María José Iglesias

SummaryDevelopmental transitions in plants require regulatory networks that are robust enough to ensure developmental progression while remaining sufficiently plastic to respond to changing environmental conditions. A central regulator of this plasticity is the conserved miR156/157–SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) module, in which these miRNAs represses SPL transcription factors to regulate flowering time and root development (Wang et al., 2009; Wu & Poethig, 2006; Yu et al., 2015). While low temperature has been reported to increase miR156 abundance and repress SPL expression in Arabidopsis (Lee et al., 2010), whether environmental signals selectively reshape the temporal coordination between specific miRNA–target pairs within this otherwise redundant regulatory module has not been established. Here, we show that low temperature specifically advances the phase of MIR157C expression, and that this response requires phytochrome B (phyB). This phase advance aligns miR157 accumulation with peak SPL3 expression, promoting its repression, while other miR156/157 family members remain unaffected. This phase advance is rapidly reversed upon return to warm temperature, restoring the temporal expression profiles of MIR157C and SPL3. Functionally, this selective regulation shapes developmental responses to cold in Arabidopsis plants. Together, our findings reveal that temporal coordination between a miRNA and its target can provide functional specificity, offering a mechanism through which environmental signals can fine-tune developmental responses.

Alternative splicing expands proteome diversity and enables phenotypic plasticity across eukaryotes. In plants, mutations in spliceosomal components impair development and stress responses, but the molecular mechanisms remain unclear. Here, we define the molecular function of SPLICING FACTOR 1 (AtSF1) in Arabidopsis thaliana using individual-nucleotide resolution UV crosslinking and immunoprecipitation combined with RNA sequencing of sf1 mutants. We identify the in vivo branch point sequences bound by AtSF1 and delineate its RNA-binding landscape, revealing pervasive splicing defects dominated by aberrant 3′ splice-site selection. Structural comparison with human SF1 indicates that AtSF1 retains branch point recognition capacity but features a distinct domain organization, including a restructured C-terminal region absent in metazoans, suggesting a divergent RNA-binding mode that evolved to meet plant-specific splicing demands. AtSF1 targets are enriched for core circadian clock and defense genes, consistent with the long-period phenotype and immune-compromised phenotypes of sf1 mutants. Together, these findings establish that AtSF1 orchestrates alternative 3′ splice-site choice through intron binding and branch point recognition, coupling RNA processing with circadian and immune regulation in plants.

Alternative splicing expands proteome diversity and enables phenotypic plasticity across eukaryotes. In plants, mutations in spliceosomal components impair development and stress responses, but the molecular mechanisms remain unclear. Here, we define the molecular function of SPLICING FACTOR1 (AtSF1) in Arabidopsis thaliana using individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) combined with RNA sequencing of sf1 mutants. We identify the in vivo branch point sequences bound by AtSF1 and delineate its RNA- binding landscape, revealing pervasive splicing defects dominated by aberrant 3′ splice site selection. Structural comparison with human SF1 indicates that AtSF1 retains branch point recognition capacity but features a distinct domain organization, including a restructured C-terminal region absent in metazoans, suggesting a divergent RNA-binding mode that evolved to meet plant-specific splicing demands. AtSF1 targets are enriched for core circadian clock and defense genes, consistent with the long-period phenotype and immune-compromised phenotypes of sf1 mutants. Together, these findings establish that AtSF1 orchestrates alternative 3 ́ splice site choice through intron binding and branch point recognition, coupling RNA processing with circadian and immune regulation in plants.

In plants, the ubiquitin–proteasome system (UPS) plays a central role in hormonal regulation, including the action of the phytohormone auxin, which orchestrates numerous aspects of growth and development. Auxin modulates redox metabolism and promotes the accumulation of nitric oxide (NO) in various tissues and physiological contexts. NO functions as a redox signaling molecule, exerting its effects in part through the reversible oxidation of cysteine residues via a post-translational modification known as S-nitrosylation. Recent findings highlight a dynamic interplay between S-nitrosylation and the ubiquitination machinery, shaping critical aspects of auxin-mediated plant responses. In this review, we summarize current knowledge on redox regulation of UPS components involved in auxin-mediated pathways and propose new perspectives on the integration of hormonal and redox signaling in plants. We describe and discuss the complexity of the latest evidence supporting the role of NO as a second messenger in auxin signaling, with S-nitrosylation acting as a regulatory mechanism that fine-tunes the UPS to control developmental outcomes. We focused on the direct effects of NO that include S-nitrosylation of specific cysteine residues of substrates, adaptors, and substrate receptors belonging to different CULLIN1- and CULLIN4-based E3 ubiquitin ligase complexes.

