Pub Date : 2025-12-17DOI: 10.1016/j.bbabio.2025.149576
Michael Lynch
A recent paper in this journal claims that prior estimates of the bioenergetic costs of producing cells are off by more than 100-fold. Here, it is shown that this conclusion is based on an erroneous interpretation of the methods previously employed by a diversity of authors and that the downstream arguments are conceptually flawed. Likewise, the author's claim that the establishment of the mitochondrion caused a quantum leap in bioenergetic capacity that spurred a revolution in eukaryotic innovation is inconsistent with empirical data and evolutionary theory.
{"title":"Energetics and evolution: Response to Martin.","authors":"Michael Lynch","doi":"10.1016/j.bbabio.2025.149576","DOIUrl":"https://doi.org/10.1016/j.bbabio.2025.149576","url":null,"abstract":"<p><p>A recent paper in this journal claims that prior estimates of the bioenergetic costs of producing cells are off by more than 100-fold. Here, it is shown that this conclusion is based on an erroneous interpretation of the methods previously employed by a diversity of authors and that the downstream arguments are conceptually flawed. Likewise, the author's claim that the establishment of the mitochondrion caused a quantum leap in bioenergetic capacity that spurred a revolution in eukaryotic innovation is inconsistent with empirical data and evolutionary theory.</p>","PeriodicalId":50731,"journal":{"name":"Biochimica et Biophysica Acta-Bioenergetics","volume":" ","pages":"149576"},"PeriodicalIF":2.7,"publicationDate":"2025-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145794981","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}
Pub Date : 2025-12-01DOI: 10.1016/j.bbabio.2025.149575
Katharina Trost , Robert B. Gennis , John F. Allen , Daniel B. Mills , William F. Martin
The history of Earth's atmospheric oxygen is a cornerstone of evolutionary biology. While unequivocal evidence for an increase in atmospheric O2 marks the Great Oxidation Event (GOE) roughly 2.4 billion years ago, evidence underlying proposals for pre-GOE O2 accumulation is debated. Here we have investigated the distribution of genes for oxygen reductases, the enzymes that consume O2 in respiratory chains, across independently generated molecular timescales of prokaryotic evolution. The data indicate that cytochrome bd-oxidases, heme-copper oxidases and alternative oxidases arose in the wake of the GOE ca. 2.4 billion years ago, after which the genes were subjected to abundant lateral gene transfer, a reflection of their utility in redox balance and membrane bioenergetics. The data lead us to propose a straightforward four-stage model for O2 accumulation surrounding the GOE: (i) Negligible O2 existed prior to the GOE. (ii) Cyanobacterial O2 production started at the GOE, yet was capped at 2 % [v/v] atmospheric O2, the threshold at which cyanobacterial nitrogenase is inhibited by O2. (iii) Production of 0.02 atm of O2 (2 % [v/v]) at the GOE buried roughly the entire atmospheric CO2 inventory, causing sudden enrichment of 13C in dissolved inorganic carbon (the Lomagundi 13C anomaly), through RuBisCO isotope discrimination, without atmospheric O2 exceeding 2 % [v/v]. (iv) High atmospheric 12C at the end of the Lomagundi excursion marks the origin of oxygen reductases, their rapid spread via function in respiratory CO2 liberation, and the onset of equilibrium between photosynthetic O2 production and respiratory O2 consumption at 2 % atmospheric O2.
