Cryo-EM structure of respiratory complex I at work

Parey, Kristian; Brandt, Ulrich; Xie, Hao; Mills, Deryck J.; Siegmund, Karin; Vonck, Janet; Kühlbrandt, Werner; Zickermann, Volker

doi:10.7554/elife.39213

Cited by 97 publications

(95 citation statements)

References 51 publications

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“…In plant, 25 proteins shared with aerobic yeast or mammals are present. Similarly to the previously obtained complex I structure 4,6,9,16 , the supernumerary subunits, specific to mitochondrial complex I, form a shell around the core subunits, adding nearly 400kDa of proteins to the conserved subunits (Extended Data Fig. 6).…”

Section: General Descriptionsupporting

confidence: 57%

Specific features and assembly of the plant mitochondrial complex I revealed by cryo-EM

Soufari

Parrot

Kuhn

et al. 2020

Preprint

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Mitochondria are the powerhouses of eukaryotic cells and the site of essential metabolic reactions. Their main purpose is to maintain the high ATP/ADP ratio that is required to fuel the countless biochemical reactions taking place in eukaryotic cells 1 . This high ATP/ADP ratio is maintained through oxidative phosphorylation (OXPHOS). Complex I or NADH:ubiquinone oxidoreductase is the main entry site for electrons into the mitochondrial respiratory chain and constitutes the largest of the respiratory complexes 2 . Its structure and composition varies across eukaryotes species. However, high resolution structures are available only for one group of eukaryotes, opisthokonts 3-6 . In plants, only biochemical studies were carried out, already hinting the peculiar composition of complex I in the green lineage. Here, we report several cryoelectron microscopy structures of the plant mitochondrial complex I at near-atomic resolution. We describe the structure and composition of the plant complex I including the plant-specific additional domain composed by carbonic anhydrase proteins. We show that the carbonic anhydrase is an heterotrimeric complex with only one conserved active site. This domain is crucial for the overall stability of complex I as well as a peculiar lipid complex composed cardiolipin and phosphatidylinositols. Moreover we also describe the structure of one of the plant-specific complex I assembly intermediate, lacking the whole PD module, in presence of the maturation factor GLDH. GLDH prevents the binding of the plant specific P1 protein, responsible for the linkage of the PP to the PD module. Finally, as the carbonic anhydrase domain is likely to be associated with complex I from numerous other known eukaryotes, we propose that our structure unveils an ancestral-like organization of mitochondrial complex I.Complex I is the largest multimeric enzyme of the respiratory chain, composed of more than 40 protein subunits. 14 are strictly conserved proteins subunits, vestige of complex I of bacterial origin 7 . The additional subunits, referred to as supernumerary subunits, were acquired during eukaryotes evolution. Part of these additional subunits are conserved among other eukaryotes and play essential roles for the structure, function and the association with the other respiratory chain complexes, eg. to assemble into respirasome in animals 8 . Recently, several high resolution 3D structures of the complete mitochondrial complex I of opisthokonts were determined by cryo-EM in mammalian species 4-6 and in the aerobic yeast Yarrowia lipolytica 3,9 , revealing the organization of their additional specie-specific subunits. However, in plants, even though extensive biochemical characterization was conducted 10,11 , high-resolution structures of mitochondrial complex I are yet to be derived. Early negative staining studies 12 revealed the presence of a large additional membrane attached domain, absent from animal and yeast species, hinting at the peculiar structure and composition of the plant complex I.In order...

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Section: General Descriptionsupporting

confidence: 57%

Specific features and assembly of the plant mitochondrial complex I revealed by cryo-EM

Soufari

Parrot

Kuhn

et al. 2020

Preprint

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“…If IACS-010759 enters the channel and is in direct contact with Leu 55 , the channel is almost completely covered by this compound. In that case, quinazoline-type inhibitors (such as [ 125 I]AzQ), which are supposed to enter and transit to near the "top" of the channel (40,42), would no longer enter the channel; but, this was not the case. An excess amount of IACS-010759 did not suppress the binding of [ 125 I]AzQ to the 49-kDa subunit (Figure 4).…”

Section: Discussionmentioning

confidence: 99%

IACS-010759, a potent inhibitor of glycolysis-deficient hypoxic tumor cells, inhibits mitochondrial respiratory complex I through a unique mechanism

