bims-cytox1 2021-09-26 papers

Issue of 2021–09–26
six papers selected by
Gavin McStay, Staffordshire University

Front Cell Dev Biol. 2021 ;9 720656

Redox-Mediated Regulation of Mitochondrial Biogenesis, Dynamics, and Respiratory Chain Assembly in Yeast and Human Cells.

Stefan Geldon, Erika Fernández-Vizarra, Kostas Tokatlidis.

Mitochondria are double-membrane organelles that contain their own genome, the mitochondrial DNA (mtDNA), and reminiscent of its endosymbiotic origin. Mitochondria are responsible for cellular respiration via the function of the electron oxidative phosphorylation system (OXPHOS), located in the mitochondrial inner membrane and composed of the four electron transport chain (ETC) enzymes (complexes I-IV), and the ATP synthase (complex V). Even though the mtDNA encodes essential OXPHOS components, the large majority of the structural subunits and additional biogenetical factors (more than seventy proteins) are encoded in the nucleus and translated in the cytoplasm. To incorporate these proteins and the rest of the mitochondrial proteome, mitochondria have evolved varied, and sophisticated import machineries that specifically target proteins to the different compartments defined by the two membranes. The intermembrane space (IMS) contains a high number of cysteine-rich proteins, which are mostly imported via the MIA40 oxidative folding system, dependent on the reduction, and oxidation of key Cys residues. Several of these proteins are structural components or assembly factors necessary for the correct maturation and function of the ETC complexes. Interestingly, many of these proteins are involved in the metalation of the active redox centers of complex IV, the terminal oxidase of the mitochondrial ETC. Due to their function in oxygen reduction, mitochondria are the main generators of reactive oxygen species (ROS), on both sides of the inner membrane, i.e., in the matrix and the IMS. ROS generation is important due to their role as signaling molecules, but an excessive production is detrimental due to unwanted oxidation reactions that impact on the function of different types of biomolecules contained in mitochondria. Therefore, the maintenance of the redox balance in the IMS is essential for mitochondrial function. In this review, we will discuss the role that redox regulation plays in the maintenance of IMS homeostasis as well as how mitochondrial ROS generation may be a key regulatory factor for ETC biogenesis, especially for complex IV.

Keywords: MIA; ROS; biogenesis; mitochondria; protein import; redox signaling; respiratory chain assembly

DOI: https://doi.org/10.3389/fcell.2021.720656

EMBO J. 2021 Sep 20. e108648

Ablation of mitochondrial DNA results in widespread remodeling of the mitochondrial complexome.

Sergio Guerrero-Castillo, Joeri van Strien, Ulrich Brandt, Susanne Arnold.

So-called ρ0 cells lack mitochondrial DNA and are therefore incapable of aerobic ATP synthesis. How cells adapt to survive ablation of oxidative phosphorylation remains poorly understood. Complexome profiling analysis of ρ0 cells covered 1,002 mitochondrial proteins and revealed changes in abundance and organization of numerous multiprotein complexes including previously not described assemblies. Beyond multiple subassemblies of complexes that would normally contain components encoded by mitochondrial DNA, we observed widespread reorganization of the complexome. This included distinct changes in the expression pattern of adenine nucleotide carrier isoforms, other mitochondrial transporters, and components of the protein import machinery. Remarkably, ablation of mitochondrial DNA hardly affected the complexes organizing cristae junctions indicating that the altered cristae morphology in ρ0 mitochondria predominantly resulted from the loss of complex V dimers required to impose narrow curvatures to the inner membrane. Our data provide a comprehensive resource for in-depth analysis of remodeling of the mitochondrial complexome in response to respiratory deficiency.

Keywords: OXPHOS; complexome profiling; mitochondria; mtDNA; rho0 cells

DOI: https://doi.org/10.15252/embj.2021108648

Proc Natl Acad Sci U S A. 2021 09 28. pii: e2106950118. [Epub ahead of print]118(39):

Molecular characterization of a complex of apoptosis-inducing factor 1 with cytochrome c oxidase of the mitochondrial respiratory chain.

Johannes F Hevler, Riccardo Zenezeni Chiozzi, Alfredo Cabrera-Orefice, Ulrich Brandt, Susanne Arnold, Albert J R Heck.

Combining mass spectrometry-based chemical cross-linking and complexome profiling, we analyzed the interactome of heart mitochondria. We focused on complexes of oxidative phosphorylation and found that dimeric apoptosis-inducing factor 1 (AIFM1) forms a defined complex with ∼10% of monomeric cytochrome c oxidase (COX) but hardly interacts with respiratory chain supercomplexes. Multiple AIFM1 intercross-links engaging six different COX subunits provided structural restraints to build a detailed atomic model of the COX-AIFM12 complex (PDBDEV_00000092). An application of two complementary proteomic approaches thus provided unexpected insight into the macromolecular organization of the mitochondrial complexome. Our structural model excludes direct electron transfer between AIFM1 and COX. Notably, however, the binding site of cytochrome c remains accessible, allowing formation of a ternary complex. The discovery of the previously overlooked COX-AIFM12 complex and clues provided by the structural model hint at potential roles of AIFM1 in oxidative phosphorylation biogenesis and in programmed cell death.