{"title":"Oxygen reductase origin followed the great oxidation event and terminated the Lomagundi excursion","authors":"Katharina Trost , Robert B. Gennis , John F. Allen , Daniel B. Mills , William F. Martin","doi":"10.1016/j.bbabio.2025.149575","DOIUrl":"10.1016/j.bbabio.2025.149575","url":null,"abstract":"<div><div>The history of Earth's atmospheric oxygen is a cornerstone of evolutionary biology. While unequivocal evidence for an increase in atmospheric O<sub>2</sub> marks the Great Oxidation Event (GOE) roughly 2.4 billion years ago, evidence underlying proposals for pre-GOE O<sub>2</sub> accumulation is debated. Here we have investigated the distribution of genes for oxygen reductases, the enzymes that consume O<sub>2</sub> in respiratory chains, across independently generated molecular timescales of prokaryotic evolution. The data indicate that cytochrome <em>bd</em>-oxidases, heme-copper oxidases and alternative oxidases arose in the wake of the GOE ca. 2.4 billion years ago, after which the genes were subjected to abundant lateral gene transfer, a reflection of their utility in redox balance and membrane bioenergetics. The data lead us to propose a straightforward four-stage model for O<sub>2</sub> accumulation surrounding the GOE: (i) Negligible O<sub>2</sub> existed prior to the GOE. (ii) Cyanobacterial O<sub>2</sub> production started at the GOE, yet was capped at 2 % [<em>v</em>/v] atmospheric O<sub>2</sub>, the threshold at which cyanobacterial nitrogenase is inhibited by O<sub>2</sub>. (iii) Production of 0.02 atm of O<sub>2</sub> (2 % [<em>v</em>/v]) at the GOE buried roughly the entire atmospheric CO<sub>2</sub> inventory, causing sudden enrichment of <sup>13</sup>C in dissolved inorganic carbon (the Lomagundi <sup>13</sup>C anomaly), through RuBisCO isotope discrimination, without atmospheric O<sub>2</sub> exceeding 2 % [<em>v</em>/v]. (iv) High atmospheric <sup>12</sup>C at the end of the Lomagundi excursion marks the origin of oxygen reductases, their rapid spread via function in respiratory CO<sub>2</sub> liberation, and the onset of equilibrium between photosynthetic O<sub>2</sub> production and respiratory O<sub>2</sub> consumption at 2 % atmospheric O<sub>2</sub>.</div></div>","PeriodicalId":50731,"journal":{"name":"Biochimica et Biophysica Acta-Bioenergetics","volume":"1867 2","pages":"Article 149575"},"PeriodicalIF":2.7,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145670512","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}
Pub Date : 2025-11-22DOI: 10.1016/j.bbabio.2025.149574
Italo Lorandi , José Alfredo Hernández-Zúñiga , Mercedes Esparza-Perusquía , Genaro Matus-Ortega , Héctor Vázquez-Meza , Héctor Flores-Herrera , Juan Pablo Pardo , Federico Martínez , Oscar Flores-Herrera
Complex I is absent in mitochondria from Saccharomyces cerevisiae; instead, three rotenone-insensitive NADH dehydrogenases are present: two on the external (Nde1 and Nde2) and one on the internal (Ndi1) leaf of the inner mitochondrial membrane. In a previous work (1), we reported the presence of a supercomplex in S. cerevisiae constituted by the Ndi1 and complexes III2 and IV with an apparent MW of 1600 kDa. In this work, respirasomes from WT and NDE1Δ/NDE2Δ strains were isolated, and their activities characterized. Kinetic characterization of NADH:DBQ oxidoreductase activity from respirasomes, as well as free Ndi1, showed Vmax values of 0.85 ± 0.01, 0.82 ± 0.02, and 0.51 ± 0.02 μmol NADH oxidized·min−1·mg−1 for WT respirasome, NDE1Δ/NDE2Δ respirasome, and free Ndi1, respectively. The kinetic model for WT- and NDE1Δ/NDE2Δ respirasome was a Ping Pong Bi-Bi mechanism with two different stable enzyme forms, free (E) and modified enzyme (F); while the free Ndi1 exhibited a Random Bi-Bi mechanism with the ternary complex NADH-Ndi1-ubiquinone. This suggests that the interaction of Ndi1 with complexes III2 and IV in the respirasome modifies its kinetic mechanism. Oxygen consumption values were 0.35 ± 0.07 and 0.34 ± 0.07 μmol O2·min−1·mg−1 for WT and NDE1Δ/NDE2Δ respirasomes, respectively. The values for NADH/O2 ratio were 2.4 ± 1.4 and 2.4 ± 1.6 for WT and NDE1Δ/NDE2Δ respirasomes, respectively, suggesting that electron flux from NADH to oxygen occurs in the S. cerevisiae respirasome. The electron transfer from NADH to oxygen was inhibited by flavone, antimycin A, or cyanide, but the NADH dehydrogenase activity of the respirasome was insensitive to antimycin A or cyanide, indicating that no codependence of respirasomal-Ndi1 activity occurs as reported in the Ustilago maydis respirasome. This result indicates that the activity of respirasomal Ndi1 may contribute to the quinol pool with no evidence of direct substrate channeling. This is the first evidence of the Ndi1 role as the electron input in the respirasome from S. cerevisiae.
