Biology subjects

Blein-Nicolas, M.

Publications and source records attributed to Blein-Nicolas, M..

8 recordsLinked to original sources

bioRxiv2026

Spatiotemporal pectin remodelling, glycoproteins, and LEA proteins maintain cell wall integrity during desiccation and rehydration in Ramonda serbica

Vegetative desiccation tolerance requires specialised cell wall (CW) adaptations to withstand severe mechanical stress during dehydration and rehydration. While intracellular protective strategies in resurrection plants, including Ramonda serbica, are well documented, the CW response remains poorly understood. Here, we integrated immunocytochemical profiling, FTIR spectroscopy, quantification of CW-bound phenolics, transcriptomics, and ionically bound CW proteomics across hydrated (HL), desiccated (DL), and rehydrated states (R1-1h, R2-24h, R3-48h). Reversible CW folding was facilitated by condensed arabinogalactan-proteins (AGPs) and extensins, alongside a site-specific balance between pectin methylesterification and demethylesterification. Structural compaction was further reinforced by the accumulation of CW-bound hydroxycinnamates, which persisted through R1 phase. Moreover, basic 7S globulin, miraculin, -galactosidase, and two LEA4 protein family members were strongly accumulated during DL and R1, providing the first evidence of ionically CW-bound LEA proteins. Initial rewatering (R1) triggered a rapid transcriptomic reactivation of pectin-degrading/modifying enzymes, carbohydrate-active enzymes, and subtilases, accompanied by unesterified pectin enrichment. By 24-48 h (R2-R3), CW-bound hydroxycinnamic acids declined, and CW architecture, gene expression, and proteome profiles returned to baseline levels. Overall, our findings reveal a coordinated spatiotemporal apoplastic network - driven by glycoproteins, pectin modulation, CW-bound hydroxycinnamates, and LEA4 proteins - essential for rapid desiccation recovery.

plant biology↗

bioRxiv2026

Proteomic reprogramming underlies climate-associated variation in seed dormancy and germination of European beech

The ability of seeds to survive until dormancy recedes and the germination requirements are met is an adaptive strategy. Proteomics improves our understanding of the mechanisms that control the adaptation to environmental heterogeneity. In this study, we investigated two European beech populations from different habitats that differed in dormancy and germination traits. We found that the populations exhibited different germination strategies, which were reflected in coordinated but quantitatively different proteomic reprogramming. The Miekinia population exhibited stronger accumulation of proteins involved in nucleotide sugar biosynthesis, S-adenosylmethionine metabolism, and flavonoid biosynthesis. Enhanced nucleotide sugar biosynthesis indicates more intensive cell wall remodelling and carbohydrate metabolism, which support embryo growth and faster germination. Increased S-adenosylmethionine metabolism suggests the epigenetic and hormonal regulation of germination differences between populations. Higher flavonoid biosynthesis indicates an enhanced antioxidant capacity associated with environmental protection. In contrast, the Wisa population showed stronger accumulation of proteins involved in RNA processing, suggesting tighter post-transcriptional regulation and proteome reorganization during germination. Consistent with its deeper dormancy and later germination, the Wisa population appears to rely more on RNA-level regulation, whereas the Miekinia population prioritizes metabolic activation. These contrasting proteomic profiles likely reflect population-specific physiological strategies associated with dormancy depth and adaptation to different climatic conditions. HighlightProteomic reprogramming reveals population-specific germination strategies in European beech, linking dormancy depth with contrasting metabolic activation and RNA-level regulation during the transition from dormancy to germination.

plant biology↗

bioRxiv2026

Apoplast multi-omics profiling during fungal infection uncovers new players of basal and early induced immunity

The extracellular space in plant tissues, known as the apoplast, remains one of the least characterized cellular compartments. The apoplastic fluid (APF), akin to mammalian extracellular fluid, serves as the primary interface between pathogens and their host. It allows the exchange of signalling molecules, coordinates host cell responses, and enables the circulation of pathogen effectors that modulate the immune response. We describe here the first multi-omics analysis of the APF content just 6 h after the onset of A. thaliana infection with B. cinerea, a fast-killing necrotrophic fungus. By varying plant nitrogen nutrition, known to affect both plant defenses and pathogen virulence, we identify candidates that do not stand out under optimal conditions. Our analysis uncovers novel nitrogen-dependent mechanisms that regulate both basal and early induced apoplastic immunity, revealing the presence of previously unidentified, potentially protective apoplastic metabolites as well as the intercellular transport of nuclear proteins, thereby offering new insights into early apoplastic immune responses.

plant biology↗

bioRxiv2025

Unravelling the Genetic Architecture of Field Traits through Multi-Omics Platform Data integration

BackgroundIdentifying the genes and regulatory regions underlying a complex trait is a long-standing challenge. GWAS is generally used, but it suffers from insufficient power, lack of resolution and inefficiency to systematically screen for epistasis. We propose a systems genetics approach integrating multi-omics to overcome these limits. It was applied to a panel of maize with the objective to analyze the genetic determinism of yield in a multi-environment trials by combining genomics with transcriptomics measured on a platform. ResultsDespite the contrasted conditions between the platform and the fields, transcriptomics could be used to identify candidate genes. A presence-absence variation was in particular detected, and the transcripts allowed the identification of causal genes, increasing resolution in comparison to GWAS. In total, 47 genes were identified along the genome, and we could characterize their contrasted effect on yield according to environmental covariates. We demonstrated that the cis- and also the trans-eQTLs of these genes had an important contribution to genetic variance, suggesting a key role of epistatic interactions. In terms of predictive ability, the cis-eQTL resulted in an increase of 39 to 52% on average across the environments, in comparison to random SNP sets. ConclusionsBy efficiently combining multi-omics, it is possible to considerably increase our understanding of genetic architecture in comparison to standard GWAS. We demonstrated that omics data even measured on a phenotyping platform can be used for the analysis of field traits, opening the way for their routine use in plant breeding both for marker-assisted selection and bio-informed predictions.

