Article
Biology
Maria Maldonado, Fei Guo, James A. Letts
Summary: This study determined the atomic structures of mitochondrial complex III (CIII2), complex IV (CIV), and their supercomplex in Vigna radiata using single-particle cryoEM. The findings showed specific differences in plant complexes and challenged long-standing assumptions, providing new mechanistic hypotheses for proton translocation and complex interactions. The structures revealed coordinated movements and conformational heterogeneity within the complexes, offering insights into the unique features of plant respiration machinery.
Article
Chemistry, Multidisciplinary
Agnes Moe, Pia Adelroth, Peter Brzezinski, Linda Nasvik Ojemyr
Summary: This study investigates the structure and function of respiratory complex IV from the fission yeast Schizosaccharomyces pombe. The authors reveal the arrangement of subunits and the reaction sequence of O-2 reduction. The results suggest that Rcf2 is a component of CIV and its binding does not require the presence of a CIII-CIV supercomplex.
COMMUNICATIONS CHEMISTRY
(2023)
Article
Plant Sciences
Liping Che, Han Meng, Junxiang Ruan, Lianwei Peng, Lin Zhang
Summary: RBD1 is crucial for PSII assembly in higher plants, as it not only contributes to the formation of functional PSII core complex, but also participates in the translation of D1 protein.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
M. Adamiec, L. Misztal, M. Ciesielska, R. Lucinski
Summary: The study revealed that EGY1 protease plays a crucial role in maintaining the stoichiometry of PSII complexes, with its deficiency leading to changes in PSII complexes, premature senescence, and decreased chlorophyll content. This reduction is related to chlorophyll b deficiency and not to chlorophyllide a oxygenase abundance.
Article
Biochemistry & Molecular Biology
Tom Schwartz, Mariia Fadeeva, Daniel Klaiman, Nathan Nelson
Summary: The mutant TSP9 of Chlamydomonas reinhardtii, isolated through negative selection of UV irradiation-mutated cells, has a single amino acid mutation in the Rieske protein. It loses its function at 37 degrees C but recovers at 25 degrees C. The mutant showed structural alterations in photosystem I and II supercomplexes, suggesting a possible response mechanism involving the exclusion of certain subunits.
Article
Plant Sciences
Carlos A. Elena-Real, Katiuska Gonzalez-Arzola, Gonzalo Perez-Mejias, Antonio Diaz-Quintana, Adrian Velazquez-Campoy, Benedicte Desvoyes, Crisanto Gutierrez, Miguel A. De la Rosa, Irene Diaz-Moreno
Summary: The study reveals the important role of cytochrome c in cell death in both plants and humans, particularly in its similarity in inhibiting caspase-like protease activity. The 14-3-3 iota protein plays a crucial role in the process of plant H2O2-induced PCD.
Article
Plant Sciences
Xiaoying Niu, Lu Chen, Atsushi Kato, Hidetaka Ito
Summary: The DDR complex plays an essential role in regulating the activity of the retrotransposon ONSEN in Arabidopsis. Loss of any component of the DDR complex increases ONSEN transcript levels and leads to transgenerational transposition under heat stress. The components of the DDR complex, DRD1, DMS3, and RDM1, independently suppress ONSEN transcription and transposition. The duration of heat stress also affects ONSEN activity.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Amy Leanne Whitbread, Annika Dorn, Sarah Roehrig, Holger Puchta
Summary: The RTR complex is essential for genome stability in eukaryotes, with TOP3α and RMI1 mutants in tomato showing significantly different phenotypes compared to Arabidopsis. While the TOP3α mutant in tomato is embryo-lethal, the RMI1 mutant does not exhibit detectable defects in somatic DNA repair or meiosis. This differentiation of function in RTR complex partners between plant species suggests caution in generalizing knowledge obtained in Arabidopsis to the entire plant kingdom.
