Biology subjects

Caius, J.

Publications and source records attributed to Caius, J..

8 recordsLinked to original sources

bioRxiv2026

Defects in the Arabidopsis V-ATPase associated RAVE complex affects endosomal pH and triggers the onset of leaf cell clusters upon TOR inhibition

The TOR kinase is an important and conserved signaling hub in plants, as in other eukaryotes. However, the identification of the TOR pathway components and regulators in plants is still fragmentary. Using a genetic screen based on altered sensitivity to TOR inhibitors, we have selected an Arabidopsis mutant that develops leaf ectopic cell clusters of enlarged cells in a TOR-inhibition dependent manner. We have named this mutant loki (Localized growth depending on TOR Kinase Inhibition) and identified the causal mutation in a gene coding for the Arabidopsis homolog of the yeast Rav1 protein. This protein serves as the scaffold for the RAVE complex (Regulator of the ATPase of Vacuolar and Endosomal membranes), which regulates the V-ATPase activity in yeasts and animals. The overall V-ATPase activity is decreased in loki mutants and consistently the endosomal pH is increased. However, the vacuolar pH was found to be unaffected by this mutation. Interestingly, the det3 mutant, which is affected in the C subunit of the V-ATPase, also develops similar cell clusters. Finally, transcriptomic and metabolic analyses revealed that many pathways are affected by both the loki and det3 mutations, including cell wall integrity. This study establishes a new connection between the V-ATPase and the central TOR kinase in plants.

plant biology↗

bioRxiv2025

Enterobacter sp. SA187-induced coordinated regulation of high-affinity nitrate transporters and ethylene signaling enhances nitrogen content and plant growth under low nitrate

O_LISustainable crop production demands solutions to reduce the overuse of synthetic nitrogen fertilizers, and plant-growth-promoting bacteria offer a promising strategy by enhancing nutrients acquisition. This study investigated ability of a non-diazotrophic bacterium, Enterobacter sp. SA187 (SA187), in enhancing Arabidopsis growth under low nitrate conditions and the underlying mechanisms. C_LIO_LIArabidopsis seedlings were grown under different nitrate concentrations with or without SA187 inoculation. Growth traits were quantified alongside shoot and root nitrate and total nitrogen contents, and C:N ratios. Transcriptomic profiling (RNA-seq) and qRT-PCR were used to assess modified gene expression. Functional validation was conducted using ethylene-insensitive (ein2-1) and high-affinity nitrate transporter (HATS) mutants (nrt2.5, nrt2.6). C_LIO_LISA187 significantly enhanced fresh weight, primary root length, and lateral root density under low nitrate, with benefits increasing as nitrate availability decreased. SA187 improved nitrate accumulation and shoot nitrogen allocation, reducing shoot C:N ratios. SA187 regulated expression of HATS and hormone-responsive genes. The growth-promoting effects were abolished in ein2-1, nrt2.5, and nrt2.6 mutants, and SA187-induced regulation of NRT2.5 occurred downstream of ethylene signaling, while NRT2.6 was partly ethylene-independent. C_LIO_LISA187 promotes growth under low nitrate possibly through ethylene-mediated and HATS-dependent reprogramming of nitrate accumulation and nitrogen allocation, supporting its use as a microbial solution for low-input agriculture. C_LI

plant biology↗

bioRxiv2024

A multidisciplinary on-farm survey of maize-bean intercropping shows that revival of traditionalagricultural systems requires careful consideration of partner varieties and agronomic practices.

