Artículos (Bioquímica Vegetal y Biología Molecular)

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

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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
Non-Canonical, Extralysosomal Activities of Lysosomal Peptidases in Physiological and Pathological Conditions: New Clinical Opportunities for Cancer Therapy
(Multidisciplinary Digital Publishing Institute (MDPI), 2025-01-07) Conesa Bakkali, Ryan; Morillo Huesca, Macarena; Martínez Fábregas, Jonathan; Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular; Junta de Andalucía; European Union (UE); Ministerio de Ciencia e Innovación (MICIN). España; Universidad de Sevilla
Lysosomes are subcellular compartments characterised by an acidic pH, containing an ample variety of acid hydrolases involved in the recycling of biopolymers. Among these hydrolases, lysosomal proteases have merely been considered as end-destination proteases responsible for the digestion of waste proteins, trafficked to the lysosomal compartment through autophagy and endocytosis. However, recent reports have started to unravel specific roles for these proteases in the regulation of initially unexpected biological processes, both under physiological and pathological conditions. Furthermore, some lysosomal proteases are no longer restricted to the lysosomal compartment, as more novel non-canonical, extralysosomal targets are being identified. Currently, lysosomal proteases are accepted to play key functions in the extracellular milieu, attached to the plasma membrane and even in the cytosolic and nuclear compartments of the cell. Under physiological conditions, lysosomal proteases, through non-canonical, extralysosomal activities, have been linked to cell differentiation, regulation of gene expression, and cell division. Under pathological conditions, these proteases have been linked to cancer, mostly through their extralysosomal activities in the cytosol and nuclei of cells. In this review, we aim to provide a comprehensive summary of our current knowledge about the extralysosomal, non-canonical functions of lysosomal proteases, both under physiological and pathological conditions, with a particular interest in cancer, that could potentially offer new opportunities for clinical intervention.
R-DeeP/TripepSVM identifies the RNA-binding OB-fold-like protein PatR as regulator of heterocyst patterning
(Oxford University Press, 2025-02-10) Brenes-Álvarez, Manuel; Ropp, Halie R.; Papagiannidis, Dimitrios; Potel, Clement M.; Stein, Frank; Scholz, Ingeborg; Steglich, Claudia; Savitski, Mikhail M.; Vioque Peña, Agustín; Muro Pastor, Alicia María; Hess, Wolfgang R.; Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular; Deutsche Forschungsgemeinschaft / German Research Foundation (DFG); Ministerio de Ciencia e Innovación (MICIN). España
RNA-binding proteins (RBPs) are central components of gene regulatory networks. The differentiation of heterocysts in filamentous cyanobacteria is an example of cell differentiation in prokaryotes. Although multiple non-coding transcripts are involved in this process, no RBPs have been implicated thus far. Here we used quantitative mass spectrometry to analyze the differential fractionation of RNA–protein complexes after RNase treatment in density gradients yielding 333 RNA-associated proteins, while a bioinformatic prediction yielded 311 RBP candidates in Nostoc sp. PCC 7120. We validated in vivo the RNA-binding capacity of six RBP candidates. Some participate in essential physiological aspects, such as photosynthesis (Alr2890), thylakoid biogenesis (Vipp1) or heterocyst differentiation (PrpA, PatU3), but their association with RNA was unknown. Validated RBPs Asl3888 and Alr1700 were not previously characterized. Alr1700 is an RBP with two oligonucleotide/oligosaccharide-binding (OB)-fold-like domains that is differentially expressed in heterocysts and interacts with non-coding regulatory RNAs. Deletion of alr1700 led to complete deregulation of the cell differentiation process, a striking increase in the number of heterocyst-like cells, and was ultimately lethal in the absence of combined nitrogen. These observations characterize this RBP as a master regulator of the heterocyst patterning and differentiation process, leading us to rename Alr1700 to PatR.
Thioredoxin A regulates protein synthesis to maintain carbon and nitrogen partitioning in cyanobacteria.
(American Society of Plant Biologists, 2024-02-22) Mallén Ponce, Manuel J.; Florencio Bellido, Francisco Javier; Huertas Romera, María José; Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular; Ministerio de Ciencia, Innovación y Universidades (MICINN). España; Agencia Estatal de Investigación. España; European Commission (EC). Fondo Europeo de Desarrollo Regional (FEDER); Junta de Andalucía; Universidad de Sevilla; Universidad de Sevilla. BIO284: Expresión Génica y Regulación Metabólica en Cianobacterias.
Thioredoxins play an essential role in regulating enzyme activity in response to environmental changes, especially in photosynthetic organisms. They are crucial for metabolic regulation in cyanobacteria, but the key redox-regulated central processes remain to be determined. Physiological, metabolic, and transcriptomic characterization of a conditional mutant of the essential Synechocystis sp. PCC 6803 thioredoxin trxA gene (STXA2) revealed that decreased TrxA levels alter cell morphology and induce a dormant-like state. Furthermore, TrxA depletion in the STXA2 strain inhibited protein synthesis and led to changes in amino acid pools and nitrogen/carbon reserve polymers, accompanied by oxidation of the elongation factor-Tu. Transcriptomic analysis of TrxA depletion in STXA2 revealed a robust transcriptional response. Downregulated genes formed a large cluster directly related to photosynthesis, ATP synthesis, and CO2 fixation. In contrast, upregulated genes were grouped into different clusters related to respiratory electron transport, carotenoid biosynthesis, amino acid metabolism, and protein degradation, among others. These findings highlight the complex regulatory mechanisms that govern cyanobacterial metabolism, where TrxA acts as a critical regulator that orchestrates the transition from anabolic to maintenance metabolism and regulates carbon and nitrogen balance.