Article
Biochemistry & Molecular Biology
Na Li, Wing Shing Wong, Lei Feng, Chunming Wang, King Shing Wong, Nianhui Zhang, Wei Yang, Yueming Jiang, Liwen Jiang, Jun-Xian He
Summary: The study reports the discovery and characterization of a new tiny albino 1 (nta1) mutant in Arabidopsis, which shows severe defects in the accumulation of cytochrome b6f (Cyt b6f) complex and chloroplast development. The nta1 phenotype is caused by disruption of a single nuclear gene, NTA1, which encodes a conserved thylakoid membrane protein. NTA1 interacts with multiple subunits of Cyt b6f and plays an essential role in its assembly and the development of chloroplast.
PLANT COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Wei-Chun Kao, Claire Ortmann de Percin Northumberland, Tat Cheung Cheng, Julio Ortiz, Alexandre Durand, Ottilie von Loeffelholz, Oliver Schilling, Martin L. Biniossek, Bruno P. Klaholz, Carola Hunte
Summary: This study presents the cryo-EM structure of the cytochrome bcc-aa(3) (III2-IV2) supercomplex from Corynebacterium glutamicum, which provides insights into the controlled electron and proton transfer in respiratory supercomplexes. The structure resolution allowed the identification of substrate mimics, lycopene, unexpected Q(c) site, proton transfer routes, and conformational states of key protonable residues. The findings contribute to the understanding of safe and efficient energy conversion in respiratory supercomplexes and have implications for drug design against actinobacteria causing diphtheria and tuberculosis.
NATURE COMMUNICATIONS
(2022)
Article
Plant Sciences
Dawid Bielewicz, Jakub Dolata, Mateusz Bajczyk, Lukasz Szewc, Tomasz Gulanicz, Susheel S. Bhat, Anna Karlik, Monika Jozwiak, Artur Jarmolowski, Zofia Szweykowska-Kulinska
Summary: HYL1, also known as DRB1, is a double-stranded RNA-binding protein involved in miRNA processing in plants. It was found to have a novel function in the transcription of MIR genes, affecting the distribution of RNA polymerase II and interacting with various transcription factors. Additionally, HYL1 was found to impact the expression of many other genes, particularly those involved in plastid organization.
PLANT AND CELL PHYSIOLOGY
(2023)
Article
Plant Sciences
Mei Xu, Xu Yan, Yutong Wang, Chan Liu, Qian Yang, Dan Tian, Sebastian Y. Bednarek, Jianwei Pan, Chao Wang
Summary: The study reveals that AP-1 plays a crucial role in pollen wall development by regulating protein transport in tapetal cells and microspores.
Article
Plant Sciences
Juan Camilo Ochoa, Soham Mukhopadhyay, Tomasz Bieluszewski, Malgorzata Jedryczka, Robert Malinowski, William Truman
Summary: The RPB1 gene plays a critical role in the defense response of Arabidopsis against Plasmodiophora brassicae infection, and its deletion renders resistant accessions susceptible to the pathogen.
Article
Plant Sciences
Thi Linh Chi Tran, Damien L. L. Callahan, Md Tohidul Islam, Yichao Wang, Tony Arioli, David Cahill
Summary: Seaweed extracts are biostimulants that enhance plant health and tolerance to stresses. Mechanisms of action of biostimulants are still unknown. In this study, a metabolic approach was used to uncover the mechanisms induced following application of a seaweed extract to Arabidopsis. The extract altered metabolomic profiles and revealed systemic responses in roots and leaves. Results suggest that the extract promotes plant growth and activates defense systems by altering physiological processes at the metabolite level.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Bruno E. Rojas, Matias D. Hartman, Carlos M. Figueroa, Alberto A. Iglesias
Summary: The study analyzed the proteolysis of PEPCK1 in germinating Arabidopsis thaliana seedlings, and found that shorter versions of the protein may be generated by metacaspase-9. Truncated mutants Delta 19 and Delta 101 of AthPEPCK1 exhibited similar kinetic parameters, but activation by malate and inhibition by glucose 6-phosphate were abolished in the .101 mutant. This proteolysis is proposed to adapt the sensitivity to allosteric regulation during the transition from sink to source in germinating seedlings.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Biochemistry & Molecular Biology
Michele Marongiu, Gonzalo Perez-Mejias, Valeria Orru, Maristella Steri, Carlo Sidore, Antonio Diaz-Quintana, Antonella Mulas, Fabio Busonero, Andrea Maschio, Klaudia Walter, Manuel Tardaguila, Parsa Akbari, Nicole Soranzo, Edoardo Fiorillo, Myriam Gorospe, David Schlessinger, Irene Diaz-Moreno, Francesco Cucca, Magdalena Zoledziewska
Summary: This study conducted a genome-wide association study (GWAS) on the genetic regulation of morphological traits of white blood cells. It identified seven significant signals, four of which were novel and one of them had a large effect size on eosinophil morphology. Computational analysis revealed a mutation in the PRG2 gene that could possibly explain the observed changes in eosinophil morphology.
