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Review

The functional significance of mitochondrial


respiratory chain supercomplexes
Andreas Kohler1,2 , Antoni Barrientos3,4 , Flavia Fontanesi4 & Martin Ott1,5,*

Abstract mitochondrial respiratory chain (MRC), where they finally reduce


molecular oxygen to form water (Fig 1). The energy of this reaction
The mitochondrial respiratory chain (MRC) is a key energy trans- is converted into an electrochemical gradient across the inner mito-

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ducer in eukaryotic cells. Four respiratory chain complexes cooper- chondrial membrane (IMM). In a subsequent step, protons flow
ate in the transfer of electrons derived from various metabolic from the mitochondrial intermembrane space (IMS) back into the
pathways to molecular oxygen, thereby establishing an electro- matrix, powering the ATP synthase (CV), which condenses ADP
chemical gradient over the inner mitochondrial membrane that and phosphate to form ATP (Fig 1).
powers ATP synthesis. This electron transport relies on mobile elec- NADH feeds two electrons into the NADH dehydrogenase (CI),
tron carries that functionally connect the complexes. While the the first and largest of the MRC multiprotein complexes in mam-
individual complexes can operate independently, they are in situ mals, consisting of 45 subunits and comprising a mass of approx.
organized into large assemblies termed respiratory supercom- 1 MDa (Kampjut & Sazanov, 2020; Fig 1). Electrons from NADH are
plexes. Recent structural and functional studies have provided thereby transferred to oxidized quinone (Q), a reaction coupled to
some answers to the question of whether the supercomplex orga- proton extrusion from the matrix into the IMS via CI’s antiporter
nization confers an advantage for cellular energy conversion. How- subunits (Jones et al, 2017; Fig 1). Q is an abundant mitochondrial
ever, the jury is still out, regarding the universality of these claims. lipid that can be reversibly reduced and oxidized, respectively, and
In this review, we discuss the current knowledge on the functional freely diffuses in the IMM. Interestingly, some species, including
significance of MRC supercomplexes, highlight experimental limi- the model organism Saccharomyces cerevisiae, do not contain a con-
tations, and suggest potential new strategies to overcome these ventional CI, but rather possess non-proton-translocating peripheral
obstacles. membrane NADH dehydrogenases (Nde1, Nde2, and Ndi1; Joseph-
Horne et al, 2001). In addition, electrons extracted from succinate
Keywords bioenergetics; electron transfer; Mitochondria; respiratory chain; can reduce Q via the succinate dehydrogenase (CII; Fig 1). Whereas
supercomplexes CI pumps protons, no H+ is translocated by CII. Of note, Q can also
Subject Categories Metabolism; Organelles be reduced by several other membrane-bound dehydrogenases
DOI 10.15252/embr.202357092 | Received 28 February 2023 | Revised 10 July (e.g., glycerol 3-phosphate dehydrogenase). The reduced quinone
2023 | Accepted 14 September 2023 | Published online 12 October 2023 (QH2) subsequently transfers two electrons to cytochrome bc1
EMBO Reports (2023) 24: e57092 reductase (CIII), which exists as an obligate homodimer (CIII2;
Fig 1) in all species (Stephan & Ott, 2020). CIII couples electron
transfer from QH2 to cytochrome c (Cytc) with the shuttling of H+
The mitochondrial respiratory chain into the IMS via a mechanism called Q-cycle (Mitchell, 1975;
Osyczka et al, 2005). In one such Q-cycle, two QH2 molecules are
As the most versatile form of chemical energy in cells, ATP is syn- oxidized to Q, releasing 4 H+ into the IMS and reducing two Cytc
thesized in large quantities by mitochondrial activity. Biochemical molecules (Fig 1). Of note, another Q is reduced to QH2 in this pro-
reactions, many occurring in the cytoplasm, convert carbohydrates cess, which can subsequently be used for another round of the Q-
and lipids to mitochondrial acetyl-CoA. This central metabolite is cycle. The protein Cytc acts as a mobile electron carrier, with a cen-
processed in the mitochondrial matrix by the tricarboxylic acid cycle tral, covalently attached heme group that can reversibly bind one
(TCA; Fig 1). Electrons originating from these TCA reactions are electron. Cytc transfers electrons from CIII to Cytc oxidase (CIV),
passed over to the typically four multiprotein complexes (CI-CIV) of where molecular oxygen is reduced to water (Fig 1). In this last step
the electron transport chain. In a process termed oxidative phos- of the electron transport chain, another 4 H+ are pumped into the
phorylation (OXPHOS), the electrons are transported through the IMS by oxidizing 4 Cytc molecules (Wikstrom, 1977). Finally, the

1 Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden


2 Institute of Molecular Biosciences, University of Graz, Graz, Austria
3 Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL, USA
4 Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, USA
5 Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
*Corresponding author. Tel: +46 31 786 9402; E-mail: martin.ott@gu.se

ª 2023 The Authors. Published under the terms of the CC BY 4.0 license. EMBO reports 24: e57092 | 2023 1 of 14
EMBO reports Andreas Kohler et al

Glycolysis β-oxidation

Acetyl CoA

Citrate
NADH Oxaloacetate cis-Aconitate

NAD+
Isocitrate
Malate Tricarboxylic acid cycle NAD+
TCA
(TCA) NADH
Fumarate α-Ketoglutarate
FADH2
NAD+
FAD
Succinate
Succinyl CoA
NADH

GTP GDP

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OMM

CI CII CIII CIV


NADH-ubiquinone Succinate-ubiquinone Ubiquinol-cytochrome c e- cytochrome c CV
oxidoreductase oxidoreductase oxidoreductase oxidase ATPsynthase
IMS
4H+ 4H+ 2H+
cytochrome c

QH2 QH2 2Q
IMM
Q Q 2QH2
2H+ 2H+ 2.7 H+
1/2 O2
4H+
H 2O
4H+
Succinate Fumarate +
+ 2H+ 2H

