Could Causal Discovery in Proteogenomics Assist in Understanding Gene-Protein Relations? A Perennial Fruit Tree Case Study Using Sweet Cherry as a Model.

Maria Ganopoulou,Ioannis Ganopoulos,Aliki Xanthopoulou,Michail Michailidis,Athanassios Molassiotis,Lefteris Angelis,Theodoros Moysiadis

doi:10.3390/cells11010092

Maria Ganopoulou, Ioannis Ganopoulos + Show 5 more

Open Access

https://doi.org/10.3390/cells11010092

Copy DOI

Abstract

Genome-wide transcriptome analysis is a method that produces important data on plant biology at a systemic level. The lack of understanding of the relationships between proteins and genes in plants necessitates a further thorough analysis at the proteogenomic level. Recently, our group generated a quantitative proteogenomic atlas of 15 sweet cherry (Prunus avium L.) cv. ‘Tragana Edessis’ tissues represented by 29,247 genes and 7584 proteins. The aim of the current study was to perform a targeted analysis at the gene/protein level to assess the structure of their relation, and the biological implications. Weighted correlation network analysis and causal modeling were employed to, respectively, cluster the gene/protein pairs, and reveal their cause–effect relations, aiming to assess the associated biological functions. To the best of our knowledge, this is the first time that causal modeling has been employed within the proteogenomics concept in plants. The analysis revealed the complex nature of causal relations among genes/proteins that are important for traits of interest in perennial fruit trees, particularly regarding the fruit softening and ripening process in sweet cherry. Causal discovery could be used to highlight persistent relations at the gene/protein level, stimulating biological interpretation and facilitating further study of the proteogenomic atlas in plants.

Highlights

Among the numerous research areas of biology, the interactions of proteins and genes of an organism as well as the expression of genes and proteins are a topic of paramount importance [1]
A large number of studies have been use the relations between the consensus eigengenes, which are basically representatives conducted to better understand sweet cherry ripening and quality, no causal-based proof the consensus modules, and defined as the first principal component of the expression teogenomic information is available regarding the fruit ripening up to now
We further examined fruit and stem tissue-specific causal models in respect to their proteogenomic profile, which is known to interfere with the cherry ripening process [10]

Summary

Introduction

Among the numerous research areas of biology, the interactions of proteins and genes of an organism as well as the expression of genes and proteins are a topic of paramount importance [1]. New trends in research aiming at better understanding of gene function, have lead to an undiminished interest in the study of transcriptome profiles of specific tissues or cells [2]. A worthwhile application of proteogenomics in humans resulted in the creation of a global expression atlas that revealed gene/protein expression data in different tissues [7,8]. The development of a plant tissue atlas containing a combination of transcriptomic and proteomic data has been recently reported in sweet cherry (Prunus avium L.) tree [10]. The non-climacteric ripening behavior of sweet cherry fruit are different from several other Prunus species such as peach and apricot, making its study of high interest [14].

Objectives

Methods

Results

Conclusion