Proteomics research in forest trees: A 2012-2022 update

Abstract

This review is a compilation of proteomic studies on forest tree species published in the last decade (2012-2022), mostly focused on the most investigated species, including Eucalyptus, Pinus, and Quercus. Improvements in equipment, platforms, and methods in addition to the increasing availability of genomic data have favored the biological knowledge of these species at the molecular, organismal, and community levels. Integration of proteomics with physiological, biochemical and other large-scale omics in the direction of the Systems Biology, will provide a comprehensive understanding of different biological processes, from growth and development to responses to biotic and abiotic stresses. As main issue we envisage that proteomics in long-living plants will thrive light on the plant responses and resilience to global climate change, contributing to climate mitigation strategies and molecular breeding programs. Proteomics not only will provide a molecular knowledge of the mechanisms of resilience to either biotic or abiotic stresses, but also will allow the identification on key gene products and its interaction. Proteomics research has also a translational character being applied to the characterization of the variability and biodiversity, as well as to wood and non-wood derived products, traceability, allergen and bioactive peptides identification, among others. Even thought, the full potential of proteomics is far from being fully exploited in forest tree research, with PTMs and interactomics being reserved to plant model systems. The most outstanding achievements in forest tree proteomics in the last decade as well as prospects are discussed.

Proteomic and Metabolomic Analysis of the Quercus ilex–Phytophthora cinnamomi Pathosystem Reveals a Population-Specific Response, Independent of Co-Occurrence of Drought

“…This resulted in 2565 total proteins being confidently identified, 1590 in Co and 1444 in Hu individuals, with 1334 common to both (Table 1, Table S3). These data confirm the great variability commonly found in Q. ilex, with the protein profile depending on the genotype [64]. Two-dimensional PCA explained 40 and 43% of the total variability in Co and Hu, respectively (Figure 2a,b).…”

‘Omics’ Approaches for Crop Improvement

“…The authors evaluated leaf proteome responses to Botrytis fabae necrotrophic fungus in susceptible and resistant Faba bean (Vicia faba) genotypes, finding a predominant role in the chloroplast PSII protein repair cycle. More interestingly, these studies reinforce that proteomics advancements are already permeating orphan species [10], even in the forestry sector [3].…”

“…To cope with these pressures, crop improvement demands enhancing important agronomical traits beyond yield, such as adaptation, resistance, and nutritional value, by pivoting direct and indirect selection approaches [2]. The development of next-generation high-throughput screening technologies, referred to as 'omics', promises to speed up plant trait improvement [3] while producing more sustainable crops.…”

Comprehensive Organ-Specific Profiling of Douglas Fir (Pseudotsuga menziesii) Proteome

“…In addition to transcriptomic studies, proteomics provides another promising approach to obtaining genomic information [ 22 ]. Mainly in the past, proteomic studies were carried out based on 2-DE gels associated with mass spectrometry identification of the proteins to whom the spot volume changed between the two compared conditions, leading to a limited number of identified proteins [ 23 , 24 ].…”