NAD++ H+ ADP + Pi
NADH ATP

Figure 1. The tricarboxylic acid cycle (TCA) and mitochondrial respiratory chain.
Upper Panel: Acetyl-CoA is a central metabolite produced via various metabolic reaction pathways. It can subsequently be utilized in the TCA, were among others sev-
eral molecules of NADH and FADH2 are generated. Lower Panel: Electrons from these metabolites can be subsequently utilized by the mitochondrial respiratory chain
to convert energy in the form of ATP. Structures of the individual respiratory chain complexes and the electron carrier cytochrome c are shown, as well as respective
redox reactions (PDB CI: 6ZKC; PDB CII: 1ZP0; PDB CIII: 6Q9E; PDB CIV and CytC: 5IY5; PDB CV: 5ARA). IMM, inner mitochondrial membrane; IMS, intermembrane space;
OMM, outer mitochondrial membrane.

electrochemical gradient across the IMM formed by the transfer of models. The solid-state model postulates that all components of the
protons from the mitochondrial matrix into the IMS is used by the MRC (including Q and Cytc) form a single unit, which can catalyze
ATP synthase (CV), which phosphorylates ADP with inorganic the entire process of mitochondrial respiration. Thereby, Q and Cytc
phosphate to ATP, whereby the flow of protons back into the mediate electron transfer via enclosed pathways, never exchanging
matrix powers ATP synthesis (Mitchell, 1975) by a rotary mecha- with the exterior of the unit (Ragan & Heron, 1978). On the con-
nism of the ATP synthase (Fig 1). trary, the liquid-state model proposes that individual complexes
reside independently in the IMM. Likewise, Q and Cytc diffuse freely
Connectivity of mitochondrial respiratory chain complexes and randomly to transfer electrons between the individual com-
Despite detailed insights into the fundamental structural and cata- plexes (Hochli & Hackenbrock, 1976; Hackenbrock et al, 1986). The
lytic properties of the individual MRC complexes, available since liquid-state model received extensive experimental support, mostly
last century, their overall structural organization and physiological owing to the observation that individual MRC complexes could be
implications of that organization have been extensively revisited purified in active forms and that the small mobile electron carriers
over the last 20 years and are still debated today (Milenkovic et al, are freely diffusing and in large stoichiometric excess over MRC
2017). Historically, two opposing models for how the complexes are complexes. However, the solid-state model gained new experimen-
functionally connected were proposed early on, namely, the “solid- tal support. Through the use of mild detergents for mitochondrial
state” and the “liquid-state” (also referred to as “fluid-state”) membrane solubilization and the establishment of blue native

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Andreas Kohler et al EMBO reports

polyacrylamide gel electrophoresis, it was demonstrated that MRC Supercomplexes are also formed between CIII and CIV without
complexes form supramolecular assemblies, termed respiratory CI, with the stoichiometries CIII2 + CIV2 or CIII2 + CIV, respectively
chain supercomplexes (SCs) (Cruciat et al, 2000; Sch€ agger & (Fig 2A). Whereas CIII forms an obligate homodimer (CIII2), CIV
Pfeiffer, 2000). SCs were shown to exist in varying stoichiometry can occur in its monomeric, as well as in its dimeric (CIV2) form.
in different species, ranging from bacteria to plants, fungi, and
animals. Because they exist widely in multiple life forms, they The respirasomes
must confer specific, selectable advantages to organisms. In this A common feature of respirasomes is the curving of the membrane
review, we provide a comprehensive overview of the various arm of CI around the CIII dimer, which can already be observed in
forms of mitochondrial SCs, their biogenesis, and their structure the isolated CI + CIII2 complex (Letts et al, 2019). The overall struc-
and discuss the current understanding of the functional roles ture of these SCs was similar to the respirasome configuration, but
of SCs. showed at least six open states (inactive form) of CI and one closed
state (active form) (Letts et al, 2019). In structural studies for both
ovine and bovine respirasomes, two different classes had significant
Structures and assembly of different respiratory chain variations of the CIV position (Letts et al, 2016; Sousa et al, 2016).
complexes For the ovine respirasome structure, “loose” (active) and “tight”

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(inactive) conformations were shown, where CIV contacts both CI
Overview of different supercomplex configurations and CIII in the tight variant but only CI in the loose form (Letts
Only a small fraction of CI is present as a free complex in bovine et al, 2016). Class 1 of the bovine respirasome is similar to the tight
heart mitochondria, and in some studies using cell cultures, the free form and represents the most prevalent population and stable form
form of CI is even undetectable (Lobo-Jarne et al, 2018), whereas of the respirasome (Gu et al, 2016; Letts et al, 2016; Letts &
the rest is found in various SC assemblies with varying stoichiome- Sazanov, 2017). Two main interaction sites are found between CI
try (Sch€agger & Pfeiffer, 2001) (Fig 2A). The most prevalent of these and CIII2, namely, one in the membrane between NDUFA11 and the
assemblies in human cells is the respirasome, consisting of UQCRB, UQCRQ, and UQCRH subunits of CIII, and a second one in
CI + CIII2 + CIV and a size of approx. 1.7 MDa, accounting for the matrix between NDUFB4, NDUFB9, and CIII subunit UQCRC1
approximately half of CI in SCs (Sch€agger & Pfeiffer, 2001; Gu (Fig 2B). Interestingly, the contacts formed between CI and CIII
et al, 2016; Letts et al, 2016; Wu et al, 2016; Lobo-Jarne & within the respirasome involve so-called supernumerary subunits.
Ugalde, 2018; Fig 2A). Other variants of the respirasome, which Compared to the 14 conserved CI subunits of bacterial origin, these
have been proposed to contain further copies of CIV (CI + supernumerary subunits are assumed to be of eukaryotic origin
CIII2 + CIV2-4), present only minor amounts of CI-containing SCs. (Gray, 2012). As no CI-containing supercomplexes have been identi-
The second most prevalent assembly of CI is the CI + CIII2 configu- fied in bacteria so far (however, CIII2 + CIV2 supercomplexes were
ration (Sch€agger & Pfeiffer, 2001; Fig 2A). Of note, although the stoi- described, Kaila & Wikström, 2021), it is feasible that certain CI
chiometry of these assemblies is the same between yeasts, plants, supernumerary subunits evolved to form respirasomes (Letts &
and mammals, the structures and frequencies differ (Davies Sazanov, 2017). On the contrary, the contacts between CI and CIV
et al, 2018). Evidence for the existence of even larger assemblies are formed by the evolutionarily conserved core subunit ND5 of CI
than the CI + CIII2 + CIV4 respirasome comes from cryo-EM studies and the CIV subunit COX7C (Gu et al, 2016; Letts et al, 2016;
in HEK293T cells, reporting a symmetrical respiratory megacomplex Fig 2B).
with the stoichiometry CI2 + CIII2 + CIV2 (Guo et al, 2017). Different states of the respirasome can be observed when looking
Although the authors also speculate that two units of CII could at the four major rotational axes of its structure, including the hinge
potentially bind to this megacomplex, a corresponding unassigned between the matrix and membrane arms of CI, the pivot between CI
density could not be observed in their data, and so far, no direct and CIII2, the rotation along the two-fold-symmetry axis of CIII2,
experimental evidence for the participation of CII in supercomplex and the internal asymmetric rotation of CIV (Letts et al, 2016; Letts
assembly of metazoa or plants was reported (Caruana & & Sazanov, 2017). Whereas the rotation between the matrix and
Stroud, 2020). However, a recent study using the ciliate protist Tet- membrane arms of CI may be associated with the regulation of
rahymena thermophila reports a CI + CII + CIII2 + CIV2 SC, which enzymatic activity or may represent different stages in the catalytic
has important implications in the curvature of the IMM in this cycle (Letts et al, 2016; Agip et al, 2018; Blaza et al, 2018; Kravchuk
organism (Mu € hleip et al, 2023). Of note, this arrangement shows et al, 2022), physiological implications of other conformational
significant differences compared to known mammalian SCs. states remain unknown. It might be that these different

