Artículos (Bioquímica Vegetal y Biología Molecular)

URI permanente para esta colecciónhttps://hdl.handle.net/11441/10824

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Quantitative Assessment of Hormogonia Induction in Nostoc punctiforme by a Fluorescent Reporter Strain
(Oxford University Press, 2025-05-13) Neubauer, Anna; Iniesta Pallarés, Macarena; Álvarez Núñez, Consolación; Bailly, Aurélien; Szövényi, Péter; Mariscal, Vicente; Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular; Ministerio de Ciencia, Innovación y Universidades (MICIU). España; Universidad de Sevilla
While symbiotic plant–cyanobacteria interactions hold significant potential for revolutionizing agricultural practices by reducing the application of artificial nitrogen fertilizers, the genetic underpinnings of the symbiotic interaction between the plant host and the cyanobiont remain poorly understood. In particular, the molecular mechanisms through which host plants induce the formation of motile cyanobacterial filaments (hormogonia), essential for colonization and initiation of symbiosis, are not well characterized. In this study, we present a novel yet objective method for quantifying hormogonia induction, addressing limitations of traditional qualitative approaches. We have developed a reporter strain of Nostoc punctiforme PCC 73102 capable of quantifying hormogonia induction in response to diverse biotic and abiotic stimuli. This reporter strain, generated via triparental mating conjugation transformation, contains the promoter sequence of prepilin pilA fused to a green fluorescent protein (GFP) and enables quantitative and high-throughput monitoring of hormogonia induction using a microplate reader. Our innovative approach, employing a cyanobacterial hormogonia reporter strain, allows high-throughput screening of the hormogonia-inducing effect of a wide array of environmental and plant signals. This method is expected to greatly advance our understanding of the genetic determinants underpinning plant–cyanobacteria symbioses.
Hydrogen Sulfide-induced Barley Resilience to Drought and Salinity through Protein Persulfidation
(Elsevier, 2025) Carrillo, Reyes; Moreno, Inmaculada; Romero, Luis C.; Aroca Aguilar, Ángeles; Gotor, Cecilia; Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular; Junta de Andalucía; Ministerio de Ciencia e Innovación (MICIN). España; Agencia Estatal de Investigación. España
Barley (Hordeum vulgare) is a widely cultivated cereal crops, and its production is increasingly threatened by environmental stresses such as drought and salinity. Hydrogen sulfide is established as a signaling molecule that promotes tolerance to plant stress throught persulfidation, a post-translational modification of cysteine residues in proteins. The purpose of this study is to explore the impact of NaHS (sulfide donor) pretreatment on barley plants in enhancing tolerance to drought and salinity stresses, and determine if persulfidation is involved. In pretreated-plants, phenotypical traits and pigment contents showed an improvement in the survival of the plants under stress conditions. Quantification of stress-markers such as anthocyanin, proline, and reactive oxygen species also showed significant decreased contents in pretreated compared to untreated plants. In addition, the accumulation of amino acids under drought stress was significantly reduced when plants were pretreated with NaHS. Similarly, the increase of ABA content as a typical drought response was reduced in the pretreated plants. When plants are exposed to salt stress, the Na+/K+ ratio was maintained low in NaHS-pretreated plants, by increasing K+ levels. The sulfide ameliorative effect to salt was also observed during germination in previously NaHS-soaked seeds. Our findings suggest that sulfide pretreatment prepares barely plants to better deal with drought and salinity. Moreover, persulfidation was analyzed under all conditions, exhibiting enhanced levels under stress when plants were pretreated with NaHS. Our findings indicate that sulfide pretreatment induces a previous state in barley to respond more efficiently to stress and propose persulfidation is the underlying mechanism.
