Biochimica et Biophysica Acta-Bioenergetics最新文献

{"title":"Three's company: Membrane waltz among organelles","authors":"Valentin Guyard,&nbsp;Francesca Giordano","doi":"10.1016/j.bbabio.2025.149555","DOIUrl":"10.1016/j.bbabio.2025.149555","url":null,"abstract":"<div><div>The study of membrane contact sites (MCS) has profoundly transformed our understanding of inter-organelle communication. These sites, where the membranes of two organelles are closely apposed, facilitate the transfer of small molecules such as lipids and ions. They are especially crucial for the maintenance of the structure and function of organelles like mitochondria and lipid droplets, which are largely excluded from vesicular trafficking. The significant advancements in imaging techniques, and molecular and cell biology research have shown that MCS are more complex than what originally thought and can involve more than two organelles. This has revealed the intricate nature and critical importance of these subcellular connections.</div><div>Here, we provide an overview of newly described three-way inter-organelles associations, and the proteins involved in these MCS. We highlight the roles these contacts play in key cellular processes such as lipid droplet biogenesis and mitochondrial division. Additionally, we discuss the latest advances in super-resolution imaging that enable the study of these complex three-way interactions. Ongoing research, driven by technological innovations, promises to uncover further insights into their roles in fundamental cellular processes and their implications for health and disease.</div></div>","PeriodicalId":50731,"journal":{"name":"Biochimica et Biophysica Acta-Bioenergetics","volume":"1866 3","pages":"Article 149555"},"PeriodicalIF":3.4,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143781799","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Expansion microscopy reveals thylakoid organisation alterations due to genetic mutations and far-red light acclimation","authors":"Jarne Berentsen,&nbsp;Peter R. Bos,&nbsp;Emilie Wientjes","doi":"10.1016/j.bbabio.2025.149552","DOIUrl":"10.1016/j.bbabio.2025.149552","url":null,"abstract":"<div><div>The thylakoid membrane is the site of the light-dependent reactions of photosynthesis. It is a continuous membrane, folded into grana stacks and the interconnecting stroma lamellae. The CURVATURE THYLAKOID1 (CURT1) protein family is involved in the folding of the membrane into the grana stacks. The thylakoid membrane remodels its architecture in response to light conditions, but its 3D organisation and dynamics remain incompletely understood. To resolve these details, an imaging technique is needed that provides high-resolution 3D images in a high-throughput manner. Recently, we have used expansion microscopy, a technique that meets these criteria, to visualise the thylakoid membrane isolated from spinach. Here, we show that this protocol can also be used to visualise enveloped spinach chloroplasts. Additionally, we present an improved protocol for resolving the thylakoid structure of <em>Arabidopsis thaliana</em>. Using this protocol, we show the changes in thylakoid architecture in response to long-term far-red light acclimation and due to knocking out CURT1A. We show that far-red light acclimation results in higher grana stacks that are packed closer together. In addition, the distance between stroma lamellae, which are wrapped around the grana, decreases. In the <em>curt1a</em> mutant, grana have an increased diameter and height, and the distance between grana is increased. Interestingly, in this mutant, the stroma lamellae occasionally approach the grana stacks from the top. These observations show the potential of expansion microscopy to study the thylakoid membrane architecture.</div></div>","PeriodicalId":50731,"journal":{"name":"Biochimica et Biophysica Acta-Bioenergetics","volume":"1866 3","pages":"Article 149552"},"PeriodicalIF":3.4,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143631025","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of determinants for variability in mitochondrial biochemical complex activities","authors":"Sandra Monica Bach de Courtade ,&nbsp;Marte Eikenes ,&nbsp;Ying Sheng ,&nbsp;Tuula A. Nyman ,&nbsp;Yngve Thomas Bliksrud ,&nbsp;Katja Scheffler ,&nbsp;Lars Eide","doi":"10.1016/j.bbabio.2025.149553","DOIUrl":"10.1016/j.bbabio.2025.149553","url":null,"abstract":"<div><div>Diagnostics of mitochondrial disease requires a combination of clinical evaluations and biochemical characterization. However, the large normal variation in mitochondrial complex activity limits the precision of biochemical diagnostics. Thus, identifying factors that contribute to such variations could enhance diagnostic accuracy. In comparison, inbred mice demonstrate much less variations in brain mitochondrial activity, but a clear reduction with age. Interestingly, pretreatment of mouse brain mitochondria with the detergent dodecyl maltoside abolishes the reduction. We therefore postulated that DDM pretreatment could be valuable tool for distinguishing between variations caused by posttranslational modifications and those caused by genetic heterogeneity.