genetics↗

bioRxiv2024

A moderate water deficit induces profound changes in the proteome of developing maize ovaries

Water deficit is a major cause of yield loss for maize (Zea mays), leading to ovary abortion when applied at flowering time. To help understand the mechanisms involved in this phenomenon, the proteome response to water deficit has been analysed in developing ovaries at silk emergence stage and five days later. Differential analysis, abundance pattern clustering and coexpressions networks were performed in order to draw a general picture of the proteome changes all along ovary development and under the effect of water deficit. The results show that, even mild, water deficit has a major impact on ovary proteome, but that this impact is very different from a response to a stress. A part of the changes can be related to a slowdown of ovary development, while another part cannot. In particular, ovaries submitted to water deficit show an increase in proteins involved in protein biosynthesis and in vesicle transport together with a decrease in proteins involved in amino acid metabolism and proteolysis. According to the functions of increased proteins, the changes may be linked to auxin, brassinosteroids and jasmonate signalling, but not abscisic acid.

plant biology↗

bioRxiv2023

Fast alignment of mass spectra in large proteomics datasets, capturing dissimilarities arising from multiple complex modifications of peptides

BackgroundIn proteomics, the interpretation of mass spectra representing peptides carrying multiple complex modifications is still challenging, currently limited by the number of potential modifications considered in a single analysis and the need to know them in advance. Further developments must be done in the field to help the scientific community to discover new post-translational modifications that play an essential role in disease and to understand how chemical modifications carried by food proteins could impact our health. ResultsTo make progress on this issue, we implemented SpecGlobX (SpecGlob eXTended to eXperimental spectra), a standalone Java application that quickly determines the best spectral alignments of a (possibly very large) list of Peptide-to-Spectrum Matches (PSMs) provided by any open modification search method, or generated by the user. As input, SpecGlobX reads a file containing spectra in MGF or mzML format and a semicolon-delimited spreadsheet describing the PSMs. As output, SpecGlobX returns the best alignment for each PSM, splitting the mass difference between the spectrum and the peptide into one or more shifts while considering the possibility of non-aligned masses (a phenomenon resulting from many situations including neutral losses). SpecGlobX is fast, able to align one million PSMs in about 1.5 minutes on a standard desktop. Firstly, we remind the foundations of the algorithm and detail how we adapted SpecGlob (the method we previously developed following the same aim, but limited to the interpretation of perfect simulated spectra) to the interpretation of imperfect experimental spectra. Then, we highlight the interest of SpecGlobX as a complementary tool downstream to three open modification search methods on a large simulated spectra dataset. Finally, we show on a smaller dataset that SpecGlobX performs equally well on experimental and simulated spectra. ConclusionsSpecGlobX is helpful as a decision support tool, providing keys to interpret peptides carrying complex modifications still poorly considered by current open modification search software. Better alignment of PSMs enhances confidence in the identification of spectra provided by open modification search methods and should improve the interpretation rate of spectra.

bioinformatics↗

bioRxiv2020

Proteomic data from leaves of twenty-four sunflower genotypes underwater deficit

This article describes how the proteomic data were produced on sunflower plants subjected to water deficit. Twenty-four sunflower genotypes were selected to represent genetic diversity within cultivated sunflower. They included both inbred lines and their hybridsWater deficit was applied to plants in pots at the vegetative stage using the high-throughput phenotyping platform Heliaphen. Here, we provide proteomic data from sunflower leaves corresponding to the identification of 3062 proteins and the quantification of 1211 of them in these 24 genotypes grown in two watering conditions. These data differentiate both treatment and the different genotypes and constitute a valuable resource to the community to study adaptation of crops to drought and the molecular basis of heterosis.Competing Interest StatementThe authors have declared no competing interest.View Full Text

plant biology↗

bioRxiv2019

Integrating proteomics and genomics into systems genetics provides novel insights into the mechanisms of drought tolerance in maize

The effect of drought on maize yield is of particular concern in the context of climate change and human population growth. However, the complexity of drought-response mechanisms make the design of new drought-tolerant varieties a difficult task that would greatly benefit from a better understanding of the genotype-phenotype relationship. To provide novel insight into this relationship, we applied a systems genetics approach integrating high-throughput phenotypic, proteomic and genomic data acquired from 254 maize hybrids grown under two watering conditions. Using association genetics and protein co-expression analysis, we detected more than 22,000 pQTLs across the two conditions and confidently identified fifteen loci with potential pleiotropic effects on the proteome. We showed that even mild water deficit induced a profound remodeling of the proteome, which affected the structure of the protein co-expression network, and a reprogramming of the genetic control of the abundance of many proteins, notably those involved in stress response. Co-localizations between pQTLs and QTLs for ecophysiological traits, found mostly in the water deficit condition, indicated that this reprogramming may also affect the phenotypic level. Finally, we identified several candidate genes that are potentially responsible for both the co-expression of stress response proteins and the variations of ecophysiological traits under water deficit. Taken together, our findings provide novel insights into the molecular mechanisms of drought tolerance and suggest some pathways for further research and breeding.

systems biology↗