Proteomics, Holm Oak (Quercus ilex L.) and Other Recalcitrant and Orphan Forest Tree Species: How do They See Each Other?

Abstract

Proteomics has had a big impact on plant biology, considered as a valuable tool for several forest species, such as Quercus, Pines, Poplars, and Eucalyptus. This review assesses the potential and limitations of the proteomics approaches and is focused on Quercus ilex as a model species and other forest tree species. Proteomics has been used with Q. ilex since 2003 with the main aim of examining natural variability, developmental processes, and responses to biotic and abiotic stresses as in other species of the genus Quercus or Pinus. As with the progress in techniques in proteomics in other plant species, the research in Q. ilex moved from 2-DE based strategy to the latest gel-free shotgun workflows. Experimental design, protein extraction, mass spectrometric analysis, confidence levels of qualitative and quantitative proteomics data, and their interpretation are a true challenge with relation to forest tree species due to their extreme orphan and recalcitrant (non-orthodox) nature. Implementing a systems biology approach, it is time to validate proteomics data using complementary techniques and integrate it with the -omics and classical approaches. The full potential of the protein field in plant research is quite far from being entirely exploited. However, despite the methodological limitations present in proteomics, there is no doubt that this discipline has contributed to deeper knowledge of plant biology and, currently, is increasingly employed for translational purposes.

Responses and Differences in Tolerance to Water Shortage under Climatic Dryness Conditions in Seedlings from Quercus spp. and Andalusian Q. ilex Populations

“…For instance, the identification and characterization of plus or elite Q. ilex genotypes, which are more resilient and tolerant to drought, is a priority in plant breeding, reforestation, management, and conservation programs in the Mediterranean area. To enable this, ecophysiological and molecular studies are required to have a better understanding of both the variability in this species and the selection of morphometric, physiological, and molecular markers [31].…”

Dissecting the Seed Maturation and Germination Processes in the Non-Orthodox Quercus ilex Species Based on Protein Signatures as Revealed by 2-DE Coupled to MALDI-TOF/TOF Proteomics Strategy

“…Protein signatures, experimentally afforded by proteomics, determine the phenotype, characteristics and properties of biological systems and processes. We have applied this principle to study seed development and germination in the non-orthodox Quercus ilex, the most representative and emblematic forest tree species of the Mediterranean forest and of the agrosilvopastoral ecosystem "dehesa" [1]. Despite being a priority, reforestation and breeding programs with this species are hindered by its long lifespan, lack of natural regeneration, and its biological properties.…”

“…Despite being a priority, reforestation and breeding programs with this species are hindered by its long lifespan, lack of natural regeneration, and its biological properties. These latter, impede a viable and feasible germplasm conservation and propagation, which is also linked to the lack of knowledge of its biology, especially at the molecular level [1].…”

Plant Proteomic Research 2.0: Trends and Perspectives

“…Progress has been fueled by the advancement in mass spectrometry techniques, complemented with genome-sequence data and modern bioinformatic analysis; however, until now the two-dimensional electrophoresis based proteomic technique was used [2] as shown in six articles of this special issue. The review by Ray et al [3] summarized the potential and limitations of the proteomic approaches and focused on Quercus ilex as a model species for other forest tree species. Regarding the progress of techniques in proteomics with other plant species, the research in Q. ilex moved from a gel-based strategy to a gel-free shotgun workflow.…”

“…Regarding the progress of techniques in proteomics with other plant species, the research in Q. ilex moved from a gel-based strategy to a gel-free shotgun workflow. New directions in Q. ilex research leads to the identification of allergens in pollen grains/acorns and the characterization of wood materials, which are objectives clearly approached by proteomics [3]…”