</div><div>In this study, we evaluated the effects of age, DDM sensitivity, oxidative damage and single nucleotide polymorphism on biochemical complex activity and the proteome of human muscle mitochondria, which serve as reference standards for mitochondrial diagnostics. Our results indicate that mtDNA variants are the primary contributors to the diversity in biochemical activity in human muscle mitochondria from healthy individuals.</div></div>","PeriodicalId":50731,"journal":{"name":"Biochimica et Biophysica Acta-Bioenergetics","volume":"1866 2","pages":"Article 149553"},"PeriodicalIF":3.4,"publicationDate":"2025-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143601763","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pinpoint introduction of functional molecular probe into the NqrB subunit of Na+-translocating NADH-ubiquinone oxidoreductase from Vibrio cholerae","authors":"Saya Miyachi ,&nbsp;Hinako Tanaka ,&nbsp;Moe Ishikawa ,&nbsp;Danielle Mcfee ,&nbsp;Wataru Aoki ,&nbsp;Masatoshi Murai ,&nbsp;Blanca Barquera ,&nbsp;Hideto Miyoshi ,&nbsp;Takahiro Masuya","doi":"10.1016/j.bbabio.2025.149551","DOIUrl":"10.1016/j.bbabio.2025.149551","url":null,"abstract":"<div><div>The Na⁺-translocating NADH-ubiquinone oxidoreductase (Na⁺-NQR) is a key enzyme in the respiratory chain of numerous pathogenic bacteria, including <em>Vibrio cholerae</em>. The flexible cytoplasmic <em>N</em>-terminal region of the NqrB subunit (Met¹–Lys⁵⁴), which may play an important role in the final UQ reduction at the adjacent NqrA, is the target of specific inhibitors. If we can develop a new method that enables pinpoint introduction of functional probe molecules (such as fluorescent probes) into the <em>N</em>-terminal region, this could lead to new experimental ways of monitoring dynamic structural changes of the region. We previously showed that an electrophilic chemical group, which can be released from korormicin A-templated synthetic ligand, can be predominantly introduced into nucleophilic Lys²² as a “foothold” via ligand-directed (LD) substitution, but the subsequent conjugation of a functional probe molecule to the foothold by Cu⁺-catalyzed click chemistry required destruction of the enzyme. Accordingly, we now report the nondestructive conjugation of the functional molecule into the <em>N</em>-terminal region via a two-step conjugation technique: first, pinpoint introduction of a foothold tag containing a ring-strained cyclopropene by LD substitution using a new korormicin A-templated ligand (BEK-1) and second, direct conjugation of a fluorescent probe molecule containing tetrazine with the introduced cyclopropene by inverse electron-demand Diels-Alder-type click chemistry. Protein sequence analyses revealed that the fluorescent probe is attached to Lys¹⁹, His²⁰, or Lys²² in the region. The extent of conjugation of the fluorescent probe was approximately halved in the presence of different inhibitors, suggesting that the inhibitor binding induces structural changes around the residues.</div></div>","PeriodicalId":50731,"journal":{"name":"Biochimica et Biophysica Acta-Bioenergetics","volume":"1866 2","pages":"Article 149551"},"PeriodicalIF":3.4,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143574557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"New insights into the involvement of residue D1/V185 in photosystem II function in Synechocystis 6803 and Thermosynechococcus vestitus","authors":"Alain Boussac ,&nbsp;Julien Sellés ,&nbsp;Miwa Sugiura ,&nbsp;Robert L. Burnap","doi":"10.1016/j.bbabio.2025.149550","DOIUrl":"10.1016/j.bbabio.2025.149550","url":null,"abstract":"<div><div>The effects of D1-V185T and D1-V185N mutations in Photosystem II (PSII) from <em>Thermosynechococcus vestitus</em> (formerly <em>T. elongatus</em>) and <em>Synechocystis</em> 6803, respectively, were studied using both EPR and optical kinetics. EPR spectroscopy reveals the presence of a mixture of a S₂ state in a high spin configuration (S₂^HS) and in a low spin configuration (S₂^LS) in both mutants. In contrast to the S₂^HS in the wild type, the S₂^HS state in the D1-V185T mutant does not progress to the S₃ state at 198 K. This inability is likely due to alterations in the protonation state and hydrogen-bonding network around the Mn₄CaO₅ cluster. Optical studies show that these mutations significantly affect proton release during the S₃-to-S₀ transition. While the initial fast proton release associated with Tyr_Z^● formation remains unaffected within the resolution of our measurements, the second, and slower, proton release is delayed, suggesting that the mutations disrupt the hydrogen-bonding interactions necessary for efficient deprotonation of substrate water (O6). This disruption in proton transfer also correlates with slower water exchange in the S₃ state, likely due to non-native hydrogen bonds introduced by the threonine or asparagine side chains at position 185. These findings point to a critical role of D1-V185 in regulating both proton transfer dynamics and water binding, underscoring a complex interplay between structural and functional changes in PSII.