Proteomic Data Integration Highlights Central Actors Involved in Einkorn (Triticum monococcum ssp. monococcum) Grain Filling in Relation to Grain Storage Protein Composition
Albumins and globulins (AGs) of wheat endosperm represent about 20% of total grain proteins. Some of these physiologically active proteins can influence the synthesis of storage proteins (SPs) (gliadins and glutenins) and consequently, rheological properties of wheat flour and processing. To identif...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2019-07-01
|
| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fpls.2019.00832/full |
| _version_ | 1811263813271420928 |
|---|---|
| author | Emmanuelle Bancel Emmanuelle Bancel Titouan Bonnot Titouan Bonnot Marlène Davanture David Alvarez David Alvarez Michel Zivy Pierre Martre Pierre Martre Sébastien Déjean Catherine Ravel Catherine Ravel |
| author_facet | Emmanuelle Bancel Emmanuelle Bancel Titouan Bonnot Titouan Bonnot Marlène Davanture David Alvarez David Alvarez Michel Zivy Pierre Martre Pierre Martre Sébastien Déjean Catherine Ravel Catherine Ravel |
| author_sort | Emmanuelle Bancel |
| collection | DOAJ |
| description | Albumins and globulins (AGs) of wheat endosperm represent about 20% of total grain proteins. Some of these physiologically active proteins can influence the synthesis of storage proteins (SPs) (gliadins and glutenins) and consequently, rheological properties of wheat flour and processing. To identify such AGs, data, (published by Bonnot et al., 2017) concerning abundance in 352 AGs and in the different seed SPs during grain filling and in response to different nitrogen (N) and sulfur (S) supply, were integrated with mixOmics R package. Relationships between AGs and SPs were first unraveled using the unsupervised method sparse Partial Least Square, also known as Projection to Latent Structure (sPLS). Then, data were integrated using a supervised approach taking into account the nutrition and the grain developmental stage. We used the block.splda procedure also referred to as DIABLO (Data Integration Analysis for Biomarker discovery using Latent variable approaches for Omics studies). These approaches led to the identification of discriminant and highly correlated features from the two datasets (AGs and SPs) which are not necessarily differentially expressed during seed development or in response to N or S supply. Eighteen AGs were correlated with the quantity of SPs per grain. A statistical validation of these proteins by genetic association analysis confirmed that 5 out of this AG set were robust candidate proteins able to modulate the seed SP synthesis. In conclusion, this latter result confirmed that the integrative strategy is an adequate way to reduce the number of potentially relevant AGs for further functional validation. |
| first_indexed | 2024-04-12T19:51:57Z |
| format | Article |
| id | doaj.art-7055fad4dd27470a88258b3a908be2c2 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-12T19:51:57Z |
| publishDate | 2019-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-7055fad4dd27470a88258b3a908be2c22022-12-22T03:18:48ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2019-07-011010.3389/fpls.2019.00832454666Proteomic Data Integration Highlights Central Actors Involved in Einkorn (Triticum monococcum ssp. monococcum) Grain Filling in Relation to Grain Storage Protein CompositionEmmanuelle Bancel0Emmanuelle Bancel1Titouan Bonnot2Titouan Bonnot3Marlène Davanture4David Alvarez5David Alvarez6Michel Zivy7Pierre Martre8Pierre Martre9Sébastien Déjean10Catherine Ravel11Catherine Ravel12UMR GDEC, Institut National de la Recherche Agronomique (INRA), Université Clermont Auvergne, Clermont-Ferrand, FranceUMR1095, Genetics Diversity and Ecophysiology of Cereals, Clermont Auvergne University, Clermont-Ferrand, FranceUMR GDEC, Institut National de la Recherche Agronomique (INRA), Université Clermont Auvergne, Clermont-Ferrand, FranceUMR1095, Genetics Diversity and Ecophysiology of Cereals, Clermont Auvergne University, Clermont-Ferrand, FranceUMR GQE, Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS), Agro ParisTech, Université Paris-Sud – Université Paris-Saclay, Gif-sur-Yvette, FranceUMR GDEC, Institut National de la Recherche Agronomique (INRA), Université Clermont Auvergne, Clermont-Ferrand, FranceUMR1095, Genetics Diversity and Ecophysiology of Cereals, Clermont Auvergne University, Clermont-Ferrand, FranceUMR GQE, Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS), Agro ParisTech, Université Paris-Sud – Université Paris-Saclay, Gif-sur-Yvette, FranceUMR GDEC, Institut National de la Recherche Agronomique (INRA), Université Clermont Auvergne, Clermont-Ferrand, FranceUMR1095, Genetics Diversity and Ecophysiology of Cereals, Clermont Auvergne University, Clermont-Ferrand, FranceInstitut de Mathématiques de Toulouse, UMR5219 Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Toulouse, FranceUMR GDEC, Institut National de la Recherche Agronomique (INRA), Université Clermont Auvergne, Clermont-Ferrand, FranceUMR1095, Genetics Diversity and Ecophysiology of Cereals, Clermont Auvergne University, Clermont-Ferrand, FranceAlbumins and globulins (AGs) of wheat endosperm represent about 20% of total grain proteins. Some of these physiologically active proteins can influence the synthesis of storage proteins (SPs) (gliadins and glutenins) and consequently, rheological properties of wheat flour and processing. To identify such AGs, data, (published by