An Extremely Acidic Environment Microalga from Tinto River as a Novel Source of Anti-inflammatory Activity
(Elsevier, 2025) Robles, María; Viegas, Carla S. B.; Torronteras, Rafael; Garbayo, Inés; Vega Piqueres, José María; Simes, Dina C.; Vílchez, Carlos; Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular; Foundation for Science and Technology (FST); Consejo Superior de Investigaciones Científicas (CSIC)
Coccomyxa onubensis (C. onubensis) is an acidotolerant microalga isolated from the extremely acidic Tinto River (Huelva), which contains high levels of metals in solution, mainly Fe and Cu. This makes C. onubensis an adequate candidate to easily cope with high levels of oxidative stress by increasing the levels of certain molecules and enzymes, which helps them elicit an adequate antioxidant biochemical response. Thus, C. onubensis is a promising source of bioactive compounds which exhibit in vitro anti-inflammatory activity, including fatty acids, (poly)phenolic compounds and carotenoids. In this study, the correlations between the antioxidant response and anti-inflammatory activity of cell extracts obtained from Fe (III)-stressed microalgal cultures were analyzed. The results suggested a direct relationship between the antioxidant capacity of the microalgal extracts and Fe (III) concentration in the culture medium. Consequently, the production of some of the target antioxidant molecules, including carotenes, xanthophylls and (poly)phenols, increased. The levels of these molecules increased the most in cell extracts obtained from microalgal cultures at 0.25 mM of Fe (III), which was correlated with a 50 % increase in the anti-inflammatory activity of the microalgal extracts in THP-1 differentiated human macrophages. Fe (III)-modulated oxidative stress allowed us to define culture conditions that can enhance the anti-inflammatory activity of C. onubensis extracts, which are enriched in valuable antioxidant molecules. Overall, this study highlighted the utility of a microalgal species from a highly acidic environment as a novel, natural source of anti-inflammatory agents, based on its ability to cope with the oxidative conditions of its habitat.
Modulatory effects of CNNM4 on protein-L-isoaspartylO-methyltransferase repair function during alcohol-induced hepatic damage
(Wiley, 2024-03-23) González Recio, Irene; Goikoetxea Usandizaga, Naroa; Rejano Gordillo, Claudia M.; Conter, Carolina; Rodríguez Agudo, Rubén; Serrano Maciá, Marina; Díaz Moreno, Irene; Díaz Quintana, Antonio Jesús; Martínez Chantar, María Luz; Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular; Ministerio de Ciencia, Innovación y Universidades (MICINN). España; Agencia Estatal de Investigación. España; European Union (UE); Instituto de Salud Carlos III; Fundación La Caixa; Gobierno Vasco; Xunta de Galicia; Junta de Andalucía
Background and Aims: Alcohol-associated liver disease (ALD) is a,leading cause of liver-related mortality worldwide, with limited treatment,options beyond abstinence and liver transplantation. Chronic alcohol,consumption has been linked to magnesium (Mg2+) deficiency, which can,influence liver disease progression. The mechanisms underlying Mg2+,homeostasis dysregulation in ALD remain elusive. This study aimed to,investigate the role of the Mg2+ transporter Cyclin M4 (CNNM4) in ALD by,analyzing its expression patterns in patients with ALD and preclinical,animal models.,Approach and Results: In this study, CNNM4 is upregulated in the liver of,both patients with ALD and animal models. CNNM4 overexpression triggers Mg2+ homeostasis dysregulation, linked to ALD progression. We,propose a novel therapeutic approach for ALD treatment using N-acetylgalactosamine silencing RNA technology to specifically modulate,Cnnm4 expression in the liver, improving mitochondrial function and alleviating endoplasmic reticulum stress. Notably, silencing Cnnm4 restores,protein isoaspartyl methyltransferase (PCMT1) activity, essential for,repairing ethanol-induced protein damage. Enhancing mitochondrial,activity through Cnnm4-dependent mechanisms increases S-adenosylmethionine levels, crucial for PCMT1 function, highlighting the interconnected roles of mitochondrial health and protein homeostasis in ALD,treatment.,Conclusions: These findings shed light on the dysregulation of Mg2+,homeostasis in ALD, providing a promising therapeutic approach targeting,CNNM4. N-acetylgalactosamine siCnnm4 therapy boosts the repair processes of ethanol-damaged proteins through the upregulation of PCMT1,activity.