{"title":"The internal alternative NADH dehydrogenase (Ndi1) is the electron input in the Saccharomyces cerevisiae respirasome","authors":"Italo Lorandi , José Alfredo Hernández-Zúñiga , Mercedes Esparza-Perusquía , Genaro Matus-Ortega , Héctor Vázquez-Meza , Héctor Flores-Herrera , Juan Pablo Pardo , Federico Martínez , Oscar Flores-Herrera","doi":"10.1016/j.bbabio.2025.149574","DOIUrl":"10.1016/j.bbabio.2025.149574","url":null,"abstract":"<div><div>Complex I is absent in mitochondria from <em>Saccharomyces cerevisiae</em>; instead, three rotenone-insensitive NADH dehydrogenases are present: two on the external (Nde1 and Nde2) and one on the internal (Ndi1) leaf of the inner mitochondrial membrane. In a previous work (1), we reported the presence of a supercomplex in <em>S. cerevisiae</em> constituted by the Ndi1 and complexes III<sub>2</sub> and IV with an apparent MW of 1600 kDa. In this work, respirasomes from WT and <em>NDE1Δ/NDE2Δ</em> strains were isolated, and their activities characterized. Kinetic characterization of NADH:DBQ oxidoreductase activity from respirasomes, as well as free Ndi1, showed V<sub>max</sub> values of 0.85 ± 0.01, 0.82 ± 0.02, and 0.51 ± 0.02 μmol NADH oxidized·min<sup>−1</sup>·mg<sup>−1</sup> for WT respirasome, <em>NDE1Δ/NDE2Δ</em> respirasome, and free Ndi1, respectively. The kinetic model for WT- and <em>NDE1Δ/NDE2Δ</em> respirasome was a Ping Pong Bi-Bi mechanism with two different stable enzyme forms, free (E) and modified enzyme (F); while the free Ndi1 exhibited a Random Bi-Bi mechanism with the ternary complex NADH-Ndi1-ubiquinone. This suggests that the interaction of Ndi1 with complexes III<sub>2</sub> and IV in the respirasome modifies its kinetic mechanism. Oxygen consumption values were 0.35 ± 0.07 and 0.34 ± 0.07 μmol O<sub>2</sub>·min<sup>−1</sup>·mg<sup>−1</sup> for WT and <em>NDE1Δ/NDE2Δ</em> respirasomes, respectively. The values for NADH/O<sub>2</sub> ratio were 2.4 ± 1.4 and 2.4 ± 1.6 for WT and <em>NDE1Δ/NDE2Δ</em> respirasomes, respectively, suggesting that electron flux from NADH to oxygen occurs in the <em>S. cerevisiae</em> respirasome. The electron transfer from NADH to oxygen was inhibited by flavone, antimycin A, or cyanide, but the NADH dehydrogenase activity of the respirasome was insensitive to antimycin A or cyanide, indicating that no codependence of respirasomal-Ndi1 activity occurs as reported in the <em>Ustilago maydis</em> respirasome. This result indicates that the activity of respirasomal Ndi1 may contribute to the quinol pool with no evidence of direct substrate channeling. This is the first evidence of the Ndi1 role as the electron input in the respirasome from <em>S. cerevisiae</em>.</div></div>","PeriodicalId":50731,"journal":{"name":"Biochimica et Biophysica Acta-Bioenergetics","volume":"1867 1","pages":"Article 149574"},"PeriodicalIF":2.7,"publicationDate":"2025-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145589806","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}
Under drought, lack of an electron source (water) reduces the capacity of oxygen-evolving photosynthesis.
•
Consequently, even under low light, excess excitation energy may be generated, which is harmful as it leads to generation of reactive oxygen species.
•
When the desert green alga Chlorella ohadii undergoes desiccation, first photosystem II binds to photosystem I via LHCII to establish energy transfer pathways, and then excitation energy dissipation induced by a quencher is initiated.
•
This strategy may provide efficient protection of the entire photosynthetic apparatus during early stages of desiccation, when the available quencher may be insufficient.
{"title":"Increase in spillover and excitation energy dissipation during wet–dry transitions in the desert green alga Chlorella ohadii","authors":"Soma Kawamura , Makio Yokono , Chiyo Noda , Jun Minagawa","doi":"10.1016/j.bbabio.2025.149573","DOIUrl":"10.1016/j.bbabio.2025.149573","url":null,"abstract":"<div><div><ul><li><span>•</span><span><div>Under drought, lack of an electron source (water) reduces the capacity of oxygen-evolving photosynthesis.</div></span></li><li><span>•</span><span><div>Consequently, even under low light, excess excitation energy may be generated, which is harmful as it leads to generation of reactive oxygen species.</div></span></li><li><span>•</span><span><div>When the desert green alga <em>Chlorella ohadii</em> undergoes desiccation, first photosystem II binds to photosystem I via LHCII to establish energy transfer pathways, and then excitation energy dissipation induced by a quencher is initiated.</div></span></li><li><span>•</span><span><div>This strategy may provide efficient protection of the entire photosynthetic apparatus during early stages of desiccation, when the available quencher may be insufficient.</div></span></li></ul></div></div>","PeriodicalId":50731,"journal":{"name":"Biochimica et Biophysica Acta-Bioenergetics","volume":"1867 1","pages":"Article 149573"},"PeriodicalIF":2.7,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145092999","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}
Pub Date : 2025-09-04DOI: 10.1016/j.bbabio.2025.149571
Victor V. Lemeshko
A recent revision of the chemiosmotic theory was reported by Hernansanz-Agustín and coauthors as a discovery that a Na+ gradient across the mitochondrial inner membrane equates with the H+ gradient and contributes up to half of the inner membrane potential, without an explanation of the possible underlying mechanism. Based on the experimental data of these and other authors, and performed biophysical estimations, I propose a mechanism by which both the reported fast-acting Na+/H+ exchanger, associated with the complex I of the respiratory chain, and Na+ electrodiffusion in the intracristae space and the matrix allow maintenance of a high membrane potential.