Figure 2. Respiratory chain supercomplex assemblies.


(A) Stoichiometry of several mitochondrial respiratory chain supercomplexes. (B) Main interaction surfaces of mammalian respirasomes (CI + CIII2 + CIV, PDB: 5j4z).
Close-up of interactions between CI (green) and CIII (blue) subunits NDUFA11, UQCRB, UQCRQ, and UQCRH (left panel), as well as NDUFB4 and NDUFB9 with UQCRC1

(lower right panel) are shown, as well as the interaction surface between CIII and CIV (red), formed by the CI subunit ND5 and the CIV subunit COX7C (upper right
panel). Visualization is adapted from (Letts et al, 2016). (C) Interaction surfaces of the Saccharomyces cerevisiae respiratory chain supercomplex CIII2 + CIV (PDB: 6YMX).
The inner membrane protein–lipid–protein interaction between Rip1 (CIII, blue, cardiolipin (CL) and Cox5 (CIV, red) are shown (left panel), as well as the matrix-situated
protein–protein interaction between Cor1 and Cox5a). Visualization was modified from (Berndtsson et al, 2020). (D) Structure of the mammalian respiratory chain
supercomplex CIII2 + CIV in the unlocked configuration (PDB: 7O3C, upper panel). The lower panel shows a transparent visualization of the same structure to display
interactions between the CIII (blue) subunit Sub9 and the CIV (red) subunit SCAF1.

 2023 The Authors EMBO reports 24: e57092 | 2023 3 of 14


EMBO reports Andreas Kohler et al

A
CI + CIII2 + CIV CI + CIII2 CIII2 + CIV2 CIII2 + CIV

CI Complex I CIII Complex III CIV Complex IV

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COX7C
UQCRB NDUFA11

ND5

UQCRQ NDUFB4 UQCR1

UQCRH

NDUFB9

C D

Qcr8 Cox5

CL
Cor1 SCAF1

Rip1 Cox5

Sub9

Figure 2.

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Andreas Kohler et al EMBO reports

conformations present intermediate states of respirasome assembly (Sch€agger & Pfeiffer, 2000). The first elucidated high-resolution
or that some configurations (e.g., the loose form of the respirasome) structure for mitochondrial CIII2 + CIV came from Saccharomyces
are sample preparation artifacts (Letts et al, 2016). cerevisiae (Hartley et al, 2019; Rathore et al, 2019). The association
The exact mechanism of respirasome formation, particularly between CIII2 and CIV occurs via protein–protein interactions
involving SC assembly factors, is still a matter of debate. The CIV between the CIII subunit Cor1 and the CIV subunit Cox5, stabilizing
subunit COX7A has two tissue-specific isoforms, namely, COX7A1 the complex from the matrix side, and a protein–lipid–protein inter-
in the heart and skeletal muscles and COX7A2 in the liver. However, action between Cor1, cardiolipin, and the CIV subunit Rip1 (Fig 2C).
both isoforms can be found in heart-derived mitochondria, whereas Whereas alanine substitutions in Cor1 abolished the formation of
COX7A2 is found in liver mitochondria only. Further, a homolog of SCs, the reduction of cardiolipin content via deletion of the cardio-
COX7A2, COX7A2L, or SCAF1 was described, initially thought to be lipin synthase Crd1 had no direct consequence on SC formation
essential for both respirasome and CIII2 + CIV SC formation (Ikeda (Pfeiffer et al, 2003), showing that the protein–protein interaction
et al, 2013; Lapuente-Brun et al, 2013). It was postulated that SCAF1 between Cor1 and Cox5 is necessary and sufficient for the formation
is required to form respirasomes in all tissues except in the heart of CIII2 + CIV SCs in yeast (Berndtsson et al, 2020). However, the
and skeletal muscle (Cogliati et al, 2016). However, overwhelming yeast and mammalian CIII2 + CIV differ substantially in their struc-
evidence shows that SCAF1 is only required for CIII2 + CIV SC for- ture. In yeast, CIV binds to CIII2 at the same site as CI does in the

