Biology subjects

Carpentier, S.

Publications and source records attributed to Carpentier, S..

7 recordsLinked to original sources

bioRxiv2026

Pre-chlorotic Mg2+ deficiency impairs guard-cell PSII and leaf gas exchange in Vicia faba

Magnesium deficiency impairs photosynthesis and transpiration before visible chlorosis, but whether guard cells themselves are affected at this early stage remains unresolved. We combined whole-leaf gas exchange and chlorophyll fluorescence with cell-specific fluorescence measurements of individual guard cell pairs, together with elemental analysis, metabolite profiling, adenosine triphosphate quantification, and proteome profiling of guard cell-enriched material in hydroponically grown Vicia faba. Magnesium deficiency reduced magnesium concentrations in both whole leaves and guard cell-enriched fractions. Under red light, magnesium-deficient leaves showed reduced effective quantum yield of photosystem II, CO2 assimilation, transpiration, and stomatal conductance, whereas intercellular CO2 concentration remained unchanged. Individual guard cell pairs likewise showed reduced effective quantum yield of photosystem II, demonstrating that the early deficiency response extended to guard cells. Electron transport rate and non-photochemical quenching in guard cells were not significantly altered. Only a small set of metabolites in guard cell-enriched material, mainly fatty acids and citrate, responded to magnesium deficiency, whereas ATP abundance and light-induced proton extrusion remained unchanged. In contrast, the guard cell-enriched proteome showed higher abundance of photosynthesis- and translation-related proteins despite reduced guard-cell PSII efficiency. Together, these findings identify guard cells as an early responsive cell type under magnesium deficiency and show that guard-cell photochemistry is impaired before visible chlorosis, alongside reduced whole-leaf carbon gain and water loss.

physiology↗

bioRxiv2024

Unlocking the power of gene banks: diversity in base growth temperature provides opportunities for climate-smart agriculture

Implementation of context-specific solutions, including cultivation of varieties adapted to current and future climatic conditions, were found to be effective in establishing resilient, climate-smart agricultural systems. Gene banks play a pivotal role in this. However, a large fraction of the collections remains neither genotyped nor phenotyped. Hypothesising that significant genotypic diversity in Musa temperature responses exists, this study aimed to assess the diversity in the worlds largest banana gene bank in terms of base temperature (Tbase) and to evaluate its impact on plant performance in the East African highlands during a projected climate scenario. 116 gene bank accessions were evaluated in the BananaTainer, a tailor-made high throughput phenotyping installation. Plant growth was quantified in response to temperature and genotype-specific Tbase were modelled. Growth response of two genotypes was validated under greenhouse conditions, and gas exchange capacity measurements were made. The model revealed genotype-specific Tbase, with 30 % of the accessions showing a Tbase below the reference of 14 {degrees}C. The Mutika/Lujugira subgroup, endemic to the East African highlands, appeared to display a low Tbase, although within subgroup diversity was revealed. Greenhouse validation further showed low T sensitivity/tolerance to be related to the photosynthetic capacity. This study, therefore, significantly advances the debate of within species diversity in temperature growth responses, while at the same time unlocking the power of gene banks. Moreover, we provide a high throughput method to reveal the existing genotypic diversity in temperature responses, paving the way for future research to establish climate-smart varieties.

physiology↗

bioRxiv2024

Transcriptome Analysis of Archived Tumor Tissues by Visium, GeoMx DSP, and Chromium Methods Reveals Inter- and Intra-Patient Heterogeneity

Recent advancements in probe-based, full-transcriptome, high-resolution technologies for Formalin-Fixed Paraffin-Embedded (FFPE) tissues, such as Visium CytAssist, Chromium Flex (10X Genomics), and GeoMx DSP (Nanostring), have opened new opportunities for studying decades-old archival samples in biobanks, facilitating the generation of data from extensive cohorts. However, the experimental protocols can be labor-intensive and costly; therefore, it is thus essential for researchers to carefully evaluate the strengths and limitations of each technology in relation to their specific research objectives. Here, we report the results of a comparative analysis of the three methods mentioned above on FFPE archival tumor samples from four non-small cell lung cancer, four breast cancer and six diffuse large B-cell lymphoma. We highlight some relative advantages and disadvantages of each method in the context of operational challenges, bioinformatic analysis and biological discovery. Our results show that: 1) all three methods yielded good-quality, highly reproducible transcriptomic data from serial sections of the same FFPE block; 2) GeoMx data contained mixtures of cell types, even when pre-selecting areas with cell type-specific markers; 3) high-throughput spot-level (Visium) or cell-level (Chromium) data enabled the identification of tumor heterogeneity within and between patients, which could be used to identify targeted therapies. Our data support the use of Visium and Chromium for high-throughput and discovery-driven projects, while the GeoMx platform could be suited for addressing specialized questions on targeted regions. All data generated from this study, including GeoMx, Visium, Chromium, H&E, and expert annotations are publicly available.

bioinformatics↗

bioRxiv2024

MLX phosphorylation stabilizes the ChREBP-MLX heterotetramer on tandem E-boxes to control carbohydrate and lipid metabolism