{"title":"Mechanism of Na+ ions contribution to the generation and maintenance of a high inner membrane potential in mitochondria","authors":"Victor V. Lemeshko","doi":"10.1016/j.bbabio.2025.149571","DOIUrl":"10.1016/j.bbabio.2025.149571","url":null,"abstract":"<div><div>A recent revision of the chemiosmotic theory was reported by Hernansanz-Agustín and coauthors as a discovery that a Na<sup>+</sup> gradient across the mitochondrial inner membrane equates with the H<sup>+</sup> gradient and contributes up to half of the inner membrane potential, without an explanation of the possible underlying mechanism. Based on the experimental data of these and other authors, and performed biophysical estimations, I propose a mechanism by which both the reported fast-acting Na<sup>+</sup>/H<sup>+</sup> exchanger, associated with the complex I of the respiratory chain, and Na<sup>+</sup> electrodiffusion in the intracristae space and the matrix allow maintenance of a high membrane potential.</div></div>","PeriodicalId":50731,"journal":{"name":"Biochimica et Biophysica Acta-Bioenergetics","volume":"1867 1","pages":"Article 149571"},"PeriodicalIF":2.7,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145007521","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}
Pub Date : 2025-08-25DOI: 10.1016/j.bbabio.2025.149570
Andrei G. Yakovlev , Alexandra S. Taisova
Photosynthesis in bacteria, algae, and plants begins with the absorption of light energy by (bacterio)chlorophyll molecules, part of which is then converted into heat, leading to a transient change in molecular temperature. We investigated this phenomenon in reaction centers (RCs) of the purple bacterium Rhodobacter (Rba.) sphaeroides using picosecond fluorescence spectroscopy. Exclusion of charge separation processes using the VR(L157) mutation allowed us to record the spectral dynamics of fluorescence of monomeric BChl a molecules. We found that excitation of RCs into the Soret band results in significant heating of BChl a by ~160 K with subsequent vibrational cooling, which manifests itself in a dynamic narrowing of the BChl a fluorescence spectrum with two characteristic times of 5 and 16 ps. The weaker heating by ~65 K and cooling with a characteristic time of 7.5 ps are observed upon excitation of RCs into the Qx band. Excitation into the Qу band does not result in any noticeable heating of BChl a. Difference absorption spectroscopy of tryptophan in the 280 nm region showed that the observed dynamics of the BChl a fluorescence spectrum are not associated with the dielectric rearrangement of the RCs protein matrix. Analysis of the obtained data using the phenomenological model of vibrational cooling led to the conclusion that during heat diffusion from excited BChl a, several amino acid residues from the immediate environment of BChl a act as the first solvation shell (FSS). At the first, faster stage, heat is transferred from BChl a to FSS, and at the second stage, FSS transfers heat to the protein matrix of RCs. Our work has shown the importance of taking into account vibrational cooling when studying the primary processes of photosynthesis.