Keywords: AIFM1; COX; complexome profiling; cross-linking mass spectrometry; mitochondria

DOI: https://doi.org/10.1073/pnas.2106950118

Methods Mol Biol. 2022 ;2363 101-110

Complexome Profiling of Plant Mitochondrial Fractions.

Lucie Schröder, Holger Eubel, Hans-Peter Braun.

Most molecular functions depend on defined associations of proteins. Protein-protein interactions may be transient or long-lasting; they may lead to labile assemblies or more stable particles termed protein complexes. Studying protein-protein interactions is of prime importance for understanding molecular functions in cells. The complexome profiling approach allows to systematically analyze protein assemblies of cells or subcellular compartments. It combines separation of intact protein fractions by blue native (BN) polyacrylamide gel electrophoresis (PAGE) and protein identification as well as quantification by mass spectrometry. Complexome profiling has been successfully applied to characterize mitochondrial fractions of plants. In a typical experiment, more than 1000 mitochondrial proteins are identified and assigned to defined protein assemblies. It allows discovering so far unknown protein complexes, studying assembly pathways of protein complexes and even characterizing labile super- and megacomplexes in the >10 mega-Dalton range. We here present a complexome profiling protocol for the straightforward definition of the protein complex inventory of mitochondria or other subcellular compartments from plants.

Keywords: Arabidopsis thaliana; Blue native polyacrylamide gel electrophoresis; Complexome profiling; Mass spectrometry; Plant mitochondria; Respiration; Viscum album

DOI: https://doi.org/10.1007/978-1-0716-1653-6_9

Methods Mol Biol. 2022 ;2363 111-119

High-Throughput BN-PAGE for Mitochondrial Respiratory Complexes.

Lilian Vincis Pereira Sanglard, Catherine Colas des Francs-Small.

Blue native electrophoresis (BN-PAGE) is a highly resolutive method suited to the study of high molecular weight protein complexes between 100 and >3000 kDa. One of the drawbacks of this method is that it is very time-consuming and requires high quantities of purified organelles. Here we describe a high throughput BN-PAGE method allowing to screen libraries of plants potentially altered in respiratory metabolism.

Keywords: Blue Native PAGE; Immunoblots; Mitochondria; Respiratory complexes

DOI: https://doi.org/10.1007/978-1-0716-1653-6_10

J Inorg Biochem. 2021 Aug 27. pii: S0162-0134(21)00240-3. [Epub ahead of print]225 111593

Protonation of the oxo-bridged heme/copper assemblies: Modeling the oxidized state of the cytochrome c oxidase active site.

Maria C Carrasco, Katherine J Dezarn, Firoz Shah Tuglak Khan, Shabnam Hematian.

In this study on model compounds for the resting oxidized state of the iron‑copper binuclear center in cytochrome c oxidase (CcO), we describe the synthesis of a new μ-oxo-heme/Cu complex, [(TPP)FeIII-O-CuII(tmpa)][B(C6F5)4] (2) {TPP: tetraphenyl porphyrinate(2-); TMPA: tris(2-pyridylmethylamine)}, as well as two protonation events for three μ-oxo-heme/Cu complexes with varying peripheral substituents on the heme site. The addition of increasing amounts of strong acid to these μ-oxo-heme/Cu systems successively led to the generation of the corresponding μ-hydroxo, μ-aquo, and the dissociated complexes. The heme/Cu assemblies bridged through a water ligand are reported here for the first time and the 1H NMR and 19F NMR spectral properties are consistent with antiferromagnetically coupled high-spin iron(III) and copper(II) centers. By titration using a series of protonated amines, the pKa values for the corresponding μ-hydroxo-heme/Cu species (i.e., the first protonation event) have been reported and compared with the pKa ranges previously estimated for related systems. These synthetic systems may represent structural models for the oxidized FeIII-X-CuII resting state, or turnover intermediates and can be employed to clarify the nature of proton/electron transfer events in CcO. SYNOPSIS: The resting oxidized state of the cytochrome c oxidase active site contains an Fea3-OHx-CuB moiety. Here, we investigated two successive protonation events, for a series of μ-oxo-heme/Cu assemblies and reported the pKa values for the first protonation event. The μ-aquo-heme/Cu complexes described here are the first examples of such systems.

Keywords: Acid dissociation constant; Antiferromagnetic coupling; Bridging ligand; Cytochrome c oxidase; Paramagnetic NMR; Protonation

DOI: https://doi.org/10.1016/j.jinorgbio.2021.111593