The transcriptional regulator BBX24 impairs DELLA activity to promote shade avoidance in Arabidopsis thaliana

[EN] In response to canopy shade, plant vegetative structures elongate to gain access to light. However, the mechanism that allows a plastic transcriptional response to canopy shade light is not fully elucidated. Here we propose that the activity of PIF4, a key transcription factor in the shade signalling network, is modulated by the interplay between the BBX24 transcriptional regulator and DELLA proteins, which are negative regulators of the gibberellin (GA) signalling pathway. We show that GA-related targets are enriched among genes responsive to BBX24 under shade and that the shade-response defect in bbx24 mutants is rescued by a GA treatment that promotes DELLA degradation. BBX24 physically interacts with DELLA proteins and alleviates DELLA-mediated repression of PIF4 activity. The proposed molecular mechanism provides reversible regulation of the activity of a key transcription factor that may prove especially relevant under fluctuating light conditions.We thank Santiago Mora Garcia for valuable initial discussions and Peter Quail for the PIL1::LUC construct. This work was supported by grants from Agencia Nacional de Promocion Cientifica y Tecnologica, and Universidad de Buenos Aires (to J.F.B), and the Spanish Ministry of Science, BIO2010-15071 (to M.A.B.).Crocco, C.; Locascio ., AAM.; Escudero, CM.; Alabadí Diego, D.; Blazquez Rodriguez, MA.; Botto, J. (2015). The transcriptional regulator BBX24 impairs DELLA activity to promote shade avoidance in Arabidopsis thaliana. Nature Communications. 6:1-10. https://doi.org/10.1038/ncomms7202S1106Valladares, F. & Niinemets, U. Shade tolerance, a key plant feature of complex nature and consequences. Annu. Rev. Ecol. Evol. Syst. 39, 237–257 (2008).Casal, J. J. Photoreceptor signaling networks in plant responses to shade. Annu. Rev. Plant Biol. 64, 403–427 (2013).Botto, J. F. & Coluccio, M. P. Seasonal and plant-density dependency for quantitative trait loci affecting flowering time in multiple populations of Arabidopsis thaliana. Plant Cell Environ. 30, 1465–1479 (2007).Coluccio, M. P., Sánchez, S., Kasulin, L., Yanovsky, M. J. & Botto, J. F. Genetic mapping of natural variation in a shade avoidance response: ELF3 is the candidate gene for a QTL in hypocotyl growth regulation. J. Exp. Bot. 62, 167–176 (2011).Filiault, D. L. & Maloof, J. N. A genome-wide association study identifies variants underlying the Arabidopsis thaliana shade avoidance response. PLoS. Genet. 8, e1002589 (2012).Kasulin, L., Agrofoglio, Y. & Botto, J. F. The receptor-like kinase ERECTA contributes to the shade-avoidance syndrome in a background-dependent manner. Ann. Bot. 111, 811–819 (2013).Leivar, P. & Monte, E. PIFs: systems integrators in plant development. Plant Cell 26, 56–78 (2014).Lorrain, S., Allen, T., Duek, P. D., Whitelam, G. C. & Fankhauser, C. Phytochrome-mediated inhibition of shade avoidance involves degradation of growth-promoting bHLH transcription factors. Plant J. 53, 312–323 (2008).Hornitschek, P., Lorrain, S., Zoete, V., Michielin, O. & Fankhauser, C. Inhibition of the shade avoidance response by formation of non-DNA binding bHLH heterodimers. EMBO J. 28, 3893–3902 (2009).Gangappa, S. N. & Botto, J. F. The BBX family of plant transcription factors. Trends Plant Sci. 19, 460–470 (2014).Crocco, C. D., Holm, M., Yanovsky, M. J. & Botto, J. F. AtBBX21 and COP1 genetically interact in the regulation of shade avoidance. Plant J. 64, 551–562 (2010).Gangappa, S. N. et al. The Arabidopsis B-BOX protein BBX25 interacts with HY5, negatively regulating BBX22 expression to suppress seedling photomorphogenesis. Plant Cell 25, 1243–1257 (2013).Devlin, F. P., Yanovsky, M. J. & Kay, S. A. A genomic analysis of the shade avoidance response in Arabidopsis. Plant Physiol. 133, 1–13 (2003).Hisamatsu, T., King, R. W., Helliwell, C. A. & Koshioka, M. The involvement of gibberellin 20-oxidase genes in phytochrome-regulated petiole elongation of Arabidopsis. Plant Physiol. 138, 1106–1116 (2005).Locascio, A., Blázquez, M. A. & Alabadí, D. Genomic analysis of DELLA protein activity. Plant Cell Physiol. 54, 1229–1237 (2013).de Lucas, M. et al. A molecular framework for light and gibberellin control of cell elongation. Nature 451, 480–486 (2008).Feng, S. et al. Coordinated regulation of Arabidopsis thaliana development by light and gibberellins. Nature 451, 475–480 (2008).Djakovic-Petrovic, T., de Wit, M., Voesenek, L. A. C. J. & Pierik, R. DELLA protein function in growth responses to canopy signals. Plant J. 51, 117–126 (2007).Pierik, R., de Wit, M. & Voesenek, L. A. C. J. Growth-mediated stress escape: convergence of signal transduction pathways activated upon exposure to two different environmental stresses. New Phytol. 189, 122–134 (2011).Colebrook, E. H., Thomas, S. G., Phillips, A. L. & Hedden, P. The role of gibberellin signalling in plant responses to abiotic stress. J. Exp. Biol. 217, 67–75 (2014).Holtan, H. E. et al. BBX32, an Arabidopsis B-Box protein, functions in light signaling by suppressing HY5-regulated gene expression and interacting with STH2/BBX21. Plant Physiol. 156, 2109–2123 (2011).Xu, D. et al. Convergence of light and ABA signaling on the ABI5 promoter. PLoS. Genet. 