Pub Date : 2025-06-17DOI: 10.1016/j.bbabio.2025.149563
Cristina Pecorilla , Anton Altmeyer , Outi Haapanen , Yongchan Lee , Volker Zickermann , Vivek Sharma
Multisubunit Mrp (multiple resistance and pH adaptation) type sodium proton antiporters are indispensable for the growth of alkali and salt tolerant bacteria and archaea. They share sequence and structural similarity with the membrane domain of respiratory complex I, a key mitochondrial enzyme. The molecular mechanism of complex I and Mrp antiporters has remained largely unknown and is the subject of intense debate. Here, by combining site-directed mutagenesis with large-scale molecular dynamics simulations, we explore the conformational dynamics of a key histidine residue in the MrpA subunit of the antiporter. We show that point mutations perturbing the conformational mobility of the histidine sidechain directly affect the transport activity of the antiporter. We identify that protonation state variations in conserved lysine residues around the histidine drive hydrogen bonding rearrangements and hydration changes coupled to sidechain and backbone conformational dynamics. Finally, we develop detailed and testable mechanistic models of proton transfer in Mrp antiporter and complex I, in which the histidine switch functions as a unique gating element.
多亚基Mrp （multiple resistance and pH adaptation）型钠质子反转运蛋白是耐碱耐盐细菌和古细菌生长所必需的。它们与呼吸复合体I（一种关键的线粒体酶）的膜结构域具有序列和结构相似性。复合体I和Mrp反转运蛋白的分子机制在很大程度上仍然是未知的，是激烈争论的主题。在这里，通过结合位点定向突变和大规模分子动力学模拟，我们探索了反转运蛋白MrpA亚基中一个关键组氨酸残基的构象动力学。我们发现扰乱组氨酸侧链构象迁移的点突变直接影响反转运蛋白的转运活性。我们发现，组氨酸周围保守赖氨酸残基的质子化状态变化驱动氢键重排和水合作用变化，以及侧链和主链构象动力学。最后，我们建立了Mrp反转运体和复合体I中质子转移的详细和可测试的机制模型，其中组氨酸开关作为独特的门控元件起作用。
{"title":"Conformational dynamics of a histidine molecular switch in a cation/proton antiporter","authors":"Cristina Pecorilla , Anton Altmeyer , Outi Haapanen , Yongchan Lee , Volker Zickermann , Vivek Sharma","doi":"10.1016/j.bbabio.2025.149563","DOIUrl":"10.1016/j.bbabio.2025.149563","url":null,"abstract":"<div><div>Multisubunit Mrp (<u>m</u>ultiple <u>r</u>esistance and <u>p</u>H adaptation) type sodium proton antiporters are indispensable for the growth of alkali and salt tolerant bacteria and archaea. They share sequence and structural similarity with the membrane domain of respiratory complex I, a key mitochondrial enzyme. The molecular mechanism of complex I and Mrp antiporters has remained largely unknown and is the subject of intense debate. Here, by combining site-directed mutagenesis with large-scale molecular dynamics simulations, we explore the conformational dynamics of a key histidine residue in the MrpA subunit of the antiporter. We show that point mutations perturbing the conformational mobility of the histidine sidechain directly affect the transport activity of the antiporter. We identify that protonation state variations in conserved lysine residues around the histidine drive hydrogen bonding rearrangements and hydration changes coupled to sidechain and backbone conformational dynamics. Finally, we develop detailed and testable mechanistic models of proton transfer in Mrp antiporter and complex I, in which the histidine switch functions as a unique gating element.</div></div>","PeriodicalId":50731,"journal":{"name":"Biochimica et Biophysica Acta-Bioenergetics","volume":"1866 4","pages":"Article 149563"},"PeriodicalIF":3.4,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144481769","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 : 2025-06-12DOI: 10.1016/j.bbabio.2025.149561
Pardis Taheri , Devanshi D. Dave , Abraham Taye , Anne V. Clough , Elizabeth R. Jacobs , Ranjan K. Dash , Said H. Audi
Adult rats exposed to hyperoxia (>95 % O2) die within 60–72 h from respiratory failure. However, when preconditioned with either >95 % O2 for 48 h followed by 24 h in room air (H-T) or 60 % O2 for 7 days (H-S), they acquire tolerance or susceptibility to hyperoxia, respectively. The aim was to quantify H2O2 production rate and identify sources in isolated lung mitochondria and isolated perfused lungs (IPLs) of normoxia, H-T, and H-S rats. Mitochondria were isolated from lungs, and H2O2 production rates were quantified in the presence of pyruvate-malate or succinate, with and without inhibitors of mitochondrial complex I (CI), complex II (CII), and/or H2O2 scavenging systems. Lung rate of H2O2 release was quantified in IPLs with and without CII inhibitor. Results from isolated mitochondria show that CII is the main H2O2 source, and that both H2O2 production rate and scavenging capacity were ~48 % lower in H-S mitochondria compared to normoxia. Results from IPLs show that CII is also the dominant H2O2 source from lung tissue, and that H2O2 release rate was lower in H-T lungs compared to normoxia and H-S lungs. These results suggest that for H-S rats, both mitochondrial rate of H2O2 production and scavenging capacity were significantly lower than those in normoxia mitochondria and may contribute to their increased hyperoxia susceptibility. The lower H2O2 release rate from H-T IPLs, along with no change in mitochondrial H2O2 production rate, is consistent with higher antioxidant capacity in the lungs of H-T rats, which may contribute to their hyperoxia tolerance.