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mation but not for the respirasome (Davoudi et al, 2016; Jha respirasome, resulting in different binding modes between CIII and
et al, 2016; Perez-Perez et al, 2016; Sun et al, 2016; Williams CIV in yeast and mammals (Rathore et al, 2019). CIII2 + CIV of
et al, 2016). Although SCAF1 is essential for the assembly of the mammals was observed in two different conformations, a locked
CIII2 + CIV SC (as discussed in more detail below), it does not con- and an unlocked state (Vercellino & Sazanov, 2021). In the unlocked
tribute to the assembly of the respirasome, as the formation of state, CIV is peripherally attached to CIII2, and almost 180° rotated
the CIII2 + CIV SC is not necessary for respirasome formation (Pe- compared to the yeast form of this assembly. Whereas the unlocked
rez-Perez et al, 2016). Likewise, SCAF1 was not detected in the conformation contained both fully mature CIII2 and CIV, the locked
structure of the respirasome. However, a recent analysis of human form harbors assembly intermediates of CIII2.
cells by complexome profiling has led to the identification of two The assembly of mammalian CIII2 + CIV has been shown to fol-
distinct respirasome forms that present slightly different electropho- low a specific sequence. The assembly factor SCAF1 binds to a pre-
retic mobility and contain either SCAF1 or COX7A2 isoforms (Fern a- mature form of CIII2 and drives the docking of CIV to form an
ndez-Vizarra et al, 2022). intermediate-locked assembly. This is followed by the maturation of
CIII2, forming the locked conformation. Subsequently, CIV shifts to
Supercomplex CI + CIII2 and CIII2 + CIV the unlocked state, in which the newly added subunits of the mature
Although the configuration of CI + CIII2 is observed much less fre- CIII2 form contacts with CIV (Vercellino & Sazanov, 2021; Fig 2D).
quently in mammalian cells as compared to the respirasome The yeast proteins Rcf1 (and its mammalian homolog HIGD2A),
(approx. 17% of total complex I in mitochondria compared to as well as Rcf2 (yeast-specific), were previously suggested to medi-
approx. 54% for the respirasome) (Sch€agger & Pfeiffer, 2001), this ate assembly and stability of CIII2 + CIV SCs (Chen et al, 2012; Stro-
arrangement is widely observed across kingdoms (Davies golova et al, 2012; Vukotic et al, 2012; Zhou et al, 2018). However,
et al, 2018). Rcf1 was later shown to interact with CIV, thereby regulating the
Recently, high-resolution structures of T. thermophila respiratory late stages of its assembly (Su et al, 2014; Garlich et al, 2017). In
chain complexes have been solved, including CI + CIII2 (Zhou addition, a recent study showed that Rcf1 and Rcf2 regulate respira-
et al, 2022). Interestingly, the overall arrangement is similar to that tion of yeast cells, without significantly affecting the assembly of
of mammalian CI + CIII2 SCs as discussed above. However, signifi- SCs (Dawitz et al, 2020). It was also shown that Rcf1 and Rcf2 are
cant differences in the interaction sites were observed, with more not stoichiometric subunits of CIV, and thus, they were also not pre-
contacts in both the matrix and the IMM, as well as an IMS bridge sent in the cryo-EM structure of yeast SCs under physiological con-
present in T. thermophila SCs. Thereby, these interactions cause ditions (Rathore et al, 2019). However, Rcf2 could be detected in SC
structural and functional symmetry breaking in CIII2. The authors structures under hypoxia-mimicking conditions (Hartley et al,
further suggested that no free CI is present in T. thermophila and 2020). This is in line with the observation that Rcf1 and Rcf2 regu-
that the CI + CIII2 represents the minimal organization of CI (Zhou late CIV activity, in particular under energy-demanding conditions
et al, 2022). Moreover, very recent cryo-EM structures of Arabi- (Dawitz et al, 2020). These results suggest that the primary func-
dopsis thaliana CI + CIII2 showed a plant-specific additional interac- tions of Rcf1 and Rcf2 are related to the assembly of individual com-
tion site between the complexes compared to ovine CI + CIII2 plexes and regulating their function rather than specifically
structures, potentially contributing to the unusual stability of the mediating SC formation. In mammals, other relevant HIGD family
plant SC (Klusch et al, 2023). Similar plant-specific interaction sur- proteins are HIGD1A and HIGD1C. HIGD1A impacts the assembly of
face between CI and CIII2 was also shown for Vigna radiata (Maldo- CIII (Timon-Gomez et al, 2020), and in addition, it binds to Cytc and
nado et al, 2023). CIV in the respirasome to enhance electron transfer (Hayashi
In the yeast S. cerevisiae that lacks a canonical CI, the ratio et al, 2015; Guerra-Castellano et al, 2018). In agreement, HIGD1A
between the two SC species CIII2 + CIV2 or CIII2 + CIV reflects the overexpression improves cellular respiration in models of mitochon-
cellular energy demands under different growth conditions drial disorders (Nagao et al, 2020). Differently, HIGD1C is almost
(Sch€agger & Pfeiffer, 2000). In particular, the abundance of SC exclusively expressed in glomus cells, where it also interacts with
CIII2 + CIV2 is enhanced in cells propagating in respiratory CIV to negatively regulate its activity and facilitate oxygen sensing
media and is mainly controlled by the amount of CIV available (Tim on-Gomez et al, 2022).

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EMBO reports Andreas Kohler et al

Physiological functions of supercomplexes the overall pathway (and hence, the flux control coefficient is 1),
this step has complete control over the pathway. Such an analysis
The physiological functions of SCs remain controversial, despite has been performed for the NADH oxidation pathway with the
more than two decades of research (Sch€agger & Pfeiffer, 2000). Sev- inhibitors rotenone and mucidin, and it was shown that CI and CIII
eral hypotheses regarding their physiological significance were behave as a single functioning unit (Blanchi et al, 2004). In support
made and will be discussed in this section. of this model, Q and Cytc were found in respirasomes and shown to
be able to transfer electrons from NADH to O2 (Acın-Perez
Free diffusion versus substrate channeling et al, 2008). It was therefore proposed that neither Q nor Cytc form
The random collision model suggests that the electron transport homogeneous pools, but instead, each respirasome contains a dedi-
within mitochondria is a diffusion-based process. The mechanistic cated small pool of Q and Cytc, which are not exchanged and allow
role of Q to transport electrons from NADH or succinate oxidation to a localized electron transfer via substrate channeling (Lapuente-
CIII was established in the 1960s, when it was demonstrated that a Brun et al, 2013; Fig 3A and B). Substrate channeling in complexes
surprisingly high concentration of Q was found in the IMM, where it of enzymes that act sequentially in a pathway is a process where a
behaves as a pool, binding electrons (and protons) to the Q head- specific substrate is transferred from one enzymatic activity to the
group, and thereby helps to connect electron flow in the MRC next without allowing free diffusion of the substrate into the bulk

