A three-dimensional topology of complex I inferred from evolutionary correlations

Abstract

Background: The quaternary structure of eukaryotic NADH:ubiquinone oxidoreductase (complex I), the largest complex of the oxidative phosphorylation, is still mostly unresolved. Furthermore, it is unknown where transiently bound assembly factors interact with complex I. We therefore asked whether the evolution of complex I contains information about its 3D topology and the binding positions of its assembly factors. We approached these questions by correlating the evolutionary rates of eukaryotic complex I subunits using the mirror-tree method and mapping the results into a 3D representation by multidimensional scaling.

Results: More than 60% of the evolutionary correlation among the conserved seven subunits of the complex I matrix arm can be explained by the physical distance between the subunits. The three-dimensional evolutionary model of the eukaryotic conserved matrix arm has a striking similarity to the matrix arm quaternary structure in the bacterium Thermus thermophilus (rmsd=19 Å) and supports the previous finding that in eukaryotes the N-module is turned relative to the Q-module when compared to bacteria. By contrast, the evolutionary rates contained little information about the structure of the membrane arm. A large evolutionary model of 45 subunits and assembly factors allows to predict subunit positions and interactions (rmsd=52.6 Å). The model supports an interaction of NDUFAF3, C8orf38 and C2orf56 during the assembly of the proximal matrix arm and the membrane arm. The model further suggests a tight relationship between the assembly factor NUBPL and NDUFA2, which both have been linked to iron-sulfur cluster assembly, as well as between NDUFA12 and its paralog, the assembly factor NDUFAF2.

Conclusions: The physical distance between subunits of complex I is a major correlate of the rate of protein evolution in the complex I matrix arm and is sufficient to infer parts of the complex's structure with high accuracy. The resulting evolutionary model predicts the positions of a number of subunits and assembly factors.

Figure 1

Co-evolutionary distance correlates with physical distance. The figure shows the distances for the subunits in the evolutionary conserved core in T. thermophilus[5] (PDB:3M9S). Note that in the bacterial structure NADH3, 4L and 6 were not identified individually but are neighboring. Therefore, we calculated the co-evolutionary distances with concatenated alignments of these subunits. The red line is the regression line for the matrix arm and the black line is the regression line for the complete set of points.

Figure 2

Superimposition of the subunit centers predicted by the evolutionary model and those of the experimental model from T. thermophilus [[5]]. The arrowheads point towards the coordinates in the evolutionary configuration while the labeled arrow origins correspond to the coordinates in the experimental structure. (a) and (b) show the results for the evolutionary model of the seven conserved matrix arm subunits. The axes are the first three principal components (PC) of the evolutionary configuration. Figure (c) shows the results for the evolutionary model of all 14 conserved membrane and matrix arm subunits. The axes are the first two PCs derived from a PCA on the evolutionary coordinates. Blue: distal matrix arm/N-module; purple: proximal matrix arm/Q-module; red: membrane arm/P-module. Subunit names were abbreviated by omitting the “NDUF” or “NADH” prefixes.

Figure 3

Evolutionary model of 38 subunits and seven assembly factors of human complex I. Only the predicted subunit centers are displayed. The evolutionary model was first rotated and scaled to fit to the bacterial structure and both models were then manually rotated into the orientations of the bacterial complex shown in the insets. The symbols code the sub-complex association according to Vogel et al. [93]. Sub-complex Iα-λ represents the fraction of large sub-complex Iα that is not also contained in the smaller matrix arm sub-complex Iλ. Category “?” represents subunits that have not been assigned to any sub-complex. Assembly factors are labeled in italics and red. Subunit names were abbreviated by omitting the “NDUF” or “NADH” prefixes where applicable. N: NUBPL; O7: C20orf7; O38: C8orf38; O56: C2orf56. An interactive three-dimensional model of the evolutionary configuration is provided in Additional file 2.