ROS signaling capacity of cytochrome bc1: Opposing effects of adaptive and pathogenic mitochondrial mutations

Daphnia stress response to environmental concentrations of chloramphenicol-multi-omics approach

Commonly used medicines, when discarded or improperly disposed of, are known to contaminate freshwater ecosystems. Pharmaceuticals can be toxic and mutagenic, and can modify freshwater organisms, even at environmentally relevant concentrations. Chloramphenicol (CAP) is an antibiotic banned in Europe. However, it is still found in surface waters around the world. The aim of this study was to evaluate the impact of chloramphenicol contamination in freshwater on the model organism Daphnia magna. Specific life history parameters, proteome, and host-associated microbiome of four D. magna clones were analyzed during a three-generation exposure to CAP at environmental concentrations (32 ng L-1). In the first generation, no statistically significant CAP effect at the individual level was detected. After three generations, exposed animals were smaller at first reproduction and on average produced fewer offspring. The differences in D. magna's life history after CAP treatment were in accordance with proteome changes. D. magna's response to CAP presence indicates the high stress that the tested organisms are under, e.g., male production, upregulation of ubiquitin-conjugating enzyme E2 and calcium-binding protein, and downregulation of glutathione transferase. The CAP-exposed D. magna proteome profile confirms that CAP, being reactive oxygen species (ROS)-inducing compounds, contributes to structural changes in mitochondria. Microbiome analysis showed a significant difference in the Shannon index between control and CAP-exposed animals, the latter having a more diverse microbiome. Multilevel analyses, together with long exposure in the laboratory imitating conditions in a polluted environment, allow us to obtain a more complete picture of the impact of CAP on D. magna.

ROS production by cytochrome bc1: Its mechanism as inferred from the effects of heme b cofactor mutants

Cytochrome bc1 is one of the enzymes of electron transport chain responsible for generation of reactive oxygen species (ROS). While ROS are considered to be products of side reactions of quinol oxidation site (Qo), molecular aspects of their generation remain unclear. One of them concerns significance of hemes b (bL and bH) redox potentials (Em) and properties on ROS generation by Qo. Here we addressed this question by examining ROS production in mutants of bacterial cytochrome bc1 that replaced one of the His ligand of either heme bL or bH with Lys or Asn. We observed that severe slowing down of electron flow by the Asn mutants induces similar effects on ROS production as inhibition by antimycin in the native cytochrome bc1 (WT). An increase in the Em of hemes b (either bL or bH) in Lys mutants does not exert major effect on the ROS production level, compared to WT. The experimental data were analyzed in the frame of a dynamic model to conclude that the observed ROS rates and levels reflect a combinatory effect of two factors: probability of heme bL being in the reduced state and probability of electron transfer from heme bL towards Qo. A significant contribution from short-circuits maintains the ROS levels at ~15 % in all tested forms. Overall, ROS production by cytochrome bc1 shows remarkably low susceptibility to changes in the Em of heme b cofactors, leaving significance of tuning the Em of hemes b as factor limiting superoxide production an open question.

Mitochondrial Cristae Morphology Reflecting Metabolism, Superoxide Formation, Redox Homeostasis, and Pathology

Significance: Mitochondrial (mt) reticulum network in the cell possesses amazing ultramorphology of parallel lamellar cristae, formed by the invaginated inner mitochondrial membrane. Its non-invaginated part, the inner boundary membrane (IBM) forms a cylindrical sandwich with the outer mitochondrial membrane (OMM). Crista membranes (CMs) meet IBM at crista junctions (CJs) of mt cristae organizing system (MICOS) complexes connected to OMM sorting and assembly machinery (SAM). Cristae dimensions, shape, and CJs have characteristic patterns for different metabolic regimes, physiological and pathological situations. Recent Advances: Cristae-shaping proteins were characterized, namely rows of ATP-synthase dimers forming the crista lamella edges, MICOS subunits, optic atrophy 1 (OPA1) isoforms and mitochondrial genome maintenance 1 (MGM1) filaments, prohibitins, and others. Detailed cristae ultramorphology changes were imaged by focused-ion beam/scanning electron microscopy. Dynamics of crista lamellae and mobile CJs were demonstrated by nanoscopy in living cells. With tBID-induced apoptosis a single entirely fused cristae reticulum was observed in a mitochondrial spheroid. Critical Issues: The mobility and composition of MICOS, OPA1, and ATP-synthase dimeric rows regulated by post-translational modifications might be exclusively responsible for cristae morphology changes, but ion fluxes across CM and resulting osmotic forces might be also involved. Inevitably, cristae ultramorphology should reflect also mitochondrial redox homeostasis, but details are unknown. Disordered cristae typically reflect higher superoxide formation. Future Directions: To link redox homeostasis to cristae ultramorphology and define markers, recent progress will help in uncovering mechanisms involved in proton-coupled electron transfer via the respiratory chain and in regulation of cristae architecture, leading to structural determination of superoxide formation sites and cristae ultramorphology changes in diseases. Antioxid. Redox Signal. 39, 635-683.

The evolution of the human mitochondrial bc1 complex- adaptation for reduced rate of superoxide production?