Mutational analysis of the inactivating factors, IF7 and IF17 from Synechocystis sp. PCC 6803: Critical role of arginine amino acid residues for glutamine synthetase inactivation
(John Wiley & Sons, 2011-11) Saelices, Lorena; Galmozzi, Carla V.; Florencio Bellido, Francisco Javier; Muro Pastor, María Isabel; Universidad de Sevilla. Departamento de Genética; Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular; Ministerio de Ciencia e Innovación (MICIN). España; Junta de Andalucía
The Synechocystis sp. PCC 6803 glutamine synthetase type I (GS) activity is controlled by a process that involves protein-protein interaction with two inactivating factors (IF7 and IF17). IF7 is a natively unfolded, 65-residue-long protein, homologous to the carboxy-terminal region of IF17. Both proteins have abundance of positively charged amino acid residues and a high isoelectric point. In this study, we analyse the IF amino acid residues involved in GS inactivation by a mutational approach, both in vitro and in vivo. The results clearly indicate that the GS-IF complex formation must be determined mainly by electrostatic interactions. We have identified three conserved arginine residues of IF7 and IF17 that are essential for the interaction of these proteins with GS. All these residues map in the homologous region of IFs. Furthermore, in vitro analysis of a truncated IF17 protein without the 82-residue-long amino-terminal part, together with the analysis of a Synechocystis strain expressing a chimeric protein, containing this amino-terminal part of IF17 fused to IF7, demonstrates that amino-terminal region of IF17 mostly confers a higher stability to this protein.
The inactivating factor of glutamine synthetase IF17 Is an intrinsically disordered protein, which folds upon binding to its target
(American Chemical Society, 2011-10-12) Saelices, Lorena; Galmozzi, Carla V.; Florencio Bellido, Francisco Javier; Muro Pastor, María Isabel; Neira, José L.; Universidad de Sevilla. Departamento de Genética; Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular; Ministerio de Ciencia e Innovación (MICIN). España; Generalitat Valenciana; Junta de Andalucía
In cyanobacteria, ammonium is incorporated into carbon skeletons by the sequential action of glutamine synthetase and glutamate synthase (GOGAT). The activity of Synechocystis sp. PCC 6803 glutamine synthetase type I (GS) is controlled by a post-transcriptional process involving protein-protein interactions with two inactivating factors: the 65-residue-long protein (IF7) and the 149-residue-long one (IF17). The sequence of the C terminus of IF17 is similar to IF7; IF7 is an intrinsically disordered protein (IDP). In this work, we study the structural propensities and affinity for GS of IF17 and a chimera protein, IF17N/IF7 (constructed by fusing the first 82 residues of IF17 with the whole IF7) by fluorescence, CD, and NMR. IF17 and IF17N/IF7 are IDPs with residual non-hydrogen-bonded structure, probably formed by α-helical, turn-like, and PPII conformations; several theoretical predictions support these experimental findings. IF17 seems to fold upon binding to GS, as suggested by CD thermal denaturations and steady-state far-UV spectra. The apparent affinity of IF17 for GS, as measured by fluorescence, is slightly smaller (K D ∼1 μM) than that measured for IF7 (∼0.3 μM). The K Ds determined by CD are similar to those measured by fluorescence, but slightly larger, suggesting possible conformational rearrangements in the IFs and/or GS upon binding. Further, the results with IFN17/IF7 suggest that (i) binding of IF17 to the GS is modulated not only by its C-terminal region but also by its N-terminus and (ii) there are weakly structured (that is, "fuzzy") complexes in the ternary GS-IF system.
N and C control of ABC-type bicarbonate transporter Cmp and its LysR-type transcriptional regulator CmpR in a heterocyst-forming cyanobacterium, Anabaena sp.
(Wiley, 2012-06-06) López Igual, Rocío; Picossi, S.; López-Garrido, J.; Flores, E.; Herrero, A.; Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular; Ministerio de Ciencia e Innovación (MICIN). España; European Commission (EC). Fondo Europeo de Desarrollo Regional (FEDER)
In the model, heterocyst-forming cyanobacterium Anabaena sp. PCC 7120, gene cluster alr2877-alr2880, which encodes an ABC-type transport system, was induced under conditions of carbon limitation and its inactivation impaired the uptake of bicarbonate. Thus, this gene cluster encodes a Cmp bicarbonate transporter. ORF all0862, encoding a LysR-type transcriptional regulator, was expressed under carbon limitation and at higher levels in the absence than in the presence of combined nitrogen, with a positive effect of the N-control transcription factor NtcA. all0862 was expressed from two putative transcription start sites located 164 and 64 bp upstream from the gene respectively. The latter was induced under carbon limitation and was dependent on positive autoregulation by All0862. All0862 was required for the induction of the Cmp bicarbonate transporter, thus representing a CmpR regulator of Anabaena sp. These results show a novel mode of co-regulation by C and N availability through the concerted action of N- and C-responsive transcription factors.

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