O_LICereal-legume intercropping is a promising strategy for sustainable agroecosystems. The traditional intercropping of maize and bean is experiencing a revival in some modern agricultural settings, such as in southwestern France, where maize hybrids are intercropped with the commercialized Tarbais bean. We conducted on-farm surveys and a field assay to address the following questions: How does the cropping system impact yield, nutrient uptake, and rhizosphere bacterial assemblages? Do positive or negative interactions between maize and beans dominate in intercropping? What is the effect of intercropping on plant transcriptomics? C_LIO_LIWe recorded farming practices, conducted yield and nutrient measurements, and characterized soil bacterial assemblages to compare sole-cropped maize and beans with intercropped plants. A controlled field assay was also established to extend this comparison to plant gene expression differences. C_LIO_LIIntercropping was associated with a trend towards increased bacterial diversity. The cropping system significantly influenced agronomic traits, with frequent farm-by-cropping system interactions underscoring the critical role of farming practices. Competition dominated maize-bean intercropping, with 34 negative correlations among the 47 significant ones between maize and bean traits. This competition affected yield and nutrition, but primarily impacted beans, which produced fewer but bigger/heavier seeds. Transcriptomic results concurred with these findings, revealing no differentially expressed genes in maize but 5,070 in beans under competition. C_LIO_LIOverall, our findings suggest that beneficial interactions between the two crops are hindered under current field conditions, underscoring the importance of carefully considering partner varieties and farming practices to revive traditional agricultural systems. C_LI Societal Impact StatementCereal-legume intercropping is a promising strategy for sustainable agroecosystems that leverages the biological complementarities between plant species, reducing the need for chemical inputs while enhancing field biodiversity. Here, we focused on maize-bean intercropping, which is experiencing a revival in modern conventional agricultural settings. We found a trend towards an increased soil bacterial diversity in intercropping. However, competition between the two crops dominated and primarily impacted yield and gene expression in beans. Despite lower yield, bean seeds exhibited greater size. Our study indicates that implementing variety selection of both species and adapting farming practices is essential to fully harness the potential of intercropping.

plant biology↗

bioRxiv2021

A ppGpp-mediated brake on photosynthesis is required for acclimation to nitrogen limitation in Arabidopsis.

Guanosine pentaphosphate and tetraphosphate (together referred to as ppGpp) are hyperphosphorylated nucleotides found in bacteria and the chloroplasts of plants and algae. In plants and algae artificial ppGpp accumulation can inhibit chloroplast gene expression, and influence photosynthesis, nutrient remobilisation, growth, and immunity. However, it is so far unknown whether ppGpp is required for abiotic stress acclimation in plants. Here, we demonstrate that ppGpp biosynthesis is necessary for acclimation to nitrogen starvation in Arabidopsis. We show that ppGpp is required for remodeling the photosynthetic electron transport chain to downregulate photosynthetic activity and for protection against oxidative stress. Furthermore, we demonstrate that ppGpp is required for coupling chloroplastic and nuclear gene expression during nitrogen starvation. Altogether, our work indicates that ppGpp is a pivotal regulator of chloroplast activity for stress acclimation in plants.

plant biology↗

bioRxiv2020

A derived ZW chromosome system in Amborella trichopoda, the sister species to all other extant flowering plants

Sex determination is poorly understood in plants. Amborella trichopoda is a well-known plant model for evo-devo studies, which is also dioecious (has male and female individuals), with an unknown sex determination mechanism. A. trichopoda is a "sex switcher", which points to possible environmental factors that act on sex, but populations grown from seed under greenhouse conditions exhibit a 50:50 sex ratio, which indicates the operation of genetic factors. Here, we use a new method (SDpop) to identify sex-linked genes from genotyping data of male and female individuals sampled in the field, and find that A. trichopoda has a ZW sex-chromosome system. The sex-linked genes map to a 4 Mb sex-determining region on chromosome 9. The low extent of ZW divergence suggests these sex chromosomes are of recent origin, which is consistent with dioecy being derived character in the A. trichopoda lineage. Our work has uncovered clearly formed sex chromosomes in a species in which both genetic and environmental factors can influence sex. One Sentence SummaryAmborella trichopoda, a dioecious species in which both genetics and the environment influence sex, possesses a pair of quite recently evolved ZW chromosomes.

plant biology↗

bioRxiv2020

The genomic impact of mycoheterotrophy: targeted gene losses but extensive expression reprogramming.