10, e1004197 (2014).Pierik, R., Djakovic-Petrovic, T., Keuskamp, D. H., de Wit, M. & Voesenek, L. A. C. J. Auxin and ethylene regulate elongation responses to neighbor proximity signals independent of gibberellin and DELLA proteins in Arabidopsis. Plant Physiol. 149, 1701–1712 (2009).Keuskamp, D. H. et al. Blue-light-mediated shade avoidance requires combined auxin and brassinosteroid action in Arabidopsis seedlings. Plant J. 67, 208–217 (2011).Li, L. et al. Linking photoreceptor excitation to changes in plant architecture. Genes Dev. 26, 785–790 (2012).Hornitschek, P. et al. Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling. Plant J. 71, 699–711 (2012).Leivar, P. et al. Dynamic antagonism between phytochromes and PIF family basic helix-loop-helix factors induces selective reciprocal responses to light and shade in a rapidly responsive transcriptional network in Arabidopsis. Plant Cell 24, 1398–1419 (2012).Oh, E., Zhu, J.-Y. & Wang, Z.-Y. Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses. Nat. Cell Biol. 14, 802–809 (2012).Dill, A. & Sun, T. P. Synergistic derepression of gibberellin signaling by removing RGA and GAI function in Arabidopsis thaliana. Genetics 159, 777–785 (2001).Cole, B., Kay, S. A. & Chory, J. Automated analysis of hypocotyl growth dynamics during shade avoidance in Arabidopsis. Plant J. 65, 991–1000 (2011).Zhang, Y. et al. A quartet of PIF bHLH factors provides a transcriptionally centered signaling hub that regulates seedling morphogenesis through differential expression-patterning of shared target genes in Arabidopsis. PLoS. Genet. 9, e1003244 (2013).Leivar, P. et al. Definition of early transcriptional circuitry involved in light-induced reversal of PIF-imposed repression of photomorphogenesis in young Arabidopsis seedlings. Plant Cell 21, 3535–3553 (2009).Willige, B. C. et al. The DELLA domain of GA INSENSITIVE mediates the interaction with the GA INSENSITIVE DWARF1A gibberellin receptor of Arabidopsis. Plant Cell 19, 1209–1220 (2007).Davière, J.-M. & Achard, P. Gibberellin signaling in plants. Develop 140, 1147–1151 (2013).Lim, S. et al. ABA-INSENSITIVE3, ABA-INSENSITIVE5, and DELLAs interact to activate the expression of SOMNUS and other high-temperature-inducible genes in imbibed seeds in Arabidopsis. Plant Cell 25, 4863–4878 (2013).Yoshida, H. et al. DELLA protein functions as a transcriptional activator through the DNA binding of the indeterminate domain family proteins. Proc. Natl Acad. Sci. USA 111, 7861–7866 (2014).Yamaguchi, N. et al. Gibberellin acts positively then negatively to control onset of flower formation in Arabidopsis. Science 344, 638–641 (2014).Stavang, J. et al. Hormonal regulation of temperature-induced growth in Arabidopsis. Plant J. 60, 589–601 (2009).Achard, P. et al. DELLAs contribute to plant photomorphogenesis. Plant Physiol. 143, 1163–1172 (2007).Arana, M. V., Marín-de la Rosa, N., Maloof, J. N., Blázquez, M. A. & Alabadí, D. Circadian oscillation of gibberellin signaling in Arabidopsis. Proc. Natl Acad. Sci. USA 108, 9292–9297 (2011).Bai, M.-Y., Fan, M., Oh, E. & Wang, Z.-Y. A triple helix-loop-helix/basic helix-loop-helix cascade controls cell elongation downstream of multiple hormonal and environmental signaling pathways in Arabidopsis. Plant Cell 24, 4917–4929 (2012).Ikeda, M., Fujiwara, S., Mitsuda, N. & Ohme-Takagi, M. A triantagonistic basic helix-loop-helix system regulates cell elongation in Arabidopsis. Plant Cell 24, 4483–4497 (2012).Yang, D.-L. et al. Plant hormone jasmonate prioritizes defense over growth by interfering with gibberellin signaling cascade. Proc. Natl Acad. Sci. USA 109, E1192–E1200 (2012).Ciolfi, A. et al. Dynamics of the shade-avoidance response in Arabidopsis. Plant Physiol. 163, 331–353 (2013).Indorf, M., Cordero, J., Neuhaus, G. & Rodríguez-Franco, M. Salt tolerance (STO), a stress-related protein, has a major role in light signalling. Plant J. 51, 563–574 (2007).Gallego-Bartolomé, J., Kami, C., Fankhauser, C., Alabadí, D. & Blázquez, M. A. A hormonal regulatory module that provides flexibility to tropic responses. Plant Physiol. 156, 1819–1825 (2011).Earley, K. W. et al. Gateway-compatible vectors for plant functional genomics and proteomics. Plant J. 45, 616–629 (2006).Tusher, V. G., Tibshirani, R. & Chu, G. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci. USA 98, 5116–5121 (2001).Gallego-Bartolomé, J. et al. Molecular mechanism for the interaction between gibberellin and brassinosteroid signaling pathways in Arabidopsis. Proc. Natl Acad. Sci. USA 109, 13446–13451 (2012).Belda-Palazón, B. et al. Aminopropyltransferases involved in polyamine biosynthesis localize preferentially in the nucleus of plant cells. PLoS ONE 7, e46907 (2012).Gallego-Bartolomé, J., Alabadí, D. & Blázquez, M. A. DELLA-induced early transcriptional changes during etiolated development in Arabidopsis thaliana. PLoS ONE 6, e23918 (2011).Piskurewicz, U. et al. The gibberellic acid signaling repressor RGL2 inhibits Arabidopsis seed germination by stimulating abscisic acid synthesis and ABI5 activity. Plant Cell 20, 2729–2745 (2008).Paz-Ares, J. REGIA, an EU project on functional genomics of transcription factors from Arabidopsis thaliana. Comp. Funct. Genomics 3, 102–108 (2002)