{"title":"Mitochondrial reactive oxygen species production in lungs of rats with different susceptibilities to hyperoxia-induced acute lung injury","authors":"Pardis Taheri , Devanshi D. Dave , Abraham Taye , Anne V. Clough , Elizabeth R. Jacobs , Ranjan K. Dash , Said H. Audi","doi":"10.1016/j.bbabio.2025.149561","DOIUrl":"10.1016/j.bbabio.2025.149561","url":null,"abstract":"<div><div>Adult rats exposed to hyperoxia (>95 % O<sub>2</sub>) die within 60–72 h from respiratory failure. However, when preconditioned with either >95 % O<sub>2</sub> for 48 h followed by 24 h in room air (H-T) or 60 % O<sub>2</sub> for 7 days (H-S), they acquire tolerance or susceptibility to hyperoxia, respectively. The aim was to quantify H<sub>2</sub>O<sub>2</sub> production rate and identify sources in isolated lung mitochondria and isolated perfused lungs (IPLs) of normoxia, H-T, and H-S rats. Mitochondria were isolated from lungs, and H<sub>2</sub>O<sub>2</sub> production rates were quantified in the presence of pyruvate-malate or succinate, with and without inhibitors of mitochondrial complex I (CI), complex II (CII), and/or H<sub>2</sub>O<sub>2</sub> scavenging systems. Lung rate of H<sub>2</sub>O<sub>2</sub> release was quantified in IPLs with and without CII inhibitor. Results from isolated mitochondria show that CII is the main H<sub>2</sub>O<sub>2</sub> source, and that both H<sub>2</sub>O<sub>2</sub> production rate and scavenging capacity were ~48 % lower in H-S mitochondria compared to normoxia. Results from IPLs show that CII is also the dominant H<sub>2</sub>O<sub>2</sub> source from lung tissue, and that H<sub>2</sub>O<sub>2</sub> release rate was lower in H-T lungs compared to normoxia and H-S lungs. These results suggest that for H-S rats, both mitochondrial rate of H<sub>2</sub>O<sub>2</sub> production and scavenging capacity were significantly lower than those in normoxia mitochondria and may contribute to their increased hyperoxia susceptibility. The lower H<sub>2</sub>O<sub>2</sub> release rate from H-T IPLs, along with no change in mitochondrial H<sub>2</sub>O<sub>2</sub> production rate, is consistent with higher antioxidant capacity in the lungs of H-T rats, which may contribute to their hyperoxia tolerance.</div></div>","PeriodicalId":50731,"journal":{"name":"Biochimica et Biophysica Acta-Bioenergetics","volume":"1866 4","pages":"Article 149561"},"PeriodicalIF":3.4,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144295269","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 : 2025-05-27DOI: 10.1016/j.bbabio.2025.149560
Shu En Lee , Willem van de Poll , Volha Chukhutsina
The polar oceanic environment poses extreme challenges to photosynthetic organisms, which have evolved atypical strategies to maintain efficient photosynthesis in cold temperatures. Here, the psychrophilic diatom Chaetoceros simplex (C. simplex) is studied in vivo in the dark-adapted state using steady-state and time-resolved fluorescence methods. Our results show that all fucoxanthin chlorophyll a/c protein (FCP) antenna transfer energy to photosystem I (PSI) or photosystem II (PSII), with no detached FCPs. PSI exhibits no fluorescence of ‘red’ forms of chlorophyll (chl) beyond 700 nm in both 279 K and 77 K conditions. Despite this, it apparently has a long decay time of ~85 ps indicating the presence of a large core-antenna supercomplex. PSII has an average lifetime of ~500 ps in open state (QA oxidized) and ~1220 ps in closed state (QA reduced). PSII of C. simplex has kinetics that are slightly slower than temperate diatoms, suggesting larger antenna. In addition, fucoxanthin (fx) molecules of FCP that absorb in the 500–550 nm range (fx-red) transfer more energy to PSII than fx that absorb in the blue range (fx-blue, 462 nm max absorption). A subpopulation of red-shifted, aggregated FCPs are detected at 77 K, that are active in energy transfer uphill at 279 K. Overall, our results indicate relatively larger antenna of PSI and PSII and an absence of red chls in PSI of cold-adapted species, compared to temperate species.