HUMAN MOLECULAR GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Jose L. Neira, Bruno Rizzuti, Salome Araujo-Abad, Olga Abian, Maria Esther Farez-Vidal, Adrian Velazquez-Campoy, Camino de Juan Romero
Summary: This study describes the interaction between PKP1 and PADI4 and provides insights into their binding mode and binding hot-spot. This is of importance for understanding tumor development and the formation of neutrophil extracellular traps.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2023)
Article
Biochemistry & Molecular Biology
David Ortega-Alarcon, Rafael Claveria-Gimeno, Sonia Vega, Olga C. Jorge-Torres, Manel Esteller, Olga Abian, Adrian Velazquez-Campoy
Summary: Hydroxymethylated cytosine (5hmC) is a stable DNA epigenetic mark that interacts with MeCP2 in a distinct mode with a specific thermodynamic signature. Mutations associated with Rett syndrome alter the interaction between MeCP2 and dsDNA in a cytosine modification-specific manner, which may be correlated with disease onset time and clinical severity score.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Multidisciplinary Sciences
Jorge Lozano-Juste, Lourdes Infantes, Irene Garcia-Maquilon, Rafael Ruiz-Partida, Ebe Merilo, Juan Luis Benavente, Adrian Velazquez-Campoy, Alberto Coego, Mar Bono, Javier Forment, Begona Pampin, Paolo Destito, Adrian Monteiro, Ramon Rodriguez, Jacobo Cruces, Pedro L. Rodriguez, Armando Albert
Summary: Through structure-based targeted design, a chemical-genetic orthogonal approach was used to generate an ABA receptor agonist molecule (iSB09) and engineer a CsPYL1 ABA receptor, named CsPYL1(5m), which efficiently binds iSB09. This optimized receptor-agonist pair leads to activation of ABA signaling and significant improvement in drought tolerance.
Article
Oncology
Sonia Hermoso-Duran, Maria Jose Domper-Arnal, Pilar Roncales, Sonia Vega, Oscar Sanchez-Gracia, Jorge L. L. Ojeda, Angel Lanas, Adrian Velazquez-Campoy, Olga Abian
Summary: The aim of this study was to investigate the interference of colonoscopy bowel preparation on the results of thermal liquid biopsy (TLB). The results showed that bowel preparation altered serum protein levels, affected TLB parameters, and may compromise the diagnostic capability of other liquid-biopsy-based methods. Therefore, blood extraction after bowel preparation for colonoscopy should be avoided.
