Luis Valledor

University of Oviedo | UNIOVI · Department of Organisms and Systems Biology

Chlamydomonas reinhardtii is one of the most important model organisms nowadays phylogenetically situated between higher plants and animals (Merchant et al. 2007). Stress adaptation of this unicellular model algae is in the focus because of its relevance to biomass and biofuel production. Here, we have studied cold stress adaptation of C. reinhardt...

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 allows also separation of metabolites into polar and lipid fractions, as well as RNA fractionat...

Nitrogen starvation is known to cause drastic alterations in physiology and metabolism leading to the accumulation of lipid bodies in many microalgae, and it thus presents an important alternative for biofuel production. However, despite the importance of this process, the molecular mechanisms that mediate the metabolic remodeling induced by N star...

Natural variation of the metabolome of Pinus pinaster was studied to improve understanding of its role in the adaptation process and phenotypic diversity. The metabolomes of needles and the apical and basal section of buds were analyzed in ten provenances of P. pinaster, selected from France, Spain, and Morocco, grown in a common garden for five ye...

The SnRK (Snf1-Related protein Kinase) gene family plays an important role in energy sensing and stress-adaptive responses in plant systems. In this study, Chlamydomonas CKIN family (SnRK in Arabidopsis) was defined after a genome-wide analysis of all sequenced Chlorophytes. Twenty-two sequences were defined as plant SnRK orthologs in Chlamydomonas...

The increasing availability of massive omics data requires improving the quality of reference databases and their annotations. The combination of full-length isoform sequencing (Iso-Seq) with short-read transcriptomics and proteomics has been successfully used for increasing proteoform characterization, which is a main ongoing goal in biology. Howe...

Current scenario of climate change has led to increase number of studies describing main drivers in abiotic stress. Recent findings suggest that alternative splicing (AS) has a critical role in controlling plant response to high temperature. AS is a mechanism that allows organisms to create an assortment of RNA transcripts and proteins using single...

In an era of climate change and global trade, forests sustainability is endangered by several biotic threats. Pine pitch canker (PPC), caused by Fusarium circinatum, is one of the most important disease affecting conifers worldwide. To date, no effective control measures have been found for this disease. Earlier studies on PPC were mainly focused o...

The holm oak (Quercus ilex L.) is the dominant tree species of the Mediterranean forest and the Spanish agrosilvopastoral ecosystem, "dehesa." It has been, since the prehistoric period, an important part of the Iberian population from a social, cultural, and religious point of view, providing an ample variety of goods and services, and forming the...

Introduction: Different gene expression between male and female bovine embryos leads to metabolic differences. Objective: We used UHPLC-MS/MS to identify sex metabolite biomarkers in embryo culture medium (CM). Methods: Embryos were produced in vitro under highly variable conditions, i.e., fertilized with 7 bulls, two breeds, and cultured with...

Climate warming is causing quick changes in mean annual temperature and more severe drought period. These are major contributors of forest dieback, which is becoming more frequent and widespread, particularly in warm and drought-prone regions. Despite being a hot topic in non-woody plant sciences, the information about how heatwaves impact in tree...

Plants do have stress memory and chloroplast signaling has been revealed as crucial element to acquire and extend this memory into future generations, allowing plant adaptation to changing environments and providing novel tools in the field of crop improvement. Despite the process is known, how a plant is capable to transfer some aspects of its “li...

In the era of plastic pollution, plants have been discarded as a system that is not affected by micro and nanoplastics, but contrary to beliefs that plants cannot absorb plastic particles, recent research proved otherwise. The presented review gives insight into known aspects of plants' interplay with plastics and how plants' ability to absorb plas...

The recovery and maintenance of plant homeostasis under stressful environments are complex processes involving organelle crosstalk for a coordinated cellular response. Here, we revealed through nuclear and chloroplast subcellular proteomics, biochemical cell profiles and targeted transcriptomics how chloroplasts and nuclei developed their responses...

Fusarium circinatum, causing pine pitch canker (PPC), affects conifers productivity and health worldwide. Selection and breeding for resistance arises as the most promising approach to fight PPC. Therefore, it is crucial to explore the response of hosts with varying levels of susceptibility to PPC to unveil the genes/pathways behind these phenotype...

In vitro produced (IVP) embryos show large metabolic variability induced by breed, culture conditions, embryonic stage and sex and gamete donors. We hypothesized that the birth potential could be accurately predicted by UHPLC-MS/MS in culture medium (CM) with the discrimination of factors inducing metabolic variation. Day-6 embryos were developed i...

