Analysis of Human Mutations in the Supernumerary Subunits of Complex I

Abstract

Complex I is the largest member of the electron transport chain in human mitochondria. It comprises 45 subunits and requires at least 15 assembly factors. The subunits can be divided into 14 "core" subunits that carry out oxidation-reduction reactions and proton translocation, as well as 31 additional supernumerary (or accessory) subunits whose functions are less well known. Diminished levels of complex I activity are seen in many mitochondrial disease states. This review seeks to tabulate mutations in the supernumerary subunits of humans that appear to cause disease. Mutations in 20 of the supernumerary subunits have been identified. The mutations were analyzed in light of the tertiary and quaternary structure of human complex I (PDB id = 5xtd). Mutations were found that might disrupt the folding of that subunit or that would weaken binding to another subunit. In some cases, it appeared that no protein was made or, at least, could not be detected. A very common outcome is the lack of assembly of complex I when supernumerary subunits are mutated or missing. We suggest that poor assembly is the result of disrupting the large network of subunit interactions that the supernumerary subunits typically engage in.

Keywords: Leigh syndrome; NADH dehydrogenase; complex I assembly; complex I deficiency; complex I structure; electron transport chain; mammalian complex I; mitochondria; mitochondrial dysfunction; supernumerary subunits.

Figure 1

Structure of complex I with supernumerary subunits highlighted. Core subunits in the matrix arm are colored light blue. Core subunits in the membrane arm are colored beige. Supernumerary subunits that are described in this review are colored and labeled. Other supernumerary subunits are white. The two views are rotated 180° relative to each other. The structure is from the Protein Data Bank file 5xtd (PDB id = 5xtd) [9]. All structural images were generated using Jmol (http://www.jmol.org).

Figure 2

Location of NDUFA2 and NDUFV3. Most of Complex I is colored gray. Core subunits in the N-module arm are colored light blue (NDUFV1, NDUFV2, and NDUFS1). NDUFA2 and NDUFV3 are shown in ribbons, with NDUFA2 colored purple and NDUFV3 colored red. The two views are rotated 180° relative to each other. The structure is from PDB id = 5xtd [9].

Figure 3

Structural features of NDUFA2 from the N-module. The protein is portrayed in a purple-colored ribbon. Sites of mutations are shown in space-filling views: Lys45Thr and Glu57Ala are mitochondrial disease mutations (colored lime). Asn50Asp has been found in breast cancer patients (colored pink). Two Cys residues are colored yellow.

Figure 4

Location of NDUFS4, NDUFS6, and NDUFA9. Most of Complex I is colored gray. Core subunits in the Q-module are colored light blue (NDUFS2, NDUFS3, NDUFS7, and NDUFS8). NDUFS4, NDUFS6, and NDUFA9 are shown in ribbons, with NDUFS4 colored magenta, NDUFS6 colored green, and NDUFA9 colored cyan. The two views are rotated 180° relative to each other. The structure is from PDB id = 5xtd [9].

Figure 5

Structural features of 3 interacting subunits from the Q-module. The proteins are portrayed in ribbons. NDUFS4 is colored magenta. The sites of two mutations in this subunit, Trp114Arg and Asp119His, are shown in space-filling and are colored blue. NDUFS6 is colored green. The zinc bind residues are shown in space-filling, with Cys colored yellow and His colored green. The site of the mutation, Cys115Tyr is colored black. NDUFA9 is colored cyan, and its bound ligand NADP⁺ is shown in space-filling with CPK colors (e.g., carbon gray, nitrogen blue, oxygen red, phosphorus orange). The sites of 2 mutations, Arg321Pro and Arg360Cys, are shown in space-filling and are colored red.

Figure 6

Location of NDUFA1, NDUFA3, and NDUFA13. Most of Complex I is colored gray. Core subunits in the ND1-modules are colored light blue (ND1). NDUFA1, NDUFA3, and NDUFA13 are shown in ribbons, with NDUFA1 colored blue, NDUFA3 colored orange, and NDUFA13 colored pink. The two views are rotated 180° relative to each other. The structure is from PDB id = 5xtd [9].

Figure 7

Structural features of ND1-module subunits. The proteins are portrayed in ribbons. ND1 is in the background and colored light gray. NDUFA1 is colored blue with the sites of 4 mutations, Gly8Arg, Pro19Ser, Gly32Arg, and Arg37Ser, shown in space-filling and colored yellow. NDUFA3 is shown in orange. No point mutations have been discovered yet. NDUFA13 is colored pink. The site of one mutation, Arg57His, is shown in space-filling and colored black.