Article
Chemistry, Medicinal
Maria Nuria Peralta-Moreno, Vanessa Anton-Munoz, David Ortega-Alarcon, Ana Jimenez-Alesanco, Sonia Vega, Olga Abian, Adrian Velazquez-Campoy, Timothy M. Thomson, Jose Manuel Granadino-Roldan, Claudia Machicado, Jaime Rubio-Martinez
Summary: Since the outbreak of the COVID-19 pandemic, there have been over 750 million reported cases of COVID-19 caused by SARS-CoV-2. In order to find effective treatments, intensive research has been conducted on therapeutic agents derived from pharmaceutical repositioning or natural products. This study focuses on identifying inhibitors for the SARS-CoV-2 M-pro main protease dimer using virtual screening of natural compounds derived from Peruvian flora. The compound Hyperoside displayed inhibitory activity against M-pro in vitro, with a K-i value lower than 20 μM, possibly through allosteric modulation.
Article
Cell Biology
Maria J. Gonzalez-Rellan, Uxia Fernandez, Tamara Parracho, Eva Novoa, Marcos F. Fondevila, Natalia da Silva Lima, Lucia Ramos, Amaia Rodriguez, Marina Serrano-Macia, Gonzalo Perez-Mejias, Pilar Chantada-Vazquez, Cristina Riobello, Christelle Veyrat-Durebex, Sulay Tovar, Roberto Coppari, Ashwin Woodhoo, Markus Schwaninger, Vincent Prevot, Teresa C. Delgado, Miguel Lopez, Antonio Diaz-Quintana, Carlos Dieguez, Diana Guallar, Gema Fruhbeck, Irene Diaz-Moreno, Susana B. Bravo, Maria L. Martinez-Chantar, Ruben Nogueiras
Summary: Neddylation is a post-translational modification mechanism that regulates metabolism in the liver of mice and is associated with liver pathology in patients with type 2 diabetes. Fasting or calorie restriction leads to neddylation of phosphoenolpyruvate carboxykinase 1 (PCK1), affecting its metabolic activity.
Review
Biochemistry & Molecular Biology
Katiuska Gonzalez-Arzola, Antonio Diaz-Quintana
Summary: The origin of eukaryotic organisms involved the integration of mitochondria into the ancestor cell, with a massive gene transfer from the original proteobacterium to the host nucleus. Mitochondrial performance relies on a mosaic of nuclear gene products, and their synthesis is regulated by crosstalk between mitochondrial, cytoplasmic, and nuclear factors. Mitochondrial metabolites and proteins can target the cell nucleus and modulate gene expression, chromatin state, and even cause DNA fragmentation in response to stress conditions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Salome Araujo-Abad, Bruno Rizzuti, Adrian Villamarin-Ortiz, David Pantoja-Uceda, Celia M. Moreno-Gonzalez, Olga Abian, Adrian Velazquez-Campoy, Jose L. Neira, Camino de Juan Romero
Summary: PADI4 and MDM2 were found to interact in the nucleus and cytosol of various cancer cell lines, and this binding was inhibited by GSK484. Further experiments revealed that the N-terminal region of MDM2 interacted with PADI4, and certain amino acid residues were affected by the enzyme. This finding suggests potential therapeutic value in utilizing MDM2 citrullination to improve cancer treatment.
Article
Chemistry, Multidisciplinary
Pedro Buzon, Alejandro Velazquez-Cruz, Laura Corrales-Guerrero, Antonio Diaz-Quintana, Irene Diaz-Moreno, Wouter H. Roos
Summary: This article investigates the crucial role of chromatin homeostasis in eukaryotes, with a focus on the function of histone chaperones in DNA replication, repair, and transcription. The authors use fluorescence optical tweezers to study the dynamics of histone chaperones in real time. They find that SET/template-activating factor-I beta and nucleophosmin 1, representing the two most common histone chaperone folds, exhibit binding specificity for fully dismantled nucleosomes and can disrupt non-native histone-DNA interactions. Additionally, the process of histone eviction and its regulation by cytochrome c are examined. This study reveals conserved mechanisms of action in nucleosome remodeling for these structurally distinct chaperones.
