Large Scale Proteomic Data and Network-Based Systems Biology Approaches to Explore the Plant World

Dario Di Silvestre, Andrea Bergamaschi, Edoardo Bellini, PierLuigi Mauri
2018 Proteomes  
The investigation of plant organisms by means of data-derived systems biology approaches based on network modeling is mainly characterized by genomic data, while the potential of proteomics is largely unexplored. This delay is mainly caused by the paucity of plant genomic/proteomic sequences and annotations which are fundamental to perform mass-spectrometry (MS) data interpretation. However, Next Generation Sequencing (NGS) techniques are contributing to filling this gap and an increasing
more » ... of studies are focusing on plant proteome profiling and protein-protein interactions (PPIs) identification. Interesting results were obtained by evaluating the topology of PPI networks in the context of organ-associated biological processes as well as plant-pathogen relationships. These examples foreshadow well the benefits that these approaches may provide to plant research. Thus, in addition to providing an overview of the main-omic technologies recently used on plant organisms, we will focus on studies that rely on concepts of module, hub and shortest path, and how they can contribute to the plant discovery processes. In this scenario, we will also consider gene co-expression networks, and some examples of integration with metabolomic data and genome-wide association studies (GWAS) to select candidate genes will be mentioned. Proteomes 2018, 6, 27 2 of 34 level [7], while computational tools and algorithms assist biologists in data processing to extract the most relevant information in an objective way [8]. Plasma membrane Gene mRNA Protein Metabolite Cell wall miRNA BIOTIC STRESS ABIOTIC STRESS ORGANS CELLS METABOLIC NETWORKS PROTEOMIC NETWORKS GENOMIC NETWORKS Figure 1. Holistic view of plant organisms. (A) Like each living organism, it is assumed that plants are made up of networks integrated and communicating on a multiple scale. They include molecular networks, where genes, transcripts, proteins and metabolites interact to carry out biological functions and processes, and social networks, where plants interact with other organisms/factors and are subjected to abiotic and biotic stresses; (B) Steps and main components to perform data-derived systems biology approaches.
doi:10.3390/proteomes6020027 pmid:29865292 pmcid:PMC6027444 fatcat:cs7o46lztfgtrh2bzi65hu7cti