Structural characterization of the B800–850 and B875 light-harvesting antenna complexes from Rhodobacter sphaeroides by electron microscopy

The C-terminus of PufX plays a key role in dimerisation and assembly of the reaction center light-harvesting 1 complex from Rhodobacter sphaeroides

In bacterial photosynthesis reaction center-light-harvesting 1 (RC-LH1) complexes trap absorbed solar energy by generating a charge separated state. Subsequent electron and proton transfers form a quinol, destined to diffuse to the cytochrome bc₁ complex. In bacteria such as Rhodobacter (Rba.) sphaeroides and Rba. capsulatus the PufX polypeptide creates a channel for quinone/quinol traffic across the LH1 complex that surrounds the RC, and it is therefore essential for photosynthetic growth. PufX also plays a key role in dimerization of the RC-LH1-PufX core complex, and the structure of the Rba. sphaeroides complex shows that the PufX C-terminus, particularly the region from X49-X53, likely mediates association of core monomers. To investigate this putative interaction we analysed mutations PufX R49L, PufX R53L, PufX R49/53L and PufX G52L by measuring photosynthetic growth, fractionation of detergent-solubilised membranes, formation of 2-D crystals and electron microscopy. We show that these mutations do not affect assembly of PufX within the core or photosynthetic growth but they do prevent dimerization, consistent with predictions from the RC-LH1-PufX structure. We obtained low resolution structures of monomeric core complexes with and without PufX, using electron microscopy of negatively stained single particles and 3D reconstruction; the monomeric complex with PufX corresponds to one half of the dimer structure whereas LH1 completely encloses the RC if the gene encoding PufX is deleted. On the basis of the insights gained from these mutagenesis and structural analyses we propose a sequence for assembly of the dimeric RC-LH1-PufX complex.

Light-harvesting antenna system from the phototrophic bacterium Roseiflexus castenholzii

Photosynthetic organisms have evolved diverse light-harvesting complexes to harness light of various qualities and intensities. Photosynthetic bacteria can have (bacterio)chlorophyll Q(y) antenna absorption bands ranging from approximately 650 to approximately 1100 nm. This broad range of wavelengths has allowed many organisms to thrive in unique light environments. Roseiflexus castenholzii is a niche-adapted, filamentous anoxygenic phototroph (FAP) that lacks chlorosomes, the dominant antenna found in most green bacteria, and here we describe the purification of a full complement of photosynthetic complexes: the light-harvesting (LH) antenna, reaction center (RC), and core complex (RC-LH). By high-performance liquid chromatography separation of bacteriochlorophyll and bacteriopheophytin pigments extracted from the core complex and the RC, the number of subunits that comprise the antenna was determined to be 15 +/- 1. Resonance Raman spectroscopy of the carbonyl stretching region displayed modes indicating that 3C-acetyl groups of BChl a are all involved in molecular interactions probably similar to those found in LH1 complexes from purple photosynthetic bacteria. Finally, two-dimensional projections of negatively stained core complexes and the LH antenna revealed a closed, slightly elliptical LH ring with an average diameter of 130 +/- 10 A surrounding a single RC that lacks an H-subunit but is associated with a tetraheme c-type cytochrome.

The peripheral light-harvesting complexes from purple sulfur bacteria have different 'ring' sizes

The integral membrane light-harvesting (LH) proteins from purple photosynthetic bacteria form circular oligomers of an elementary unit that is composed of two very hydrophobic polypeptides, termed alpha and beta. These apoprotein dimers are known to associate into closed circular arrays of 8, 9 and 16 alpha/beta-mers. We report the existence of peripheral LH proteins purified from Allochromatium vinosum with two intermediate ring sizes and postulate that one is a 13 alpha/beta-mer. This shows that LH proteins are able to form membrane rings of continuously increasing diameter from 68 to 115A. The presence of these new ring sizes warrants further study, as it will help to further validate the structure-function models of LH proteins currently found in the literature.

Effect of the in situ electrochemical oxidation on the pigment–protein arrangement and energy transfer in light-harvesting complex from Rhodobacter sphaeroides 601

The oxidation of bacteriochlorophylls (BChls) in peripheral light-harvesting complexes (LH2) from Rhodobacter sphaeroides was investigated by spectroelectrochemistry of absorption, fluorescence emission, and femtosecond (fs) pump-probe, with the aim obtaining information about the effect of in situ electrochemical oxidation on the pigment-protein arrangement and energy transfer within LH2. The experimental results revealed that: (a) the generation of the BChl radical cation in both B800 and B850 rings dramatically induced bleaching of the characteristic absorption in the NIR region and quenching of the fluorescence emission from the B850 ring for the electrochemical oxidized LH2; (b) the BChl-B850 radical cation might act as an additional channel to compete with the unoxidized BChl-B850 molecules for rapidly releasing the excitation energy, however the B800-B850 energy transfer rate remained almost unchanged during the oxidation process.