{"title":"Antarctic photosynthesis: energy transfer and charge separation in the diatom Chaetoceros simplex","authors":"Shu En Lee , Willem van de Poll , Volha Chukhutsina","doi":"10.1016/j.bbabio.2025.149560","DOIUrl":"10.1016/j.bbabio.2025.149560","url":null,"abstract":"<div><div>The polar oceanic environment poses extreme challenges to photosynthetic organisms, which have evolved atypical strategies to maintain efficient photosynthesis in cold temperatures. Here, the psychrophilic diatom <em>Chaetoceros simplex</em> (<em>C. simplex</em>) is studied <em>in vivo</em> in the dark-adapted state using steady-state and time-resolved fluorescence methods. Our results show that all fucoxanthin chlorophyll <em>a</em>/c protein (FCP) antenna transfer energy to photosystem I (PSI) or photosystem II (PSII), with no detached FCPs. PSI exhibits no fluorescence of ‘red’ forms of chlorophyll (chl) beyond 700 nm in both 279 K and 77 K conditions. Despite this, it apparently has a long decay time of ~85 ps indicating the presence of a large core-antenna supercomplex. PSII has an average lifetime of ~500 ps in open state (Q<sub>A</sub> oxidized) and ~1220 ps in closed state (Q<sub>A</sub> reduced). PSII of <em>C. simplex</em> has kinetics that are slightly slower than temperate diatoms, suggesting larger antenna. In addition, fucoxanthin (fx) molecules of FCP that absorb in the 500–550 nm range (fx-red) transfer more energy to PSII than fx that absorb in the blue range (fx-blue, 462 nm max absorption). A subpopulation of red-shifted, aggregated FCPs are detected at 77 K, that are active in energy transfer uphill at 279 K. Overall, our results indicate relatively larger antenna of PSI and PSII and an absence of red chls in PSI of cold-adapted species, compared to temperate species.</div></div>","PeriodicalId":50731,"journal":{"name":"Biochimica et Biophysica Acta-Bioenergetics","volume":"1866 3","pages":"Article 149560"},"PeriodicalIF":3.4,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144183016","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 : 2025-05-26DOI: 10.1016/j.bbabio.2025.149559
Anna.B. Nikiforova, Maxim.V. Molchanov, Alexey G. Kruglov
Inorganic phosphate (Pi) is essential for Ca2+ buffering by mitochondria. Adenine nucleotides (AN) are known to strongly increase the Ca2+-retention capacity (CRC) of mitochondria even in the absence of Pi in the medium. Several mechanisms can explain this phenomenon. Here we examined these mechanisms in detail in isolated rat liver mitochondria. We found that, in Pi-free medium, AN dose-dependently increased the CRC. The FOF1-ATP synthase (F-ATPase) inhibitor oligomycin decreased the CRC and the Ca2+ uptake rate to a minor extent. Nuclear magnetic resonance (NMR) analysis showed that Pi in suspensions of oligomycin-treated mitochondria was formed due to AN hydrolysis. In the absence and presence of Ca2+, mitochondria accumulated small and large (50 and > 1000 nmol/mg protein) amounts of Pi, respectively, without detectable accumulation of AN. The average ratio of Ca2+ to Pi accumulated by intact mitochondria in the presence of ADP, ATP, and ATP plus Pi was about 0.68, 1, and 1.25, respectively, or lower. These values correspond to the formation of calcium dihydrogen and hydrogen orthophosphates, and tricalcium phosphate/whitlockite in different proportions. AN increased the CRC in the presence of inhibitors of both F-ATPase and adenylate translocase, the known regulators of the permeability transition pore (PTP). The PTP inhibitor NADH did not increase the CRC in the absence of Pi. Thus, the mechanism of the AN-dependent increase in the CRC in the absence of Pi includes the F-ATPase-independent production of Pi and suppression of the PTP at the site other than F-ATPase and adenylate translocase.