Fusarium circinatum causes one of the most important diseases of conifers worldwide, the pine pitch canker (PPC). However, no effective field intervention measures aiming to control or eradicate PPC are available. Due to the variation in host genetic resistance, the development of resistant varieties is postulated as a viable and promising strategy...

The elucidation of plant health status requires quantifying multiple molecular metabolism markers. Until now, the extraction of these biomarkers is performed independently, with different extractions and protocols. This approach is inefficient, since it increases laboratory time, amount of sample, and could introduce biases or difficulties when com...

Presently, pearl millet and wheat are belonging to highly important cereal crops. Pearl millet, however, is an under-utilized crop, despite its superior resilience to drought and heat stress in contrast to wheat. To investigate this in more detail, we performed comparative physiological screening and large scale proteomics of drought stress respons...

During its life, freshwater microalgae need to grow under varying water availabilities such as seasonal dryness of puddles or tidal variations. A vast knowledge of the physiological and molecular responses to osmotic stress is available for land plants, however these responses have been scarcely studied in microalgae. In this work we described the...

Pine pitch canker (PPC), caused by Fusarium circinatum Nirenberg & 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 t...

Bud maturation is a physiological process which implies a set of morphophysiological changes which lead to the transition of growth patterns from young to mature. This transition defines tree growth and architecture, and in consequence traits such as biomass production and wood quality. In Pinus pinaster, a conifer of great timber value, bud matura...

Background: The exposure of microalgae and plants to low UV-C radiation dosages can improve their biomass composition and stress tolerance. Despite UV-C sharing these effects with UV-A/B but at much lower dosages, UV-C sensing and signal mechanisms are still mostly unknown. Thus, we have described and integrated the proteometabolomic and physiolog...

Microalgae are gaining attention in industry for their high value–added biomolecules and biomass production and for studying fundamental processes in biology. The introduction of novel approaches for understanding and modeling molecular networks at different omic levels is paramount for increasing the productivity of these organisms. However, the c...

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. This chapter...

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...

B-cell acute lymphoblastic leukemia (B-ALL) is the most common pediatric cancer, and high-hyperdiploidy (HyperD) identifies the most common subtype of pediatric B-ALL. Despite HyperD is an initiating oncogenic event affiliated to childhood B-ALL, the mitotic and chromosomal defects associated to HyperD B-ALL (HyperD-ALL) remain poorly characterized...

Background The exposition of microalgae and plants to low UV-C radiation dosages can improve their biomass composition and stress tolerance. Despite UV-C shares these effects with UV-A/B but at much lower dosages, UV-C sensing and signal mechanisms are still mostly unknown. Thus, we have described and integrated the proteometabolomic and physiologi...

Background: The exposition of microalgae and plants to low UV-C radiation dosages can improve their biomass composition and stress tolerance. Despite UV-C shares these effects with UV-A/B but at much lower dosages, UV-C sensing and signal mechanisms are still mostly unknown. Thus, we have described and integrated the proteometabolomic and physiolog...

Climate change is increasing the intensity and incidence of environmental stressors, reducing the biomass yields of forestry species as Pinus pinaster. Selection of new stress-tolerant varieties is thus required. Many genes related to plant stress signaling pathways have proven useful for this purpose with sucrose non-fermenting related kinases (Sn...

This third edition details recent advances made in the field of proteomics and the application to plant biology and translational research. In recent years, improvements have been made to protocols on high-throughput proteomics at all workflow stages, from wet to dry labs. Chapters are divided into nine parts, covering methods and protocols such as...

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 the...

Histone H4 acetylation at Lysine 16 (H4K16ac) is a key epigenetic mark involved in gene regulation, DNA repair and chromatin remodeling, and though it is known to be essential for embryonic development, its role during adult life is still poorly understood. Here we show that this lysine is massively hyperacety-lated in peripheral neutrophils. Genom...

While reviewing the plant proteomics topic, both from a conceptual and methodological point of view and with a historical perspective, recent advances, current states, challenges, and future directions of the field are discussed. Proteomics is moving, even though very slowly, from the descriptive era to a new era in which data start to be validated...

Trees are sessile and long-lived organism so they have to rapidly adapt to dynamic and unfavorable environments (drought, soil salinity, heat, …) for ensure their survival. Acclimation is mostly related to epigenetic regulation mechanisms that act responding to environmental stimuli and thus regulating gene expression during leaf development, flora...

