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Two independent structures of the proton-pumping, respiratory cytochrome bo₃ ubiquinol oxidase (cyt bo₃) have been determined by cryogenic electron microscopy (cryo-EM) in styrene–maleic acid (SMA) copolymer nanodiscs and in membrane scaffold protein (MSP) nanodiscs to 2.55- and 2.19-Å resolution, respectively. The structures include the metal redox centers (heme b, heme o₃, and CuB), the redox-active cross-linked histidine–tyrosine cofactor, and the internal water molecules in the proton-conducting D channel. Each structure also contains one equivalent of ubiquinone-8 (UQ8) in the substrate binding site as well as several phospholipid molecules. The isoprene side chain of UQ8 is clamped within a hydrophobic groove in subunit I by transmembrane helix TM0, which is only present in quinol oxidases and not in the closely related cytochrome c oxidases. Both structures show carbonyl O1 of the UQ8 headgroup hydrogen bonded to D75I and R71I. In both structures, residue H98I occupies two conformations. In conformation 1, H98I forms a hydrogen bond with carbonyl O4 of the UQ8 headgroup, but in conformation 2, the imidazole side chain of H98I has flipped to form a hydrogen bond with E14I at the N-terminal end of TM0. We propose that H98I dynamics facilitate proton transfer from ubiquinol to the periplasmic aqueous phase during oxidation of the substrate. Computational studies show that TM0 creates a channel, allowing access of water to the ubiquinol headgroup and to H98I.

Cytochrome bo₃ ubiquinol oxidase is a transmembrane protein, which oxidizes ubiquinone and reduces oxygen, while pumping protons. Apart from its combination with F₁Fₒ-ATPase to assemble a minimal ATP regeneration module, the utility of the proton pump can be extended to other applications in the context of synthetic cells such as transport, signaling, and control of enzymatic reactions. In parallel, polymers have been speculated to be phospholipid mimics with respect to their ability to self-assemble in compartments with increased stability. However, their usability as interfaces for complex membrane proteins has remained questionable. In the present work, we optimized a fusion/electroformation approach to reconstitute bo₃ oxidase in giant unilamellar vesicles made of PDMS-g-PEO and/or phosphatidylcholine (PC). This enabled optical access, while microfluidic trapping allowed for online analysis of individual vesicles. The tight polymer membranes and the inward oriented enzyme caused 1 pH unit difference in 30 min, with an initial rate of 0.35 pH·min−1. To understand the interplay in these composite systems, we studied the relevant mechanical and rheological membrane properties. Remarkably, the proton permeability of polymer/lipid hybrids decreased after protein insertion, while the latter also led to a 20% increase of the polymer diffusion coefficient in polymersomes. In addition, PDMS-g-PEO increased the activity lifetime and the resistance to free radicals. These advantageous properties may open diverse applications, ranging from cell-free biotechnology to biomedicine. Furthermore, the presented study serves as a comprehensive road map for studying the interactions between membrane proteins and synthetic membranes, which will be fundamental for the successful engineering of such hybrid systems.