The heterodimeric ChREBP-MLX transcription factor complex is a key mediator that couples intracellular sugar levels to carbohydrate and lipid metabolism. To promote the expression of target genes, two ChREBP-MLX heterodimers form a heterotetramer to bind a tandem element with two adjacent E-boxes, called Carbohydrate Responsive Element (ChoRE). How the ChREBP-MLX hetero-tetramerization is achieved and regulated, remains poorly understood. Here we show that MLX phosphorylation on an evolutionarily conserved motif is necessary for the heterotetramer formation on the ChoRE and the transcriptional activity of the ChREBP-MLX complex. We identified CK2 and GSK3 as MLX kinases that coordinately phosphorylate MLX. High intracellular glucose-6-phosphate accumulation inhibits MLX phosphorylation and heterotetramer formation on the ChoRE, impairing ChREBP-MLX activity. Physiologically, MLX phosphorylation is necessary in Drosophila to maintain sugar tolerance and lipid homeostasis. Our findings suggest that MLX phosphorylation is a key mechanism for the ChREBP-MLX heterotetramer formation to regulate carbohydrate and lipid metabolism.

cell biology↗

bioRxiv2023

Enhanced protein secretion in reduced genome strains of Streptomyces lividans

S. lividans TK24 is a popular host for the production of small molecules and for the secretion of heterologous proteins. TK24 has a large genome with at least 29 secondary metabolite gene clusters that are non-essential for viability and undergo complex regulation. To optimize heterologous protein secretion, we previously constructed ten chassis strains that are devoid of several secondary metabolite gene clusters. Genome reduction was aimed at reducing carbon flow to secondary metabolites and pigmentation in the spent growth medium and improving colony morphology. Strains RG1.0-RG1.10 contain various deletion combinations of the blue actinorhodin cluster (act), the calcium-dependent antibiotic (cda), the undecylprodigiosin (red) and coelimycin A (cpk) clusters, the melanin cluster (mel), the matAB genes that affect mycelial aggregation and the non-essential sigma factor hrdD that controls the transcription of Act and Red regulatory proteins. Two derivative strains, RG1.5 and 1.9, showed a [~]15% reduction in growth rate, >2-fold increase in the total mass yield of their native secretome and altered abundance of several specific proteins compared with TK24. Metabolomics and RNAseq analysis revealed that genome reduction led to rapid cessation of growth due to aminoacid depletion and caused both redox and cell envelope stresses, upregulation of the Sec-pathway components secDF and chaperones and a cell envelope two component regulator. RG1.9 maintained elevated heterologous secretion of mRFP and mTNF by 12-70%. An integrated model is presented linking genome reduction and enhanced secretion.

systems biology↗

bioRxiv2022

Diverse responses among wild banana species to vapour pressure deficit, a solution for drought tolerance breeding?

1The predicted rise in global temperature is not only affecting plant functioning directly, but is also increasing air vapour pressure deficit (VPD). The yield of banana is heavily affected by water deficit but so far breeding programs have never addressed the issue. A reduction in transpiration at high VPD has been suggested as a key drought tolerance breeding trait to avoid excessive water loss, hydraulic failure and to increase water use efficiency. In this study, stomatal and transpiration responses under increasing VPD at the leaf and whole-plant level of 8 wild banana (sub)species were evaluated, displaying significant differences in stomatal reactivity. Three different groups were identified under increasing VPD. M. acuminata spp. errans (group I), M. acuminata spp. zebrina (group II) and M. balbisiana (group II) showed the highest transpiration rate limitations to increasing VPD. In contrast to group I, group II only showed strong reductions at high VPD levels, limiting the cost of reduced photosynthesis and strongly increasing their water use efficiency. Group II genotypes thus show favourable responses for high water use efficiency in regions with high VPDs. This provides a basis for the identification of potential parent material within their wild populations for drought tolerance breeding. HighlightWild banana species respond significantly different to water deficit caused by VPD increases and differ in the rate of stomatal reduction, revealing opportunities for drought tolerance breeding.

plant biology↗

bioRxiv2021

From fruit growth to ripening in plantain: a careful balance between carbohydrate synthesis and breakdown

We investigated the fruit development in two plantain banana cultivars from two weeks after bunch emergence till twelve weeks through high-throughput proteomics, major metabolite quantification and metabolic flux analyses. We give for the first time an insight at early stages of starch synthesis and breakdown. Starch and sugar synthesis and breakdown are processes that take place simultaneously. During the first eight to ten weeks the balance between synthesis and breakdown is clearly in favour of sugar breakdown and a net starch synthesis occurs. During this period, plantain fruit accumulates up to 48% of starch. The initiation of the ripening process is accompanied with a shift in balance towards net starch breakdown. The key enzymes related to this are phosphoglucan water dikinase (PWD), phosphoglucan phosphatase, -1,6-glucosidase starch debranching enzyme (DBE), alpha glucan phosphorylase (PHS) and 4-alpha glucanotransferase disproportioning enzyme (DPE). The highest correlations with sucrose have been observed for PHS and DPE. There is also a significant correlation between the enzymes involved in ethylene biosynthesis, starch breakdown, pulp softening and ascorbate biosynthesis. The faster ending of maturation and starting of ripening in the Agbagba cultivar are linked to the key enzymes 1-aminocyclopropane-1-carboxylate oxidase and DPE. This knowledge of the mechanisms that regulate starch and sugar metabolisms during maturation and ripening is fundamental to determine the harvest moment, reduce postharvest losses and improve final product quality of breeding programs.

plant biology↗