Alterations in nitrogen metabolism caused by heavy metals in the acid-tolerant microalga Coccomyxa onubensis
(Elsevier, 2024-12) Romero Cruz, María del Carmen; Leon Vaz, Antonio; Vega Piqueres, José María; Vigara, Javier; Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular; Universidad de Huelva
The microalga Coccomyxa onubensis is an extremophile microorganism with a unique ecosystem (Río Tinto,,Huelva, Spain) that contains high amounts of contaminants, including heavy metals, sulphates, and nitrates, in,acidic environments (pH 2.5). The current work presents an evaluation of the capacity of Coccomyxa onubensis to,assimilate different nitrogen sources under Cu2+, Cd2+, AsO3,3− , AsO4,3− and Hg2+ stress, and the metabolic implications of these stressors. The results showed that ammonium consumption was less affected than nitrate,consumption when microalgae were cultivated with heavy metals (except cadmium). The activities of enzymes,involved in nitrogen metabolism, such as nitrite reductase (NiR; EC:1.7.7.1), glutamine synthetase (GS;,EC:6.3.2.1) and glutamate dehydrogenase (GDH; EC:1.4.1.2) were characterised to determine the MichaelisMenten constant (Km) and optimal temperature and pH values, being 45, 40 and 60 ◦C and pH values of 7.5,,6.0 and 9.0 for NiR, GS, and GDH, respectively. The effects of different heavy metals on these enzymes were,assessed at multiple levels, and the results showed that the enzymatic activity of NiR was downregulated,,specially under copper stress, maintaining 23 % of control NiR activity at 2 mM Cu2+. The enzymatic activity of,GS was upregulated at low concentrations under cadmium and mercury stress (115–120 % of control cultures GS,activity at 25 μM Cd2+ and 50 nM Hg2+, respectively) and downregulated at high concentrations of these elements. GDH activity was upregulated in the presence of Cu2+, Cd2+, and Hg2+, with increases up to 192, 155 and,154 % at 1 mM Cu2+, 300 μM Cd2+, and 250 nM Hg2+, respectively. These results provide a better explanation of,the effects of heavy metal stress on N metabolism in Coccomyxa onubensis, which may be used as a model,eukaryotic organism of the Tinto River acidophilic ecosystem.
The two yeast cytochrome c isoforms differentially regulate supercomplex assembly and mitochondrial electron flow
(Elsevier, 2025-06) Guerra Castellano, Alejandra; Aneas, Manuel; Tamargo Azpilicueta, Joaquín; Márquez Escudero, Inmaculada; Olloqui Sariego, José Luis; Calvente Pacheco, Juan José; Rosa Acosta, Miguel Ángel de la; Díaz Moreno, Irene; Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular; Universidad de Sevilla. Departamento de Química Física; Ministerio de Ciencia, Innovación y Universidades (MICIU). España; Junta de Andalucía
Mitochondria play a crucial role in cellular energy production, signaling and homeostasis. Respiratory supercomplexes represent evolutionary well-conserved, stable associations between membrane complexes and molecules, including proteins and lipids, within the inner mitochondrial membrane. They dynamically respond to metabolic demands and enhance the electron transfer rate, thereby reducing the production of ROS. Recent research has unveiled cytochrome c, a mobile electron carrier between complexes III and IV, as a potential key player in orchestrating the formation of these supra-associations. This study centers on elucidating the role of cytochrome c in modulating the assembly of supercomplexes, using the Saccharomyces cerevisiae yeast as a model system for mitochondrial metabolism. BN-PAGE and mass spectrometry-based proteomic analysis were employed to examine supercomplex organization in yeast strains expressing different cytochrome c isoforms, grown under fermentative and respiratory conditions. Our results demonstrate that both isoforms of cytochrome c contribute to supercomplex assembly, with isoform-2 significantly improving electron transfer and lowering ROS levels. We propose a model in which cytochrome c acts as a scaffold for the recruitment of assembly factors, facilitating the formation of higher order supercomplexes such as III2IV2. This model highlights cytochrome c's role beyond electron transfer, as it regulates supercomplex assembly and mitochondrial homeostasis.
Phototropin connects blue light perception to starch metabolism in green algae
(Springer Nature, 2025-03-15) Yuan, Yizhong; Iannetta, Anthony A.; Kim, Minjae; Sadecki, Patric W.; Arend, Marius; Tsichla, Angeliki; Ruiz Sola, M. Águila; Kepesidis, Georgios; Petroutsos, Dimitris; Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular; Human Frontiers Science Program; rench National Research Agency
In photosynthetic organisms, light acts as an environmental signal to control their development and physiology, as well as energy source to drive the conversion of CO2 into carbohydrates used for growth or storage. The main storage carbohydrate in green algae is starch, which accumulates during the day and is broken down at night to meet cellular energy demands. The signaling role of light quality in the regulation of starch accumulation remains unexplored. Here, we identify PHOTOTROPIN-MEDIATED SIGNALING KINASE 1 (PMSK1) as a key regulator of starch metabolism in Chlamydomonas reinhardtii. In its phosphorylated form (PMSK1-P), it activates GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE (GAP1), promoting starch biosynthesis. We show that blue light, perceived by PHOTOTROPIN, induces PMSK1 dephosphorylation that in turn represses GAP1 mRNA levels and reduces starch accumulation. These findings reveal a previously uncharacterized blue light-mediated signaling pathway that advances our understanding of photoreceptor-controlled carbon metabolism in microalgae.
