# Integrated Proteomics and Metabolomics Emphasized Nutritional Benefits Driven by Lentil (Lens culinaris Medik) Seed Germination

Shuang Peng, Luiza Avezum, Gwendal Cueff, Gilles Clément, Thierry Balliau, Jordan Brulé, Loïc Rajjou

► To cite this version:

Shuang Peng, Luiza Avezum, Gwendal Cueff, Gilles Clément, Thierry Balliau, et al.. Integrated Proteomics and Metabolomics Emphasized Nutritional Benefits Driven by Lentil (Lens culinaris Medik) Seed Germination. The 14th International Society for Seed Science (ISSS) biennial conference, Jul 2023, Paris, France. . [hal-04551806](https://hal.science/hal-04551806)

HAL Id: hal-04551806

https://hal.science/hal-04551806

Submitted on 18 Apr 2024

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# Integrated Proteomics and Metabolomics Emphasized Nutritional Benefits Driven by Lentil (Lens culinaris Medik) Seed Germination.

Shuang Peng<fnref n="1" />, Luiza Avezum¹², Gwendal Cueff<fnref n="1" />, Gilles Clément<fnref n="1" />, Thierry Balliau³, Jordan Brulé<fnref n="1" />, Loïc Rajjou*<fnref n="1" />

<figure><img src="image_1.png" /></figure>

## Introduction

1. Lentils are small, lens-shaped legumes that are a great source of protein, fiber, and various vitamins and minerals, easy to cook and versatile in dishes, and are considered an environmentally friendly and sustainable food source.
2. Until now, lentil seed germination has been poorly described. The present work displays an original systems biology approach to address this gap in knowledge.
3. This study investigated lentil seeds at different germination stages and temperature conditions through a multi-omics approach, including:
   - Statistical analysis was performed on the proteome and metabolome separately to screen for markers with significant control differences;
   - Functional annotation of lentil protein-coding sequences was done based on homologous alignment against well-annotated plant genomes;
   - Study of physiological and metabolic changes during lentil germination based on annotation enrichment and Multi-Omics Integration (MOI).

## Germination Data Description

<figure><img src="image_2.png" /><figcaption>Figure 1. Germination kinetics presented by the simulating hill-function (left) and PCA projection of Germination Indices (right)</figcaption></figure>

<figure><img src="image_3.png" /><figcaption>Figure 2. PCA Sample projection by 300 metabolomic features (left) and 1275 proteomic features (right)</figcaption></figure>

<figure><img src="image_4.png" /><figcaption>Figure 3. Metabolite Fold-Change Heat-map with total 88 significant features (left) and Protein Fold-Change Heat-map with 136 significant features (right)</figcaption></figure>

## Omics Profiling/GO Enrichment

<figure><img src="image_5.png" /></figure>

<figure><img src="image_6.png" /><figcaption>Figure 4. Top Proteomic GO enrichment (In total 1377 biological processes) by statistical profiles (above) and Top KEGG pathway enrichment (In total 85) network from Multi-Omics Integration (below)</figcaption></figure>

## Conclusions

- This is the first descriptive analysis about Lentil seed germination by Multi-Omics approach. with no significant differences found in the germination patterns of the two different temperature treatments
- The metabolic dynamics give us the guidance of improving the nutritional quality of Lentil seed as food.
- The biological process revealed the important physiological turn-over during germination process, including central metabolism, hormone signaling, response to abiotic/biotic stress etc.

## Future Work

- Adding another omics dimensions (eg. transcriptomics) to reinforce the model interpretability.

- We will access the reproducibility of our results.

*This study was funded by the PROVEGGAS (Protéines Végétales Gastronomiques) project*

<figure><img src="image_7.png" /></figure>

AgroParisTech
Talents d'une planète soutenable

<figure><img src="image_8.png" /></figure>

INRAE

université

PARIS-SACLAY

<footnote n="1">¹Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France.
²QualiSud, Université de Montpellier, CIRAD, Institut Agro, Université d'Avignon, Université de La Réunion, Montpellier, France.
³GQE - Le Moulon, Génétique Quantitative et Évolution - PAPPSO, Plateforme d'Analyse de Proteomique Paris-Sud-Ouest, 91190, Gif-sur-Yvette, France.</footnote>
# Integrated Proteomics and Metabolomics Emphasized Nutritional Benefits Driven by Lentil (Lens culinaris Medik) Seed Germination.

Shuang Peng<fnref n="1" />, Luiza Avezum¹², Gwendal Cueff<fnref n="1" />, Gilles Clément<fnref n="1" />, Thierry Balliau³, Jordan Brulé<fnref n="1" />, Loïc Rajjou*<fnref n="1" />

<figure><img src="image_1.png" /></figure>

## Introduction

1. Lentils are small, lens-shaped legumes that are a great source of protein, fiber, and various vitamins and minerals, easy to cook and versatile in dishes, and are considered an environmentally friendly and sustainable food source.
2. Until now, lentil seed germination has been poorly described. The present work displays an original systems biology approach to address this gap in knowledge.
3. This study investigated lentil seeds at different germination stages and temperature conditions through a multi-omics approach, including:
   - Statistical analysis was performed on the proteome and metabolome separately to screen for markers with significant control differences;
   - Functional annotation of lentil protein-coding sequences was done based on homologous alignment against well-annotated plant genomes;
   - Study of physiological and metabolic changes during lentil germination based on annotation enrichment and Multi-Omics Integration (MOI).

## Germination Data Description

<figure><img src="image_2.png" /><figcaption>Figure 1. Germination kinetics presented by the simulating hill-function (left) and PCA projection of Germination Indices (right)</figcaption></figure>

<figure><img src="image_3.png" /><figcaption>Figure 2. PCA Sample projection by 300 metabolomic features (left) and 1275 proteomic features (right)</figcaption></figure>

<figure><img src="image_4.png" /><figcaption>Figure 3. Metabolite Fold-Change Heat-map with total 88 significant features (left) and Protein Fold-Change Heat-map with 136 significant features (right)</figcaption></figure>

## Omics Profiling/GO Enrichment

<figure><img src="image_5.png" /></figure>

<figure><img src="image_6.png" /><figcaption>Figure 4. Top Proteomic GO enrichment (In total 1377 biological processes) by statistical profiles (above) and Top KEGG pathway enrichment (In total 85) network from Multi-Omics Integration (below)</figcaption></figure>

## Conclusions

- This is the first descriptive analysis about Lentil seed germination by Multi-Omics approach. with no significant differences found in the germination patterns of the two different temperature treatments
- The metabolic dynamics give us the guidance of improving the nutritional quality of Lentil seed as food.
- The biological process revealed the important physiological turn-over during germination process, including central metabolism, hormone signaling, response to abiotic/biotic stress etc.

## Future Work

- Adding another omics dimensions (eg. transcriptomics) to reinforce the model interpretability.
- We will access the reproducibility of our results

This study was funded by the PROVEGGAS (Protéines Végétales Gastronomiques) project

<figure><img src="image_7.png" /></figure>

Ijpb

AgroParisTech

Talents d'une planète soutenable

<figure><img src="image_8.png" /></figure>

INRAE

université
PARIS-SACLAY

<footnote n="1">¹Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France.
²QualiSud, Université de Montpellier, CIRAD, Institut Agro, Université d'Avignon, Université de La Réunion, Montpellier, France.
³GQE - Le Moulon, Génétique Quantitative et Évolution - PAPPSO, Plateforme d'Analyse de Proteomique Paris-Sud-Ouest, 91190, Gif-sur-Yvette, France.</footnote>