS1 is involved in the red light-mediated degradation of CO. Besides, we have demonstrated that PhyB physically interacts in vivo with HOS1 and CO, suggesting that the mechanism by which CO is degraded under red light relies on the formation of a tripartite complex between these proteins that may be essential to modulate a correct photoperiodic response in Arabidopsis (Lázaro et al, 2015).
 

Hypothetical model for HOS1 function in the photoperiodic flowering control.
 

Arabidopsis DNA Polymerase ɛ recruits components of POLYCOMB REPRESSOR COMPLEX to mediate epigenetic gene silencing of floral integrators.

We have provided an enlightening model for targeting of POLYCOMB REPRESSIVE COMPLEX 2 (PRC2) to newly synthesized DNA for reestablishment of repressive epigenetic marks after dilution by replication, which has important implications in the understanding of epigenetic inheritance in eukaryotic organisms. We have taken advantage of viable PRC2 and DNA polymerase ε esd7 mutations in Arabidopsis to address the mechanism underlying the maintenance of the epigenetic states during replication. We have also presented sound evidence supporting a role for the catalytic subunit of DNA polymerase ϵ ESD7 in preserving high H3K27me3 levels at floral target loci. Using flowering time control as a subject, we have examined the function of the Pol ϵ in epigenetic transcriptional silencing and demonstrated the genetic and molecular interaction of this replication protein with PRC2 (del Olmo et al., 2016). Our studies have also contributed to reveal a role for the plant DNA Pol ϵ in sensing replicative stress (Pedroza Garcia et al., 2017) as well as the involvement of the DNA Pol ϵ regulatory subunit DPB2 in DNA replication, cell cycle regulation and the response to DNA damage (Pedroza Garcia et al., 2016).
 

Working model for the recruitment of components of polycomb repressor complex via Arabidopsis DNA polymerase ε to mediate epigenetic gene silencing.
 

Histone variant H2A.Z and histone acetylation mediate different aspects of chromatin function and modulate flowering responses in Arabidopsis.

During recent years our lab has got a deeper insight into the epigenetic mechanisms that participate in the regulation of the floral transition through the molecular and genetic characterization of several Arabidopsis mutations affecting subunits of the plant SWR1 chromatin remodeling complex, which catalyzes the exchange of H2A histone by the H2A.Z variant and that regulates flowering time in plants. Previously, we have characterized the ESD1 locus, encoding ARP6, a nuclear protein similar to conventional actin, and also the AtSWC6 locus, that encodes a zinc finger-harboring protein. Both proteins are part of the SWR1 complex and mutations in the corresponding genes cause an acceleration of flowering (Jarillo & Piñeiro, 2015). In addition, we have studied AtSWC4 and AtYAF9-like proteins, whose yeast orthologues are present in the SWR1 complex and are shared by the HAT complex NuA4, indicating a possible functional interplay between these two complexes. We have already demonstrated that mutations in these homologues and in other NuA4-C subunits such as EAF3 and ING homologues confer alterations in flowering time and in other developmental responses. Remarkably, we have recently showed that SWC4 specifically binds AT-rich elements in regulatory regions of target genes such as the floral integrator FT, and participates in the recruitment of the SWR1 complex and H2A.Z deposition to modulate gene expression (Gómez-Zambrano et al., 2018). On the same way, we have demonstrated that Arabidopsis YAF9 histone readers modulate flowering time through NuA4-complex-dependent H4 and H2A.Z histone acetylation at FLC chromatin (Crevillen et al., 2019).


We are currently analyzing the function displayed by additional NuA4 complex subunits in the regulation of flowering time in response to environmental factors and in other biological processes (Espinosa-Cores et al., 2020). Our analyses will shed light on the distinct roles that different NuA4 components play in the flowering response of Arabidopsis and Brassica crops to temperature and photoperiodic cues.
 

Functions of the putative NuA4 subunits in different plant biological responses..
 

Securing yield stability of Brassica crops in changing climate conditions.

Our group is not only translating the knowledge from model species such as Arabidopsis to crops, but we are also addressing biological problems with impact in crop yield in cultivated species. Crop yield stability relies on the adaptive response of key developmental traits to fluctuating environmental cues often associated to climate change. In this context, the interest of the laboratory aims at understanding the mechanisms of adaptability of oilseed rape to suboptimal environmental conditions by uncovering the genetic, physiological and molecular bases of the regulation of flowering time in relation to environmental factors such as temperature and their impact on crop yield. Our group is currently focused on assessing the influence of warm temperature on oilseed rape (canola; Brassica napus), B. rapa and B. oleraceae flowering and understanding how epigenetic mechanisms and chromatin remodelling processes mediate flowering responses to temperature in crop species. We have recently revealed that high ambient temperature leads to reduced FT expression and delayed flowering in Brassica rapa via a mechanism associated with H2A.Z dynamics (Del Olmo et al., 2019).

Further work in other crop species like tomato has led us to reveal the involvement of chromatin –associated proteins in the regulation of developmental processes such as pollen ontogeny (Pérez-Martín et al., 2018).