Radiotherapy Resistance Driven by Asparagine Endopeptidase through ATR Pathway Modulation in Breast Cancer
(BioMed Central, 2025) Morillo Huesca, Macarena; G. López Cepero, Ignacio; Conesa Bakkali, Ryan; Tomé, Mercedes; Watts, Colin; Huertas Sánchez, Pablo; Moreno Bueno, Gema; Durán, Raúl V.; Martínez Fábregas, Jonathan; Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular; Universidad de Sevilla. Departamento de Genética; European Union (UE). H2020; Ministerio de Ciencia e Innovación (MICIN). España; Universidad de Sevilla; Instituto de Salud Carlos III
Background: Tumor resistance represents a major challenge in the current oncology landscape. Asparagine endopeptidase (AEP) overexpression correlates with worse prognosis and reduced overall survival in most human solid tumors. However, the underlying mechanisms of the connection between AEP and reduced overall survival in cancer patients remain unclear. Methods: High-throughput proteomics, cellular and molecular biology approaches and clinical data from breast cancer (BC) patients were used to identify novel, biologically relevant AEP targets. Immunoblotting and qPCR analyses were used to quantify protein and mRNA levels. Flow cytometry, confocal microscopy, chemical inhibitors, siRNA- and shRNA-silencing and DNA repair assays were used as functional assays. In-silico analyses using the TCGA BC dataset and immunofluorescence assays in an independent cohort of invasive ductal (ID) BC patients were used to validate the clinical relevance of our findings. Results: Here we showed a dual role for AEP in genomic stability and radiotherapy resistance in BC patients by suppressing ATR and PPP1R10 levels. Reduced ATR and PPP1R10 levels were found in BC patients expressing high AEP levels and correlated with worst prognosis. Mechanistically, AEP suppresses ATR levels, reducing DNA damage-induced cell death, and PPP1R10 levels, promoting Chek1/P53 cell cycle checkpoint activation, allowing BC cells to efficiently repair DNA. Functional studies revealed AEP-deficiency results in genomic instability, increased DNA damage signaling, reduced Chek1/P53 activation, impaired DNA repair and cell death, with phosphatase inhibitors restoring the DNA damage response in AEP-deficient BC cells. Furthermore, AEP inhibition sensitized BC cells to the chemotherapeutic reagents cisplatin and etoposide. Immunofluorescence assays in an independent cohort of IDBC patients showed increased AEP levels in ductal cells. These analyses showed that higher AEP levels in radioresistant IDBC patients resulted in ATR nuclear eviction, revealing AEPhigh/ATRlow protein levels as an efficient predictive biomarker for the stratification of radioresistant patients. Conclusion: The newly identified AEP/ATR/PPP1R10 axis plays a dual role in genomic stability and radiotherapy resistance in BC. Our work provides new clues to the underlying mechanisms of tumor resistance and strong evidence validating the AEP/ATR axis as a novel predictive biomarker and therapeutic target for the stratification and treatment of radioresistant BC patients.
Evolutionary Pro-To-Thr Mutation in the Intrinsically Disordered Domain of ANP32 Family Members Modulates Their Target Binding Modes
(John Wiley and Sons, 2025) Baños Jaime, Blanca; Uceda Mayo, A. B.; Rivero Rodríguez, Francisco; Casado Combreras, Miguel Ángel; Velázquez Cruz, Alejandro; Velázquez Campoy, A.; Corrales Guerrero, Laura; Rosa Acosta, Miguel Ángel de la; Díaz Moreno, Irene; Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular; Ministerio de Ciencia e Innovación (MICIN). España; Junta de Andalucía; Universidad de Sevilla; Ministerio de Educación, Cultura y Deporte (MECD). España; European Commission. Fondo Social Europeo (FSO)
Gene duplication has allowed protein evolution toward novel functions and mechanisms. The differences between paralogous genes frequently rely on the sequence of disordered regions. For instance, in mammals, the chaperones ANP32A and ANP32B share a common evolutionary line and have some exchangeable functions based on their similar N-terminal domains. Nevertheless, their C-terminal low-complexity-acidic-regions (LCARs) display substantial sequence differences, unveiling some degree of variability between them, in agreement with their different tissue-specific expression patterns. These structural and computational results indicate that a substitution in the vicinity of the nuclear localization signal (NLS), of Pro in ANP32A for Thr in ANP32B, determines the overall compactness of the C-terminal LCAR. The different structural properties of the disordered region affect the binding mode of ANP32 members to their targets. This type of divergent binding mode is exemplified with the extra-mitochondrial cytochrome c (Cc), a well-known ANP32B partner and which now determine also binds to ANP32A; and with the RNA binding protein HuR, whose export to the cytoplasm is mediated by ANP32 proteins under stress. Therefore, differential expression patterns of ANP32A or ANP32B may affect the regulation of Cc and HuR and can help to explain the distinct roles of these proteins in diseases.
