In mitochondria, four respiratory-chain complexes drive oxidative phosphorylation by sustaining a proton-motive force across the inner membrane that is used to synthesize ATP. The question of how the densely packed proteins of the inner membrane are organized to optimize structure and function has returned to prominence with the characterization of respiratory-chain supercomplexes. Supercomplexes are increasingly accepted structural entities, but their functional and catalytic advantages are disputed. Notably, substrate “channeling” between the enzymes in supercomplexes has been proposed to confer a kinetic advantage, relative to the rate provided by a freely accessible, common substrate pool. Here, we focus on the mitochondrial ubiquinone/ubiquinol pool. We formulate and test three conceptually simple predictions of the behavior of the mammalian respiratory chain that depend on whether channeling in supercomplexes is kinetically important, and on whether the ubiquinone pool is partitioned between pathways. Our spectroscopic and kinetic experiments demonstrate how the metabolic pathways for NADH and succinate oxidation communicate and catalyze via a single, universally accessible ubiquinone/ubiquinol pool that is not partitioned or channeled. We reevaluate the major piece of contrary evidence from flux control analysis and find that the conclusion of substrate channeling arises from the particular behavior of a single inhibitor; we explain why different inhibitors behave differently and show that a robust flux control analysis provides no evidence for channeling. Finally, we discuss how the formation of respiratory-chain supercomplexes may confer alternative advantages on energy-converting membranes.Contemporary models for the organization of respiratory-chain complexes in energy-transducing membranes range from the fluid model to the respirasome model. In the fluid model each complex is a free and independent entity, and substrates exchange freely between enzymes through common ubiquinone/ubiquinol (Q) and cytochrome
cox/
cred (cyt
c) pools (
1–
3). In the respirasome model the complexes are assembled into units that contain everything required for catalysis; substrates are channeled between enzymes within the respirasome, not exchanged with external pools (
4,
5). Intermediate models, in which some enzymes are free and some assembled into multienzyme supercomplexes, or in which supercomplexes are assembled and disassembled in response to changing conditions, are increasingly considered a realistic combination of these two extremes (
6).Structural evidence for respiratory-chain supercomplexes, initiated by observations by blue native PAGE analyses of mammalian mitochondria (
4,
7), has culminated in electron microscopy data that revealed the arrangement of complexes I, III, and IV in a particular class of isolated supercomplex assembly (
8,
9); respiratory-chain supercomplexes have also been observed (at lower resolution) in the membrane (
10). Furthermore, specific proteins have been found to mediate interactions between specific pairs of respiratory complexes, and functionally removing these proteins prevents the relevant supercomplexes from forming (
11–
14). Thus, structural associations between membrane-bound respiratory complexes are increasingly accepted.Whether a catalytic or functional justification for the formation of respiratory-chain supercomplexes exists is uncertain. The most widely cited evidence for a catalytic role, from flux control analysis (
15), was considered to support substrate channeling between enzymes present within respirasomes. More recently, the existence of dedicated Q and cyt
c pools within supercomplex assemblies was proposed to determine electron transport chain flux, based on the relative rates of complex I- and complex II-linked respiration observed when complexes I and/or III are ablated (
13). Opposing these substrate channeling models, a recent time-resolved kinetic study of the respiratory chain in intact yeast cells concluded that cyt
c is not trapped within supercomplexes and encounters no restriction to its diffusion (
16).Here, we focus on the mitochondrial Q pool. We formulate and test a set of conceptually simple predictions of the behavior of the mammalian respiratory chain that depend on whether Q channeling in supercomplexes is kinetically important, and on whether the Q pool is partitioned into supercomplex assemblies. Our results are not consistent with Q channeling or partitioning. Consequently, we reevaluate the contrary evidence from flux control analysis and find that the substrate channeling proposal arose from lack of consideration of the effects of enzyme substrate and inhibitor binding properties. We conclude that Q exists as a single, common pool in mammalian mitochondria that is exchanged freely between complexes.
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