Tsuji

Akao

Masuya

et al. 2020

Journal of Biological Chemistry

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The small molecule IACS-010759 has been reported to potently inhibit the proliferation of glycolysis-deficient hypoxic tumor cells by interfering with the functions of mitochondrial NADH-ubiquinone oxidoreductase (complex I) without exhibiting cytotoxicity at tolerated doses in normal cells. Considering the significant cytotoxicity of conventional quinone-site inhibitors of complex I, such as piericidin and acetogenin families, we hypothesized that the mechanism of action of IACS-010759 on complex I differs from that of other known quinone-site inhibitors. To test this possibility, here we investigated IACS-010759's mechanism in bovine heart submitochondrial particles. We found that IACS-010759, like known quinone-site inhibitors, suppresses chemical modification by the tosyl reagent AL1 of Asp160 in the 49-kDa subunit, located deep in the interior of a previously proposed quinone-access channel. However, contrary to the other inhibitors, IACS-010759 direction-dependently inhibited forward and reverse electron transfer and did not suppress binding of the quinazoline-type inhibitor [125I]AzQ to the N terminus of the 49-kDa subunit. Photoaffinity labeling experiments revealed that the photoreactive derivative [125I]IACS-010759-PD1 binds to the middle of the membrane subunit ND1 and that inhibitors that bind to the 49-kDa or PSST subunit cannot suppress the binding. We conclude that IACS-010759's binding location in complex I differs from that of any other known inhibitor of the enzyme. Our findings, along with those from previous study, reveal that the mechanisms of action of complex I inhibitors with widely different chemical properties are more diverse than can be accounted for by the quinone-access channel model proposed by structural biology studies.

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“…The concomitant pumping of protons (H + ) across IMM the establishes an electrochemical proton gradient that is used by ATP synthase to produce ATP [1] . Whereas the atomic details of the respiratory complexes and several supercomplexes (higher-order complex assemblies) are known for yeast, mammals and bacteria [2][3][4][5][6][7][8][9][10][11][12][13] , the high-resolution structural details of the respiratory complexes and supercomplexes of plants have remained mostly unknown.…”

Section: Introductionmentioning

confidence: 99%

Atomic structures of respiratory complex III₂, complex IV and supercomplex III₂-IV from vascular plants

Maldonado

Guo

Letts

2020

Preprint

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Mitochondrial complex III (CIII2) and complex IV (CIV), which can associate into a higher-order supercomplex (SC III2+IV), play key roles in respiration. However, structures of these plant complexes remain unknown. We present atomic models of CIII2, CIV and SC III2+IV from Vigna radiata determined by single-particle cryoEM. The structures reveal plant-specific differences in the MPP domain of CIII2 and define the subunit composition of CIV. Conformational heterogeneity analysis of CIII2 revealed long-range, coordinated movements across the complex, as well as the motion of CIII2’s iron-sulfur head domain. The CIV structure suggests that, in plants, proton translocation does not occur via the H-channel. The supercomplex interface differs significantly from that in yeast and bacteria in its interacting subunits, angle of approach and limited interactions in the mitochondrial matrix. These structures challenge long-standing assumptions about the plant complexes, generate new mechanistic hypotheses and allow for the generation of more selective agricultural inhibitors.

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Cryo-EM structure of respiratory complex I at work

Cited by 97 publications

References 51 publications

Specific features and assembly of the plant mitochondrial complex I revealed by cryo-EM

Specific features and assembly of the plant mitochondrial complex I revealed by cryo-EM

IACS-010759, a potent inhibitor of glycolysis-deficient hypoxic tumor cells, inhibits mitochondrial respiratory complex I through a unique mechanism

Atomic structures of respiratory complex III₂, complex IV and supercomplex III₂-IV from vascular plants

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Cryo-EM structure of respiratory complex I at work

Cited by 97 publications

References 51 publications

Specific features and assembly of the plant mitochondrial complex I revealed by cryo-EM

Specific features and assembly of the plant mitochondrial complex I revealed by cryo-EM

IACS-010759, a potent inhibitor of glycolysis-deficient hypoxic tumor cells, inhibits mitochondrial respiratory complex I through a unique mechanism

Atomic structures of respiratory complex III2, complex IV and supercomplex III2-IV from vascular plants

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Atomic structures of respiratory complex III₂, complex IV and supercomplex III₂-IV from vascular plants