</div></div>","PeriodicalId":50731,"journal":{"name":"Biochimica et Biophysica Acta-Bioenergetics","volume":"1866 2","pages":"Article 149550"},"PeriodicalIF":3.4,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143517175","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Engineering of thermal stability in the recombinant xanthorhodopsin from Salinibacter ruber","authors":"Lada E. Petrovskaya ,&nbsp;Vadim A. Bolshakov ,&nbsp;Evgeniy P. Lukashev ,&nbsp;Elena A. Kryukova ,&nbsp;Eugene G. Maksimov ,&nbsp;Andrei B. Rubin ,&nbsp;Dmitriy A. Dolgikh ,&nbsp;Sergei P. Balashov ,&nbsp;Mikhail P. Kirpichnikov","doi":"10.1016/j.bbabio.2025.149547","DOIUrl":"10.1016/j.bbabio.2025.149547","url":null,"abstract":"<div><div>Solubilization in detergents is a widely used technique for the isolation of membrane proteins and the study of their properties. Unfortunately, protein stability in detergent micelles can sometimes be compromised. We encountered this issue with xanthorhodopsin (XR) from <em>Salinibacter ruber</em>, which had been previously engineered for expression in <em>Escherichia coli</em> cells. To explore the factors affecting stability and to enhance thermal stability of recombinant XR preparations following solubilization of membranes using n-dodecyl-β-D-maltopyranoside and nickel-affinity chromatography, we developed a series of hybrid proteins based on the homology between XR and a stable rhodopsin from <em>Gloeobacter violaceus</em> (GR). Functional studies of these hybrids and measurements of their melting temperatures revealed the structural elements of XR that account for its notable difference in stability compared to GR, despite their high overall homology of approximately 50 % identical residues.</div><div>In particular, XR variants with an engineered loop between transmembrane helices D and E, similar to that in GR, demonstrated enhanced stability. However, we found that replacing the DE loop affects carotenoid binding. Additionally, two hybrid proteins containing the C and D helices from GR exhibited increased stability as well as improved photocycle and proton transport rates. In conclusion, we have demonstrated that optimizing the amino acid sequence of xanthorhodopsin from <em>S. ruber</em> based on its homology with <em>Gloeobacter</em> rhodopsin is an effective approach to enhance its thermal stability in vitro and improve its potential for optogenetic applications.</div></div>","PeriodicalId":50731,"journal":{"name":"Biochimica et Biophysica Acta-Bioenergetics","volume":"1866 2","pages":"Article 149547"},"PeriodicalIF":3.4,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143464421","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Defining the direct electron transfer connection between alternative complex III and cytochrome oxidase in Flavobacterium johnsoniae","authors":"Katarzyna Lorencik ,&nbsp;Robert Ekiert ,&nbsp;Rafał Pietras ,&nbsp;Joanna Ner-Kluza ,&nbsp;Małgorzata Hopciaś ,&nbsp;Artur Osyczka","doi":"10.1016/j.bbabio.2025.149548","DOIUrl":"10.1016/j.bbabio.2025.149548","url":null,"abstract":"<div><div>Alternative complex III (ACIII) is an enzyme of electron transport chains in some bacterial species. ACIII, like cytochrome <em>bc</em> enzymes, oxidizes quinol and transfers electrons from quinol to electron acceptors located outside the membrane. Various proteins can functionally link ACIII with other enzymes. The structure of ACIII from <em>Flavobacterium johnsoniae</em> suggests that in this bacterium the membrane-anchored mobile mono-heme cytochrome <em>c</em> domain (mdA) of the ActA subunit of ACIII provides means for its connection with cytochrome <em>aa</em>₃ oxidase. Here, using a recently-developed genetic system for ACIII, we revealed that ACIII mutant deprived of mdA does not exhibit electron transfer activity towards cytochrome <em>aa</em>₃ oxidase in the cells and in the isolated membranes. These results indicate that mdA is the only carrier of electrons between the pentaheme core of ActA and cytochrome <em>aa</em>₃ oxidase. In addition, we heterologously expressed and purified mdA and ActE (another mono-heme subunit of ACIII) from <em>Escherichia coli</em> to identify the redox midpoint potentials of the hemes in these two domains. The obtained values analyzed in the context of the whole titration profiles of native ACIII and ACIII deprived of mdA provide first insights into the arrangement of heme redox potentials in the seven-heme chain formed by the ActA/ActE assembly.