Canopy shade enhances the activity of PHYTOCHROME INTERACTING FACTORs (PIFs) to boost auxin synthesis in the cotyledons. Auxin, together with local PIFs and their positive regulator CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1), promotes hypocotyl growth to facilitate access to light. Whether shade alters the cellular redox status thereby affecting growth responses, remains unexplored. Here, we show that, under shade, high auxin levels increased reactive oxygen species and nitric oxide accumulation in the hypocotyl of Arabidopsis. This nitroxidative environment favored the promotion of hypocotyl growth by COP1 under shade. We demonstrate that COP1 is S-nitrosylated, particularly under shade. Impairing this redox regulation enhanced COP1 degradation by the proteasome and diminished the capacity of COP1 to interact with target proteins and to promote hypocotyl growth. Disabling this regulation also generated transversal asymmetries in hypocotyl growth, indicating poor coordination among different cells, which resulted in random hypocotyl bending and predictably low ability to compete with neighbors. These findings highlight the significance of redox signaling in the control of diffuse growth during shade avoidance.

PROTEIN ARGININE METHYLTRANSFERASES (PRMTs) catalyze arginine (R) methylation that is critical for transcriptional and post-transcriptional gene regulation. In Arabidopsis, PRMT5 that catalyzes symmetric R dimethylation is best characterized. PRMT5 mutants are late-flowering and show altered responses to environmental stress. Among PRMT5 targets are Arabidopsis thaliana GLYCINE RICH RNA BINDING PROTEIN 7 (AtGRP7) and AtGRP8 that promote the transition to flowering. AtGRP7 R141 has been shown to be modified by PRMT5. Here, we tested whether this symmetric dimethylation of R141 is important for AtGRP7’s physiological role in flowering time control. We constructed AtGRP7 mutant variants with non-methylable R141 (R141A, R141K). Genomic clones containing these variants complemented the late-flowering phenotype of the grp7-1 mutant to the same extent as wild-type AtGRP7. Furthermore, overexpression of AtGRP7 R141A or R141K promoted flowering similar to overexpression of the wild-type protein. Thus, flowering time does not depend on R141 and its modification. However, germination experiments showed that R141 contributes to the activity of AtGRP7 in response to abiotic stress reactions mediated by abscisic acid during early development. Immunoprecipitation of AtGRP7-GFP in the prmt5 background revealed that antibodies against dimethylated arginine still recognized AtGRP7, suggesting that additional methyltransferases may be responsible for modification of AtGRP7.

Arginine (R) methylation, catalyzed by PROTEIN ARGININE METHYLTRANSFERASES (PRMTs), is critical for regulation of gene expression at the transcriptional and post-transcriptional level. Among nine PRMT genes in Arabidopsis, PRMT5 catalyzing symmetric R dimethylation of its targets is best characterized. PRMT5 mutants are late flowering and show altered responses to environmental stress. Among PRMT5 targets are Arabidopsis thaliana GLYCINE RICH RNA BINDING PROTEIN 7 ( At GRP7) and At GRP8 that promote the transition to flowering. At GRP7 R141 has been shown to be modified by PRMT5. Here, we tested whether this symmetric dimethylation of R141 is important for At GRP7’s physiological role in flowering time control. We constructed At GRP7 mutant variants with non-methylable R141 (R141A, R141K). Genomic clones containing these variants complemented the late flowering phenotype of the grp7-1 mutant to the same extend as wild-type At GRP7. Furthermore, overexpression of At GRP7 R141A or R141K promoted flowering similar to overexpression of the wild-type protein. Thus, flowering time does not depend on R141 and its modification. However, At GRP7 R141 contributes to the activity of GRP7 in response to abscisic. Immunoprecipitation of At GRP7-GFP in the prmt5 background revealed that antibodies against dimethylated arginine still recognized At GRP7, suggesting that additional methyltransferases may be responsible for modification of At GRP7.