The mitochondrial bc1 complex is a major source of mitochondrial superoxide. While bc1-generated superoxide plays a beneficial signaling role, excess production of superoxide lead to aging and degenerative diseases. The catalytic core of bc1 comprises three peptides -cytochrome b, Fe-S protein, and cytochrome c1. All three core peptides exhibit accelerated evolution in anthropoid primates. It has been suggested that the evolution of cytochrome b in anthropoids was driven by a pressure to reduce the production of superoxide. In humans, the bc1 core peptides exhibit anthropoid-specific substitutions that are clustered near functionally critical sites that may affect the production of superoxide. Here we compare the high-resolution structures of bovine, mouse, sheep and human bc1 to identify structural changes that are associated with human-specific substitutions. Several cytochrome b substitutions in humans alter its interactions with other subunits. Most significantly, there is a cluster of seven substitutions, in cytochrome b, the Fe-S protein, and cytochrome c1 that affect the interactions between these proteins at the tether arm of the Fe-S protein and may alter the rate of ubiquinone oxidation and the rate of superoxide production. Another cluster of substitutions near heme bH and the ubiquinone reduction site, Qi, may affect the rate of ubiquinone reduction and thus alter the rate of superoxide production. These results are compatible with the hypothesis that cytochrome b in humans (and other anthropoid primates) evolve to reduce the rate of production of superoxide thus enabling the exceptional longevity and exceptional cognitive ability of humans.

Analysis of the conformational heterogeneity of the Rieske iron-sulfur protein in complex III2 by cryo-EM

Movement of the Rieske domain of the iron-sulfur protein is essential for intramolecular electron transfer within complex III₂ (CIII₂) of the respiratory chain as it bridges a gap in the cofactor chain towards the electron acceptor cytochrome c. We present cryo-EM structures of CIII₂ from Yarrowia lipolytica at resolutions up to 2.0 Å under different conditions, with different redox states of the cofactors of the high-potential chain. All possible permutations of three primary positions were observed, indicating that the two halves of the dimeric complex act independently. Addition of the substrate analogue decylubiquinone to CIII₂ with a reduced high-potential chain increased the occupancy of the Q_o site. The extent of Rieske domain interactions through hydrogen bonds to the cytochrome b and cytochrome c₁ subunits varied depending on the redox state and substrate. In the absence of quinols, the reduced Rieske domain interacted more closely with cytochrome b and cytochrome c₁ than in the oxidized state. Upon addition of the inhibitor antimycin A, the heterogeneity of the cd₁-helix and ef-loop increased, which may be indicative of a long-range effect on the Rieske domain.

Isoquercitrin Attenuates Osteogenic Injury in MC3T3 Osteoblastic Cells and the Zebrafish Model via the Keap1-Nrf2-ARE Pathway

Isoquercitrin (IQ) widely exists in natural products, with a variety of pharmacological activities. In this study, the anti-apoptotic and antioxidative activities of IQ were evaluated. IQ showed protective activity against 2, 2′-azobis [2-methylpropionamidine] dihydrochloride (AAPH)-induced cell damage, as well as a marked reduction in reactive oxygen species (ROS). The evidence of IQ regulating Keap1-Nrf2-ARE and the mitochondrial-mediated Caspase 3 pathway were found in the MC3T3 osteoblastic cell line. Furthermore, IQ significantly decreased ROS production, apoptosis, and lipid peroxidation in AAPH-treated 72 h post-fertilization (hpf) zebrafish, as observed via DCFH-DA, acridine orange (AO), and a 1,3-bis(diphenylphosphino) propane (DPPP) probe, respectively. In AAPH-treated 9 day post-fertilization (dpf) zebrafish, IQ strongly promoted osteogenic development, with increased concentrations by calcein staining, compared with the untreated group. In a molecular docking assay, among all signal proteins, Keap1 showed the strongest affinity with IQ at −8.6 kcal/mol, which might be the reason why IQ regulated the Keap1-Nrf2-ARE pathway in vitro and in vivo. These results indicated that IQ promotes bone development and repairs bone injury, which is valuable for the prevention and treatment of bone diseases.

Recent Progress of Surface Modified Nanomaterials for Scavenging Reactive Oxygen Species in Organism

Reactive oxygen species (ROS) are essential for normal physiological processes and play important roles in signal transduction, immunity, and tissue homeostasis. However, excess ROS may have a negative effect on the normal cells leading to various diseases. Nanomaterials are an attractive therapeutic alternative of antioxidants and possess an intrinsic ability to scavenge ROS. Surface modification for nanomaterials is a critical strategy to improve their comprehensive performances. Herein, we review the different surface modified strategies for nanomaterials to scavenge ROS and their inherent antioxidant capability, mechanisms of action, and biological applications. At last, the primary challenges and future perspectives in this emerging research frontier have also been highlighted. It is believed that this review paper will offer a top understanding and guidance on engineering future high-performance surface modified ROS scavenging nanomaterials for wide biomedical applications.