Ferroptosis, a form of regulated cell death that is induced by excessive lipid peroxidation, is a key tumour suppression mechanism 1 – 4 . Glutathione peroxidase 4 (GPX4) 5 , 6 and ferroptosis suppressor protein 1 (FSP1) 7 , 8 constitute two major ferroptosis defence systems. Here we show that treatment of cancer cells with GPX4 inhibitors results in acute depletion of N -carbamoyl- l -aspartate, a pyrimidine biosynthesis intermediate, with concomitant accumulation of uridine. Supplementation with dihydroorotate or orotate—the substrate and product of dihydroorotate dehydrogenase (DHODH)—attenuates or potentiates ferroptosis induced by inhibition of GPX4, respectively, and these effects are particularly pronounced in cancer cells with low expression of GPX4 (GPX4 low ). Inactivation of DHODH induces extensive mitochondrial lipid peroxidation and ferroptosis in GPX4 low cancer cells, and synergizes with ferroptosis inducers to induce these effects in GPX4 high cancer cells. Mechanistically, DHODH operates in parallel to mitochondrial GPX4 (but independently of cytosolic GPX4 or FSP1) to inhibit ferroptosis in the mitochondrial inner membrane by reducing ubiquinone to ubiquinol (a radical-trapping antioxidant with anti-ferroptosis activity). The DHODH inhibitor brequinar selectively suppresses GPX4 low tumour growth by inducing ferroptosis, whereas combined treatment with brequinar and sulfasalazine, an FDA-approved drug with ferroptosis-inducing activity, synergistically induces ferroptosis and suppresses GPX4 high tumour growth. Our results identify a DHODH-mediated ferroptosis defence mechanism in mitochondria and suggest a therapeutic strategy of targeting ferroptosis in cancer treatment. DHO dehydrogenase regulates ferroptosis by preventing mitochondrial lipid peroxidation and its inhibition suppresses growth in tumours with low levels of GPX4.

We engineered Escherichia coli to grow on CO 2 and formic acid alone by introducing the synthetic CO 2 and formic acid assimilation pathway, expressing two formate dehydrogenase genes, fine-tuning metabolic fluxes and optimizing the levels of cytochrome bo 3 and bd -I ubiquinol oxidase. Our engineered strain can grow to an optical density at 600 nm of 7.38 in 450 h, and shows promise as a platform strain growing on CO 2 and formic acid alone. Growth of Escherichia coli on carbon dioxide and formate is achieved by rational metabolic engineering alone.

Ferroptosis is an iron-dependent form of necrotic cell death marked by oxidative damage to phospholipids 1 , 2 . To date, ferroptosis has been thought to be controlled only by the phospholipid hydroperoxide-reducing enzyme glutathione peroxidase 4 (GPX4) 3 , 4 and radical-trapping antioxidants 5 , 6 . However, elucidation of the factors that underlie the sensitivity of a given cell type to ferroptosis 7 is crucial to understand the pathophysiological role of ferroptosis and how it may be exploited for the treatment of cancer. Although metabolic constraints 8 and phospholipid composition 9 , 10 contribute to ferroptosis sensitivity, no cell-autonomous mechanisms have been identified that account for the resistance of cells to ferroptosis. Here we used an expression cloning approach to identify genes in human cancer cells that are able to complement the loss of GPX4. We found that the flavoprotein apoptosis-inducing factor mitochondria-associated 2 ( AIFM2 ) is a previously unrecognized anti-ferroptotic gene. AIFM2, which we renamed ferroptosis suppressor protein 1 (FSP1) and which was initially described as a pro-apoptotic gene 11 , confers protection against ferroptosis elicited by GPX4 deletion. We further demonstrate that the suppression of ferroptosis by FSP1 is mediated by ubiquinone (also known as coenzyme Q 10 , CoQ 10 ): the reduced form, ubiquinol, traps lipid peroxyl radicals that mediate lipid peroxidation, whereas FSP1 catalyses the regeneration of CoQ 10 using NAD(P)H. Pharmacological targeting of FSP1 strongly synergizes with GPX4 inhibitors to trigger ferroptosis in a number of cancer entities. In conclusion, the FSP1–CoQ 10 –NAD(P)H pathway exists as a stand-alone parallel system, which co-operates with GPX4 and glutathione to suppress phospholipid peroxidation and ferroptosis. In the absence of GPX4, FSP1 regenerates ubiquinol from the oxidized form, ubiquinone, using NAD(P)H and suppresses phospholipid peroxidation and ferroptosis in cells.