{"title":"Adenine nucleotide-dependent Ca2+ buffering by mitochondria in an inorganic phosphate-free medium","authors":"Anna.B. Nikiforova, Maxim.V. Molchanov, Alexey G. Kruglov","doi":"10.1016/j.bbabio.2025.149559","DOIUrl":"10.1016/j.bbabio.2025.149559","url":null,"abstract":"<div><div>Inorganic phosphate (P<sub>i</sub>) is essential for Ca<sup>2+</sup> buffering by mitochondria. Adenine nucleotides (AN) are known to strongly increase the Ca<sup>2+</sup>-retention capacity (CRC) of mitochondria even in the absence of P<sub>i</sub> in the medium. Several mechanisms can explain this phenomenon. Here we examined these mechanisms in detail in isolated rat liver mitochondria. We found that, in P<sub>i</sub>-free medium, AN dose-dependently increased the CRC. The F<sub>O</sub>F<sub>1</sub>-ATP synthase (F-ATPase) inhibitor oligomycin decreased the CRC and the Ca<sup>2+</sup> uptake rate to a minor extent. Nuclear magnetic resonance (NMR) analysis showed that P<sub>i</sub> in suspensions of oligomycin-treated mitochondria was formed due to AN hydrolysis. In the absence and presence of Ca<sup>2+</sup>, mitochondria accumulated small and large (50 and > 1000 nmol/mg protein) amounts of Pi, respectively, without detectable accumulation of AN. The average ratio of Ca<sup>2+</sup> to P<sub>i</sub> accumulated by intact mitochondria in the presence of ADP, ATP, and ATP plus P<sub>i</sub> was about 0.68, 1, and 1.25, respectively, or lower. These values correspond to the formation of calcium dihydrogen and hydrogen orthophosphates, and tricalcium phosphate/whitlockite in different proportions. AN increased the CRC in the presence of inhibitors of both F-ATPase and adenylate translocase, the known regulators of the permeability transition pore (PTP). The PTP inhibitor NADH did not increase the CRC in the absence of P<sub>i</sub>. Thus, the mechanism of the AN-dependent increase in the CRC in the absence of P<sub>i</sub> includes the F-ATPase-independent production of P<sub>i</sub> and suppression of the PTP at the site other than F-ATPase and adenylate translocase.</div></div>","PeriodicalId":50731,"journal":{"name":"Biochimica et Biophysica Acta-Bioenergetics","volume":"1866 3","pages":"Article 149559"},"PeriodicalIF":3.4,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144146874","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 : 2025-05-26DOI: 10.1016/j.bbabio.2025.149558
Alain Boussac , Julien Sellés , Tania Tibiletti , Miwa Sugiura , Robert L. Burnap
{"title":"Corrigendum to “New insights into the involvement of residue D1/V185 in Photosystem II function in Synechocystis 6803 and Thermosynechococcus vestitus” [Biochim. Biophys. Acta Bioenerg. 1866 (2025) 149550]","authors":"Alain Boussac , Julien Sellés , Tania Tibiletti , Miwa Sugiura , Robert L. Burnap","doi":"10.1016/j.bbabio.2025.149558","DOIUrl":"10.1016/j.bbabio.2025.149558","url":null,"abstract":"","PeriodicalId":50731,"journal":{"name":"Biochimica et Biophysica Acta-Bioenergetics","volume":"1866 3","pages":"Article 149558"},"PeriodicalIF":3.4,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144163501","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}
The role of the D1/S264 residue and the role of its environment in the proton-coupled electron transfer reaction on the acceptor side of Photosystem II were investigated. To this end, D1/S264V mutants were constructed in the thermophilic cyanobacterium Thermosynechococcus elongatus, with D1 being either PsbA1 or PsbA3. The PSII mutants were investigated using EPR spectroscopy, thermoluminescence, (time-resolved) absorption changes measurements, and oximetry. While the mutation had minor effects in PsbA1-PSII, the S264V mutation in PsbA3-PSII had significant consequences: i) thermoluminescence data show inefficient electron transfer from QA− to QB; ii) re-oxidation of QA− was slowed, by at least a factor of 10; iii) the herbicides inhibit weakly O2 evolution; iv) no Fe2+QB− EPR signal was detected in dark-adapted PSII; instead, v) a large Fe3+ signal was present with vi) modified EPR properties; vii) no QA−Fe2+QB− biradical signal was observed after illumination at 198 K following a flash illumination, confirming the inefficient formation of QB−; viii) either no proton uptake coupled to non-heme iron reduction occurred or with a very slow rate compared to PsbA3-PSII; ix) changes were noted in the electrochromic response associated with QA− formation; and x) increased production of singlet oxygen, both with and without herbicides. The S264V mutation in PsbA3-PSII leads to a significant decrease in the energy gap between the QA−QB and QAQB− states. The effects listed above are discussed regarding the differences between PsbA1-PSII and PsbA3-PSII as those related to the sulfoquinovosyldiacylglycerol, the water molecules and the H-bond network.