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(Fig 3A). Because Q is a substantially hydrophobic molecule, owing solution. For example, the large E1-E2-E3 enzymes like pyruvate
to the attachment of varying numbers of isoprenyl moieties (Stefely dehydrogenase or alpha-ketoglutarate dehydrogenase employ sub-
& Pagliarini, 2017), the coenzyme is solved in the lipidic core of the strate channeling by transferring a covalently bound substrate
membrane, where it diffuses in the plane of the lipid bilayer. In con- between the complexes’ three enzymatic entities using a highly flex-
trast, Cytc is a protein of roughly 15 kDa molecular weight that ible domain.
carries a covalently attached heme moiety enabling the transport of Although the substrate channeling hypothesis represents an
one electron at a time. Cytc belongs to the class of peripheral mem- attractive model for the physiological functions of SCs, experimental
brane proteins. In the absence of transmembrane segments, evidence against this hypothesis emerged. First, repetitions of flux
membrane association stems from its attachment to the IMM by elec- control experiments showed that the outcome of these experiments
trostatic interactions with negatively charged phospholipids, particu- strongly depended on the respective inhibitor used (Blaza
larly cardiolipin, the signature phospholipid of mitochondria et al, 2014). As certain inhibitors even resulted in a biological mean-
(Kinnunen et al, 1994). Moreover, biophysical experiments ingless flux control coefficient of > 1, this approach is not a reliable
suggested that in addition to electrostatic interactions, also an alter- method to analyze physiological functions of SCs (Blaza et al, 2014;
native form of membrane interaction could exist. In this model, an Milenkovic et al, 2017). The authors also measured substrate oxida-
acyl chain of cardiolipin might get inserted into the folded Cytc, giv- tion using NADH, succinate, or both in submitochondrial particles
ing rise to a tight membrane-bound form (Rytomaa & containing supercomplexes, prepared with and without the addition
Kinnunen, 1995). However, Cytc release from mitochondria during of Cytc to alter the rate-limiting step for substrate oxidation. The
apoptosis is a highly conserved and important event, necessitating same system with the same set of supercomplexes showed both
that the protein is detached from the IMM (Ott et al, 2007). This pro- additive and non-additive kinetics (Blaza et al, 2014). These results
pensity of Cytc, namely to interact with the IMM via various mecha- reject the hypothesis of a Q pool partitioning in SCs. Similarly, spec-
nisms and the well-documented fact that it can be detached from the troscopic measurements in living cells also demonstrated that Cytc
membrane to act as a signaling molecule during cell death execution does not face any barriers to free diffusion (Trouillard et al, 2011).
(Garrido et al, 2006), complicates the interpretation of how the pro- In an additional study, an alternative QH2 oxidase was inserted into
tein diffuses inside mitochondria. However, the general consent is mammalian heart mitochondrial membranes, which then presents a
that Cytc is freely moving in the IMS (Hochman et al, 1982), either competing pathway for QH2 oxidation (Fedor & Hirst, 2018). In the
moving in two dimensions at the level of the IMM, in three dimen- case of substrate channeling, the flux through the competing path-
sions in the IMS, or a mixture of both, whereby the actual ionic way should be negligible. However, the rate of cyanide-insensitive
strength might dictate the degree of membrane association (Fig 3B). NADH:O2 oxidoreduction via the alternative QH2 oxidase was signif-
The discovery of SCs, however, led to the hypothesis that icantly higher, revealing that CIII/CIV catalysis is rate-limiting for
respirasomes might act as solid-state units, with each respirasome both, NADH and succinate oxidation, and that Q is not channeled in
carrying its own Q and Cytc molecules and catalyzing the transfer of SCs. In addition, structures of the mammalian respirasomes (Gu
electrons from NADH to O2 (Fig 3A and B). Flux control analyses et al, 2016; Letts et al, 2016) and CIII2 + CIV SCs (Vercellino &
take advantage of inhibitors to block a certain step in a reaction Sazanov, 2021), yeast CIII2 + CIV1-2 SCs (Hartley et al, 2019;
pathway. If the effect on the isolated step is equal to the effect on Rathore et al, 2019; Berndtsson et al, 2020), or plant CIII2 + CIV SCs

Figure 3. Physiological functions of respiratory chain supercomplexes.


(A) Comparison between the free diffusion and substrate channeling model for coenzyme Q (Q) within respiratory chain supercomplexes. Arrows indicate the free
exchange with the Q pool (free diffusion model, left panel) or the direct Q transfer in the form of substrate channeling (right panel). (B) Comparison of various

postulated models for cytochrome c shuttling between complex CIII and CIV in respiratory chain supercomplex configuration. Arrows indicate the modality of
cytochrome c transfer/exchange with the free pool, similar as described for the Q pool above. (C) Potential physiological functions of different respiratory chain
supercomplex assemblies. Several of these assigned functions are controversially discussed. Arrows indicate a respective increase or decrease of the indicated
physiological functions and pathophysiological effects.

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A
Free diffusion Substrate channeling
exchange with pool no exchange with pool
CI Complex I

Q Q
Q Q Q Q Q Q CIII Complex III
Q Q
Q Q Q Q
CIV Complex IV
Q
Q Coenzyme Q

Cytochrome c

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B
Free diffusion Substrate channeling 2D diffusion 2D diffusion
exchange with pool no exchange with pool no exchange with pool exchange with pool

C
CI + CIII2 + CIV CI + CIII2 CIII2 + CIV

Oxidative stress Oxidative stress Competitive fitness


Protein aggregation Protein aggregation Protein aggregation
Cooperative assembly Cooperative assembly Cooperative assembly
Stability of complexes Metabolic efficiency

Figure 3.