Background Rising interest in creatine’s role in sperm energy metabolism highlights its potential to enhance male fertility, with semen biomarkers providing insights into its impact on sperm function and fertility.Methods Fifteen volunteers (mean age 25.0 ± 6.1 years; BMI 25.1 ± 2.0 kg/m2) were randomly assigned to one of three groups: Group 1 received received 5 g of creatine monohydrate plus 200 mg of ubiquinol, Group 2 received 5 g of creatine monohydrate, and the control group received 5 g of inulin daily for 8 weeks. Semen samples were collected after 3–5 days of abstinence and analyzed for creatine and creatine kinase (CK) levels.Results The sperm CK levels showed a non-significant increase in the creatine-ubiquinol group, from 257.5 ± 140.6 IU/L at baseline to 455.2 ± 249.2 IU/L at 8-week follow up (P = 0.07; Cohen’s d = 0.88). Sperm creatine concentration also increased non-significantly, from 455.2 ± 188.9 µmol/L to 570.7 ± 228.1 µmol/L (P = 0.06; Cohen’s d = 0.55). In the creatine-only group, sperm CK decreased from 454.3 ± 106.5 IU/L to 422.9 ± 193.7 IU/L (P = 0.58; Cohen’s d = 0.20), while sperm creatine increased slightly from 499.4 ± 180.7 µmol/L to 564.3 ± 284.4 µmol/L (P = 0.71; Cohen’s d = 0.27). In the control group, both sperm CK and creatine concentrations decreased. CK dropped from 462.1 ± 229.1 IU/L to 419.9 ± 248.5 IU/L (P = 0.76; Cohen’s d = 0.17), and creatine declined from 464.8 ± 205.1 µmol/L to 459.5 ± 236.2 µmol/L (P = 0.90; Cohen’s d = 0.02). Friedman’s two-way ANOVA by ranks indicated a significant interaction effect for both sperm creatine and CK concentrations between the intervention groups (P < 0.05).Conclusion Creatine, both alone and in combination with ubiquinol, led to increases in sperm creatine and CK concentrations, while these biomarkers remained unchanged in the control group. These results highlight the potential metabolic effects of creatine supplementation, warranting further investigation.

Background: The toxic gas carbon monoxide (CO) is abundantly present in synthesis gas (syngas) and certain industrial waste gases that can serve as feedstocks for the biological production of industrially significant chemicals and fuels. For efficient bacterial growth to occur, and to increase productivity and titres, a high resistance to the gas is required. The aerobic bacterium Cupriavidus necator H16 can grow on CO 2 + H 2 , although it cannot utilise CO as a source of carbon and energy. This study aimed to increase its CO resistance through adaptive laboratory evolution. Results: To increase the tolerance of C. necator to CO, the organism was continually subcultured in the presence of CO both heterotrophically and autotrophically. Ten individual cultures were evolved heterotrophically with fructose in this manner and eventually displayed a clear growth advantage over the wild type strain. Next-generation sequencing revealed several mutations, including a single point mutation upstream of a cytochrome bd ubiquinol oxidase operon ( cydA2B2 ), which was present in all evolved isolates. When a subset of these mutations was engineered into the parental H16 strain, only the cydA2B2 upstream mutation enabled faster growth in the presence of CO. Expression analysis, mutation, overexpression and complementation suggested that cydA2B2 transcription is upregulated in the evolved isolates, resulting in increased CO tolerance under heterotrophic but not autotrophic conditions. However, through subculturing on a syngas-like mixture with increasing CO concentrations, C. necator could also be evolved to tolerate high CO concentrations under autotrophic conditions. A mutation in the gene for the soluble [NiFe]-hydrogenase subunit hoxH was identified in the evolved isolates. When the resulting amino acid change was engineered into the parental strain, autotrophic CO resistance was conferred. A strain constitutively expressing cydA2B2 and the mutated hoxH gene exhibited high CO tolerance under both heterotrophic and autotrophic conditions. Conclusion: C. necator was evolved to tolerate high concentrations of CO, a phenomenon which was dependent on the terminal respiratory cytochrome bd ubiquinol oxidase when grown heterotrophically and the soluble [NiFe]-hydrogenase when grown autotrophically. A strain exhibiting high tolerance under both conditions was created and presents a promising chassis for syngas-based bioproduction processes.