Combined Effect of Temperature and Different Light Regimes on the Photosynthetic Activity and Lipid Accumulation in the Diatom Phaeodactylum tricornutum
(Multidisciplinary Digital Publishing Institute (MDPI), 2025) Díaz Santos, Encarnación; Heredia Martínez, Luis G.; López Maury, Luis; Hervás Morón, Manuel; Ortega Rodríguez, José María; Navarro, J. A.; Roncel Gil, Mercedes; Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular; Ministerio de Ciencia e Innovación (MICIN). España; Universidad de Sevilla; Junta de Andalucía
The aim of this study was to investigate the combined effects of temperature and light on the photosynthetic parameters and lipid accumulation in the diatom Phaeodactylum tricornutum, a model organism widely used for studies on diatom physiology, ecology, and biotechnology. Our results highlight the importance of the interaction between temperature and light intensity in influencing growth rates, pigments and active photosystems content, photosynthetic efficiency, lipid production and fatty acid composition in P. tricornutum. Measurements of the maximum electron transport rate (rETRmax) and rETR at maximum PAR (830 µmol m−2 s−1) confirmed that P. tricornutum exhibits significantly higher light sensitivity as growth temperature increases under light/dark cycles at two light intensities (25–60 µmol m−2 s−1). However, this trend was reversed under continuous light (25 µmol m−2 s−1). Moreover, higher rETRmax values (up to double) were observed at higher irradiance, either in intensity or under continuous light regimes, at the two temperatures tested. On the other hand, increasing light intensity amplified the observed effect of temperature on photosystem I (PSI) activity under light/dark regimes, but not under continuous light conditions. This resulted in a greater deficiency in PSI activity, likely due to limitations in electron supply to this photosystem. Furthermore, increasing the culture temperature from 20 °C to 25 °C triggered an increase in the number and size of cytoplasmic lipid droplets under conditions of increased light intensity, with an even more pronounced effect under continuous illumination. Notably, the combination of 25 °C and continuous illumination resulted in a more than twofold increase in triacylglyceride (TAG) content, reaching approximately 17 mg L−1. This condition also caused a substantial rise (up to ≈90%) in the proportions of palmitoleic and palmitic acids in the TAG fatty acid profile.
Transcriptomic analysis reveals the participation of NTRC in iron homeostasis in Arabidopsis
(Wiley, 2025-04-10) Rodríguez Marín, Fernando; Pérez Ruiz, Juan Manuel; Cejudo Fernández, Francisco Javier; Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular; Ministerio de Ciencia, Innovación y Universidades (MICIU). España; Agencia Estatal de Investigación. España
NADPH-dependent thioredoxin reductase C (NTRC) plays a central role in redox regulation of chloroplast photosynthetic metabolism. Accordingly, Arabidopsis (Arabidopsis thaliana) NTRC-null mutants show defective photosynthetic performance and growth inhibition. Remarkably, these mutants show almost a wild-type phenotype at the seedling stage, which raises the question of whether NTRC plays different functions throughout plant development. In this work, we have addressed this issue by performing transcriptome comparisons of Arabidopsis wild-type and ntrc mutant lines at seedling and adult stages of development. In contrast with the high impact of NTRC on leaves from adult plants, the low transcriptomic differences in seedlings suggested a less relevant function of NTRC at this stage of plant development. Notably, the ntrc mutant showed transcriptomic changes resembling the response to Fe excess throughout plant development, though this response was almost unique at the seedling stage. The lack of NTRC caused altered levels of Mn, Zn, Cu, S, P, K and Na, but no significant differences in the content of Fe, as compared with the wild type. Moreover, at the seedling stage, the lack of NTRC caused hypersensitivity to Fe deficit but a protective effect in response to Fe excess, most likely due to lower ROS accumulation in the mutant seedlings. Our results reveal the different impacts of NTRC throughout plant development and identify Fe homeostasis as a process highly affected by NTRC, most notably at the seedling stage.