Fusarium circinatum, the causal agent of pine pitch canker (PPC), is an emergent and still understudied risk that threatens Pinus forests worldwide, with potential production and sustainability losses. In order to explore the response of pine species with distinct levels of susceptibility to PPC, we investigated changes in physiology, hormones, spe...

Plants have evolved a suite of photoreceptors to perceive information from the surrounding light conditions. The aim of this study was to examine photomorphogenic effects of light quality on the growth of Scots pine (Pinus sylvestris L.)seedlings representing southern (60 °N)and northern (68 °N)origins in Finland. We measured the growth characteris...

Holm oak (Quercus ilex), is the most representative forest species of the Mediterranean forest and the agro-silvo-pastoral system of the “dehesa”, having therefore an ecological as well as economic interest. However, the number of works at the molecular level that can be found in the bibliography is quite small. A mRNA level study of the drought re...

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....

Previous knowledge suggested the involvement of specific pathways/proteins that could be identified as potential molecular indicators linked to enhanced drought tolerance in Eucalyptus globulus. Here, we looked for specific variations in key transcripts of two Eucalyptus globulus clones (AL-18 and AL-13) exposed to water deficit and rehydration wit...

Systems biology has emerged in the last years as a comprehensive set of tools which provides rich biological information by integrating different cell organization levels (genome, epigenome, transcripts, proteins, and metabolites) and providing not only the relationships and correlations among them but also giving the possibility of modeling how an...

Proteomics, either considered as being a scientific discipline or a methodological approach, will be presented from a historical perspective, as the heir of the classical protein chemistry or biochemistry. In the last 20 years, classical techniques for protein extraction and resolution such as electrophoresis and liquid chromatography have been con...

Long-lived conifers are vulnerable to climate change because classical evolutionary processes are slow in developing adaptive responses. Therefore, the capacity of a genotype to adopt different phenotypes is important. Gene expression is the primary mechanism to convert genome-encoded information into phenotypes, and further, DNA methylation is emp...

Comparison of KEGG pathways of different species.

Enzymes (transcript level and protein level) assigned to the glycolysis/gluconeogenesis.

Density histogram for proteins in the different biological processes of Q. ilex annotated transcriptome.

Density histogram for proteins in the different cellular components of Q. ilex annotated transcriptome.

Density histogram for proteins in the different molecular functions of Q. ilex annotated transcriptome.

GC-MS metabolomic data. Mean values of normalized peak areas, as well as SD (standard deviation) and CV% (percentage of coefficient of variation) were determined for replicates of the metabolite extract.

Comparison of in silico proteomes.

KEGG pathways with metabolites, proteins, and transcripts.

Shotgun LC-MS/MS proteomic data. Mean values of normalized peak areas, as well as SD (standard deviation) and CV% (percentage of coefficient of variation) were determined for replicates of protein extract (Jorge et al., 2005, 2006). The area values correspond to replicate 1 (0.6 μg of protein), replicate 2 (0.8 μg of protein), and replicate 3 (1 μg...

The metabolite profiles of acorns in Holm oak (Quercus ilex L. subsp. ballota [Desf.] Samp.) have been analyzed from different trees by a non-targeted LC-MS approach. This work has a double objective, first to characterize population variability and diversity through the chemical compositions of acorns, and second to search for bioactive compounds....

Aiming to mimic a more realistic field condition and to determine convergent and divergent responses of individual stresses in relation to their combination, we explored physiological, biochemical, and metabolomic alterations after drought and heat stress imposition (alone and combined) and recovery, using a drought-tolerant Eucalyptus globulus clo...

Holm oak (Quercus ilex) is the most important and representative species of the Mediterranean forest and of the Spanish agrosilvo-pastoral “dehesa” ecosystem. Despite its environmental and economic interest, Holm oak is an orphan species whose biology is very little known, especially at the molecular level. In order to increase the knowledge on the...

Background: Holm oak (Quercus ilex) is the most important and representative species of the Mediterranean forest and of the Spanish agrosilvo-pastoral “dehesa” ecosystem. Despite its environmental and economic interest, Holm oak is an orphan species whose biology is very little known, especially at the molecular level. In order to increase the know...

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, Pinus radiata 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...

Global DNA methylation was classically considered the relative percentage of 5-methylcysine (5mC) with respect to total cytosine (C). Early approaches were based on the use of high-performance separation technologies and UV detection. However, the recent development of protocols using mass spectrometry for the detection has increased sensibility an...