Biology subjects

Cubas, P.

Publications and source records attributed to Cubas, P..

8 recordsLinked to original sources

bioRxiv2026

The miR319-targeted TCP transcription factors play crucial roles in the establishment of Arabidopsis thaliana shoot architecture in response to carbon and nitrogen availability.

Shoot branching is a highly plastic developmental process that allows plants to adjust their architecture to environmental conditions, such as carbon and nitrogen availability. Although the class II TCP transcription factor BRANCHED1 is a well-established repressor of shoot branching, the contribution of other TCP factors during this process remains less well understood. Here, we show that the miR319-targeted TCP module promotes shoot branching in Arabidopsis thaliana. Overexpression of miR319 reduced rosette branch production, whereas repression of TCP3 activity or triple knockout (KO) mutation in TCP3, TCP4 and TCP10 inhibited branching. Conversely, expression of a miR319-resistant TCP3 triggered a highly branched phenotype, indicating that TCP3 and related miR319 targets act as positive regulators of shoot branching. Genetic analysis with the strigolactone-deficient max4 mutant showed that strigolactones mediate, at least partly, the reduced branching observed in the miR319 overexpressing line and in the tcp3,4,10 triple mutant. Transcriptomic and DNA-binding analyses indicated indirect effect of TCP3 on strigolactone biosynthesis genes. Instead, miR319 overexpression increased the sensitivity of branching to nitrogen limitation and reduced nitrate uptake, thereby increasing the expression of strigolactone synthesis genes. We further show that carbon starvation reduced the transcription levels of miR319-targeted TCPs, independently of miR319 accumulation, and that TCP3 may connect carbon availability to sugar signalling via HEXOKINASE1. Together, our results identify the miR319-targeted TCP module as a positive regulator of shoot branching that links plant architecture to carbon and nitrogen availability.

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

UNVEILING STEM CELL INDUCTION MECHANISMS FROM SPATIOTEMPORAL CELL-TYPE-SPECIFIC GENE REGULATORY NETWORKS IN POSTEMBRYONIC ROOT ORGANOGENSIS

Plants grow continuously by developing new organs, a complex process that requires the formation of specific and functional tissue patterns. Tap root systems, as observed in Arabidopsis thaliana, undergo lateral root formation, a developmental mechanism that necessitates the establishment of stem cell lineages. However, the underlying mechanisms remain poorly understood. We have reconstructed a spatiotemporal cell-type-specific transcriptional map of early lateral root organogenesis in Arabidopsis, profiling single and double fluorescent markers across 8 different cell types in the root stem cell lineage. Employing dynamic Bayesian network inference, based on time-course experiments and developmental time, alongside tree-based methods, we investigated lineage developmental progression and precursor stem-cell specification. Our results reveal a morphogenic cascade of hierarchical interdependent transcription factors driving stem cell initiation, and identify the QC/Endodermis transitioning cells as root stem cell progenitors. The associated formative program involves a profound transcriptomic re-arrangement, which, remarkably, precedes the activation of known stem-cell transcriptional signatures. Our data support a model in which root-stem-cell networks do not initiate stem formation, although various stem cell regulators are involved. Collectively, our study identifies core transcriptional signatures associated with stem cell induction and elucidates the dynamic regulatory mechanism driving early stem cell lineage establishment.

developmental biology↗

bioRxiv2024

Novel Mechanisms of Strigolactone-Induced DWARF14 Degradation in Arabidopsis thaliana

Strigolactones (SLs) are carotenoid-derived compounds that regulate various aspects of plant development, physiological responses and plant interactions with microorganisms. In angiosperms, the SL receptor is the /{beta} hydrolase D14 that, upon SL binding, undergoes conformational changes, triggers SL-dependent responses and hydrolyses SLs. Arabidopsis SL signalling involves the formation of a complex between SL-bound D14, the E3-ubiquitin ligase SCFMAX2 and the transcriptional corepressors SMXL6/7/8 (SMXLs), which become ubiquitinated and degraded by the proteasome. However, the sequence of events that result in SL signalling and the requirement of SL hydrolysis for this process remain unclear. In addition, SL destabilises the D14 receptor. The biological significance of SL-induced D14 degradation is unclear, although it has been proposed to create a negative feedback loop in SL signalling. The current model proposes that D14 degradation occurs after SMXLs ubiquitination and proteolysis, via the same E3-ubiquitin ligase that targets the repressors. In this work we quantitatively studied the degradation dynamics of Arabidopsis D14 in response to SLs in planta. For this, we conducted fluorescence and luminescence assays to monitor D14 stability dynamics upon SL treatments, in transgenic lines expressing D14 fused to GREEN FLUORESCENT PROTEIN (GFP) or LUCIFERASE (LUC), in wild-type and SL-signalling mutant backgrounds. Mutant D14 proteins predicted to be non-functional for SL signalling were also examined, and their capability to bind SLs in vitro was studied using Differential Scanning Fluorimetry (DSF). Finally, we used a non-hydrolysable SL to test the requirements of SL hydrolysis for D14 and SMXL7 degradation. Our research revealed that SL-induced D14 degradation may occur in the absence of SCFMAX2 and/or SMXLs by a proteasome-independent mechanism. Additionally, we observed conditions in which the efficiency of SL-induced degradation of D14 is not aligned with that of SMXL7 degradation. Finally, our results indicate that the hydrolysis of SLs is not a prerequisite to trigger either D14 or SMXL7 degradation. These findings suggest the existence of a regulatory mechanism governing D14 degradation more complex than anticipated, and provide novel insights into the dynamics of SL signalling in Arabidopsis.

plant biology↗

bioRxiv2023

Long noncoding RNA-mediated epigenetic regulation of auxin-related genes controlling shade avoidance syndrome in Arabidopsis thaliana