Applying an NMR-based metabolomic workflow to unveil strawberry molecular mechanisms in vernalization
(Elsevier, 2025-03-31) Fernández Veloso, Andrea; Hiniesta Valero, Jaime; Guerra Castellano, Alejandra; Tomás Gallardo, Laura; Rosa Acosta, Miguel Ángel de la; Díaz Moreno, Irene; Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular; Ministerio de Ciencia e Innovación (MICIN). España; European Union (UE)
Nuclear Magnetic Resonance (NMR) is a mature technique in metabolomics due to its non-invasive, highly reproducible, and inherently quantitative nature. However, difficulties in data analysis hinder its standardization in research. Herein, we propose an NMR-based metabolomic workflow that comprises data preprocessing, metabolite annotation, and data analysis. In this work, we apply such workflow to study vernalization, which is a critical process for crop development with largely unknown molecular mechanisms. Our findings suggest that sugar mobility, accessibility, and increased photosynthetic activity support plant viability post-vernalization. In other words, these processes ensure successful transplanting of the plant, highlighting the importance of sufficient cold exposure for flowering, fruiting, and ripening. This study demonstrates that the proposed workflow is suitable to capture metabolic changes in plant development. Such methodology underscores the potential of NMR-based metabolomics as a powerful tool for crop monitoring, aiding in improved agricultural practices and yield optimization.
A machine learning-based nuclear magnetic resonance profiling model to authenticate ’Jerez-Xérès-Sherry’ wines
(Elsevier, 2025-03-26) Hiniesta Valero, Jaime; Guerra Castellano, Alejandra; Fernández Veloso, Andrea; Rosa Acosta, Miguel Ángel de la; Díaz Moreno, Irene; Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular
Traditionally, wine quality and certification have been assessed through sensory analysis by trained tasters. However, this method has the limitation of relying on highly specialized individuals who are typically trained to evaluate only specific types of products, such as those associated with a particular Denomination of Origin (D.O.), etc. While tasters can often identify instances of fraud, they are generally unable to pinpoint its origins or explain the mechanisms behind it. On the other hand, classical biochemistry has made significant progress in understanding various aspects of winemaking. However, it has yet to identify the specific metabolites responsible for the unique characteristics of wines, particularly those influenced by complex variables involving multiple compounds, such as geographical differences between regions or vineyards. The concept of the “Terroir fingerprint” has emerged as a novel approach to wine certification. The concept refers to the unique characteristics imparted to a wine by its geography, climate, and aging process. Nuclear Magnetic Resonance (NMR) technology plays a pivotal role in establishing this “Terroir fingerprint” because it enables precise identification, quantification, and differentiation of the compounds present in wine. NMR provides a highly reproducible and specific method for certification. This work introduces an innovative project that combines NMR technology with Artificial Intelligence to create a profiling model for certifying the authenticity and quality of ‘Jerez-Xérès-Sherry’ wines.
PharaohFUN: PHylogenomic Analysis foR plAnt prOtein History and FUNction elucidation
(2023) Ramos González, Marcos; Ramos González, Víctor; Arvanitidou, Christina; Hernández García, Jorge; García González, Mercedes; Romero Campero, Francisco José; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular
Motivation Since DNA sequencing has turned commonplace, the development of efficient methods and tools to explore gene sequences has become indispensable. In particular, despite photosynthetic eukaryotes constituting the largest percentage of terrestrial biomass, computational functional characterization of gene sequences in these organisms still predominantly relies on comparisons with Arabidopsis thaliana and other angiosperms. This paper introduces PharaohFUN, a web application designed for the evolutionary and functional analysis of protein sequences in photosynthetic eukaryotes, leveraging orthology relationships between them. Results PharaohFUN incorporates a homogeneous representative sampling of key species in this group, bridging clades that have traditionally been studied separately, thus establishing a comprehensive evolutionary framework to draw conclusions about sequence evolution and function. For this purpose, it incorporates modules for exploring gene tree evolutionary history, domain identification, multiple sequence alignments, and functional annotation. The study of the CCA1 protein exemplifies how PharaohFUN unifies results for both land plants and chlorophyte microalgae, accurately tracing the evolutionary history of this protein.