{"title":"Differential effects of the D1/S264V mutation in photosystem II with either PsbA1 or PsbA3 on QB, non-heme Iron, and the associated hydrogen-bond network","authors":"Kosuke Tada , Kaho Yamagata , Kazumi Koyama , Julien Sellés , Alain Boussac , Miwa Sugiura","doi":"10.1016/j.bbabio.2025.149557","DOIUrl":"10.1016/j.bbabio.2025.149557","url":null,"abstract":"<div><div>The role of the D1/S264 residue and the role of its environment in the proton-coupled electron transfer reaction on the acceptor side of Photosystem II were investigated. To this end, D1/S264V mutants were constructed in the thermophilic cyanobacterium <em>Thermosynechococcus elongatus</em>, with D1 being either PsbA1 or PsbA3. The PSII mutants were investigated using EPR spectroscopy, thermoluminescence, (time-resolved) absorption changes measurements, and oximetry. While the mutation had minor effects in PsbA1-PSII, the S264V mutation in PsbA3-PSII had significant consequences: <em>i</em>) thermoluminescence data show inefficient electron transfer from Q<sub>A</sub><sup>−</sup> to Q<sub>B</sub>; <em>ii</em>) re-oxidation of Q<sub>A</sub><sup>−</sup> was slowed, by at least a factor of 10; <em>iii</em>) the herbicides inhibit weakly O<sub>2</sub> evolution; <em>iv</em>) no Fe<sup>2+</sup>Q<sub>B</sub><sup>−</sup> EPR signal was detected in dark-adapted PSII; instead, <em>v</em>) a large Fe<sup>3+</sup> signal was present with <em>vi</em>) modified EPR properties; <em>vii</em>) no Q<sub>A</sub><sup>−</sup>Fe<sup>2+</sup>Q<sub>B</sub><sup>−</sup> biradical signal was observed after illumination at 198 K following a flash illumination, confirming the inefficient formation of Q<sub>B</sub><sup>−</sup>; <em>viii</em>) either no proton uptake coupled to non-heme iron reduction occurred or with a very slow rate compared to PsbA3-PSII; <em>ix</em>) changes were noted in the electrochromic response associated with Q<sub>A</sub><sup>−</sup> formation; and <em>x</em>) increased production of singlet oxygen, both with and without herbicides. The S264V mutation in PsbA3-PSII leads to a significant decrease in the energy gap between the Q<sub>A</sub><sup>−</sup>Q<sub>B</sub> and Q<sub>A</sub>Q<sub>B</sub><sup>−</sup> states. The effects listed above are discussed regarding the differences between PsbA1-PSII and PsbA3-PSII as those related to the sulfoquinovosyldiacylglycerol, the water molecules and the H-bond network.</div></div>","PeriodicalId":50731,"journal":{"name":"Biochimica et Biophysica Acta-Bioenergetics","volume":"1866 3","pages":"Article 149557"},"PeriodicalIF":3.4,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144116512","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}
Xenorhodopsin (XeR) is the first identified light-driven inward proton pump, exhibiting proton translocation vectoriality opposite to that of bacteriorhodopsin (BR)—a well-characterized outward proton pump rhodopsin. The molecular mechanism governing this vectoriality remains a fundamental question. A distinguishing feature of XeRs is the substitution of the second counterion (Asp212 in BR) with a proline residue located near the protonated retinal Schiff base (PRSB). The absence of a negatively charged residue in XeRs may hinder proton transfer from the Schiff base to the primary counterion (Asp85 in BR), a key determinant of vectoriality. Several studies have reported that XeR from Nanosalina (NsXeR) exhibits higher inward proton-pumping activity than other XeRs, although the underlying molecular mechanism remains unclear. In this study, we analyzed the early photointermediate (K) of NsXeR using light-induced difference Fourier transform infrared spectroscopy, revealing two characteristic features. First, the distinct hydrogen out-of-plane (HOOP) vibrations—indicative of retinal distortion—were absent, suggesting a minimally distorted retinal chromophore post-photoisomerization in NsXeR. Second, the PRSB exhibited a weaker hydrogen bond in the dark state. Interestingly, substituting Pro209 at the second counterion position with alanine or glycine (P209A and P209G) restored HOOP band intensity and strengthened the PRSB hydrogen bond. Importantly, the P209A and P209G mutants demonstrated reduced inward proton-pumping activity and slower recovery in the final thermal isomerization process compared to the wild type. These findings suggest that photoisomerization without retinal distortion enhances inward proton transport in NsXeR.