Moreover, our group has contributed to unveil the involvement of regulatory pathways controlling flowering time in additional biological processes such as the interaction of plants with parasitic nematodes. Specifically, we have shown that the regulatory module miRNA172/TOE1/FT, previously implicated in the regulation of floral transition, plays a key role in the cellular and molecular alterations that take place in the feeding sites of root nematodes during infection (Diaz-Manzano et al., 2018). Recently, we have also contributed to uncover a new spliceosome component, SME1, which controls plant development (Including floral transition) and responses to abiotic stress by determining spliceosome activity specificity (Huertas et al., 2019).


Representative Publications

Boter, M., Pozas, J., Jarillo, J.A., Piñeiro, M., Pernas, M. 2023. Brassica napus Roots Use Different Strategies to Respond to Warm Temperatures. International Journal of Molecular Sciences 24,1143. DOI: 10.3390/ijms24021143

Abelenda, J.A., Trabanco, N., Olmo, I. del, Pozas, J., Martín-Trillo, M. del M., Gómez-Garrido, J., Esteve-Codina, A., Pernas, M., Jarillo, J.A., Piñeiro, M. 2022. High ambient temperature impacts on flowering time in Brassica napus through both H2A.Z-dependent and independent mechanisms. Plant, Cell & Environment. DOI: 10.1111/pce.14526

Barrero-Gil, J., Bouza-Morcillo, L., Espinosa-Cores, L., Piñeiro, M., Jarillo, J.A. 2022. H4 acetylation by the NuA4 complex is required for plastid transcription and chloroplast biogenesis. Nature Plants 1–12. DOI: 10.1038/s41477-022-01229-4

Poza-Viejo, L., Payá-Milans, M., Martín-Uriz, P.S., Castro-Labrador, L., Lara-Astiaso, D., Wilkinson, M.D., Piñeiro, M., Jarillo, J.A., Crevillén, P. 2022. Conserved and distinct roles of H3K27me3 demethylases regulating flowering time in Brassica rapa. Plant, Cell & Environment n/a. DOI: 10.1111/pce.14258

Barrero-Gil, J., Mouriz, A., Piqueras, R., Salinas, J., Jarillo, J.A., Piñeiro, M. 2021. A MRG-operated chromatin switch at SOC1 attenuates abiotic stress responses during the floral transition. Plant Physiology. DOI: 10.1093/plphys/kiab275

Espinosa-Cores, L., Bouza-Morcillo, L., Barrero-Gil, J., Jiménez-Suárez, V., Lázaro, A., Piqueras, R., Jarillo, J.A., Piñeiro, M. 2020. Insights Into the Function of the NuA4 Complex in Plants. Frontiers in Plant Science 11, 125. DOI: 10.3389/fpls.2020.00125

del Olmo, I., Poza‐Viejo, L., Piñeiro, M., Jarillo, J.A., Crevillén, P. 2019. High ambient temperature leads to reduced FT expression and delayed flowering in Brassica rapa via a mechanism associated with H2A.Z dynamics. The Plant Journal. DOI: 10.1111/tpj.14446

Crevillén, P., Gómez‐Zambrano, Á., López, J.A., Vázquez, J., Piñeiro, M., Jarillo, J.A. 2019. Arabidopsis YAF9 histone readers modulate flowering time through NuA4-complex-dependent H4 and H2A.Z histone acetylation at FLC chromatin. New Phytologist. DOI: 10.1111/nph.15737

Huertas, R., Catalá, R., Jimenez-Gomez, J., Castellano, M.M., Crevillén, P., Piñeiro, M., Jarillo, J.A., Salinas, J. 2019. Arabidopsis SME1 regulates plant development and response to abiotic stress by determining spliceosome activity specificity. The Plant Cell tpc.00689.2018. DOI: 10.1105/tpc.18.00689

Pérez-Martín, F; Yuste-Lisbona, FJ; Pineda, B; García-Sogo, B; del Olmo, I; Alché, JdD; Egea, I; Flores, FB; Piñeiro, M; Jarillo, JA; Angosto, T; Capel, J; Moreno, V; Lozano, R. 2018. "Developmental role of the tomato Mediator complex subunit MED18 in pollen ontogeny". Plant Journal. DOI: 10.1111/tpj.14031".

Jarillo, JA; Komar, DN; Piñeiro, M. 2018. "The use of the chromatin immunoprecipitation technique for in vivo identification of plant protein–DNA interactions", p. 323-334. In L. Oñate-Sánchez (ed.), Two-Hybrid Systems: Methods and Protocols. Springer New York, New York, NY. DOI: 10.1007/978-1-4939-7871-7_23".

Gómez-Zambrano, Á; Crevillén, P; Franco-Zorrilla, JM; López, JA; Moreno-Romero, J; Roszak, P; Santos-González, J; Jurado, S; Vázquez, J; Köhler, C; Solano, R; Piñeiro, M; Jarillo, JA. 2018. "Arabidopsis SWC4 binds DNA and recruits the SWR1 complex to modulate histone H2A.Z deposition at key regulatory genes". Molecular Plant. DOI: 10.1016/j.molp.2018.03.014".