</div></div>","PeriodicalId":50731,"journal":{"name":"Biochimica et Biophysica Acta-Bioenergetics","volume":"1866 2","pages":"Article 149548"},"PeriodicalIF":3.4,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143434190","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Corrigendum to “Structural robustness of the NADH binding site in NADH: Ubiquinone oxidoreductase (complex I)” [Biochim. Biophys. Acta (BBA) – Bioenerg. (2024)/149491]","authors":"Sanaz Göppert-Asadollahpour,&nbsp;Daniel Wohlwend,&nbsp;Thorsten Friedrich","doi":"10.1016/j.bbabio.2025.149549","DOIUrl":"10.1016/j.bbabio.2025.149549","url":null,"abstract":"","PeriodicalId":50731,"journal":{"name":"Biochimica et Biophysica Acta-Bioenergetics","volume":"1866 2","pages":"Article 149549"},"PeriodicalIF":3.4,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143434225","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural study of the chlorophyll between Lhca8 and PsaJ in an Antarctica green algal photosystem I-LHCI supercomplex revealed by its atomic structure","authors":"Pi-Cheng Tsai,&nbsp;Koji Kato,&nbsp;Jian-Ren Shen,&nbsp;Fusamichi Akita","doi":"10.1016/j.bbabio.2025.149543","DOIUrl":"10.1016/j.bbabio.2025.149543","url":null,"abstract":"<div><div><em>Coccomyxa subellipsoidea</em> is an oleaginous, non-motile unicellular green microalga isolated from Antarctica, and is an attractive candidate for CO₂ fixation and biomass production. <em>C. subellipsoidea</em> is the first polar green alga whose genome has been sequenced. Understanding the structure of photosystems from <em>C. subellipsoidea</em> can provide more information about the conversion of light energy into chemical energy under extreme environments. Photosystems I (PSI) is one of the two photosystems highly conserved from cyanobacteria to vascular plants, and associates with a large amount of outer light-harvesting complex (LHC) which absorb light energy and transfer them to the core complex. Here, we determined the structure of the PSI-10 LHCIs and PSI-8 LHCIs supercomplexes from <em>C. subellipsoidea</em> at 1.92 Å and 2.06 Å resolutions by cryo-electron microscopy, respectively. The supercomplex is similar to PSI-LHCI from other green algae, whereas a large amount of water molecules is observed in our structure because of the high-resolution map. Two novel chlorophylls (Chls), Chl <em>a</em>321 in Lhca4 and Chl <em>a</em>314 in Lhca8, are observed at the lumenal side in our structure, in which Lhca8-Chl <em>a</em>314 provides a potential excitation energy transfer (EET) pathway between the inner-belt of LHCI and the core at the lumenal side. A total of three major EET pathways from LHCIs to PSI core are proposed, and <em>C. subellipsoidea</em> might adapt to the extreme environment by transferring energy in these three different EET pathways instead of by two major pathways proposed in other organisms.</div></div>","PeriodicalId":50731,"journal":{"name":"Biochimica et Biophysica Acta-Bioenergetics","volume":"1866 2","pages":"Article 149543"},"PeriodicalIF":3.4,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143402854","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mitochondrial potassium channels: New properties and functions","authors":"Adam Szewczyk ,&nbsp;Piotr Bednarczyk ,&nbsp;Bogusz Kulawiak ,&nbsp;Monika Żochowska ,&nbsp;Barbara Kalenik ,&nbsp;Joanna Lewandowska ,&nbsp;Karolina Pytlak ,&nbsp;Shur Gałecka ,&nbsp;Antoni Wrzosek ,&nbsp;Piotr Koprowski","doi":"10.1016/j.bbabio.2025.149546","DOIUrl":"10.1016/j.bbabio.2025.149546","url":null,"abstract":"<div><div>Mitochondria are recently implicated in phenomena such as cytoprotection, cellular senescence, tumor metabolism, and inflammation. The basis of these processes relies on biochemical functions of mitochondria such as the synthesis of reactive oxygen species or biophysical properties such as the integrity of the inner mitochondrial membrane. The transport of potassium cations plays an important role in all these events. The K⁺ influx is mediated by potassium channels present in the inner mitochondrial membrane. In this article, we present an overview of our new findings on the properties of mitochondrial large-conductance calcium-activated and mitochondrial ATP-regulated potassium channels. This concerns the role of mitochondrial potassium channels in cellular senescence, and interactions with other mitochondrial proteins or small molecules such as quercetin, hemin, and hydrogen sulfide. We also discuss the prospects of research on potassium channels present in mitochondria.</div></div>","PeriodicalId":50731,"journal":{"name":"Biochimica et Biophysica Acta-Bioenergetics","volume":"1866 2","pages":"Article 149546"},"PeriodicalIF":3.4,"publicationDate":"2025-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143376895","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}