Figure 8

Location of NDUFA6 and NDUFB9. Most of Complex I is colored gray. They are shown in ribbons, with NDUFA6 colored yellow and NDUFB9 colored lime. The two views are rotated 180° relative to each other. The structure is from PDB id = 5xtd [9].

Figure 9

Structural features of the LYR proteins, NDUFA6 and NDUFB9. (a) NDUFA6 (colored yellow) is shown with its partner NDUFAB1 (colored gray), known as one of the two acyl carrier proteins (ACPs). NDUFA6 binds the 4′-phosphopantethiene (4′-PPT) analog substrate for the ACP. Tyr36 and Arg37 of the LYR motif are shown in space-filling and colored cyan. The site of the Arg64Pro mutation is shown in space-filling and colored blue. (b) NDUFB9 (colored lime) is shown with its partner NDUFAB1 (colored gray), the other one of the two ACPs. NDUFB9 binds the 4′-PPT analog substrate for the ACP. Tyr20 and Lys21 of the LYR motif are shown in space-filling and colored pink. The site of the Arg64Pro mutation is shown in space-filling and colored magenta.

Figure 10

Location of NDUFS5, NDUFA8, and NDUFB10. Most of Complex I is colored gray. NDUFS5, NDUFA8, and NDUFB10 are shown as ribbons, with NDUFS5 colored red, NDUFA8 colored green, and NDUFB10 colored blue. They are found facing the intermembrane space. The two views are rotated 180° relative to each other. The structure is from PDB id = 5xtd [9].

Figure 11

Structural features of NDUFA8, a member of the twin C–X₉–C. The proteins are portrayed in ribbons. NDUFA8 is colored green, NDUFC2 is colored gold, and NDUFB5 is colored blue. In NDUFA8, the eight Cys residues that form disulfide bonds are shown in space-filling and colored yellow. The sites of three mutations, Arg47Cys, Glu109Lys, and Arg135Gln, are shown in space-filling and colored black. NDUFB5 makes contact near Arg47, and both NDUFB5 and NDUFA8 contact NDUFC2. The site of one mutation in NDUFC2, His58Leu, is shown in space-filling and colored red.

Figure 12

Location of NDUFA10 and NDUFC2. Most of Complex I is colored gray. Core subunits in the ND2-module are colored light blue (ND2). NDUFA10 and NDUFC2 are shown in ribbons, with NDUFA10 colored red and NDUFC2 colored gold. The two views are rotated 180° relative to each other. The structure is from PDB id = 5xtd [9].

Figure 13

Structural features of two subunits from the ND2-module. NDUFA10, colored red, and NDUFC2, colored gold, are portrayed in ribbons. The site of one mutation, His48Leu in NDUFC2, is shown in space-filling and colored blue. The sites of three mutations in NDUFA10—Gly99Glu, Gln142Arg, and Leu294Pro—are shown in space-filling and colored yellow. The site of phosphorylation by PINK1, Ser250, is shown in space-filling and colored cyan. NDUFA10 likely binds an adenosine nucleoside, not shown.

Figure 14

Location of NDUFA11 and NDUFB11. Most of Complex I is colored gray. Core subunits in the ND4-module are colored light blue (ND4). NDUFA11 and NDUFB11are shown in ribbons, NDUFA11 colored blue and NDUFB11 colored purple. The two views are rotated 180° relative to each other. The structure is from PDB id = 5xtd [9].

Figure 15

Structural features of NDUFB11 of the ND4-module. The proteins are shown as ribbons, with NDUFB11 colored purple and ND4 colored light gray. The sites of two mutations are shown in space-filling, Phe93 (a deletion) and Glu121Lys (in the IMS).

Figure 16

Location of NDUFB3, NDUFB6, and NDUFB8. Most of Complex I is colored gray. Core subunits in the ND5-module are colored light blue (ND5). NDUFB3, NDUFB6, and NDUFB8 are shown in ribbons, with NDUFB3 colored violet, NDUFB6 colored salmon, and NDUFB8 colored pink. The two views are rotated 180° relative to each other. The structure is from PDB id = 5xtd [9].

Figure 17

Structural features of NDUFB8 from the ND5-module. The sites of three mutations in NDUFB8 are shown in space-filling. NDUFB8 is colored pink, while the sites of Pro76Gln and Tyr62His are shown in blue on the matrix side, and Cys144Trp is shown in yellow. The Cys279 of ND5 is shown in orange, and it appears to form a disulfide with Cys144 of NDUFB8.