Cell wall modifications of two Arabidopsis thaliana ecotypes, Col and Sha, in response to sub-optimal growth conditions: An integrative study

Duruflé, Harold; Hervé, Vincent; Ranocha, Philippe; Balliau, Thierry; Zivy, Michel; Chourré, Josiane; Clemente, Hélène San; Burlat, Vincent; Albenne, Cècile; Déjean, Sébastien; Jamet, Élisabeth; Dunand, Christophe

doi:10.1016/j.plantsci.2017.07.015

Cited by 21 publications

(44 citation statements)

References 71 publications

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“…The significant changes in arabinose content suggest a similar environmental effect on nonstarch polysaccharide composition. This is consistent with the effect of different environments on monosaccharide levels in Arabidopsis (Duruflé et al, ) and many other species.…”

Section: Discussionsupporting

confidence: 90%

Genetic and environmental factors contribute to variation in cell wall composition in mature desi chickpea (Cicer arietinumL.) cotyledons

et al. 2018

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Chickpea (Cicer arietinum L.) is an important nutritionally rich legume crop that is consumed worldwide. Prior to cooking, desi chickpea seeds are most often dehulled and cleaved to release the split cotyledons, referred to as dhal. Compositional variation between desi genotypes has a significant impact on nutritional quality and downstream processing, and this has been investigated mainly in terms of starch and protein content. Studies in pulses such as bean and lupin have also implicated cell wall polysaccharides in cooking time variation, but the underlying relationship between desi chickpea cotyledon composition and cooking performance remains unclear. Here, we utilized a variety of chemical and immunohistological assays to examine details of polysaccharide composition, structure, abundance, and location within the desi chickpea cotyledon. Pectic polysaccharides were the most abundant cell wall components, and differences in monosaccharide and glycosidic linkage content suggest both environmental and genetic factors contribute to cotyledon composition. Genotype-specific differences were identified in arabinan structure, pectin methylesterification, and calcium-mediated pectin dimerization. These differences were replicated in distinct field sites and suggest a potentially important role for cell wall polysaccharides and their underlying regulatory machinery in the control of cooking time in chickpea.

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Section: Discussionsupporting

confidence: 90%

Genetic and environmental factors contribute to variation in cell wall composition in mature desi chickpea (Cicer arietinumL.) cotyledons

et al. 2018

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“…Additionally, peptides derived from ArathEULS3 were found in the cell wall proteome of A. thaliana rosettes and mature stems [50,51]. Moreover, the experiment investigating the cell wall proteome of two Arabidopsis ecotypes Columbia (Col) and Shahdara (Sha) grown at 22 • C and at 15 • C, respectively, revealed an increase in ArathEULS3 peptides in both ecotypes at a lower temperature [52]. All these data can serve as additional proof to show that ArathEULS3 is secreted to the extracellular space under stress conditions.…”

Section: Discussionmentioning

confidence: 96%

The ArathEULS3 Lectin Ends up in Stress Granules and Can Follow an Unconventional Route for Secretion

Dubiel

Coninck

Osterne

et al. 2020

IJMS

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Stress granules are cytoplasmic compartments, which serve as mRNA storage units during stress, therefore regulating translation. The Arabidopsis thaliana lectin ArathEULS3 has been widely described as a stress inducible gene. This study aimed to examine in detail the localization of ArathEULS3 lectin in normal and stressed cells. Colocalization experiments revealed that the nucleo-cytoplasmic lectin ArathEULS3 relocates to stress granules after stress. The ArathEULS3 sequence encodes a protein with a EUL lectin domain and an N-terminal domain with unknown structure and function. Bioinformatics analyses showed that the N-terminal domain sequence contains intrinsically disordered regions and likely does not exhibit a stable protein fold. Plasmolysis experiments indicated that ArathEULS3 also localizes to the apoplast, suggesting that this protein might follow an unconventional route for secretion. As part of our efforts we also investigated the interactome of ArathEULS3 and identified several putative interaction partners important for the protein translation process.

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“…Theoretical cell wall polysaccharide composition was inferred, based on the monosaccharide analyses according to (Duruflé et al, 2017;Houben et al 2011;Duruflé, 2019a).…”

Section: Omics Data Sets and Curationmentioning

confidence: 99%

A powerful framework for an integrative study with heterogeneous omics data: from univariate statistics to multi-block analysis

Duruflé¹,

Selmani²,

Ranocha³

et al. 2018

Preprint

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The high-throughput data generated by new biotechnologies used in biological studies require specific and adapted statistical treatments. In this work, we propose a novel and powerful framework to manage and analyse multi-omics heterogeneous data to carry out an integrative analysis. We illustrate it using the package mixOmics for the R software as it specifically addresses data integration issues. Our work also aims at confronting the most recent functionalities of mixOmics to real data sets because, even if multi-block integrative methodologies exist, they still have to be used to enlarge our know-how and to provide an operational framework to biologists. Natural populations of the model plantArabidopsis thalianaare employed in this work but the framework proposed is not limited to this plant and can be deployed whatever the organisms of interest and the biological question. Four omics data sets (phenomics, metabolomics, cell wall proteomics and transcriptomics) have been collected, analysed and integrated in order to study the cell wall plasticity of plants exposed to sub-optimal temperature growth conditions. The methodologies presented start from basic univariate statistics and lead to multi-block integration analysis, and we highlight the fact that each method is associated to one biological issue. Using this powerful framework led us to novel biological conclusions that could not have been reached using standard statistical approaches.

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Cell wall modifications of two Arabidopsis thaliana ecotypes, Col and Sha, in response to sub-optimal growth conditions: An integrative study

Cited by 21 publications

References 71 publications

Genetic and environmental factors contribute to variation in cell wall composition in mature desi chickpea (Cicer arietinumL.) cotyledons

Genetic and environmental factors contribute to variation in cell wall composition in mature desi chickpea (Cicer arietinumL.) cotyledons

The ArathEULS3 Lectin Ends up in Stress Granules and Can Follow an Unconventional Route for Secretion

A powerful framework for an integrative study with heterogeneous omics data: from univariate statistics to multi-block analysis

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