Age-Dependent Evolution of the Yeast Protein Interaction Network Suggests a Limited Role of Gene Duplication and Divergence
Figure 6
The spatial subunit arrangement of known multi-protein complexes is consistent with the CG model.
Subunits of all 12 known multi-protein complexes with at least three proteins and two-age groups are colored according to their age groups: The most ancient group, ABE, is colored in red tones (yellow, pink, magenta, orange, red). The AB, AE, or BE groups are in green tone, and the most recent A, B, and E groups are in blue. For visual clarity, the older group(s) is presented in cartoon models and the youngest group in space-filling models in each complex. The age group assignments in (K) and (L) were ambiguous because the chains assigned AE could be assigned to ABE if the BLAST hit cut-off was slightly relaxed to 25% instead of 30% sequence identity (the “twilight zone” for homology detection). Therefore, (K) and (L) may, in fact, consist of the subunits of the ABE group only. The subunits are in various configurations. In (A) and (L), the younger subunits are spatially separated, but the older subunits are aggregated. In (B–E), two old subunits (three in (E)) and one young subunit are linearly connected. In all four cases, the older subunits are all connected without insertion of the younger subunit in the middle. In (F–H), the subunits form a trans-membrane helix bundle, where young subunits are always located at the periphery while old subunits are at the center. In (I) and (J), all the subunits are in contact with each other. In the case of (K), there are two modules—the clamp (upper homo-trimeric ring) and the clamp loader (lower hetero-pentameric ring). Considering the clamp loader alone, both younger and older subunits are separated. (A) APRIL and TACI (TNF receptor) complex (Protein databank code 1xu2). (B) Urokinase receptor, urokinase, and vitronectin complex (3bt1). (C) Factor Xa/NAP5 complex (2p3f). (D) Thrombin-PAR4 complex (2pv9). (E) Complexin/SNARE complex. (F) Cytochrome b6f complex (2e76). (G) Cyanobacterial photosystem I (1jb0). (H) Photosynthetic Oxygen-Evolving Center. A cross-section of the trans-membrane helix bundle is shown (1s5l). (I) APPBP1-UBA3-NEDD8 complex (1r4m). (J) Cytochrome ba3 Oxidase (1xme). (K) DNA clamp–clamp loader complex (1sxj). (L) Cythochrome bc complex (1ezv).