ABSTRACTMycoheterotrophic plants have lost the ability to photosynthesize and they parasitize their associated fungus to get the mineral and organic nutrients they need. Despite involving radical changes in life history traits and ecological requirements, the transition from autotrophy to mycoheterotrophy occurred independently in almost all major lineages of land plants, but most often in Orchidaceae. Yet the molecular mechanisms underlying this shift are still poorly understood. The comparison of the transcriptomes of Epipogium aphyllum and Neottia nidus-avis, two mycoheterotrophic orchids, to other autotrophic and mycoheterotrophic orchids showed massive molecular function losses restricted to photosynthetic activities. In addition to these targeted losses, the analysis of their expression profiles showed that many orthologs had inverted root/shoot ratios compared to autotrophic species. Fatty acid and amino acid biosynthesis as well as primary cell wall metabolism were among the pathways most impacted by this expression reprogramming. Our study suggests that, while associated with function losses rather than metabolic innovations, the shift in nutritional mode from autotrophy to mycoheterotrophy remodeled the architecture of the plant metabolism.View Full Text

plant biology↗

bioRxiv2020

Hypomethylated poplars show higher tolerance to water deficit and highlight a dual role for DNA methylation in shoot meristem: regulation of stress response and genome integrity

As fixed and long living organisms subjected to repeated environmental stresses, trees have developed mechanisms such as phenotypic plasticity that help them to cope with fluctuating environmental conditions. Here, we tested the role DNA methylation as a hub of integration, linking plasticity and physiological response to water deficit in the shoot apical meristem of the model tree poplar (Populus). Using a reverse genetic approach, we compared hypomethylated RNAi-ddm1 lines to wild-type trees for drought tolerance. An integrative analysis was realized with phytohormone balance, methylomes, transcriptomes and mobilomes. Hypomethylated lines were more tolerant when subjected to moderate water deficit and were intrinsically more tolerant to drought-induced cavitation. The alteration of the DDM1 machinery induced variation in DNA methylation in a cytosine context dependent manner, both in genes and transposable elements. Hypomethylated lines subjected to water deficit showed altered expression of genes involved in phytohormone pathways, such as salicylic acid and modified hormonal balance. Several transposable elements showed stress- and/or line-specific patterns of reactivation, and we could detect copy number variations for two of them in stressed ddm1 lines. Overall, our data highlight two major roles for DNA methylation in the shoot apical meristem: control of stress response and plasticity through transduction of hormone signaling and maintenance of genome integrity through the control of transposable elements.

plant biology↗

bioRxiv2019

Transcriptomics at maize embryo/endosperm interfaces identify a novel transcriptionally distinct endosperm sub-domain adjacent to the embryo scutellum (EAS)

Seeds are complex biological systems comprising three genetically distinct tissues nested one inside another (embryo, endosperm and maternal tissues). However, the complexity of the kernel makes it difficult to understand inter compartment interactions without access to spatially accurate information. Here we took advantage of the large size of the maize kernel to characterize genome-wide expression profiles of tissues at embryo/endosperm interfaces. Our analysis identifies specific transcriptomic signatures in two interface tissues compared to whole seed compartments: The scutellar aleurone layer (SAL), and the newly named endosperm adjacent to scutellum (EAS). The EAS, which appears around 9 days after pollination and persists for around 11 days, is confined to one to three endosperm cell layers adjacent to the embryonic scutellum. Its transcriptome is enriched in genes encoding transporters. The absence of the embryo in an embryo specific (emb) mutant can alter the expression pattern of EAS marker genes. The detection of cell death in some EAS cells together with an accumulation of crushed cell walls suggests that the EAS is a dynamic zone from which cell layers in contact with the embryo are regularly eliminated, and to which additional endosperm cells are recruited as the embryo grows.

plant biology↗