{"title":"Vibrational cooling of monomeric bacteriochlorophylls in reaction centers of purple bacteria studied by time-resolved fluorescence spectroscopy","authors":"Andrei G. Yakovlev , Alexandra S. Taisova","doi":"10.1016/j.bbabio.2025.149570","DOIUrl":"10.1016/j.bbabio.2025.149570","url":null,"abstract":"<div><div>Photosynthesis in bacteria, algae, and plants begins with the absorption of light energy by (bacterio)chlorophyll molecules, part of which is then converted into heat, leading to a transient change in molecular temperature. We investigated this phenomenon in reaction centers (RCs) of the purple bacterium <em>Rhodobacter</em> (<em>Rba</em>.) <em>sphaeroides</em> using picosecond fluorescence spectroscopy. Exclusion of charge separation processes using the VR(L157) mutation allowed us to record the spectral dynamics of fluorescence of monomeric BChl <em>a</em> molecules. We found that excitation of RCs into the Soret band results in significant heating of BChl <em>a</em> by ~160 K with subsequent vibrational cooling, which manifests itself in a dynamic narrowing of the BChl <em>a</em> fluorescence spectrum with two characteristic times of 5 and 16 ps. The weaker heating by ~65 K and cooling with a characteristic time of 7.5 ps are observed upon excitation of RCs into the Q<sub>x</sub> band. Excitation into the Q<sub>у</sub> band does not result in any noticeable heating of BChl <em>a</em>. Difference absorption spectroscopy of tryptophan in the 280 nm region showed that the observed dynamics of the BChl <em>a</em> fluorescence spectrum are not associated with the dielectric rearrangement of the RCs protein matrix. Analysis of the obtained data using the phenomenological model of vibrational cooling led to the conclusion that during heat diffusion from excited BChl <em>a</em>, several amino acid residues from the immediate environment of BChl <em>a</em> act as the first solvation shell (FSS). At the first, faster stage, heat is transferred from BChl <em>a</em> to FSS, and at the second stage, FSS transfers heat to the protein matrix of RCs. Our work has shown the importance of taking into account vibrational cooling when studying the primary processes of photosynthesis.</div></div>","PeriodicalId":50731,"journal":{"name":"Biochimica et Biophysica Acta-Bioenergetics","volume":"1866 4","pages":"Article 149570"},"PeriodicalIF":2.7,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144904589","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}
Pub Date : 2025-08-11DOI: 10.1016/j.bbabio.2025.149569
Cleo Bagchus , Herbert van Amerongen , Emilie Wientjes
Photosynthesis is driven by light absorbed in photosystem (PS) I and II. Paradoxically, light can also inactivate photosynthesis, mainly by damage to PSII. The light-dependent decrease in functional PSII, referred to as photoinhibition, is initially accompanied by an increase of excitation quenching, energy dissipation characterized by a decline in the lifetime and yield of chlorophyll fluorescence. In plants, research has not yet been performed on the effect of photoinhibition on the fluorescence lifetime of PSII in conditions where the PSII reaction centers are closed or remain open (capable of performing photochemistry).
In this work, we studied the effect of photoinhibition on the fluorescence lifetime of PSII in Arabidopsis thaliana using time-resolved fluorescence measurements with a streak-camera setup in both closing (Fm) and non-closing (Fo) conditions. Measurements under Fm conditions in the chlorina mutant, lacking peripheral antenna, demonstrate formation of a photoinhibitory quencher in the PSII core complex. In Fo, the average fluorescence lifetime of PSII increases upon induction of photoinhibition. This could be due to the degradation of quenched PSII core reaction center protein by FtsH proteases, which leads to unquenched and dysfunctional PSII. We tested this hypothesis by comparing WT plants with the FtsH2 lacking mutant. Based on the similar behavior, we conclude that degradation by FtsH proteases is not the main cause of the increase. Instead this increase is caused by the larger antenna size of still functional PSII. These findings provide new insights into the impact of photoinhibition on the PSII fluorescence lifetime in A. thaliana.
