Cryo-EM Structure of the Photosynthetic LH1-RC Complex from Rhodospirillum rubrum

Abstract

Rhodospirillum (Rsp.) rubrum is one of the most widely used model organisms in bacterial photosynthesis. This purple phototroph is characterized by the presence of both rhodoquinone (RQ) and ubiquinone as electron carriers and bacteriochlorophyll (BChl) a esterified at the propionic acid side chain by geranylgeraniol (BChl a G ) instead of phytol. Despite intensive efforts, the structure of the light-harvesting-reaction center (LH1-RC) core complex from Rsp. rubrum remains at low resolutions. Using cryo-EM, here we present a robust new view of the Rsp. rubrum LH1-RC at 2.76 Å resolution. The LH1 complex forms a closed, slightly elliptical ring structure with 16 αβ-polypeptides surrounding the RC. Our biochemical analysis detected RQ molecules in the purified LH1-RC, and the cryo-EM density map specifically positions RQ at the Q A site in the RC. The geranylgeraniol side chains of BChl a G coordinated by LH1 β-polypeptides exhibit a highly homologous tail-up conformation that allows for interactions with the bacteriochlorin rings of nearby LH1 αassociated BChls a G . The structure also revealed key protein−protein interactions in both Nand C-terminal regions of the LH1 αβ-polypeptides, mainly within a face-to-face structural subunit. Our high-resolution Rsp. rubrum LH1-RC structure provides new insight for evaluating past experimental and computational results obtained with this old organism over many decades and lays the foundation for more detailed exploration of light-energy conversion, quinone transport, and structure−function relationships in this pigment−protein complex.

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

“…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).…”

Cryo-EM structure of the monomeric Rhodobacter sphaeroides RC–LH1 core complex at 2.5 Å

“…The structure of the monomeric RC–LH1–PufX–protein-Y complex shows an interesting variation in roles for the 14 LH1 αβ subunits, as opposed to the relatively undifferentiated LH1 subunits found in the RC–LH1 16 complex of Rsp. rubrum , for example [ 6 , 7 ]. In Rba.…”

Recent advances in single-molecule spectroscopy studies on light-harvesting processes in oxygenic photosynthesis

“…Figure 1 clearly shows that the pigment arrangements in oxygenic photosynthetic complexes contrast sharply with those in photosynthetic bacteria. While the latter seem to prefer rather periodic and ordered pigment arrays (see, for example, [ 10 – 12 ]), the former rarely show periodic arrangements of pigments. In these systems, chlorophylls (Chls) seem to be placed at random positions with random orientations.…”