Multiomics analyses reveal the central role of the nucleolus and its machinery during heat stress acclimation in Pinus radiata.

Global warming is causing rapid changes in mean annual temperature and more severe drought periods. These are major contributors of forest dieback, which is becoming more frequent and widespread. In this work, we investigated how the transcriptome of Pinus radiata changed during initial heat stress response and acclimation.

Multiomic Data Integration in the Analysis of Drought-Responsive Mechanisms in Seedlings.

The integrated analysis of different omic layers can provide new knowledge not provided by their individual analysis. This approach is also necessary to validate data and reveal post-transcriptional and post-translational mechanisms of gene expression regulation. In this work, we validated the possibility of applying this approach to non-model species such as .

Identification of Proteases and Protease Inhibitors in Seeds of the Recalcitrant Forest Tree Species .

Proteases and protease inhibitors have been identified in the recalcitrant species using and wet methods, with focus on those present in seeds during germination. analyses showed that the transcriptome database contained 2,240 and 97 transcripts annotated as proteases and protease inhibitors, respectively. They belonged to the different families according to MEROPS, being the serine and metallo ones the most represented.

GeLC-Orbitrap/MS and 2-DE-MALDI-TOF/TOF comparative proteomics analysis of seed cotyledons from the non-orthodox Quercus ilex tree species.

Gel electrophoresis-based and shotgun approaches are the most employed proteomic platforms in plant biology research, with the latter replacing the former in the last years. We have compared 2-DE-MALDI-TOF/TOF and GeLC-Orbitrap/MS analyses using the same protein extracts from Quercus ilex cotyledons at different development stages. The results obtained (ProteomeXchange available data, PXD020603) showed that both platforms were complementary, showing common and specific proteins identified in each case, but leading to similar biological conclusions.

Temporal physiological response of pine to Fusarium circinatum infection is dependent on host susceptibility level: the role of ABA catabolism.

Pine pitch canker (PPC), caused by Fusarium circinatum Nirenberg and O'Donnell, represents an important threat to conifer forests worldwide, being associated with significant economic losses. Although essential to develop disease mitigation strategies, little research focused on host susceptibility/resistance mechanisms has been conducted. We aimed to explore the response of a highly susceptible (Pinus radiata D.

In-depth analysis of the Quercus suber metabolome under drought stress and recovery reveals potential key metabolic players.

Cork oak (Quercus suber L.) is a species of ecological, social and economic importance in the Mediterranean region. Given its xerophytic adaptability, the study of cork oak's response to drought stress conditions may provide important data in the global scenario of climate change.

A Pipeline for Metabolic Pathway Reconstruction in Plant Orphan Species.

In the era of high-throughput biology, it is necessary to develop a simple pipeline for metabolic pathway reconstruction in plant orphan species. However, obtaining a global picture of the plant metabolism may be challenging, especially in nonmodel species. Moreover, the use of bioinformatics tools and statistical analyses is required.

Protein Interaction Networks: Functional and Statistical Approaches.

The evolution of next-generation sequencing and high-throughput technologies has created new opportunities and challenges in data science. Currently, a classic proteomics analysis can be complemented by going a step beyond the individual analysis of the proteome by using integrative approaches. These integrations can be focused either on inferring relationships among proteins themselves, with other molecular levels, phenotype, or even environmental data, giving the researcher new tools to extract and determine the most relevant information in biological terms.

Integrative analysis of the nuclear proteome in Pinus radiata reveals thermopriming coupled to epigenetic regulation.

Despite it being an important issue in the context of climate change, for most plant species it is not currently known how abiotic stresses affect nuclear proteomes and mediate memory effects. This study examines how Pinus radiata nuclei respond, adapt, 'remember', and 'learn' from heat stress. Seedlings were heat-stressed at 45 °C for 10 d and then allowed to recover.

Metabolome Integrated Analysis of High-Temperature Response in .

The integrative omics approach is crucial to identify the molecular mechanisms underlying high-temperature response in non-model species. Based on future scenarios of heat increase, plants were exposed to a temperature of 40°C for a period of 5 days, including recovered plants (30 days after last exposure to 40°C) in the analysis. The analysis of the metabolome using complementary mass spectrometry techniques (GC-MS and LC-Orbitrap-MS) allowed the reliable quantification of 2,287 metabolites.

System-wide analysis of short-term response to high temperature in Pinus radiata.

Pinus radiata seedlings, the most widely planted pine species in the world, were exposed to temperatures within a range mimicking future scenarios based on current models of heat increase. The short-term heat response in P. radiata was studied in detail by exploring the metabolome, proteome and targeted transcriptome.

Integrated Physiological, Proteomic, and Metabolomic Analysis of Ultra Violet (UV) Stress Responses and Adaptation Mechanisms in .

Globally expected changes in environmental conditions, especially the increase of UV irradiation, necessitate extending our knowledge of the mechanisms mediating tree species adaptation to this stress. This is crucial for designing new strategies to maintain future forest productivity. Studies focused on environmentally realistic dosages of UV irradiation in forest species are scarce.

The variations in the nuclear proteome reveal new transcription factors and mechanisms involved in UV stress response in Pinus radiata.

Unlabelled: The importance of UV stress and its side-effects over the loss of plant productivity in forest species demands a deeper understanding of how pine trees respond to UV irradiation. Although the response to UV stress has been characterized at system and cellular levels, the dynamics within the nuclear proteome triggered by UV is still unknown despite that they are essential for gene expression and regulation of plant physiology. To fill this gap this work aims to characterize the variations in the nuclear proteome as a response to UV irradiation by using state-of-the-art mass spectrometry-based methods combined with novel bioinformatics workflows.

Integrated physiological and hormonal profile of heat-induced thermotolerance in Pinus radiata.

Despite great interest, not only from the economic point of view but also in terms of basic science, research on heat stress tolerance in conifers remains scarce. To fill this gap, a time-course experiment using expected temperature increase was performed aiming to identify physiological and biochemical traits that allow the characterization of heat-induced thermotolerance and recovery in Pinus radiata D. Don plants.

Conserved Epigenetic Mechanisms Could Play a Key Role in Regulation of Photosynthesis and Development-Related Genes during Needle Development of Pinus radiata.

Needle maturation is a complex process that involves cell growth, differentiation and tissue remodelling towards the acquisition of full physiological competence. Leaf induction mechanisms are well known; however, those underlying the acquisition of physiological competence are still poorly understood, especially in conifers. We studied the specific epigenetic regulation of genes defining organ function (PrRBCS and PrRBCA) and competence and stress response (PrCSDP2 and PrSHMT4) during three stages of needle development and one de-differentiated control.

A universal protocol for the combined isolation of metabolites, DNA, long RNAs, small RNAs, and proteins from plants and microorganisms.

Here, we describe a method for the combined metabolomic, proteomic, transcriptomic and genomic analysis from one single sample as a major step for multilevel data integration strategies in systems biology. While extracting proteins and DNA, this protocol also allows the separation of metabolites into polar and lipid fractions, as well as RNA fractionation into long and small RNAs, thus allowing a broad range of transcriptional studies. The isolated biomolecules are suitable for analysis with different methods that range from electrophoresis and blotting to state-of-the-art procedures based on mass spectrometry (accurate metabolite profiling, shot-gun proteomics) or massive sequencing technologies (transcript analysis).