{"title":"Photodamage and excitation energy quenching in PSII: A time-resolved fluorescence study in Arabidopsis","authors":"Cleo Bagchus , Herbert van Amerongen , Emilie Wientjes","doi":"10.1016/j.bbabio.2025.149569","DOIUrl":"10.1016/j.bbabio.2025.149569","url":null,"abstract":"<div><div>Photosynthesis is driven by light absorbed in photosystem (PS) I and II. Paradoxically, light can also inactivate photosynthesis, mainly by damage to PSII. The light-dependent decrease in functional PSII, referred to as photoinhibition, is initially accompanied by an increase of excitation quenching, energy dissipation characterized by a decline in the lifetime and yield of chlorophyll fluorescence. In plants, research has not yet been performed on the effect of photoinhibition on the fluorescence lifetime of PSII in conditions where the PSII reaction centers are closed or remain open (capable of performing photochemistry).</div><div>In this work, we studied the effect of photoinhibition on the fluorescence lifetime of PSII in <em>Arabidopsis thaliana</em> using time-resolved fluorescence measurements with a streak-camera setup in both closing (F<sub>m</sub>) and non-closing (F<sub>o</sub>) conditions. Measurements under F<sub>m</sub> conditions in the <em>chlorina</em> mutant, lacking peripheral antenna, demonstrate formation of a photoinhibitory quencher in the PSII core complex. In F<sub>o</sub><sub>,</sub> the average fluorescence lifetime of PSII increases upon induction of photoinhibition. This could be due to the degradation of quenched PSII core reaction center protein by FtsH proteases, which leads to unquenched and dysfunctional PSII. We tested this hypothesis by comparing WT plants with the FtsH2 lacking mutant. Based on the similar behavior, we conclude that degradation by FtsH proteases is not the main cause of the increase. Instead this increase is caused by the larger antenna size of still functional PSII. These findings provide new insights into the impact of photoinhibition on the PSII fluorescence lifetime in <em>A. thaliana</em>.</div></div>","PeriodicalId":50731,"journal":{"name":"Biochimica et Biophysica Acta-Bioenergetics","volume":"1866 4","pages":"Article 149569"},"PeriodicalIF":2.7,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144849506","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}
Pub Date : 2025-08-11DOI: 10.1016/j.bbabio.2025.149568
Bradley A. Ruple , Soung Hun Park , Jesse C. Craig , Matthew T. Lewis , Joel D. Trinity , Russell S. Richardson , Ryan M. Broxterman
Skeletal muscle mitochondrial respiration is commonly assessed ex vivo using permeabilized fibers in media with high oxygen (O2) concentrations to ensure that O2 availability does not limit respiration. However, high O2 concentrations also increase the production of reactive O2 species that can negatively affect respiration. In this study, we tested the hypotheses that permeabilized fiber mitochondria in a high, compared to low, O2 concentration would (i) not be different at maximal state 3 respiration rate (Vmax), (ii) have lower submaximal respiration rates at submaximal O2 concentrations, and (iii) have greater total cumulative hydrogen peroxide (H2O2) appearance. We continuously monitored mitochondrial state 3 respiration and H2O2 appearance rates using high-resolution respirometry in permeabilized skeletal muscle fibers (12 untrained participants; 22 ± 4 yrs) with either control (~127 mmHg; CON) or high (~327 mmHg; HIGH) partial pressures of O2 (PO2). Vmax was not different between conditions (HIGH: 80.7 ± 16.7 vs. CON: 82.3 ± 18.7 pmol/s/mg, p = 0.695). The PO2 at 80 % Vmax (P80) was greater in HIGH (73.9 ± 25.5 vs. 28.0 ± 7.1 mmHg, p < 0.001) and respiration rates at 5–60 mmHg PO2 were lower for HIGH than CON (all p < 0.001). Additionally, the total cumulative H2O2 appearance was greater in HIGH than CON (n = 11; 51.5 ± 23.2 vs. 18.3 ± 10.3 pmol/mg, p < 0.001), and this difference was directly correlated with the difference in P80 (r = 0.655, p = 0.029). The current findings support that a high O2 concentration, by itself, does not appear to affect Vmax in the permeabilized skeletal muscle fiber preparation, but the corollary increase in H2O2 exposure may diminish mitochondrial state 3 respiratory function.
