Biology subjects

Jimenez-Gomez, J. M.

Publications and source records attributed to Jimenez-Gomez, J. M..

9 recordsLinked to original sources

bioRxiv2026

Differential photoperiodic control of morning and evening expressed transcripts in tomato

Photoperiod, the daily duration of light, is a key environmental cue that varies with season and latitude. Photoperiod signals profoundly influence plant growth and development, and play a central role in crop adaptation across latitudes. Deciphering how plants perceive these seasonal light cues at the molecular level is essential for understanding crop evolution and shaping their geographical distribution. In this study, we investigated how photoperiod influences gene expression dynamics in tomato (Solanum lycopersicum) by performing an RNA-seq time-course across three photoperiod regimes, sampling at two-hour intervals. We use isogenic lines segregating for wild alleles of genes involved in circadian rhythm domestication in tomato to describe their contributions to the circadian clock and flowering time pathways. The high temporal resolution of our experiment allowed precise characterization of transcriptional dynamics and their responses to photoperiod, including shifts in phase, amplitude, and waveform. We found that most transcripts time their expression to dawn or approximately 12 hours later, resulting in a systematic misalignment between evening transcripts and the actual timing of dusk. Morning- and evening-phased transcripts differ markedly in expression levels and waveform responses to changes in photoperiod. Together, these patterns suggest that morning transcripts sense photoperiod transcriptionally, and serve as zeitgeber references for evening transcripts, that could measure photoperiod length by coincidence with external cues. Together, our results provide new insight into the molecular basis of photoperiodic adaptation in plants.

plant biology↗

bioRxiv2025

Glycan recognition by a plant sentinel immune receptor

Pathogens target and degrade the extracellular matrix surrounding plant cells. A central question is how cell wall-derived damage-associated molecular patterns (DAMPs) are recognized and integrated to trigger immune responses. We address this question by determining the structure of the multidomain receptor IGP1 in both apo form and bound to the cellulose-derived DAMP cellotriose. Structural analyses reveal that constitutive Leucine Rich Repeat-malectin interactions preconfigure IGP1 for ligand recognition and that the receptor features a highly specific sugar-binding pocket in the LRR domain capable of distinguishing fine variations in glycan structures. By directly sensing cello-oligomers, IGP1 acts as a cell wall sentinel that links pathogen-induced wall degradation to immune alerting, equipping plants to mount rapid and robust defense responses.

plant biology↗

bioRxiv2024

Parallel Evolution of Salinity Tolerance in Arabidopsis thaliana Accessions from Cape Verde Islands

Soil salinization poses a significant threat to crop production impacting one fifth of all cultivated land. The Cape Verde Islands are located 600 km from the coast of Africa and are characterized by high salinity soils and inland water sources. In this study we find that Arabidopsis thaliana plants native to these islands accumulate a metabolite that protects them from salt stress. We partially characterized this metabolite as glucuronyl-mannose. We find that the ability to produce glucuronyl-mannose evolved independently in two different islands from the same archipelago through mutations in the same gene, an alpha glycosidase protein that we named GH38cv. These cases of parallel evolution suggest positive selection towards the increase of salt tolerance with low fitness costs. Indeed, plants carrying derived alleles of GH38cv do not present growth defects or low defenses under normal conditions, but show better germination rates, longer roots and better hydric status than non-mutated plants when exposed to salt stress. These findings provide a knowledge-based method to develop salt resilient crops using natural mechanisms, which could be attractive both to conventional and organic agriculture.

plant biology↗

bioRxiv2024

Repairing a deleterious domestication variant in a floral regulator of tomato by base editing

Crop genomes accumulated deleterious mutations, a symptom known as the cost of domestication. Precision genome editing has been proposed to eliminate such potentially harmful mutations, however, experimental demonstration is lacking. Here, we identified a deleterious mutation in the tomato transcription factor SUPPRESSOR OF SP2 (SSP2), which became prevalent in the domesticated germplasm and diminished DNA-binding to genome-wide targets. We found that SSP2 acts partially redundant with its paralog SSP to regulate shoot and inflorescence architecture. However, redundancy was compromised during tomato domestication and completely lost in the closely-related species Physalis grisea, in which a single ortholog regulates shoot branching. We applied base editing to directly repair the deleterious mutation in cultivated tomato and obtained plants with compact growth that provide an early fruit yield. Our work shows how deleterious variants sensitized modern genotypes for phenotypic tuning and illustrates how repairing deleterious mutations with genome editing may allow predictable crop improvement.

genetics↗

bioRxiv2022

SELF PRUNING 3C is a flowering repressor that modulates seed germination, root architecture and drought responses

Allelic variation in the CETS (CENTRORADIALIS, TERMINAL FLOWER 1, SELF PRUNING) gene family has been shown to control agronomically important traits in many crops. CETS genes encode phosphatidylethanolamine binding proteins (PEBPs) that have a central role in flowering time control as florigenic and anti-florigenic signals. The great expansion of CETS genes in many species suggests that the functions of this family go beyond flowering. Here, we characterize the tomato SELF PRUNING 3C (SP3C) gene, and show that besides acting as a flowering repressor it also regulates seed germination and modulates root architecture. We show that loss of SP3C function in CRISPR/Cas9-generated mutant lines accelerates seed germination and increases root length with lower root side branching. Higher SP3C expression in transgenic lines promotes the opposite effects and also improves tolerance to water stress in seedlings. These discoveries provide insights into the role of SP paralogs in agronomically relevant traits and support future exploration of the involvement of CETS genes in abiotic stress responses. HighlightThe SELF PRUNING 3C (SP3C) gene is a repressor of flowering in tomato and exhibits additional functions, acting as a repressor of seed germination and modulating root architecture.

