Lipid functions in cytochrome bc complexes: an odd evolutionary transition in a membrane protein structure

Abstract

Lipid-binding sites and properties were compared in the hetero-oligomeric cytochrome (cyt) b(6)f and the yeast bc(1) complexes that function, respectively, in photosynthetic and respiratory electron transport. Seven lipid-binding sites in the monomeric unit of the dimeric cyanobacterial b(6)f complex overlap four sites in the Chlamydomonas reinhardtii algal b(6)f complex and four in the yeast bc(1) complex. The proposed lipid functions include: (i) interfacial-interhelix mediation between (a) the two 8-subunit monomers of the dimeric complex, (b) between the core domain (cyt b, subunit IV) and the six trans membrane helices of the peripheral domain (cyt f, iron-sulphur protein (ISP), and four small subunits in the boundary 'picket fence'); (ii) stabilization of the ISP domain-swapped trans-membrane helix; (iii) neutralization of basic residues in the single helix of cyt f and of the ISP; (iv) a 'latch' to photosystem I provided by the β-carotene chain protruding through the 'picket fence'; (v) presence of a lipid and chlorophyll a chlorin ring in b(6)f in place of the eighth helix in the bc(1) cyt b polypeptide. The question is posed of the function of the lipid substitution in relation to the evolutionary change between the eight and seven helix structures of the cyt b polypeptide. On the basis of the known n-side activation of light harvesting complex II (LHCII) kinase by the p-side level of plastoquinol, one possibility is that the change was directed by the selective advantage of p- to n-side trans membrane signalling functions in b(6)f, with the lipid either mediating this function or substituting for the trans membrane helix of a signalling protein lost in crystallization.

Figure 1.

Cytochrome b₆f complex of Mastigocladus laminosus (PDB 2E74). (a) Redox groups in the cyt b₆f complex. The trans membrane b-haems (b_p and b_n) are shown in green, and haem c_n in black. Haem of cyt f soluble domain is shown in red; [2Fe–2S] cluster of the ISP is shown as brown and yellow spheres (brown, Fe; yellow, S). The eight polypeptides in cyt b₆f monomer are shown as ribbons (cyt f, cyan; cyt b₆, light brown; ISP, pink; subIV, yellow; Pet G, gray; Pet L, green; Pet M, wheat; Pet N, dark blue). (b) Lipid-, detergent- and pigment-binding sites in cyt b₆f. Natural acidic sulfolipid is shown in wheat. Natural galactolipid, monogalactosyl-diacylglycerol (MGDG), in C. reinhardtii b₆f structure (PDB 1Q90) are in cyan and red. The synthetic lipid, dioleoylphosphatidylcholine (DOPC), used for crystallization of b₆f from M. laminosus and Nostoc PCC 7120 is shown in red. Ordered molecules of the detergent n-undecyl-β-d-maltopyranoside (UDM) found in the cyanobacterial b₆f structures are shown as, white and red sticks. Native chlorophyll a (chl-a), β-carotene (β-car) and eicosane (from C. reinhardtii b₆f) are shown as green, yellow and dark blue sticks. Figure was generated by superposition of C. reinhardtii (PDB 1Q90) and M. laminosus b₆f (PDB 1VF5, 2E74).

Figure 2.

The exposed (11 Å) chain of β-carotene that is proposed to be a ‘latch’ to photosystem I, mediating the formation of a super-complex [30]. The b₆f complex has a peripheral β-carotene inserted into the trans membrane core of the complex (PDB 2E74). This pigment overlaps with the position of a peripheral cardiolipin of the yeast respiratory cyt bc₁ complex (PDB 3CX5) that mediates the formation of a bc₁–cyt c oxidase super-complex. The extension of the b₆f β-carotene into the lipid bilayers is proposed to allow it to act as a structural antenna for the formation of b₆f–photosystem I super-complex. 2Fo-Fc map, 1.0σ (approx. 0.1 e⁻/ų).

Figure 3.

The missing helix; trans membrane signalling. Substitution of the eighth helix in the bc₁ complex with a lipid in b₆f. Trans membrane signalling by cyt b₆f; p-side niche between the ‘F’ and ‘C’ TMHs defines a portal for passage of lipophilic quinol/quinone. (a) The eight TMHs of the respiratory bc₁ complex and the seven (four + three) TMHs in b₆f; (b) Domain containing F, G and H TMHs in the yeast bc₁ complex and the F and G TMHs in b₆f. (b) binding niche of quinone analogue inhibitor, tridecyl-stigmatellin. (c) Ribbon diagram showing superposition of bc₁ H-helix (orange) and, in b₆f, DOPC lipid (yellow) and the chlorophyll a chlorin ring and phytyl tail (green). Binding site of p-side quinone analogue inhibitor, tridecyl-stigmatellin (blue). (d) Inferred structure–function equivalence of bc₁ TMH ‘H’ and (lipid together with chlorophyll a) in b₆f complex.