骨骼肌线粒体呼吸通常在高氧（O2）浓度的培养基中使用渗透性纤维进行体外评估，以确保O2的可用性不会限制呼吸。然而，高浓度的氧气也会增加活性氧的产生，从而对呼吸产生负面影响。在本研究中，我们测试了以下假设：与低氧浓度相比，高氧浓度下的通透性纤维线粒体(i)在最大状态3呼吸速率（Vmax）下没有差异，（ii）在次最大O2浓度下具有较低的次最大呼吸速率，以及（iii）具有更大的过氧化氢（H2O2）总累积量。我们在渗透骨骼肌纤维中使用高分辨率呼吸仪连续监测线粒体状态3呼吸和H2O2出现率(12名未经训练的参与者；22±4年)，对照组(~127 mmHg；CON)或高(~327 mmHg；高)分压O2 （PO2）。不同条件下Vmax无差异（HIGH: 80.7±16.7 vs CON: 82.3±18.7 pmol/s/mg, p = 0.695）。80% Vmax时的PO2 （P80）在HIGH组更高(73.9±25.5比28.0±7.1 mmHg, p <；0.001)， 5-60 mmHg PO2下HIGH组的呼吸速率低于CON组(p <；0.001)。此外，HIGH组H2O2总累积量大于CON组(n = 11；51.5±23.2 vs 18.3±10.3 pmol/mg, p <；0.001)，这一差异与P80的差异直接相关（r = 0.655, p = 0.029）。目前的研究结果支持，高浓度的O2本身似乎并不影响渗透性骨骼肌纤维制备中的Vmax，但H2O2暴露的必然增加可能会降低线粒体状态3呼吸功能。
{"title":"Chamber oxygen concentration impacts mitochondrial function and hydrogen peroxide appearance in permeabilized human skeletal muscle fibers","authors":"Bradley A. Ruple , Soung Hun Park , Jesse C. Craig , Matthew T. Lewis , Joel D. Trinity , Russell S. Richardson , Ryan M. Broxterman","doi":"10.1016/j.bbabio.2025.149568","DOIUrl":"10.1016/j.bbabio.2025.149568","url":null,"abstract":"<div><div>Skeletal muscle mitochondrial respiration is commonly assessed ex vivo using permeabilized fibers in media with high oxygen (O<sub>2</sub>) concentrations to ensure that O<sub>2</sub> availability does not limit respiration. However, high O<sub>2</sub> concentrations also increase the production of reactive O<sub>2</sub> species that can negatively affect respiration. In this study, we tested the hypotheses that permeabilized fiber mitochondria in a high, compared to low, O<sub>2</sub> concentration would (i) not be different at maximal state 3 respiration rate (V<sub>max</sub>), (ii) have lower submaximal respiration rates at submaximal O<sub>2</sub> concentrations, and (iii) have greater total cumulative hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>) appearance. We continuously monitored mitochondrial state 3 respiration and H<sub>2</sub>O<sub>2</sub> appearance rates using high-resolution respirometry in permeabilized skeletal muscle fibers (12 untrained participants; 22 ± 4 yrs) with either control (~127 mmHg; CON) or high (~327 mmHg; HIGH) partial pressures of O<sub>2</sub> (PO<sub>2</sub>). V<sub>max</sub> was not different between conditions (HIGH: 80.7 ± 16.7 vs. CON: 82.3 ± 18.7 pmol/s/mg, <em>p</em> = 0.695). The PO<sub>2</sub> at 80 % V<sub>max</sub> (P<sub>80</sub>) was greater in HIGH (73.9 ± 25.5 vs. 28.0 ± 7.1 mmHg, <em>p</em> < 0.001) and respiration rates at 5–60 mmHg PO<sub>2</sub> were lower for HIGH than CON (all <em>p</em> < 0.001). Additionally, the total cumulative H<sub>2</sub>O<sub>2</sub> appearance was greater in HIGH than CON (<em>n</em> = 11; 51.5 ± 23.2 vs. 18.3 ± 10.3 pmol/mg, <em>p</em> < 0.001), and this difference was directly correlated with the difference in P<sub>80</sub> (<em>r</em> = 0.655, <em>p</em> = 0.029). The current findings support that a high O<sub>2</sub> concentration, by itself, does not appear to affect V<sub>max</sub> in the permeabilized skeletal muscle fiber preparation, but the corollary increase in H<sub>2</sub>O<sub>2</sub> exposure may diminish mitochondrial state 3 respiratory function.</div></div>","PeriodicalId":50731,"journal":{"name":"Biochimica et Biophysica Acta-Bioenergetics","volume":"1866 4","pages":"Article 149568"},"PeriodicalIF":2.7,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144842126","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}
Pub Date : 2025-07-14DOI: 10.1016/j.bbabio.2025.149567
Emil Jakobsen , Jacob M. Bech , Jens V. Andersen , Emil W. Westi , Martin R. Larsen , Niels H. Skotte , José M.A. Moreira , Blanca I. Aldana , Lasse K. Bak
The Warburg effect is the reprogramming of cancer cells towards glycolytic metabolism, likely producing and releasing lactate into the tumor microenvironment. This lactate has been suggested to partly drive tumor growth by signaling through the lactate receptor, GPR81. Thus, reprogramming cancer cells away from glycolytic activity may be beneficial for cancer treatment. Here, we show that deletion of ADCY8 (coding for adenylyl cyclase 8; AC8) employing the CRISPR-Cas9 technology in U87MG glioma cells, changes the proteome of these cells through a system-wide transformation in expression of mitochondrial proteins. These changes shift the metabolic balance towards oxidative phosphorylation, as shown by an increase in oxygen consumption, an elevation in tricarboxylic acid cycle flux, and a concomitant decrease in glycolytic flux. This metabolic shift is likely driven by the absence of AC8-mediated transcriptional regulation and may suggest that inhibition of AC8 activity could hold therapeutic potential in the treatment of cancer.