Díaz-Manzano, FE; Cabrera, J; Ripoll, J-J; del Olmo, I; Andrés, MF; Silva, AC; Barcala, M; Sánchez, M; Ruíz-Ferrer, V; de Almeida-Engler, J; Yanofsky, MF; Piñeiro, M; Jarillo, JA; Fenoll, C; Escobar, C. 2018. "A role for the gene regulatory module microRNA172/TARGET OF EARLY ACTIVATION TAGGED 1/FLOWERING LOCUS T (miRNA172/TOE1/FT) in the feeding sites induced by Meloidogyne javanica in Arabidopsis thaliana". New Phytologist. DOI: 10.1111/nph.14839".

Narro-Diego, L; López-González, L; Jarillo, JA; Piñeiro, M. 2017. "The PHD-containing protein EARLY BOLTING IN SHORT DAYS regulates seed dormancy in Arabidopsis". Plant, Cell & Environment. DOI: 10.1111/pce.13046".

Pedroza-Garcia, J-A; Mazubert, C; del Olmo, I; Bourge, M; Domenichini, S; Bounon, R; Tariq, Z; Delannoy, E; Piñeiro, M; Jarillo, JA; Bergounioux, C; Benhamed, M; Raynaud, C. 2017. "Function of the plant DNA Polymerase epsilon in replicative stress sensing, a genetic analysis". Plant Physiology. DOI: 10.1104/pp.17.00031".

Pedroza-Garcia, JA; Domenichini, S; Mazubert, C; Bourge, M; White, C; Hudik, E; Bounon, R; Tariq, Z; Delannoy, E; del Olmo, I; Piñeiro, M; Jarillo Quiroga, Jose A; Bergounioux, C; Benhamed, M; Raynaud, C. 2016. "Role of the Polymerase ϵ sub-unit DPB2 in DNA replication, cell cycle regulation and DNA damage response in Arabidopsis". Nucleic Acids Research. DOI: 10.1093/nar/gkw449".

Olmo, ID; López, JA; Vázquez, J; Raynaud, C; Piñeiro, M; Jarillo, JA. 2016. "Arabidopsis DNA polymerase epsilon recruits components of Polycomb repressor complex to mediate epigenetic gene silencing". Nucleic Acids Research. DOI: 10.1093/nar/gkw156".

Komar, DN; Mouriz, A; Jarillo, JA; Piñeiro, M. 2016. "Chromatin Immunoprecipitation Assay for the Identification of Arabidopsis Protein-DNA Interactions In Vivo". Journal of Visualized Experiments. DOI: 10.3791/53422".

Lazaro, A; Mouriz, A; Piñeiro, M; Jarillo, JA. 2015. "Red light-mediated degradation of CONSTANS by the E3 ubiquitin ligase HOS1 regulates photoperiodic flowering in Arabidopsis". Plant Cell. DOI: 10.1105/tpc.15.00529".

Jarillo, JA; Piñeiro, M. 2015. "H2A.Z mediates different aspects of chromatin function and modulates flowering responses in Arabidopsis". Plant Journal. DOI: 10.1111/tpj.12873".

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".

Jarillo, JA; Gaudin, V; Hennig, L; Köhler, C; Piñeiro, M. 2014. "Plant chromatin warms up in Madrid: Meeting summary of the 3rd European Workshop on Plant Chromatin 2013, Madrid, Spain". Epigenetics. DOI: 10.4161/epi.28094".

López-González, L; Mouriz, A; Narro-Diego, L; Bustos, R; Martínez-Zapater, JM; Jarillo, JA; Piñeiro, M. 2014. "Chromatin-dependent repression of the Arabidopsis floral integrator genes involves plant specific PHD-containing proteins". Plant Cell. DOI: 10.1105/tpc.114.130781".

Piñeiro, M; Jarillo, JA. 2013. "Ubiquitination in the control of photoperiodic flowering". Plant Science. DOI: S0168-9452(12)00216-6 [pii] 10.1016/j.plantsci.2012.10.005".

Castrillo, G; Sánchez-Bermejo, E; de Lorenzo, L; Crevillén, P; Fraile-Escanciano, A; TC, M; Mouriz, A; Catarecha, P; Sobrino-Plata, J; Olsson, S; Leo Del Puerto, Y; Mateos, I; Rojo, E; Hernández, LE; Jarillo, JA; Piñeiro, M; Paz-Ares, J; Leyva, A. 2013. "WRKY6 transcription factor restricts arsenate uptake and transposon activation in Arabidopsis". Plant Cell. DOI: tpc.113.114009 [pii] 10.1105/tpc.113.114009".

Lazaro, A.; Valverde, F.; Pineiro, M.; Jarillo, J.A. 2012. The Arabidopsis E3 Ubiquitin Ligase HOS1 Negatively Regulates CONSTANS Abundance in the Photoperiodic Control of Flowering. Plant Cell 24:982-999.