molecular biology↗

bioRxiv2022

Interaction between photoperiod and variation in circadian rhythms in tomato

Many biological processes follow circadian rhythmicity and are controlled by the circadian clock. Predictable environmental changes such as seasonal variation in photoperiod can modulate circadian rhythms, allowing organisms to adjust to the time of the year. Modification of circadian clocks is especially relevant in crops to enhance their cultivability in specific regions by changing their sensibility to photoperiod. In tomato, the appearance of mutations in EMPFINDLICHER IM DUNKELROTEN LICHT 1 (EID1, Solyc09g075080) and NIGHT LIGHT-INDUCIBLE AND CLOCK-REGULATED GENE 2 (LNK2, Solyc01g068560) during domestication delayed its circadian rhythms, and allowed its expansion outside its equatorial origin. Here we study how variation in circadian rhythms in tomato affects its perception of photoperiod. To do this, we create near isogenic lines carrying combinations of wild alleles of EID1 and LNK2 and perform transcriptomic profiling under two different photoperiods. We observe that EID1, but not LNK2, has a large effect on the tomato transcriptome and its response to photoperiod. This large effect of EID1 is likely a consequence of the global phase shift elicited by this gene in tomatos circadian rhythms.

plant biology↗

bioRxiv2021

The VIL gene CRAWLING ELEPHANT controls maturation and differentiation in tomato via polycomb silencing

VERNALIZATION INSENSITIVE 3-LIKE (VIL) proteins are PHD-finger proteins that recruit the repressor complex Polycomb Repressive Complex 2 (PRC2) to the promoters of target genes. Most known VIL targets are flowering repressor genes. Here, we show that the tomato VIL gene CRAWLING ELEPHANT (CREL) promotes differentiation throughout plant development by facilitating the trimethylation of Histone H3 on lysine 27 (H3K27me3). We identified the crel mutant in a screen for suppressors of the simple-leaf phenotype of entire (e), a mutant in the AUX/IAA gene ENTIRE/SlIAA9, involved in compound-leaf development in tomato. crel mutants have increased leaf complexity, and suppress the ectopic blade growth of e mutants. In addition, crel mutants are late flowering, and have delayed and aberrant stem, root and flower development. Consistent with a role for CREL in recruiting PRC2, crel mutants present altered H3K27me3 modifications at a subset of PRC2 targets throughout the genome. Our results uncover a wide role for CREL in plant and organ differentiation in tomato and suggest that CREL is required for targeting PRC2 activity to, and thus silencing, a specific subset of polycomb targets. Author summaryPlants form organs continuously throughout their lives, and the number and shape of their organs is determined in a flexible manner according to the internal and external circumstances. Alongside this flexibility, plants maintain basic developmental programs to ensure proper functioning. Among the ways by which plants achieve flexible development is by tuning the pace of their maturation and differentiation, at both the plant and organ levels. One of the ways plants regulate the rate of maturation and differentiation is by changing gene expression. Here, we identified a gene that promotes plant and organ maturation and differentiation. This gene, CRAWLING ELEPHANT (CREL) acts by bringing a repressing complex to target genes. We show the importance of CREL in multiple developmental processes and in the expression of multiple genes throughout the tomato genome.

plant biology↗

bioRxiv2019

Functional Analysis of FRIGIDA Using Naturally Occurring Variation in Arabidopsis thaliana

The FRIGIDA locus (FRI, AT4G00650) has been extensively studied in Arabidopsis thaliana because of its role creating flowering time diversity. The FRI protein regulates flowering induction by binding partner proteins on its N- and C-terminus domains and creating a supercomplex that promotes transcription of the floral repressor FLC. Despite the knowledge accumulated on FRI, the function of the highly conserved central domain of the protein is still unknown. Functional characterization of naturally occurring DNA polymorphisms can provide useful information about the role of a protein and the localization of its operative domains. In the case of FRI, deleterious mutations are positively selected and widespread in nature, making them a powerful tool to study the function of the different domains of the protein. Here we explore natural sequence variation in the FRI locus in more than 1000 Arabidopsis accessions. We identify new mutations predicted to compromise the function of the protein and confirm our predictions by cloning 22 different alleles of FRI and expressing them in a common null genetic background. Our analysis allows us to pinpoint two single amino acid changes in the central domain that render the protein non-functional. We show that these two mutations determine the stability and cellular localization of the FRI protein. In summary, our work makes use of natural variants at the FRI locus to help understanding the function of the central domain of the FRI protein.

plant biology↗

bioRxiv2018

Mild drought induces phenotypic and DNA methylation plasticity but no transgenerational effects in Arabidopsis

Whether environmentally induced changes in phenotypes can be heritable is a topic with revived interest, in part because of observations in plants that heritable trait variation can occur without DNA sequence mutations. This other system of inheritance, called transgenerational epigenetics, typically involves differences in DNA methylation that are stable across multiple generations. However, it remains unknown if such a system responds to environmental changes and if it could therefore provide a rapid way for plants to generate adaptive heritable phenotypic variation. Here, we used a well-controlled phenotyping platform and whole-genome bisulfite sequencing to investigate potential heritable effects of mild drought applied over two successive generations in Arabidopsis thaliana. Plastic phenotypic responses were observed in plants exposed to drought. After an intervening generation without stress, descendants of stressed and non-stressed plants were phenotypically indistinguishable, except for very few trait-based parental effects, and irrespective of whether they were grown in control conditions or under water deficit. Moreover, while mild drought induced changes to the DNA methylome of exposed plants, DNA methylation variants were not inherited. These findings add to the growing body of evidence indicating that transgenerational epigenetics is not a common response of plants to environmental changes.

plant biology↗