Biology subjects

Calonje, M.

Publications and source records attributed to Calonje, M..

5 recordsLinked to original sources

bioRxiv2026

SELF-PRUNING 5G interplays with age and gibberellin pathways downstream of SlCOL1 to orchestrate photoperiodic tomato flowering

Tomato (Solanum lycopersicum) is classified as a day-neutral plant, whereas its wild relatives exhibit delayed flowering under long day (LD) conditions due to higher activity of the SELF-PRUNING 5G (SP5G). In Arabidopsis thaliana, CONSTANS (CO) activates FLOWERING LOCUS T (FT), a homolog of SP5G, but whether and how CO integrates with SP5G in tomato flowering was unclear. Here, we demonstrate that SlCOL1 (the tomato CO homolog) delays flowering by directly activating SP5G in a PHYTOCHROME B1 (PHYB1)-dependent manner. Importantly, genetic and molecular analyses combining a photoperiod-responsive tomato line carrying the wild SP5G allele from S. pennellii, together with SlCOL1 and flowering-pathway mutants, revealed synergistic crosstalk among the photoperiodic SlCOL1-SP5G module, age-dependent pathway (mediated mainly by the microRNA156-SlSBP module), gibberellin (GA) pathway, and SINGLE FLOWER TRUSS (SFT) pathway. Mechanistically, we show that SP5G forms a complex with miR156-targeted SlSBP13 to directly regulate SFT expression, and that GA may interfere with SP5G activity. Together, these findings revealed a coordinated network that integrates multiple flowering signals to modulate both shared and pathway-specific targets. Our findings provide a significant advance in understanding the molecular regulation of tomato flowering and offer promising avenues for breeding strategies optimized for diverse environmental conditions and latitudes.

plant biology↗

bioRxiv2026

Noncanonical loops regulated by EMF1 and cohesin-associated factors shape the distinct 3D genome architecture in plants

In mammals, cohesin-mediated chromatin loop extrusion is blocked at boundaries, where CTCF, WAPL, and PDS5s co-bind and regulate cohesin, establishing an impermeable barrier with no exceptions. In contrast, our study revealed that in Arabidopsis, some noncanonical contacts have emerged between the boundary flanking regions, which suggest that cohesin is not absolutely blocked but enables sliding beyond boundaries. We identified these interactions as noncanonical loops and clarified their regulatory proteins. Firstly, the plant-specific boundary binding protein EMF1 is essential for noncanonical loops formation. Surprisingly, although both Arabidopsis WAPLs and PDS5s inhibit loop extension as mammals, PDS5s do not co-bind and cooperate with WAPLs at boundaries. Instead, PDS5s bind to boundary-flanking regions enriched with H3K4me1 through their Tudor domains, restricting further extension of noncanonical loops. Consequently, pds5a/b/c mutants lose noncanonical loops, resulting in emergence of larger canonical loops but anchored on boundaries and co-upregulation of anchored gene pairs. Collectively, our findings reveal that the plant-specific noncanonical loop, regulated by plant-specific EMF1 and PDS5 proteins, is the fundamental structure of the distinctive chromatin organization of plants, which provides novel mechanistic insights into eukaryotic chromatin architecture regulation.

plant biology↗

bioRxiv2022

Cycad phylogeny predicts host plant use of Eumaeus butterflies

Eumaeus butterflies are obligate herbivores of Zamia, the most diverse neotropical genus of cycads. Eumaeus-Zamia interactions have been mainly characterized for species distributed in North and Central America. However, host plant use by the southern Eumaeus clade remains largely unknown, precluding a comprehensive study of co-evolution between the genera. Here, we combine fieldwork with museum and literature surveys to expand herbivory records for Eumaeus from 21 to 38 Zamia species. We inferred a time-calibrated phylogeny of Eumaeus to test for distinct macroevolutionary scenarios of host plant conservatism and co-evolution. We found remarkable coincidence between Eumaeus and Zamia diversification, with the butterfly stem group diverging at the same time as the most recent radiation of Zamia in the Miocene. Cophylogenetic reconciliation analyses show a strong cophylogenetic signal between cycads and their butterfly herbivores. Bipartite model-based approaches indicate that this is because closely related Zamia species are used by the same Eumaeus species, suggesting host plant resource tracking by the butterfly herbivores. Our results highlight a case of tight evolution between Eumaeus butterflies and cycads, pointing to the generality of correlated evolution and phylogenetic tracking in plant-herbivore interactions across seed plants.