Review: Using isolated mitochondria to investigate mitochondrial hydrogen peroxide metabolism

Mitochondria are recognized as centrally important to cellular reactive oxygen species (ROS), both as a potential source and due to their substantial antioxidant capacity. While much of the initial ROS formed by mitochondria is superoxide, this is rapidly converted to hydrogen peroxide (H₂O₂) which more readily crosses membranes making H₂O₂ important in both redox signalling mechanisms and conditions of oxidative stress. Here I outline our studies on mitochondrial H₂O₂ metabolism with a focus on some of the challenges and strategies involved with developing an integrated model of mitochondria being intrinsic regulators of H₂O₂. This view of mitochondria as regulators of H₂O₂ goes beyond the simpler contention of them being net producers or consumers. Moreover, the integration of both consumption and production can then be tied to a putative mechanism linking energy sensing at the level of the mitochondrial protonmotive force. This mechanism would provide a means of mitochondria communicating their energetic status the extramitochondrial compartment via local H₂O₂ concentrations. I conclude by explaining how these concepts developed using rodent muscle as a model have high relevance and applicability to comparative studies.

The High-Spin Heme b L Mutant Exposes Dominant Reaction Leading to the Formation of the Semiquinone Spin-Coupled to the [2Fe-2S]+ Cluster at the Qo Site of Rhodobacter capsulatus Cytochrome bc 1

Cytochrome bc ₁ (mitochondrial complex III) catalyzes electron transfer from quinols to cytochrome c and couples this reaction with proton translocation across lipid membrane; thus, it contributes to the generation of protonmotive force used for the synthesis of ATP. The energetic efficiency of the enzyme relies on a bifurcation reaction taking place at the Q_o site which upon oxidation of ubiquinol directs one electron to the Rieske 2Fe2S cluster and the other to heme b _L. The molecular mechanism of this reaction remains unclear. A semiquinone spin-coupled to the reduced 2Fe2S cluster (SQ_o-2Fe2S) was identified as a state associated with the operation of the Q_o site. To get insights into the mechanism of the formation of this state, we first constructed a mutant in which one of the histidine ligands of the iron ion of heme b _L Rhodobacter capsulatus cytochrome bc ₁ was replaced by asparagine (H198N). This converted the low-spin, low-potential heme into the high-spin, high-potential species which is unable to support enzymatic turnover. We performed a comparative analysis of redox titrations of antimycin-supplemented bacterial photosynthetic membranes containing native enzyme and the mutant. The titrations revealed that H198N failed to generate detectable amounts of SQ_o-2Fe2S under neither equilibrium (in dark) nor nonequilibrium (in light), whereas the native enzyme generated clearly detectable SQ_o-2Fe2S in light. This provided further support for the mechanism in which the back electron transfer from heme b _L to a ubiquinone bound at the Q_o site is mainly responsible for the formation of semiquinone trapped in the SQ_o-2Fe2S state in R. capusulatus cytochrome bc ₁.

Redox Active Antimicrobial Peptides in Controlling Growth of Microorganisms at Body Barriers

Epithelia in the skin, gut and other environmentally exposed organs display a variety of mechanisms to control microbial communities and limit potential pathogenic microbial invasion. Naturally occurring antimicrobial proteins/peptides and their synthetic derivatives (here collectively referred to as AMPs) reinforce the antimicrobial barrier function of epithelial cells. Understanding how these AMPs are functionally regulated may be important for new therapeutic approaches to combat microbial infections. Some AMPs are subject to redox-dependent regulation. This review aims to: (i) explore cysteine-based redox active AMPs in skin and intestine; (ii) discuss casual links between various redox environments of these barrier tissues and the ability of AMPs to control cutaneous and intestinal microbes; (iii) highlight how bacteria, through intrinsic mechanisms, can influence the bactericidal potential of redox-sensitive AMPs.

Catalytic Reactions and Energy Conservation in the Cytochrome bc1 and b6f Complexes of Energy-Transducing Membranes

This review focuses on key components of respiratory and photosynthetic energy-transduction systems: the cytochrome bc1 and b6f (Cytbc1/b6f) membranous multisubunit homodimeric complexes. These remarkable molecular machines catalyze electron transfer from membranous quinones to water-soluble electron carriers (such as cytochromes c or plastocyanin), coupling electron flow to proton translocation across the energy-transducing membrane and contributing to the generation of a transmembrane electrochemical potential gradient, which powers cellular metabolism in the majority of living organisms. Cytsbc1/b6f share many similarities but also have significant differences. While decades of research have provided extensive knowledge on these enzymes, several important aspects of their molecular mechanisms remain to be elucidated. We summarize a broad range of structural, mechanistic, and physiological aspects required for function of Cytbc1/b6f, combining textbook fundamentals with new intriguing concepts that have emerged from more recent studies. The discussion covers but is not limited to (i) mechanisms of energy-conserving bifurcation of electron pathway and energy-wasting superoxide generation at the quinol oxidation site, (ii) the mechanism by which semiquinone is stabilized at the quinone reduction site, (iii) interactions with substrates and specific inhibitors, (iv) intermonomer electron transfer and the role of a dimeric complex, and (v) higher levels of organization and regulation that involve Cytsbc1/b6f. In addressing these topics, we point out existing uncertainties and controversies, which, as suggested, will drive further research in this field.