Bonnot et al., 2017) concerning abundance in 352 AGs and in the different seed SPs during grain filling and in response to different nitrogen (N) and sulfur (S) supply, were integrated with mixOmics R package. Relationships between AGs and SPs were first unraveled using the unsupervised method sparse Partial Least Square, also known as Projection to Latent Structure (sPLS). Then, data were integrated using a supervised approach taking into account the nutrition and the grain developmental stage. We used the block.splda procedure also referred to as DIABLO (Data Integration Analysis for Biomarker discovery using Latent variable approaches for Omics studies). These approaches led to the identification of discriminant and highly correlated features from the two datasets (AGs and SPs) which are not necessarily differentially expressed during seed development or in response to N or S supply. Eighteen AGs were correlated with the quantity of SPs per grain. A statistical validation of these proteins by genetic association analysis confirmed that 5 out of this AG set were robust candidate proteins able to modulate the seed SP synthesis. In conclusion, this latter result confirmed that the integrative strategy is an adequate way to reduce the number of potentially relevant AGs for further functional validation.https://www.frontiersin.org/article/10.3389/fpls.2019.00832/fullalbumin-globulindata integrationnitrogenproteomicgrain developmentstorage protein |
| spellingShingle | Emmanuelle Bancel Emmanuelle Bancel Titouan Bonnot Titouan Bonnot Marlène Davanture David Alvarez David Alvarez Michel Zivy Pierre Martre Pierre Martre Sébastien Déjean Catherine Ravel Catherine Ravel Proteomic Data Integration Highlights Central Actors Involved in Einkorn (Triticum monococcum ssp. monococcum) Grain Filling in Relation to Grain Storage Protein Composition Frontiers in Plant Science albumin-globulin data integration nitrogen proteomic grain development storage protein |
| title | Proteomic Data Integration Highlights Central Actors Involved in Einkorn (Triticum monococcum ssp. monococcum) Grain Filling in Relation to Grain Storage Protein Composition |
| title_full | Proteomic Data Integration Highlights Central Actors Involved in Einkorn (Triticum monococcum ssp. monococcum) Grain Filling in Relation to Grain Storage Protein Composition |
| title_fullStr | Proteomic Data Integration Highlights Central Actors Involved in Einkorn (Triticum monococcum ssp. monococcum) Grain Filling in Relation to Grain Storage Protein Composition |
| title_full_unstemmed | Proteomic Data Integration Highlights Central Actors Involved in Einkorn (Triticum monococcum ssp. monococcum) Grain Filling in Relation to Grain Storage Protein Composition |
| title_short | Proteomic Data Integration Highlights Central Actors Involved in Einkorn (Triticum monococcum ssp. monococcum) Grain Filling in Relation to Grain Storage Protein Composition |
| title_sort | proteomic data integration highlights central actors involved in einkorn triticum monococcum ssp monococcum grain filling in relation to grain storage protein composition |
| topic | albumin-globulin data integration nitrogen proteomic grain development storage protein |
| url | https://www.frontiersin.org/article/10.3389/fpls.2019.00832/full |
| work_keys_str_mv | AT emmanuellebancel proteomicdataintegrationhighlightscentralactorsinvolvedineinkorntriticummonococcumsspmonococcumgrainfillinginrelationtograinstorageproteincomposition AT emmanuellebancel proteomicdataintegrationhighlightscentralactorsinvolvedineinkorntriticummonococcumsspmonococcumgrainfillinginrelationtograinstorageproteincomposition AT titouanbonnot proteomicdataintegrationhighlightscentralactorsinvolvedineinkorntriticummonococcumsspmonococcumgrainfillinginrelationtograinstorageproteincomposition AT titouanbonnot proteomicdataintegrationhighlightscentralactorsinvolvedineinkorntriticummonococcumsspmonococcumgrainfillinginrelationtograinstorageproteincomposition AT marlenedavanture proteomicdataintegrationhighlightscentralactorsinvolvedineinkorntriticummonococcumsspmonococcumgrainfillinginrelationtograinstorageproteincomposition AT davidalvarez proteomicdataintegrationhighlightscentralactorsinvolvedineinkorntriticummonococcumsspmonococcumgrainfillinginrelationtograinstorageproteincomposition AT davidalvarez proteomicdataintegrationhighlightscentralactorsinvolvedineinkorntriticummonococcumsspmonococcumgrainfillinginrelationtograinstorageproteincomposition AT michelzivy proteomicdataintegrationhighlightscentralactorsinvolvedineinkorntriticummonococcumsspmonococcumgrainfillinginrelationtograinstorageproteincomposition AT pierremartre proteomicdataintegrationhighlightscentralactorsinvolvedineinkorntriticummonococcumsspmonococcumgrainfillinginrelationtograinstorageproteincomposition AT pierremartre proteomicdataintegrationhighlightscentralactorsinvolvedineinkorntriticummonococcumsspmonococcumgrainfillinginrelationtograinstorageproteincomposition AT sebastiendejean proteomicdataintegrationhighlightscentralactorsinvolvedineinkorntriticummonococcumsspmonococcumgrainfillinginrelationtograinstorageproteincomposition AT catherineravel proteomicdataintegrationhighlightscentralactorsinvolvedineinkorntriticummonococcumsspmonococcumgrainfillinginrelationtograinstorageproteincomposition AT catherineravel proteomicdataintegrationhighlightscentralactorsinvolvedineinkorntriticummonococcumsspmonococcumgrainfillinginrelationtograinstorageproteincomposition |