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EMBO reports Andreas Kohler et al

(Maldonado et al, 2021) do not contain barriers restricting diffusion process (Stuchebrukhov et al, 2020). Interestingly, further work
of Q or Cytc away from the complexes, features that would be neces- performed with yeast mitochondria in combination with cryo-EM
sary for substrate channeling. Direct tunneling of electrons between suggests that this kinetic advantage might be conferred by 2D diffu-
CIII2 + CIV in the MRC can also be excluded because of a too-large sion of Cytc between CIII2 and CIV in SCs rather than 3D diffusion
distance (> 6 nm) between the respective Cytc binding sites between separated, individual complexes (Moe et al, 2021) (Fig 3B).
(Rathore et al, 2019; Vercellino & Sazanov, 2021), allowing electron In line with a previous proposal (Perez-Mejıas et al, 2019), it was
transfer only by a mobile pool of Cytc. However, bacterial SCs do suggested that CIII2 + CIV SC formation provides a negatively
contain covalently bound Cytc, clearly allowing substrate channel- charged surface patch on top of this SC, on which the positively
ing to transfer electrons from CIII to CIV (Daldal et al, 2003; Gong charged Cytc can “roll”. These structural properties can also be
et al, 2018; Kao et al, 2022). found in the mammalian version of this complex (Vercellino &
Sazanov, 2021). Hence, this mechanisms might present an alterna-
Efficiency of electron transfer and competitive fitness tive to substrate channeling, for which diffusion of Cytc within the
While substrate channeling in a strict definition can be excluded as SC is favored by electrostatic interactions, but still allows a free
a possibility to explain the occurrence of SC in mitochondria, it is exchange with the universal soluble Cytc pool (Moe et al, 2021;
still feasible that a bioenergetic advantage of SC formation can Vercellino & Sazanov, 2021, 2022; Fig 3B). However, the signifi-

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derive from an increased efficiency of electron transfer between the cance of an electrostatic interaction for 2D diffusion restricted to SCs
individual complexes (Fig 3C). One approach to test this hypothesis depends on the ionic strength of the local environment and the lipid
would be to delete factors essential for the formation of SCs and composition of the IMM. Currently, these aspects have not been
then determine electron transfer efficiencies. This has been firmly determined, but are essential to establish the relevance of
performed for SCAF1, which, as stated above, does not affect the such a 2D diffusion. Moreover, whether physiological or environ-
formation of respirasomes, but the assembly of CIII2 + CIV SCs. mental factors could modulate the ratio of Cytc 2D versus 3D diffu-
The ablation of SCAF1 did not affect bioenergetics, but rather pro- sion has not been investigated. In addition, limiting the 3D diffusion
voked changes in nutrient sensing (Perez-Perez et al, 2016; Lobo- of Cytc impairs mitochondrial function and cellular viability (Toth
Jarne & Ugalde, 2018). In contrast, bioenergetic differences were et al, 2020). Of note, these results were obtained by reducing the
observed in a zebrafish model, where absence of SCAF1 caused mobility of the whole Cytc pool and not only a potential subpopula-
abnormal fat deposition and reduction in fertility (Garcıa-Poyatos tion interacting with SCs. In sum, current studies demonstrate that
et al, 2020). As further discussed below, controversial results were the formation of CIII2 + CIV SCs increases the efficiency of electron
reported in mouse models, showing either measurable or no effects transport via Cytc. However, the exact modalities and biophysical
on energy metabolism upon deletion of SCAF1 (Lapuente-Brun properties establishing this advantage remain to be investigated.
et al, 2013; Mourier et al, 2014; Shiba et al, 2017).
Moreover, in many systems, including mammalian mitochon- Mitochondrial respiratory complex stability and assembly
dria, the respiratory chain complexes assemble in a variety of super- The structural interdependence between MRC complexes was first
complexes with varying degrees of stoichiometries, thereby observed in cells from patients with mitochondrial diseases, where
complicating analyses of the bioenergetic efficiency of the different mutations affecting CIII or CIV frequently lead to a combined CI
assemblies. Here, yeast offers a unique advantage by lacking CI and deficiency (Lamantea et al, 2002; Fernandez-Vizarra et al, 2007),
having CIII and CIV organized primarily in common supercom- suggesting that SCs may play roles in CI stability. The observation
plexes. We recently used information from the cryo-EM structure of that, in a CIII mutant, CI levels could be restored by treatment with
S. cerevisiae CIII2 + CIV1-2 (Rathore et al, 2019) to selectively disrupt antioxidants, while SC-associated CI is not affected by high ROS
SCs without affecting individual complexes. We genetically engi- levels (Diaz et al, 2012), suggests that only free CI is highly sensitive
neered mutants of Cor1, expressed under their endogenous pro- to ROS-induced damage and degradation.
moter at physiological levels (Berndtsson et al, 2020). These point Another hypothesis on the physiological significance of SCs
mutations caused the disruption of CIII2 + CIV1-2 SCs as the only SC suggested that these large assemblies are scaffolds for the late stages
species present in S. cerevisiae, without affecting individual com- of CI biogenesis involving the incorporation of the NADH module to
plexes. This selective disruption impaired electron transport by the CI peripheral arm (Moreno-Lastres et al, 2012). However, this
impacting the diffusion efficiency of Cytc between the individual hypothesis has been challenged by kinetic studies of CI assembly,
complexes (Berndtsson et al, 2020). Increased concentrations of where a small amount of fully assembled CI could be detected
Cytc could correct for this defect. Interestingly, this decreased effi- before the formation of SCs (Guerrero-Castillo et al, 2017). More
ciency of electron transfer had no severe consequences on cellular recently, it was shown that the lack of CIII prevents the incorpora-
physiology, including unaltered oxidative stress levels, tion of CI NADH module from completing the functional enzyme
cellular growth, and viability in isolated cultures. However, the dis- (Protasoni et al, 2020). Moreover, the association of the late assem-
ruption of SCs caused massively reduced competitive cellular fit- bly CI precursor with CIII and/or CIV was detected in mutant cell
ness, which could be restored by the overexpression of Cytc. These lines and animal models (Alston et al, 2018; Adjobo-Hermans
results thus demonstrate that the formation of SCs in living aerobic et al, 2020; Fang et al, 2021). Additionally, data supporting the inter-
cells increases the efficiency of cellular energy conversion, which action of CIII and CIV subunits and assembly modules directly in
promotes an evolutionary advantage that can be selected for the SCs have been reported (Lazarou et al, 2009; Lobo-Jarne
(Berndtsson et al, 2020) (Fig 3C). et al, 2020; Tim on-Gomez et al, 2020). Taken together, increasing
Results on increased electron transfer efficiency established by evidence supports the existence of distinct but interconnected
this work align well with recent mathematical modeling of this assembly pathways for free complexes and SCs, a model referred to