{"title":"The role of retinal chromophore photoisomerization in enhanced inward proton-pumping activity of xenorhodopsin from Nanosalina","authors":"Yuma Ito , Tatsuro Nishikino , Hideki Kandori , Yuji Furutani","doi":"10.1016/j.bbabio.2025.149556","DOIUrl":"10.1016/j.bbabio.2025.149556","url":null,"abstract":"<div><div>Xenorhodopsin (XeR) is the first identified light-driven inward proton pump, exhibiting proton translocation vectoriality opposite to that of bacteriorhodopsin (BR)—a well-characterized outward proton pump rhodopsin. The molecular mechanism governing this vectoriality remains a fundamental question. A distinguishing feature of XeRs is the substitution of the second counterion (Asp212 in BR) with a proline residue located near the protonated retinal Schiff base (PRSB). The absence of a negatively charged residue in XeRs may hinder proton transfer from the Schiff base to the primary counterion (Asp85 in BR), a key determinant of vectoriality. Several studies have reported that XeR from <em>Nanosalina</em> (<em>Ns</em>XeR) exhibits higher inward proton-pumping activity than other XeRs, although the underlying molecular mechanism remains unclear. In this study, we analyzed the early photointermediate (K) of <em>Ns</em>XeR using light-induced difference Fourier transform infrared spectroscopy, revealing two characteristic features. First, the distinct hydrogen out-of-plane (HOOP) vibrations—indicative of retinal distortion—were absent, suggesting a minimally distorted retinal chromophore post-photoisomerization in <em>Ns</em>XeR. Second, the PRSB exhibited a weaker hydrogen bond in the dark state. Interestingly, substituting Pro209 at the second counterion position with alanine or glycine (P209A and P209G) restored HOOP band intensity and strengthened the PRSB hydrogen bond. Importantly, the P209A and P209G mutants demonstrated reduced inward proton-pumping activity and slower recovery in the final thermal isomerization process compared to the wild type. These findings suggest that photoisomerization without retinal distortion enhances inward proton transport in <em>Ns</em>XeR.</div></div>","PeriodicalId":50731,"journal":{"name":"Biochimica et Biophysica Acta-Bioenergetics","volume":"1866 3","pages":"Article 149556"},"PeriodicalIF":3.4,"publicationDate":"2025-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143916252","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 : 2025-04-01DOI: 10.1016/j.bbabio.2025.149555
Valentin Guyard, Francesca Giordano
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.
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.
{"title":"Three's company: Membrane waltz among organelles","authors":"Valentin Guyard, 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}
Pub Date : 2025-03-13DOI: 10.1016/j.bbabio.2025.149552
Jarne Berentsen, Peter R. Bos, Emilie Wientjes
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 Arabidopsis thaliana. 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 curt1a 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.
{"title":"Expansion microscopy reveals thylakoid organisation alterations due to genetic mutations and far-red light acclimation","authors":"Jarne Berentsen, Peter R. Bos, 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}
Pub Date : 2025-03-09DOI: 10.1016/j.bbabio.2025.149553
Sandra Monica Bach de Courtade , Marte Eikenes , Ying Sheng , Tuula A. Nyman , Yngve Thomas Bliksrud , Katja Scheffler , Lars Eide
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.
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.
{"title":"Identification of determinants for variability in mitochondrial biochemical complex activities","authors":"Sandra Monica Bach de Courtade , Marte Eikenes , Ying Sheng , Tuula A. Nyman , Yngve Thomas Bliksrud , Katja Scheffler , 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}
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