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 severalforest species, such as Quercus,Pines,Poplars, and Eucalyptus. This review assesses the potential andlimitations of the proteomics approaches and is focused on Quercus ilex as a model species and otherforest tree species. Proteomics has been used with Q. ilex since 2003 with the main aim of examiningnatural variability, developmental processes, and responses to biotic and abiotic stresses as in otherspecies of the genus Quercus or Pinus. As with the progress in techniques in proteomics in otherplant species, the research in Q. ilex moved from 2-DE based strategy to the latest gel-free shotgunworkflows. Experimental design, protein extraction, mass spectrometric analysis, confidence levelsof qualitative and quantitative proteomics data, and their interpretation are a true challenge withrelation 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 complementarytechniques and integrate it with the -omics and classical approaches. The full potential of the proteinfield in plant research is quite far from being entirely exploited. However, despite the methodologicallimitations present in proteomics, there is no doubt that this discipline has contributed to deeperknowledge of plant biology and, currently, is increasingly employed for translational purposes