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Andreas Kohler et al EMBO reports

as the cooperative assembly model (Fernandez-Vizarra & Ugalde, improved bioenergetics; however, possible SC-independent roles
2022). of SCAF1 in fat metabolism in fish were not fully discarded.
Two more recent studies have added support to the concept of
Mitochondrial respiratory chain organization and MRC organization-dependent metabolic remodeling. One study
metabolic adaptation showed that two separate MRC organizations co-exist in human
The plasticity model of mammalian MRC organization proposes that cells and post-mitotic tissues, which the authors called C-MRC and
individual complexes assemble into SCs in a dynamic manner to S-MRC. These are defined by the preferential expression of the CIV
adapt to changing cellular metabolic needs (Acın-Perez et al, 2008). COX7A isoforms, COX7A2 and SCAF1 (Fernandez-Vizarra et al,
However, despite the variety of MRC complexes distribution in 2022), respectively. The SCAF1-dependent S-MRC organization is
free form and SCs observed in different cell types and tissues characterized by the presence of the SCAF1-containing respirasome,
(Lapuente-Brun et al, 2013), the data reflect steady-state levels and which accounts for approximately 50% of total CIII and CIV levels.
the dynamic nature of the MRC organization has not been experi- At the same time, the remaining CIII and CIV are equally distributed
mentally demonstrated. Alternatively, adaptation to the cellular between the CIII2 + CIV SC and free complexes. On the contrary,
energetic requirements could be provided by the existence of inter- the COX7A2-dependent C-MRC organization displays a relatively
connected assembly pathways, where incorporation of late assem- low amount of the COX7A2-containing respirasome, no CIII2 + CIV

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bly catalytic modules into individual complex or SC pre-assembled SC, and abundant free CIII (~ 60% of total CIII) and CIV (~ 80% of
intermediates could modulate MRC organization (Fernandez-Vizarra total CIV). The exclusive presence of one configuration or the other
& Ugalde, 2022). Although the mechanisms behind these models are in knock-out cells of the corresponding isoform led to some changes
yet to be fully disclosed, both scenarios suggest the involvement of in mitochondrial bioenergetics. However, no differences in respira-
SC assembly/disassembly factors acting as sensors or assembly tory parameters were observed between SCAF1 or COX7A2 knock-
checkpoints. As mentioned above, the only dedicated SC out and wild-type cells, where the two MRC organizations co-exist.
assembly factor identified to date is SCAF1 (Cogliati et al, 2016). The increment in respiratory rate supported by the addition of succi-
There is a general agreement that in all cell lines and model organ- nate (a CII substrate) to permeabilized cells already respiring CI sub-
isms, the absence of or mutations in SCAF1 lead to the lack of SC strates was shown to be lower in cells expressing the S-MRC
CIII2 + CIV formation, while allowing the assembly of respirasomes compared to C-MRC, suggesting that the electrons from CI saturate
(Cogliati et al, 2016; Perez-Perez et al, 2016; Lobo-Jarne & the downstream MRC segment (Q to CIV) at a greater extent in the S
Ugalde, 2018). It is also established that the stability of respirasomes configuration. Preferential utilization of the NADH versus FADH2
and, particularly, larger SC structures is compromised to different route parallels with the fraction of total CIII and CIV distributed in
extents depending on the cell type and tissue (Cogliati et al, 2016; respirasomes. This suggests the existence of a kinetic advantage for
Perez-Perez et al, 2016; Williams et al, 2016; Lobo-Jarne & electron transfer within SCs possibly linked to the proximity of elec-
Ugalde, 2018). On the contrary, the question of whether the changes tron carrier binding sites. However, NADH- and FADH2-linked respi-
in SC organization promoted by the absence of SCAF1 ultimately ration are not fully additive in either configuration, arguing against
lead to a metabolic adaptation remains to be fully answered. Some Q pool partitioning. Moreover, the lack of COX7A2 causes a
studies concluded that SCAF1-dependent MRC remodeling is not decrease in total CIV amount and enzymatic activity by 50%, which,
essential, neither to maintain mitochondrial bioenergetics nor to although it does not affect endogenous and coupled respiration,
cope with acute cellular stresses (hypoxia or oxidative stress) in reduces spare respiratory capacity. This relevant confounding vari-
HEK293T cells (Perez-Perez et al, 2016; Lobo-Jarne & Ugalde, 2018). able can contribute to the observed decrease in CII minus CI- and
Other studies showed that in U2OS cells, ER stress and glucose ATP-driven respiration in S-MRC cells. Lastly, the authors showed
deprivation stimulate mitochondrial bioenergetics and SC forma- that stimulation of pyruvate dehydrogenase (PDH) activity to pro-
tion through protein kinase R-like ER kinase (PERK) by enhancing mote a switch toward oxidative metabolism in human fibroblasts
SCAF1 levels through the PERK-eIF2a-ATF4 axis (Balsa reduces SCAF1 steady-state levels and favors the C-MRC configura-
et al, 2019). Likewise, increased SC levels were associated with tion. This observation establishes a direct link between the MRC
mitochondrial efficiency and growth in severely hypoxic pancreatic organization and cellular metabolism, controlled by PDH activity.
cancer (Hollinshead et al, 2020). An inconsistent picture was also Intriguingly, while the study proposes that a metabolic shift toward
obtained from the study of animal models. These studies have oxidative metabolism destabilizes SCAF1, data from human and
shown that SCAF1 promotes SC formation as well as metabolic mouse tissues indicate that SCAF1 expression is induced by PGC1a
efficiency in zebrafish (Garcıa-Poyatos et al, 2020) and in some and enhances respiratory capacity (Benegiamo et al, 2022).
mouse models (Lapuente-Brun et al, 2013; Shiba et al, 2017) but A study in humans has shown significant genetic variation in
not others (Mourier et al, 2014). One of these studies showed that SCAF1 in several tissues, most prominently in skeletal muscle
SCAF1 KO mice exhibit lower blood glucose levels after insulin or (Benegiamo et al, 2022). The most significant variant was an inser-
pyruvate injection, which suggested that the protein could be tion in the 30 untranslated region of the gene that creates a short-
involved in the regulation of glucose homeostasis (Shiba repeated sequence and enhances SCAF1 expression. Human
et al, 2017). However, whether the physiological manifestations myotubes carrying this genetic variant have enhanced SC levels and
correlated with or were the cause of altered SC formation was not respiratory capacity. One would expect that the S-MRC would accu-
fully defined. Work in zebrafish models showed that SCAF1- mulate in these myotubes, but this was not determined. Neverthe-
deficient animals were smaller in size and had abnormal fat depo- less, an important finding was that this variant is associated with
sition, phenotypes that were rescued by doubling the food supply lower body fat and improved cardiorespiratory fitness in humans
(Garcıa-Poyatos et al, 2020). This phenotype rescue correlated with (Benegiamo et al, 2022). This observation was reproduced in a

