The role of proteomics in progressing insights into plant secondary metabolism

Abstract

The development of omics has enabled the genome-wide exploration of all kinds of biological processes at the molecular level. Almost every field of plant biology has been analyzed at the genomic, transcriptomic and proteomic level. Here we focus on the particular contribution that proteomic technologies have made in progressing knowledge and characterising plant secondary metabolism (SM) pathways since early expectations were created 15 years ago. We analyzed how three major issues in the proteomic analysis of plant SM have been implemented in various research studies. These issues are: (i) the selection of a suitable plant material rich in secondary metabolites of interest, such as specialized tissues and organs, and in vitro cell cultures; (ii) the proteomic strategy to access target proteins, either a comprehensive or a differential analysis; (iii) the proteomic approach, represented by the hypothesis-free discovery proteomics and the hypothesis-driven targeted proteomics. We also examine to what extent the most-advanced technologies have been incorporated into proteomic research in plant SM and highlight some cutting edge techniques that would strongly benefit the progress made in this field.

Integrated omics analysis of specialized metabolism in medicinal plants

“…A comprehensive proteome analysis provides the opportunity to verify and correct assignments of open reading frames to an annotated gene and confirms the splicing patterns, and thus improves annotation of plant genomes. Further, identification of the proteins specifically localized within tissues that biosynthesize active specialized metabolites may provide important clues for understanding the biosynthesis and regulation of secondary metabolites (Martinez-Esteso et al, 2015).…”

“…While a lack of genomics and transcriptome resources, and hence a reliable proteome database for the majority of medicinal plants, has been a major impediment for proteome-based studies of specialized metabolite biosynthesis in the past, much has changed in the last few years. Further, recent technological advances and an explosion of proteomics workflows have significantly expanded proteomics beyond the analysis of protein expression, and are promising for the study of different aspects of proteins or protein-protein interactions and in the identification of enzymes involved in secondary metabolic pathways (Martinez-Esteso et al, 2015). We expect more studies to use proteomics-based approaches together with transcriptome and metabolome analysis in the study of secondary metabolism in medicinal plants in the near future.…”

A Deep Proteomics Perspective Into Grape Berry Quality Traits During Ripening

“…The challenges in proteomics for the analysis of plant SM have been recently reviewed. [7] A common issue in grape berry proteomics shared with the rest of the plant proteomics analyses is the protein preparation and fractionation which is an important step in achieving a comprehensive and deeper coverage of the fruit proteome. An additional factor that hinders the detection of a higher protein dynamic range is the type of proteomic approach applied.…”

“…Thus, the current challenge in the studies of grape berry ripening as well as in the studies of the metabolic pathways leading to the aroma composition in ripe berries is to increase the proteome coverage in order to detect the underneath low abundance proteome. The challenges in proteomics for the analysis of plant SM have been recently reviewed . A common issue in grape berry proteomics shared with the rest of the plant proteomics analyses is the protein preparation and fractionation which is an important step in achieving a comprehensive and deeper coverage of the fruit proteome.…”

Effect of methyl jasmonate on production of 20-hydroxyecdysone and turkesterone in hairy roots of Silene linicola C.C.Gmelin

“…Some scientists suggest not to activate one or more key genes of secondary metabolism, but to develop approaches to remove inhibitor blocks and to shift the regulatory balance towards activation of the entire biosynthetic pathways [3]. Other scientists investigate the processes of enhanced secondary metabolism of in vitro cultures using proteomic methods that enable regulation of enzymes involved in biosynthesis of secondary metabolites [4]. However, most of the studies on regulation of in vitro bioactive compound accumulation focus on optimization of media and culture conditions, and on selection of growth regulators, elicitors and precursors of secondary metabolite synthesis [5,6].…”