The long noncoding RNA (lncRNA) AUXIN-REGULATED PROMOTER LOOP (APOLO) recognizes a subset of target loci across the Arabidopsis thaliana genome by forming RNA-DNA hybrids (R-loop) and modulating local three-dimensional chromatin conformation. Here we show that APOLO is involved in regulating the shade avoidance syndrome (SAS) by dynamically modulating the expression of key factors. In response to far-red (FR) light, the expression of APOLO anticorrelates with its target BRANCHED1 (BRC1), a master regulator of shoot branching in Arabidopsis thaliana. APOLO deregulation results in BRC1 transcriptional repression and an increase in the number of branches. APOLO transcriptional accumulation fine-tunes the formation of a repressive chromatin loop encompassing the BRC1 promoter, which normally occurs only in leaves as well as in a late response to FR treatment in axillary buds. In addition, our data reveal that APOLO participates in leaf hyponasty, in agreement with its previously reported role in the control of auxin homeostasis through direct modulation of YUCCA2 (auxin synthesis), PID and WAG2 (auxin efflux). We found that direct application of APOLO RNA to leaves results in a rapid increase in auxin accumulation that is associated with changes in the response of the plants to FR light. Collectively, our data support the view that lncRNAs coordinate the shade avoidance syndrome in Arabidopsis thaliana and shed light on the potential of lncRNAs as bioactive exogenous molecules. Deploying exogenous RNAs that modulate plant-environment interactions are important new tools for sustainable agriculture.

plant biology↗

bioRxiv2022

The miR156-targeted SlSBP15 represses tomato shoot branching via modulating auxin transport and interacting with GOBLET and BRANCHED1b

The microRNA156 (miR156)/SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE (SPL/SBP) regulatory hub is highly conserved among phylogenetically distinct species, but how it interconnects multiple pathways to converge to common integrators controlling shoot architecture is still unclear. Here, we demonstrated that the miR156/SlSBP15 hub modulates tomato shoot branching (SB) by connecting phytohormones with important genetic pathways regulating both axillary bud (AB) development and outgrowth. We verified that plants overexpressing the miR156 (156-OE plants) display high SB, whereas plants overexpressing a miR156-resistant SlSBP15 alelle (rSBP15 plants) display arrested SB and are able to partially restore the wild-type (WT) phenotype in156-OE background. Although rSBP15 plants showed ABs smaller than MT, its activation is dependent on shoot apex-derived auxin transport inhibition. Additionally, hormonal measurements reveal that IAA and ABA concentrations were lower in 156-OE and higher in rSBP15-OE plants. SlSBP15 regulates AB development and outgrowth by inhibiting auxin transport and the activity of GOBLET (GOB), and by interacting with BRANCHED1b (SlBRC1b) at the protein level to control abscisic acid (ABA) levels within ABs. Our data provide a new mechanism by which the miR156/SPL/SBP hub regulates SB, and suggest that SlSBP15 has potential applications in improving tomato architecture.

developmental biology↗

bioRxiv2021

Different plasticity of bud outgrowth at cauline and rosette nodes in Arabidopsis thaliana

Shoot branching is a complex mechanism in which secondary shoots grow from buds that are initiated from meristems established in leaf axils. The model plant Arabidopsis thaliana has a rosette leaf growth pattern in the vegetative stage. After flowering initiation, the main stem starts to elongate with the top leaf primordia developing into cauline leaves. Meristems in arabidopsis are initiated in the axils of rosette or cauline leaves, giving rise to rosette or cauline buds, respectively. Plasticity in the process of shoot branching is regulated by resource and nutrient availability as well as by plant hormones. However, few studies have attempted to test whether cauline and rosette branching are subject to the same plasticity. Here, we addressed this question by phenotyping cauline and rosette branching in three arabidopsis ecotypes and several arabidopsis mutants with varied shoot architectures. Our results show that there is no negative correlation between cauline and rosette branch numbers in arabidopsis, demonstrating that there is no trade-off between cauline and rosette bud outgrowth. Through investigation of the altered branching pattern of flowering pathway mutants and arabidopsis ecotypes grown in various photoperiods and light regimes, we further elucidated that the number of cauline branches is closely related to flowering time. The number or rosette branches has an enormous plasticity compared with cauline branches and is influenced by genetic background, flowering time, light intensity and temperature. Our data reveal different plasticity in the regulation of branching at rosette and cauline nodes and promote a framework for future branching analyses. One sentence summaryDifferent plasticity of branching at cauline and rosette nodes of arabidopsis is revealed through detailed correlative analyses of branching under varied genetic and environmental contexts.

plant biology↗

bioRxiv2020

A gene regulatory network critical for axillary bud dormancy directly controlled by Arabidopsis BRANCHED1

The control of branch outgrowth is critical for plant fitness, stress resilience and crop yield. The Arabidopsis thaliana transcription factor BRANCHED1 (BRC1) plays a pivotal role in this process as it integrates signals that inhibit axillary bud growth to control shoot branching. Despite the remarkable activity of BRC1 as a potent growth inhibitor, the mechanisms by which it promotes and maintains bud dormancy are still largely unknown. Here we combine ChIP-seq, transcriptomic and systems biology approaches to characterise the BRC1-regulated gene network. We identify a group of BRC1 direct target genes encoding transcription factors (BTFs) that orchestrate, together with BRC1, an intricate transcriptional network enriched in abscisic acid signalling components. The BRC1 network is enriched in feed-forward loops and feed-back loops, robust against noise and mutation, reversible in response to stimuli, and stable once established. This knowledge is fundamental to adapt plant architecture and crop production to ever-changing environmental conditions.

plant biology↗