Electron cryomicroscopy structures of respiratory supercomplexes from alphaproteobacteria suggest mechanisms to enhance catalysis and to prevent deactivation of respiratory complex I

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Yaikhomba, Mutum 

In mitochondria, the electron transport chain complexes that generate the proton motive force to drive ATP synthesis form oligomeric membrane assemblies known as supercomplexes. Even though they are found throughout nature and several physiological consequences are associated with their depletion, it is not clear why they have evolved and what their selective advantage is. While the role of mitochondrial CIII-CIV-type supercomplexes in the context of enhancing catalysis is being delineated, the function of respiratory supercomplexes, particularly at the level of complexes I and III, is unresolved. Moreover, the structures of respiratory supercomplexes comprising the entire electron transport chain in bacteria and those with a transmembrane cytochrome c are not known. Here, the structures of five distinct supercomplex assemblies are presented from Paracoccus denitrificans, a close relative of the mitochondrial progenitor. The initial part of the thesis describes the procedure to purify the respiratory supercomplexes from P. denitrificans membranes, the biochemical and mass-spectrometric characterisation of the purified samples, the single-particle data processing scheme to obtain their structures and the subsequent atomic model building for these five different supercomplexes. These supercomplexes – CI2CIII2CIV2, CI1CIII2CIV2(cbb3)1, CI1CIII2CIV2, CI1CIII2CIV1 and CIII2CIV2 were resolved at resolutions of ~3 - 7 Å. The structures demonstrate that bacterial supercomplexes are modular and assembled from minimal components essential for its catalytic function. Intriguingly, the ~200 Å interface between the bacterial complexes in the membrane is held together by predominantly lipid-mediated interactions, reminiscent of 2D crystals of bacteriorhodopsin. Despite this minimal protein-interaction interface, the bacterial structures bear a striking resemblance with the mammalian counterparts, shedding light on the evolutionary origins of eukaryotic supercomplexes. The alphaproteobacterial supercomplex may also suggest a mechanism to enhance catalysis between CI and CIII by providing structural scaffolds to increases the concentration of hydrophobic substrate ubiquinone-10 between the reaction centres. A physical tether anchors the membrane tethered cytochrome c552 not only at the CIII-CIV interface, but also to cytochrome c1, the electron donor site, explaining why cytochrome c552 can function as an efficient endogenous electron relay between them. In our supercomplex structure captured in the oxidised configuration of CIII, the cytochrome domain of cytochrome c552 fails to reach CIV, suggesting a novel ‘switch mechanism’ for its release to allow the cytochrome domain to reach CIV during catalysis. The CI1CIII2CIV2(cbb3)1, supercomplex structure reveals how this is in stark contrast to the mode of electron conduction between CIII and cbb3 oxidase by the water soluble cytochrome c550. The structure of the CI1CIII2CIV2(cbb3)1 supercomplex also reveals how the mechanism employed by the CIII-CIV supercomplex contrasts with the mechanism of electron conduction between CIII and cbb3 oxidase by the water-soluble cytochrome c550. The arrangement of CIII-cbb3 oxidase in the native CI1CIII2CIV2(cbb3)1 supercomplex, also deviates from the genetically engineered CIII-cbb3 counterpart in a related alphaproteobacterium, providing insight into the contrasting mechanism by which the water soluble cytochrome c is utilised between them. In mammals, respiratory complex I is the largest proton pump of the oxidative phosphorylation machinery and is a genetic hotspot for mitochondrial diseases. So far, fundamental mechanistic investigations have been impeded by the lack of a minimal model system which solely exhibits both structural and biochemical characteristics of the catalytically ‘active’ form of the enzyme. Here, the structure of P. denitrificans complex I is solved in a state that resembles the mammalian ‘active’ state at resolutions of 2.9 - 3.1 Å. This structure is characterised by changes in the conformation of several conserved residues along the hydrophilic axis and with a ubiquinone-10 near the active site. Comparison with other structurally resolved homologs reveals that the alphaproteobacterial complex I possesses several evolutionarily unique features that effectively seal the outlets of the quinone reaction chamber, which are prone to solvent exposure and lead to a ‘deactive’ state, an off-catalytic state. This provides a rationale for the long-standing enigma, observed biochemically, why the alphaproteobacterial enzyme does not undergo ‘deactivation’, a process otherwise suggested to be involved in a regulation of mitochondrial physiology and in preventing ischemia-reperfusion injury. Along with other characteristics, such as amenability of the whole complex to genetic manipulation and straightforward growth characteristics, this inability to transition to the ‘deactive’ form establishes the utility of P. denitrificans as a model system for further investigations of the enigmatic catalytic mechanism of complex I.

Hirst, Judy
energy transducing membrane proteins, Respiration, Supercomplexes
Doctor of Philosophy (PhD)
Awarding Institution
University of Cambridge
MRC (MC_UP_1002/1)