Mitochondrial supercomplexes containing complexes I, III, and IV of the electron transport chain are now regarded as an established entity. Supercomplex I⅐III⅐IV has been theorized to improve respiratory chain function by allowing quinone channeling between complexes I and III. Here, we show that the role of the supercomplexes extends beyond channeling. Mutant analysis in Caenorhabditis elegans reveals that complex III affects supercomplex I⅐III⅐IV formation by acting as an assembly or stabilizing factor. Also, a complex III mtDNA mutation, ctb-1, inhibits complex I function by weakening the interaction of complex IV in supercomplex I⅐III⅐IV. Other complex III mutations inhibit complex I function either by decreasing the amount of complex I (isp-1), or decreasing the amount of complex I in its most active form, the I⅐III⅐IV supercomplex (isp-1;ctb-1). ctb-1 suppresses a nuclear encoded complex III defect, isp-1, without improving complex III function. Allosteric interactions involve all three complexes within the supercomplex and are necessary for maximal enzymatic activities.A solid-state model (1) of the mitochondrial respiratory chain within the mitochondrial membrane was proposed a half-century ago. In this model, the respiratory complexes are assembled into multicomplex structures, supercomplexes. Supercomplexes are capable of substrate channeling and thus facilitate transfer of electrons from one complex to the next (2). This is in contrast to the random collision model (3), which proposes that the complexes of the mitochondrial respiratory chain are embedded in the inner mitochondrial membrane as separate entities. Individual complexes are functionally connected to each other by the small, mobile electron carriers, coenzyme Q, and cytochrome c. The random collision model became more generally accepted as kinetic studies demonstrated homogenous pool behavior of coenzyme Q (4), rates of electron transfer that did not require substrate channeling, and the successful isolation of individual respiratory complexes that were enzymatically active (3, 5). However, supercomplex structures containing complexes I, III, and IV, have been investigated by blue native polyacrylamide gel electrophoresis (BN-PAGE), 3 sucrose gradient centrifugation, and single particle analysis (6, 7). A recent study by convincingly showed that supercomplexes are functional units capable of consuming oxygen when provided appropriate electron donors. They concluded that supercomplexes are in fact the functional respiratory unit of the mitochondrion in vivo. Schagger and Pfeiffer (9) demonstrated that supercomplex I⅐III⅐IV appears on blue native gels (BNGs) with increasing stoichiometries of complex IV. They termed these entities S0 -S4, where the numeral denotes the number of complex IVs within the supercomplex.Supercomplexes provide a logical explanation for combined deficiencies of the electron transport chain (ETC) observed in patients. It is estimated that ϳ30% of all ETC disorders involve multiple complexes (10). Combined I⅐IV deficie...