Biology subjects

Mateos, J. L.

Publications and source records attributed to Mateos, J. L..

6 recordsLinked to original sources

bioRxiv2025

In vivo binding by Arabidopsis SPLICING FACTOR 1 shifts 3' splice site choice, regulating circadian rhythms and immunity 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. SignificancePre-mRNA splicing is a fundamental process that shapes gene expression and proteome diversity, yet how it integrates with physiological pathways in plants remains poorly understood. Our study identifies the spliceosomal component SPLICING FACTOR1 (AtSF1) as a central modulator of alternative 3' splice site choice in Arabidopsis thaliana. By defining branch point sequences and direct RNA targets of AtSF1 in vivo, we reveal its dual regulatory role in circadian timing and immune responses. Comparative analysis with human SF1 uncovers a distinct domain architecture in the plant homolog, suggesting an alternative RNA-binding mode that evolved to meet plant-specific demands. These findings illuminate how conserved splicing machinery was molecularly adapted in the plant lineage to coordinate RNA processing with environmental and developmental cues.

plant biology↗

bioRxiv2025

What Large Language Models Know About Plant Molecular Biology

Large language models (LLMs) are rapidly permeating scientific research, yet their capabilities in plant molecular biology remain largely uncharacterized. Here, we present MOBIPLANT, the first comprehensive benchmark for evaluating LLMs in this domain, developed by a consortium of 112 plant scientists across 19 countries. MOBIPLANT comprises 565 expert-curated multiple-choice questions and 1,075 synthetically generated questions, spanning core topics from gene regulation to plant-environment interactions. We benchmarked seven leading chat-based LLMs using both automated scoring and human evaluation of open-ended answers. Models performed well on multiple-choice tasks (exceeding 75% accuracy), although most of them exhibited a consistent bias towards option A. In contrast, expert reviews exposed persistent limitations, including factual misalignment, hallucinations, and low self-awareness. Critically, we found that model performance strongly correlated with the citation frequency of source literature, suggesting that LLM knowledge inherits the visibility distribution of the underlying scientific corpus. Consequently, models tend to be more reliable on consolidated topics and less reliable on under-cited or recently emerging ones. We also benchmarked agents equipped with web-search and additional tools in more complex tasks involving DNA sequence analysis. These agents were outperformed by domain specific models in sequence classification and regression tasks, indicating an opportunity for joint agentic systems that combine both the reasoning power of LLMs and the dedicated processing of DNA models. This understanding is key to guiding both the development of next-generation models and the informed use of current tools in the everyday work of plant researchers. MOBIPLANT is publicly available online in this link.

plant biology↗

bioRxiv2024

Assessing the role of AtGRP7 arginine 141, a target of dimethylation by PRMT5, in flowering time control

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 (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 AtGRP7s 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 extend 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, AtGRP7 R141 contributes to the activity of GRP7 in response to abscisic. 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.

plant biology↗

bioRxiv2023

Antagonistic effects of arginine methylation of LSM4 on alternative splicing during plant stress responses

Arabidopsis PROTEIN ARGININE METHYLTRANSFERASE 5 (PRMT5) post-translationally modifies RNA-binding proteins by arginine (R) methylation. The impact of this modification on the regulation of RNA processing is largely unknown. Here we use LSM4, a component of the spliceosome, as a paradigm to study the impact of R-methylation on its function in RNA processing. We identify in vivo targets of LSM4 and show that LSM4 regulates alternative splicing of a suite of them. Furthermore, LSM4 affects mRNA levels of some of the targets, showing for the first time its role in both AS and steady-state abundance. The lsm4 and prmt5 mutants show a considerable overlap of genes with altered splicing patterns, suggesting that these might be regulated by PRMT5-dependent LSM4 methylation. Wild-type LSM4 and an unmethylable version complement the lsm4-1 growth and circadian rhythms defects, suggesting that methylation is not critical for growth in normal environments. However, LSM4 methylation increases with ABA and is necessary for plants to respond properly to salt stress. In contrast, LSM4 methylation is reduced by bacterial infection, and plants expressing unmethylable LSM4 are more resistant than plants expressing wild-type LSM4. This tolerance correlates with decreased intron retention of immune-response genes upon infection, augmenting the functional isoform. Taken together, this provides the first direct evidence that R methylation adjusts LSM4 function on pre-mRNA splicing in an antagonistic manner in response to biotic and abiotic stress. HighlightPlease provide a statement that, in fewer than 30 words, highlights the novelty of the paper for the non-expert. Arginine methylation of the LSM4 spliceosome component by PROTEIN ARGININE METHYLTRANSFERASE 5 fine-tunes alternative splicing of a set of stress-related genes to antagonistically control biotic and abiotic responses in Arabidopsis.

