An LH1–RC photocomplex from an extremophilic phototroph provides insight into origins of two photosynthesis proteins

Abstract

Rhodopila globiformis is the most acidophilic of anaerobic purple phototrophs, growing optimally in culture at pH 5. Here we present a cryo-EM structure of the light-harvesting 1–reaction center (LH1–RC) complex from Rhodopila globiformis at 2.24 Å resolution. All purple bacterial cytochrome (Cyt, encoded by the gene pufC) subunit-associated RCs with known structures have their N-termini truncated. By contrast, the Rhodopila globiformis RC contains a full-length tetra-heme Cyt with its N-terminus embedded in the membrane forming an α-helix as the membrane anchor. Comparison of the N-terminal regions of the Cyt with PufX polypeptides widely distributed in Rhodobacter species reveals significant structural similarities, supporting a longstanding hypothesis that PufX is phylogenetically related to the N-terminus of the RC-bound Cyt subunit and that a common ancestor of phototrophic Proteobacteria contained a full-length tetra-heme Cyt subunit that evolved independently through partial deletions of its pufC gene. Eleven copies of a novel γ-like polypeptide were also identified in the bacteriochlorophyll a-containing Rhodopila globiformis LH1 complex; γ-polypeptides have previously been found only in the LH1 of bacteriochlorophyll b-containing species. These features are discussed in relation to their predicted functions of stabilizing the LH1 structure and regulating quinone transport under the warm acidic conditions.

Advances in the Spectroscopic and Structural Characterization of Core Light-Harvesting Complexes from Purple Phototrophic Bacteria

“…This red-shifts to 780 nm upon binding to an LH1 α- or β-polypeptide, to 820 nm by forming an αβ-subunit, and to 860–970 nm (depending on the species) by forming LH1 complexes containing 14–16 αβ-subunits arranged in a circle (Figure C). In the intact LH1–RC complex, intra-BChl a dimers and inter-BChl a dimers interact to generate exciton coupling over the LH1 BChl a ring, which is involved in the LH1 Q y transition energy. , Structural information on the LH1–RC complexes of several species of purple bacteria − indicates that the distances between the intra- and inter-BChl a dimers may also contribute to the red-shifting of the LH1 Q y bands. For example, in the Tch.…”

“…In addition, BChl a bound to α n -polypeptide and BChl a bound to β n +1 -polypeptide interact to form inter-BChl a dimers (Figure A, black-dashed line). Based on structural data, − the effects of the distances between BChls on the Q y absorption band were compared. Figure B exhibits plots of the distances for the intra- and inter-BChl dimers against the LH1 Q y peak of purple bacterial species whose LH1–RC structures are known (Table S1).…”

“…Purple phototrophic bacteria utilize NIR light captured by LH complexes and transfer the energy to the RC BChl dimer (the “special pair”) against an energetically “uphill” gap (“uphill” because LH1 BChls absorb lower-energy wavelengths than do RC BChls); this event initiates photosynthetic charge separation in the special pair followed by subsequent redox events (Figure A). The RC special pair contains only two BChls (in contrast to the 28–34 BChls present in the LH1 complex) and exhibits its Q y band at 860–870 nm although these were obtained from isolated RC-only complexes free of their LH1 component. − Recent structural analyses − have detected close associations between RC and LH1 complexes, indicating that the special pair’s Q y band peaks reported for RC-only complexes may not be the same as those of the RC in the native LH1–RC. Unfortunately, however, the intensive LH1 Q y band prevents accurate determination of the special pair peak in an LH1–RC complex.…”

“…Our light-induced FTIR approach presented here is a potential tool for this purpose and actually supported a conclusion that quinone transport in Tch. tepidum occurs through the spatially restricted hydrophobic channels in the closed LH1 ring. , Recent 3D structural studies of purple bacterial photocomplexes including their mutants − have revealed highly diversified LH1 ring structures comprised of 11–17 αβ- or αβγ-subunits with or without a gap, and because of this diversity, a variety of quinone transport pathways are likely. Several groups have resolved cryo-EM structures of LH1–RCs in which the LH1 is comprised of 14 αβ-subunits with a Puf X protein and a previously unrecognized protein U , (or protein Y ,, ), residing at a gap of the C-shaped ring.…”

“…Recent X-ray crystallographic , and cryo-EM − structural analyses have revealed the architecture of several purple bacterial LH1–RCs. An RC is enclosed by an open or closed LH1 ring comprised of 14–17 αβ (γ)-subunits, each of which binds two (or rarely, three) BChls coordinated with conserved His residues in the αβ -polypeptides and one or two carotenoid molecules (Figure B).…”