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EMBO reports Andreas Kohler et al

mouse model, where it was also shown that SCAF1 and SCAF1-
In need of answers
containing SCs are induced upon exercise, specifically in the skeletal
muscle, in a manner independent of PGC1a (Benegiamo et al, • To fully unravel the functional interplay of respiratory chain com-
2022). Taken together, these studies support the conclusion that plexes in SCs and its mechanistic benefit, it might be necessary to
SCAF1 and SC levels correlate with metabolic fitness (Fig 3C), reconstitute purified SCs into proteoliposomes to study their perfor-
mance in a minimal system, free from confounding secondary
although the cellular context may modulate the nuances of this
variables.
correlation. • The functional connectivity of the respiratory chain by mobile elec-
tron carriers is likely a key aspect of SC/respirasome formation. It
Other proposed functions of respiratory chain supercomplexes would be important to determine the absolute and relative concen-
Most studies on SCs mention that the limitation of oxidative stress trations of Cytc or Q, and RCs in order to test how they might deter-
mine the dependency on SC/respirasome formation to achieve
could be a function of these assemblies. However, only very limited
optimal electron transport rates.
evidence for such a role was provided. CI and CIII are the main pro- • While this manuscript was under editorial proof, an article was
duction sites of reactive oxygen species in mitochondria (Mur- published where a more than 50% reduction in SC and respirasome
phy, 2009), and hence, it was postulated that the formation of the formation was achieved in a mouse model, without overly perturbing
respiration or physiology (Milenkovic et al, 2023). Hence, it would be
respirasome somehow alleviates oxidative stress from these sites.
desirable for future studies to generate mutants in higher organisms,

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Indeed, an in vitro study suggests that the dissociation of CI + CIII2 where the formation of SCs and respirasomes is completely abolished.
SCs increases oxidative stress (Maranzana et al, 2013). In line with • Once these mutants are available, it would be very interesting to
these results, it was observed that the higher abundance of free CI score how they impact stress tolerance and competitive fitness.
in astrocytes compared to neurons correlates with higher oxidative • The interdependency of assembly of the different respiratory chain
complexes has suggested that mature complexes might facilitate
stress found in astrocytes (Lopez-Fabuel et al, 2016). Unfortunately,
assembly of the partner complex through direct contacts. However,
a molecular mechanism for such a potential reduction of reactive assembly also occurs in the absence of the partner complex. To
oxygen species by SC formation has not been demonstrated, and unravel the contribution for the co-assembly pathways for overall
hence, this hypothesis is only based on correlations. A causative assembly, efficiency will be an important aspect of future research.
role of SC formation to limit oxidative stress remains to be
determined.
Finally, it was also proposed that SCs prevent the aggregation of
proteins in the IMM (Blaza et al, 2014). Although this is feasible, as pathways to occur, they likely improve the overall biochemical
the IMM presents one of the most protein-dense regions of a cell, efficiency, possibly only with a small, but nevertheless selectable,
direct experimental evidence for this hypothesis is missing. margin. While these small beneficial margins may be neglectable
or even sometimes undetectable in experimental setups and
under laboratory conditions, they have impacted selection during
Summary evolution and seem to affect performance in mammalian tissues.
Particularly in the context of evolutionary pressure via
Since the discovery of SCs more than 20 years ago (Scha €gger & competition in natural environments and in stress scenarios (e.g.,
Pfeiffer, 2000), significant advances in our understanding of these high temperature, hypoxic conditions, limited nutrients), these
gigantic assemblies have been made. In particular, the latest work subtle bioenergetic advantages of SC formation can be the basis
on the structural characterization of SCs presented a giant leap in for selection. Employing the recent structural insights into respira-
the field (Gu et al, 2016; Letts et al, 2016; Hartley et al, 2019; tory SCs should allow engineering of further sets of genetic
Rathore et al, 2019; Vercellino & Sazanov, 2021; Zhou et al, 2022; mutants to fully unravel the intricacies and physiological impact of
Klusch et al, 2023; Maldonado et al, 2023). Still, the physiological SC formation.
functions of SCs remain a matter of debate (Milenkovic et al, 2017).
Recent reports have indicated that SC formation primarily enhances Acknowledgements
the efficiency of electron transport. The emerging picture favors a We would like to thank the members of our laboratory for stimulating
model in which SC formation, as such, does not modify the maximal discussions. This work was supported by Austrian Science Fund FWF (J4398-B
activity of individual complexes (Mourier et al, 2014; Berndtsson to AK), the Swedish research council (2014-4116 and 2018-03694 to MO), the
et al, 2020), but optimizes their cooperation in the context of the Knut and Alice Wallenberg foundation (2017.0091 and 2019.0319 to MO),
overall pathway. the National Institutes of Health R35 grant GM118141 (to AB), and the US
Supercomplex formation constitutes another example for a Army research office (W911NF-21-1-0359 to FF).
growing theme of gathering functionally related activities in com-
mon complexes or into proximal localization. This strategy, which Author contributions
is widely employed in life, is used extensively in mitochondria Andreas Kohler: Conceptualization; writing – original draft; writing – review
(Linden et al, 2020; Schulte et al, 2023) as exemplified by a super- and editing. Antoni Barrientos: Conceptualization; writing – original
complex collecting enzymes mediating Q biosynthesis (Marbois draft; writing – review and editing. Flavia Fontanesi: Conceptualization;
et al, 2009), the establishment of membrane subdomains where writing – original draft; writing – review and editing. Martin Ott:
early steps of MRC biogenesis are organized (Singh et al, 2020) Conceptualization; writing – original draft; writing – review and editing.
and mitochondrial RNA granules (Antonicka et al, 2013; Jourdain
et al, 2013), executing early steps of mtRNA maturation. However, Disclosure and competing interests statement
while all these organizations might not be essential for these The authors declare that they have no conflict of interest.

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Acad Sci USA 115: 3048 – 3053 terms of the Creative Commons Attribution License,
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