plant biology↗

bioRxiv2022

PICLN modulates alternative splicing and ensures adaptation to light and temperature changes in plants

Plants undergo transcriptome reprogramming to adapt to daily and seasonal fluctuations in light and temperature conditions. While most efforts have focused on the role of master transcription factors, the importance of splicing factors modulating these processes is now emerging. Efficient pre-mRNA splicing depends on proper spliceosome assembly, which in plants and animals requires the methylosome complex. PICLN is part of the methylosome complex in both humans and Arabidopsis thaliana, and we show here that the human PICLN ortholog rescues phenotypes of A. thaliana picln mutants. Altered photomorphogenic and photoperiodic responses in A. thaliana picln mutants are associated with changes in pre-mRNA splicing, which partially overlap with those in prmt5 mutants. Mammalian PICLN also acts in concert with the Survival Motor Neuron (SMN) complex component GEMIN2 to modulate the late steps of UsnRNP assembly, and many alternative splicing events regulated by PICLN but not PROTEIN-ARGININE METHYL TRANSFERASE 5 (PRMT5), the main protein of the methylosome, are controlled by A. thaliana GEMIN2. As with GEMIN2 and SME1/PCP, low temperature, which increases PICLN expression, aggravates morphological and molecular defects of picln mutants. Taken together, these results establish a key role for PICLN in the regulation of pre-mRNA splicing and in mediating plant adaptation to daily and seasonal fluctuations in environmental conditions.

plant biology↗

bioRxiv2021

Arabidopsis Mediator subunit 17 connects transcription with DNA repair after UV-B exposure

Mediator 17 (MED17) is a subunit of the Mediator complex that regulates transcription initiation in eukaryotic organisms. In yeast and humans, MED17 also participates in DNA repair, physically interacting with proteins of the Nucleotide Excision DNA Repair system. We here analyzed the role of MED17 in Arabidopsis plants exposed to UV-B radiation, which role has not been previously described. Comparison of med17 mutant transcriptome to that of WT plants showed that almost one third of transcripts with altered expression in med17 plants are also changed by UV-B exposure in WT plants. To validate the role of MED17 in UV-B irradiated plants, plant responses to UV-B were analyzed, including flowering time, DNA damage accumulation and programmed cell death in the meristematic cells of the root tips. Our results show that med17 and OE MED17 plants have altered responses to UV-B; and that MED17 participates in various aspects of the DNA damage response (DDR). Increased sensitivity to DDR after UV-B in med17 plants can be due to altered regulation of UV-B responsive transcripts; but additionally MED17 physically interacts with DNA repair proteins, suggesting a direct role of this Mediator subunit during repair. Finally, we here also show that MED17 is necessary to regulate the DDR activated by ATR, and that PDCD5 overexpression reverts the deficiencies in DDR shown in med17 mutants. Together, the data presented demonstrates that MED17 is an important regulator of the DDR after UV-B radiation in Arabidopsis plants. One sentence summaryIn Arabidopsis, MED17 regulates the DNA damage response after UV-B exposure transcriptionally modulating the expression of genes and possibly also physically interacting with DNA repair proteins.

plant biology↗