Multiomics responses to seasonal variations in diel cycles in the marine phytoplanktonic picoeukaryoteOstreococcus tauri
(2023-08) Romero Losada, Ana Belén; Arvanitidou, Christina; García Gómez, María Elena; Morales Pineda, María; Castro Pérez, M. José; García González, Mercedes; Romero Campero, Francisco José; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular
Earth tilted rotation and translation around the Sun produce one of the most pervasive periodic environmental signals on our planet giving rise to seasonal variations in diel cycles. Although marine phytoplankton plays a key role on ecosystems and present promising biotechnological applications, multiomics integrative analysis of their response to these rhythms remains largely unexplored. We have chosen the marine picoeukaryote Ostreococcus tauri as model organism grown under summer long days, winter short days, constant light and constant dark conditions to characterize these responses in marine phytoplankton. Although 80% of the transcriptome present diel rhythmicity under both seasonal conditions less than 5% maintained oscillations under all constant conditions. A drastic reduction in protein abundance rhythmicity was observed with 55% of the proteome oscillating. Seasonally specific rhythms were found in key physiological processes such as cell cycle progression, photosynthetic efficiency, carotenoid content, starch accumulation and nitrogen assimilation. A global orchestration between transcriptome, proteome and physiological dynamics was observed with specific seasonal temporal offsets between transcript, protein and physiological peaks.
Multiomics integration unveils photoperiodic plasticity in the molecular rhythms of marine phytoplankton
(Oxford University Press, 2025-02-11) Romero Losada, Ana Belén; Arvanitidou, Christina; García-Gómez, M.E.; Morales-Pineda, M.; Castro-Pérez, M.J.; Chew, Y.P.; van Ooijen, G.; García González, Mercedes; Romero Campero, Francisco José; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular; Ministerio de Ciencia e Innovación (MICIN). España
Earth’s tilted rotation and translation around the Sun produce pervasive rhythms on our planet, giving rise to photoperiodic changes in diel cycles. Although marine phytoplankton plays a key role in ecosystems, multiomics analysis of its responses to these periodic environmental signals remains largely unexplored. The marine picoalga Ostreococcus tauri was chosen as a model organism due to its cellular and genomic simplicity. Ostreococcus was subjected to different light regimes to investigate its responses to periodic environmental signals: long summer days, short winter days, constant light, and constant dark conditions. Although <5% of the transcriptome maintained oscillations under both constant conditions, 80% presented diel rhythmicity. A drastic reduction in diel rhythmicity was observed at the proteome level, with 39% of the detected proteins oscillating. Photoperiod-specific rhythms were identified for key physiological processes such as the cell cycle, photosynthesis, carotenoid biosynthesis, starch accumulation, and nitrate assimilation. In this study, a photoperiodic plastic global orchestration among transcriptome, proteome, and physiological dynamics was characterized to identify photoperiod-specific temporal offsets between the timing of transcripts, proteins, and physiological responses.
Cytochrome c prompts the recruitment of its nuclear partners SET/TAF-Iβ and NPM1 into biomolecular condensates
(Cell Press, 2024-07-02) Casado Combreras, Miguel Ángel; Velázquez Campoy, Adrián; Martinho, Marlène; Belle, Valérie; Rosa Acosta, Miguel Ángel de la; Díaz Moreno, Irene; Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular; Agencia Estatal de Investigación. España; Ministerio de Ciencia e Innovación (MICIN). España; European Commission (EC). Fondo Europeo de Desarrollo Regional (FEDER); Junta de Andalucía; Universidad de Sevilla; European Cooperation in Science and Technology (COST); University of California
Compartmentalization of proteins by liquid-liquid phase separation (LLPS) is used by cells to control biochemical reactions spatially and temporally. Among them, the recruitment of proteins to DNA foci and nucleolar trafficking occur by biomolecular condensation. Within this frame, the oncoprotein SET/ TAF-Ib plays a keyrole in bothchromatin remodelingandDNAdamageresponse,asdoesnucleophosmin (NPM1)whichindeedparticipatesinnucleolar ribosome synthesis. Whereasphase separation byNPM1is widelycharacterized,little is known aboutthatundergonebySET/TAF-Ib.Here,weshowthatSET/TAF-Ib experiences phase separation together with respiratory cytochrome c (Cc), which translocates to the nucleus upon DNA damage. Here we report the molecular mechanisms governing Cc-induced phase separation of SET/TAF-IbandNPM1,wheretwolysine-richclustersofCcareessentialtorecognizemolecular surfaces on both partners in a specific and coordinated manner. Cc thus emerges as a small, globular protein with sequence-encoded heterotypic phase-separation properties