{"title":"Deletion of AC8 in glioma cells elevates oxidative phosphorylation by system-wide remodeling of the mitochondrial proteome","authors":"Emil Jakobsen , Jacob M. Bech , Jens V. Andersen , Emil W. Westi , Martin R. Larsen , Niels H. Skotte , José M.A. Moreira , Blanca I. Aldana , Lasse K. Bak","doi":"10.1016/j.bbabio.2025.149567","DOIUrl":"10.1016/j.bbabio.2025.149567","url":null,"abstract":"<div><div>The Warburg effect is the reprogramming of cancer cells towards glycolytic metabolism, likely producing and releasing lactate into the tumor microenvironment. This lactate has been suggested to partly drive tumor growth by signaling through the lactate receptor, GPR81. Thus, reprogramming cancer cells away from glycolytic activity may be beneficial for cancer treatment. Here, we show that deletion of <em>ADCY8</em> (coding for adenylyl cyclase 8; AC8) employing the CRISPR-Cas9 technology in U87MG glioma cells, changes the proteome of these cells through a system-wide transformation in expression of mitochondrial proteins. These changes shift the metabolic balance towards oxidative phosphorylation, as shown by an increase in oxygen consumption, an elevation in tricarboxylic acid cycle flux, and a concomitant decrease in glycolytic flux. This metabolic shift is likely driven by the absence of AC8-mediated transcriptional regulation and may suggest that inhibition of AC8 activity could hold therapeutic potential in the treatment of cancer.</div></div>","PeriodicalId":50731,"journal":{"name":"Biochimica et Biophysica Acta-Bioenergetics","volume":"1866 4","pages":"Article 149567"},"PeriodicalIF":3.4,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144651137","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}
Acetogenins isolated from the Annonaceae plant family are potent inhibitors of mitochondrial NADH-ubiquinone (UQ) oxidoreductase (complex I). Since acetogenins have a markedly different chemical framework from other complex I inhibitors, studying their inhibitory action offers valuable insights into the mechanism of complex I inhibition. A cryo-EM structure of mouse complex I with a bound ~35 Å-long acetogenin derivative suggested that acetogenins bind along the full length of the predicted UQ-accessing tunnel, with their γ-lactone ring orientating toward the iron‑sulfur cluster N2. However, this binding mode does not fully explain the structure–activity relationships of various acetogenin derivatives. To further elucidate their inhibition mechanism, we conducted photoaffinity labeling experiments in bovine heart SMPs using a photoreactive acetogenin derivative DLA-1, containing a small photolabile diazirine near the γ-lactone ring. DLA-1 labeled both the complex I subunits 49-kDa and ND1, which define the architecture of “top” and “bottom” regions of the canonical UQ-accessing tunnel, respectively. Proteomic analysis revealed that the labeled sites in ND1 are not within the tunnel's interior, whereas in the case of 49-kDa subunit, part of the tunnel's inner region is labeled. To investigate the molecular basis of acetogenin binding, we performed atomistic molecular dynamics simulations of DLA-1 and a natural-type acetogenin analog in the UQ-accessing tunnel. The simulation data indicate that DLA-1 is relatively rigid yet adopts multiple conformations and interacts with several regions in the tunnel including the residues identified by photoaffinity labeling. Based on these results, we discuss the binding modes of acetogenin analogs to complex I.
{"title":"Dynamic binding of acetogenin-type inhibitors to mitochondrial complex I revealed by photoaffinity labeling","authors":"Misaki Nishida , Cristina Pecorilla , Takahiro Masuya , Keitaro Hirano , Masato Abe , Oleksii Zdorevskyi , Vivek Sharma , Hideto Miyoshi , Masatoshi Murai","doi":"10.1016/j.bbabio.2025.149566","DOIUrl":"10.1016/j.bbabio.2025.149566","url":null,"abstract":"<div><div>Acetogenins isolated from the <em>Annonaceae</em> plant family are potent inhibitors of mitochondrial NADH-ubiquinone (UQ) oxidoreductase (complex I). Since acetogenins have a markedly different chemical framework from other complex I inhibitors, studying their inhibitory action offers valuable insights into the mechanism of complex I inhibition. A cryo-EM structure of mouse complex I with a bound ~35 Å-long acetogenin derivative suggested that acetogenins bind along the full length of the predicted UQ-accessing tunnel, with their γ-lactone ring orientating toward the iron‑sulfur cluster N2. However, this binding mode does not fully explain the structure–activity relationships of various acetogenin derivatives. To further elucidate their inhibition mechanism, we conducted photoaffinity labeling experiments in bovine heart SMPs using a photoreactive acetogenin derivative DLA-1, containing a small photolabile diazirine near the γ-lactone ring. DLA-1 labeled both the complex I subunits 49-kDa and ND1, which define the architecture of “top” and “bottom” regions of the canonical UQ-accessing tunnel, respectively. Proteomic analysis revealed that the labeled sites in ND1 are not within the tunnel's interior, whereas in the case of 49-kDa subunit, part of the tunnel's inner region is labeled. To investigate the molecular basis of acetogenin binding, we performed atomistic molecular dynamics simulations of DLA-1 and a natural-type acetogenin analog in the UQ-accessing tunnel. The simulation data indicate that DLA-1 is relatively rigid yet adopts multiple conformations and interacts with several regions in the tunnel including the residues identified by photoaffinity labeling. Based on these results, we discuss the binding modes of acetogenin analogs to complex I.</div></div>","PeriodicalId":50731,"journal":{"name":"Biochimica et Biophysica Acta-Bioenergetics","volume":"1866 4","pages":"Article 149566"},"PeriodicalIF":3.4,"publicationDate":"2025-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144545921","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}
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