evolutionary biology↗

bioRxiv2020

Dissection of PRC1 and PRC2 recruitment in Arabidopsis connects EAR repressome to PRC2 anchoring

PcG complexes ensure that every cell in an organism expresses the genes needed at a particular stage, time or condition. However, it is still not fully understood how PRC1 and PRC2 are recruited to target genes in plants. Recent results in Arabidopsis support that PRC2 recruitment is mediated by different TFs. However, it is unclear how all these TFs interact with PRC2 and whether they can also recruit PRC1 activity. Here, by using a system to in vivo bind selected factors to a synthetic promoter lacking the complexity of PcG target promoters, we show that while VAL1 binding recapitulates PRC1 and PRC2 marking, the binding of other TFs only render PRC2 marking. Interestingly, all these TFs contain an EAR domain that acts as docking point for PRC2 and HDACs, connecting two different repressive mechanisms. Furthermore, we show that different TFs act synergistically in PRC2 anchoring to maintain a long-term repression.

plant biology↗

bioRxiv2020

The evolution of red colour vision is linked to coordinated rhodopsin tuning in lycaenid butterflies

Colour vision is largely mediated by changes in number, expression, and spectral properties of rhodopsins, but the genetic mechanisms underlying adaptive shifts in spectral sensitivity remain largely unexplored. Using in vivo photochemistry, optophysiology, and in vitro functional assays, we link variation in eye spectral sensitivity at long wavelengths to species-specific absorbance spectra for LW opsins in lycaenid butterflies. In addition to loci specifying an ancestral green-absorbing rhodopsin with maximum spectral sensitivity ({lambda}max) at 520-530 nm in Callophrys sheridanii and Celastrina ladon, we find a novel form of red-shifted LW rhodopsin at {lambda}max = 565-570 nm in Arhopala japonica and Eumaeus atala. Furthermore, we show that Ca. sheridanii and Ce. ladon exhibit a smaller bathochromic shift at BRh2 (480-489 nm), and with the ancestral LW rhodopsin, cannot perceive visible red light beyond 600 nm. In contrast, molecular variation at the LW opsin in A. japonica and E. atala is coordinated with tuning of the blue opsin that also shifts sensitivity to longer wavelengths enabling colour discrimination up to 617 nm. We then use E. atala as a model to examine the interplay between red and blue spectral sensitivity. Owing to blue duplicate expression, the spatial distribution of opsin mRNAs within an ommatidium defines an expanded retinal stochastic mosaic of at least six opsin-based photoreceptor classes. Our mutagenesis in vitro assays with BRh1 ({lambda}max = 435 nm) chimeric blue rhodopsins reveal four main residues contributing to the 65 nm bathochromic shift towards BRh2 ({lambda}max = 500 nm). Adaptations in this four-opsin visual system are relevant for discrimination of conspecific reflectance spectra in E. atala. Together, these findings illustrate how functional changes at multiple rhodopsins contribute to the evolution of a broader spectral sensitivity and adaptation in visual performance. Significance StatementRhodopsins are photosensitive protein molecules that absorb specific wavelengths of incoming light and convey colour information in the visual system. We show that molecular evolution in a green insect opsin gene resulted in a shift in its maximal absorbance peak, enabling some lycaenid butterflies to use spectral energy of longer wavelengths (LW) to discriminate colours in the red spectrum better than relatives bearing ancestral green LW rhodopsins. Lycaenids also evolved a duplicate blue opsin gene, and we illustrate an example where species equipped with red LW rhodopsins shifted their blue sensitivity peak to longer wavelengths due to changes in several blue-tuning residues that have evolved repeatedly in different insect lineages. We demonstrate how changes at multiple vision genes in the insect eye effectively create a coordinated mechanism expanding spectral sensitivity for visually guided behaviours such as selecting host plants and mates.

evolutionary biology↗