Antioxidant Responses and Redox Regulation Within Plant-Beneficial Microbe Interaction
(Multidisciplinary Digital Publishing Institute (MDPI), 2024-12-18) González García, María de la Cruz; Roitsch, Thomas; Pandey, Chandana; Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular; Ministerio de Ciencia e Innovación (MICIN). España; Novo Nordisk Foundation; Ministry of Education, Youth and Sports of the Czech Republic
The increase in extreme climate events associated with global warming is a great menace to crop productivity nowadays. In addition to abiotic stresses, warmer conditions favor the spread of infectious diseases affecting plant performance. Within this context, beneficial microbes constitute a sustainable alternative for the mitigation of the effects of climate change on plant growth and productivity. Used as biostimulants to improve plant growth, they also increase plant resistance to abiotic and biotic stresses through the generation of a primed status in the plant, leading to a better and faster response to stress. In this review, we have focused on the importance of a balanced redox status for the adequate performance of the plant and revisited the different antioxidant mechanisms supporting the biocontrol effect of beneficial microbes through the adjustment of the levels of reactive oxygen species (ROS). In addition, the different tools for the analysis of antioxidant responses and redox regulation have been evaluated. The importance of redox regulation in the activation of the immune responses through different mechanisms, such as transcriptional regulation, retrograde signaling, and post-translational modification of proteins, emerges as an important research goal for understanding the biocontrol activity of the beneficial microbes.
Sulfuro de hidrógeno: de gas tóxico a molécula necesaria para vivir
(Universidad de Málaga, 2018-02-18) Aroca Aguilar, Ángeles; Gotor Martínez, Cecilia; Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular; Ministerio de Ciencia e Innovación (MICIN). España; Junta de Andalucía; Agencia Estatal de Investigación. España
El sulfuro de hidrógeno siempre se ha considerado un gas nocivo. Sin embargo, investigaciones recientes han desvelado sus propiedades bioquímicas beneficiosas y su papel como molécula de señalización en numerosos procesos fisiológicos y patológicos tanto en animales como en plantas. Diversos estudios demuestran el papel protector del sulfuro de hidrógeno frente al estrés oxidativo; y tanto en sistemas animales como vegetales se ha descrito que el sulfuro de hidrógeno está implicado en la regulación de la autofagia, cuyo mecanismo de acción subyacente es la persulfuración de dianas específicas, con el objetivo de promover la supervivencia del organismo.
Seed longevity is controlled by metacaspases
(Nature Research, 2024-08-08) Liu, Chen; Hatzianestis, Ioannis H.; Pfirrmann, Thorsten; Reza, Salim H.; Minina, Elena A.; Moazzami, Ali; Gutiérrez Beltrán, Emilio; Romero Campero, Francisco José; Moschou, Panagiotis N.; Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular; European Union (UE). H2020; European Research Council (ERC)
To survive extreme desiccation, seeds enter a period of quiescence that can last millennia. Seed quiescence involves the accumulation of protective storage proteins and lipids through unknown adjustments in protein homeostasis (proteostasis). Here, we show that mutation of all six type–II metacaspase (MCA–II) proteases in Arabidopsis thaliana disturbs proteostasis in seeds. MCA–II mutant seeds fail to restrict the AAA ATPase CELL DIVISION CYCLE 48 (CDC48) at the endoplasmic reticulum to discard misfolded proteins, compromising seed storability. Endoplasmic reticulum (ER) localization of CDC48 relies on the MCA–IIs-dependent cleavage of PUX10 (ubiquitination regulatory X domain–containing 10), the adaptor protein responsible for titrating CDC48 to lipid droplets. PUX10 cleavage enables the shuttling of CDC48 between lipid droplets and the ER, providing an important regulatory mechanism sustaining spatiotemporal proteolysis, lipid droplet dynamics, and protein homeostasis. In turn, the removal of the PUX10 adaptor in MCA–II mutant seeds partially restores proteostasis, CDC48 localization, and lipid droplet dynamics prolonging seed lifespan. Taken together, we uncover a proteolytic module conferring seed longevity

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