Demographic history and genetic diversity of modern and herbarium collections of Arabidopsis thaliana from the Southern Hemisphere

The model plant, Arabidopsis thaliana, has a native range throughout Eurasia and North Africa and introduced populations have been found on several additional continents. Through the RegMap and 1001 Genomes projects, high resolution genetic data has been obtained for thousands of A. thaliana populations that are mostly distributed throughout the Northern Hemisphere. To gain insight into the genetic variation and demographic history of introduced populations of A. thaliana in the Southern Hemisphere, we collected plants from four ecologically diverse sites at the southernmost end of the species distribution in Patagonia, Argentina. Two of the sites were spaced 5 km apart on the south side of Lake Buenos Aires and two neighboring sites were selected 70 km away on the north side of the lake. Individuals collected exhibited a wide range of phenotypic characteristics. We analyzed the genetic diversity by low-resolution SNP genotyping and whole-genome sequencing. We also performed whole-genome sequencing of the DNA from an herbarium specimen collected from this region in 1967. We found that individuals from all four present-day populations were essentially genetically uniform across 149 SNP markers. Whole-genome sequencing revealed that only a small fraction of the genome was segregating among these strains. Genetic comparisons with the RegMap panel and 1001 Genomes data suggested a likely European origin for these populations. Sequencing data from the herbarium specimen revealed that the presentday populations are essentially the same as they were nearly half a century ago. We conclude that populations of A. thaliana in Patagonia were likely founded by an extremely small number of individuals and that phenotypic plasticity may have contributed to their persistence in the region despite their limited genetic diversity

Faithful modeling of transient expression and its application to elucidating negative feedback regulation

Modeling and analysis of genetic regulatory networks is essential both for better understanding their dynamic behavior and for elucidating and refining open issues. We hereby present a discrete computational model that effectively describes the transient and sequential expression of a network of genes in a representative developmental pathway. Our model system is a transcriptional cascade that includes positive and negative feedback loops directing the initiation and progression through meiosis in budding yeast. The computational model allows qualitative analysis of the transcription of early meiosis-specific genes, specifically, Ime2 and their master activator, Ime1. The simulations demonstrate a robust transcriptional behavior with respect to the initial levels of Ime1 and Ime2. The computational results were verified experimentally by deleting various genes and by changing initial conditions. The model has a strong predictive aspect, and it provides insights into how to distinguish among and reason about alternative hypotheses concerning the mode by which negative regulation through Ime1 and Ime2 is accomplished. Some predictions were validated experimentally, for instance, showing that the decline in the transcription of IME1 depends on Rpd3, which is recruited by Ime1 to its promoter. Finally, this general model promotes the analysis of systems that are devoid of consistent quantitative data, as is often the case, and it can be easily adapted to other developmental pathways