Article
Multidisciplinary Sciences
Margarida Bastos, Olga Abian, Christopher M. Johnson, Frederico Ferreira-da-Silva, Sonia Vega, Ana Jimenez-Alesanco, David Ortega-Alarcon, Adrian Velazquez-Campoy
Summary: Isothermal titration calorimetry (ITC) has become the gold standard for studying molecular interactions in solution. It is widely used for characterizing molecular interactions between ligands and macromolecules. This Primer provides an overview of ITC's foundations, instrumentation, common applications, extensions and modifications, advantages and caveats, as well as recent and future developments.
NATURE REVIEWS METHODS PRIMERS
(2023)
Article
Biochemistry & Molecular Biology
Bruno Rizzuti, Olga Abian, Adrian Velazquez-Campoy, Jose L. Neira
Summary: This study investigates the stability and conformational features of the N-terminal region of MDM2, revealing the low stability and unfolding intermediates of this region. The low stability of this protein may be related to its inherent flexibility and ability to interact with multiple molecular partners.
Article
Multidisciplinary Sciences
Nerea Novo, Silvia Romero-Tamayo, Carlos Marcuello, Sergio Boneta, Irene Blasco-Machin, Adrian Velazquez-Campoy, Raquel Villanueva, Raquel Moreno-Loshuertos, Anabel Lostao, Milagros Medina, Patricia Ferreira
Summary: AIF is a moonlighting flavoenzyme that is involved in the assembly of mitochondrial respiratory complexes in healthy cells but can also trigger DNA cleavage and cell death. This study demonstrates the molecular assembly of a DNA-degradosome complex involving AIF, CypA, and histone H2AX, and the cooperative effects of these components in degrading genomic DNA. Additionally, the study reveals that AIF possesses nuclease activity that is stimulated by the presence of Mg2+ or Ca2+, which allows it to efficiently degrade genomic DNA alone or in cooperation with CypA. It is also found that the TopIB and DEK motifs in AIF are responsible for its nuclease activity. These findings enhance our understanding of AIF's role in promoting apoptosis and provide potential avenues for the development of new therapeutic strategies.
Article
Biochemistry & Molecular Biology
Brandon P. Russell, David J. Vinyard
Summary: The Mn4CaO5 oxygen-evolving complex in Photosystem II is crucial for water oxidation. D1 residue R334 participates in proton release and interacts with PsbO. A D1-R334G mutant destabilizes the OEC but stabilizes the S2 intermediate.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2024)
Article
Biochemistry & Molecular Biology
Alexander A. Bulychev, Tatiana S. Strelets
Summary: Excitable cells of higher plants and characean algae respond to stressful stimuli by generating action potentials that influence chlorophyll fluorescence and photosynthesis for an extended period of time. While plant leaves exhibit a reversible depression in the efficiency of photosystem II reaction after an individual action potential, characean algae show long-lasting oscillations of photosystem II reaction efficiency after firing an action potential. This study investigates the possible mechanisms behind these oscillations and suggests that they are a result of metabolic rearrangements in chloroplasts and the cyclosis cessation-recovery cycle induced by calcium influx during action potentials. The findings also indicate that fluidic communications between different cell regions play a role in these oscillations, and the inhibition of oscillations occurs when these communications are restricted or eliminated.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2024)
Article
Biochemistry & Molecular Biology
Dmitry Zlenko, Elena A. Protasova, Georgy Tsoraev, Nikolai N. Sluchanko, Dmitry A. Cherepanov, Thomas Friedrich, Baosheng Ge, Song Qin, Eugene G. Maksimov, Andrew B. Rubin
Summary: The conformation of chromophores in isolated phycobiliproteins is heterogeneous, but not in the entire phycobilisome (PBS). Under low-energy excitation, there is no significant uphill energy transfer from the core to the peripheral rods of the PBS, while transfer from the terminal emitters to bulk allophycocyanin chromophores is highly probable.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2024)
Article
Biochemistry & Molecular Biology
Makio Yokono, Chiyo Noda, Jun Minagawa
Summary: This paper investigates the energy transfer between Photosystem II and Photosystem I in Arabidopsis thaliana, and finds that the fast spillover is reversibly regulated depending on pH.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2024)