Bacterial energy metabolism has become a promising target for next-generation tuberculosis chemotherapy. One strategy to hamper ATP production is to inhibit the respiratory oxidases. The respiratory chain of Mycobacterium tuberculosis comprises a cytochrome bcc:aa 3 and a cytochrome bd ubiquinol oxidase that require a combined approach to block their activity. A quinazoline-type compound called ND-011992 has previously been reported to ineffectively inhibit bd oxidases, but to act bactericidal in combination with inhibitors of cytochrome bcc:aa 3 oxidase. Due to the structural similarity of ND-011992 to quinazoline-type inhibitors of respiratory complex I, we suspected that this compound is also capable of blocking other respiratory chain complexes. Here, we synthesized ND-011992 and a bromine derivative to study their effect on the respiratory chain complexes of Escherichia coli . And indeed, ND-011992 was found to inhibit respiratory complex I and bo 3 oxidase in addition to bd -I and bd -II oxidases. The IC 50 values are all in the low micromolar range, with inhibition of complex I providing the lowest value with an IC 50 of 0.12 µM. Thus, ND-011992 acts on both, quinone reductases and quinol oxidases and could be very well suited to regulate the activity of the entire respiratory chain.

Mitochondria play a pivotal part in ATP energy production through oxidative phosphorylation, which occurs within the inner membrane through a series of respiratory complexes 1 – 4 . Despite extensive in vitro structural studies, determining the atomic details of their molecular mechanisms in physiological states remains a major challenge, primarily because of loss of the native environment during purification. Here we directly image porcine mitochondria using an in situ cryo-electron microscopy approach. This enables us to determine the structures of various high-order assemblies of respiratory supercomplexes in their native states. We identify four main supercomplex organizations: I 1 III 2 IV 1 , I 1 III 2 IV 2 , I 2 III 2 IV 2 and I 2 III 4 IV 2 , which potentially expand into higher-order arrays on the inner membranes. These diverse supercomplexes are largely formed by ‘protein–lipids–protein’ interactions, which in turn have a substantial impact on the local geometry of the surrounding membranes. Our in situ structures also capture numerous reactive intermediates within these respiratory supercomplexes, shedding light on the dynamic processes of the ubiquinone/ubiquinol exchange mechanism in complex I and the Q-cycle in complex III. Structural comparison of supercomplexes from mitochondria treated under different conditions indicates a possible correlation between conformational states of complexes I and III, probably in response to environmental changes. By preserving the native membrane environment, our approach enables structural studies of mitochondrial respiratory supercomplexes in reaction at high resolution across multiple scales, from atomic-level details to the broader subcellular context. Mammalian respiratory supercomplexes are imaged in their native membrane environment by in situ cryo-electron microscopy, providing insight into their reactive intermediates and conformational dynamics.

Membrane proteins are fundamental to many crucial cellular processes but removing them from their native environment for structural and functional studies creates experimental challenges. Numerous strategies have been developed to replicate native-like membrane environments in vitro for membrane protein research, however, most studies have focused on systems for either structural or functional characterisation, not both together. Here, we apply an in-vivo split intein strategy to produce stable circularised nanodiscs for combined structural and functional analysis of respiratory complex I, using its highly hydrophobic native ubiquinone-10 substrate and an auxiliary ubiquinol oxidase from Trypanosoma brucei brucei. We successfully reconstituted Paracoccus denitrificans complex I into circularised nanodiscs, determined its cryo-EM structure at 3.1 Å resolution and conducted biophysical and biochemical analyses to demonstrate how the ‘oversized’ nanodiscs have space to accommodate both enzymes and substrates to sustain steady-state catalysis. Our work establishes a proof-of-principle for using oversized nanodiscs as an integrated platform for structural and functional interrogation of complex membrane proteins in near-native membrane environments.