A light-harvesting antenna protein retains its folded conformation in the absence of protein-lipid and protein-pigment interactions

The first study by nmr of the integral membrane protein, the bacterial light-harvesting (LH) antenna protein LH1 beta, is reported. The photosynthetic apparatus of purple bacteria contains two different kinds of antenna complexes (LH1 and LH2), which consist of two small integral membrane proteins alpha and beta, each of approximately 6 kDa, and bacteriochlorophyll and carotenoid pigments. We have purified the antenna polypeptide LH1 beta from Rhodobacter sphaeroides, and have recorded CD spectra and a series of two-dimensional nmr spectra. A comparison of CD spectra of LH1 beta observed in organic solvents and detergent micelles shows that the helical character of the peptide does not change appreciably between the two milieus. A significantly high-field shifted methyl signal was observed both in organic solvents and in detergent micelles, implying that a similar three-dimensional structure is present in each case. However, the 1H-nmr signals observed in organic solvents had a narrower line width and better resolution, and it is shown that in this case organic solvents provide a better medium for nmr studies than detergent micelles. A sequential assignment has been carried out on the C-terminal transmembrane region, which is the region in which the pigment is bound. The region is shown to have a helical structure by the chemical shift values of the alpha-CH protons and the presence of nuclear Overhauser effects characteristic of helices. An analysis of the amide proton chemical shifts of the residues surrounding the histidine chlorophyll ligand suggests that the local structure is well ordered even in the absence of protein-lipid and protein-pigment interactions. Its structure was determined from 348 nmr-derived constraints by using distance geometry calculations. The polypeptide contains an alpha-helix extending from Leu19 (position of cytoplasmic surface) to Trp44 (position of periplasmic surface). The helix is bent, as expected from the amide proton chemical shifts, and it is similar to the polypeptide fold of the previously determined crystal structure of Rhodopseudomonas acidophila Ac10050 LH2 beta (S. M. Prince et al., Journal of Molecular Biology, 1997, Vol. 268, pp. 412-423). It is concluded that the polypeptide conformation of this region may facilitate assembly of the LH complex.

The LH1-RC core complex of Rhodobacter sphaeroides: interaction between components, time-dependent assembly, and topology of the PufX protein

Mutant strains of the photosynthetic bacterium Rhodobacter sphaeroides, lacking either LH1, the RC or PufX, were analysed by mild detergent fractionation of the cores. This reveals a hierarchy of binding of PufX in the order RC:LH1 > LH1 > RC. The assembly of photosynthetic membranes was studied by switching highly aerated cells to conditions of low aeration in the dark. The RC-H subunit appears before other components, followed by the pufBALMX then pufBA transcripts. Synthesis of the PufX polypeptide precedes that of LH1alpha and beta, which suggests that PufX associates with a limited amount of LH1alpha, beta and the RC, and prior to the encirclement of the RC by the rest of the LH1 complex. The topology of PufX within the intracytoplasmic membrane was determined by proteolytic treatment of membrane vesicles followed by protein sequencing; PufX is N-terminally exposed on the cytoplasmic surface of the photosynthetic membrane.

Model for the light-harvesting complex I (B875) of Rhodobacter sphaeroides

The light-harvesting complex I (LH-I) of Rhodobacter sphaeroides has been modeled computationally as a hexadecamer of alphabeta-heterodimers, based on a close homology of the heterodimer to that of light-harvesting complex II (LH-II) of Rhodospirillum molischianum. The resulting LH-I structure yields an electron density projection map that is in agreement with an 8.5-A resolution electron microscopic projection map for the highly homologous LH-I of Rs. rubrum. A complex of the modeled LH-I with the photosynthetic reaction center of the same species has been obtained by a constrained conformational search. This complex and the available structures of LH-II from Rs. molischianum and Rhodopseudomonas acidophila furnish a complete model of the pigment organization in the photosynthetic membrane of purple bacteria.

Two-dimensional crystallization of the light-harvesting I-reaction centre photounit from Rhodospirillum rubrum

A stoichiometric unit of the light-harvesting complex I and the reaction centre (LHI-RC complex) has been isolated from a carotenoid-less mutant of the purple non-sulphur bacterium Rhodospirillum rubrum by mild solubilization of photosynthetic membranes with the phospholipid detergent diheptylphosphatidylcholine. Dialysis of the isolated LHI-RC complexes in the presence of added dioleoyl-sn-phosphatidylcholine produced ordered two-dimensional crystals. Digital image processing revealed that the LHI-RC are packed together in a square lattice (a = b = 16.3 nm). The dimensions of the LHI ring are essentially identical with those determined from two-dimensional (2D) crystals of purified carotenoid-containing light-harvesting I complexes after analysis by cryo-electron microscopic techniques or from negatively stained 2D crystals of purified LHI complexes from a carotenoid-less mutant. Each LHI ring of the LHI-RC complex contains a central diffuse stain-excluding region, which is assigned to the reaction centre. The analysis of the LHI-RC 2D crystals strongly suggests that the geometry and subunit stoichiometry of the LHI ring is unaffected by the presence of a reaction centre that can probably assume various orientations within the ring.

Site inhomogeneity and exciton delocalization in the photosynthetic antenna

The influence of energy disorder on exciton states of molecular aggregates (the dimer and the circular aggregate) was analyzed. The dipole strength and inhomogeneous line shapes of exciton states were calculated by means of numerical diagonalization of Hamiltonian with diagonal energy disorder without intersite correlation. The disorder degree corresponding to destruction of coherent exciton states was estimated. The circular aggregates were treated as a model of light-harvesting antenna structures of photosynthetic bacteria. It was concluded that the site inhomogeneity typical for LH1 and LH2 complexes of purple bacteria cannot significantly influence the exciton delocalization over the whole antenna.

Molecular cloning, DNA sequence and transcriptional analysis of the Rhodospirillum molischianum B800/850 light-harvesting genes

The amino acid sequences of the B800/850 light-harvesting proteins from Rhodospirillum molischianum were determined by Edman degradation. On the basis of these amino acid sequences, two degenerated oligonucleotides were synthesized and used for PCR of genomic DNA. The resulting 150 bp DNA fragment was cloned, sequenced and used for subsequent Southern blot analysis of digested genomic DNA. A 2.3 kbp EcoRI fragment strongly hybridized to the probe and a size selected genomic library from genomic DNA was constructed. One clone scored positive during screening of the library with the PCR-fragment and subsequent DNA sequence analysis of the clone revealed the presence of three A-genes (A1A2A3) encoding alpha-polypeptides and of two B-genes (B1B2) encoding beta-polypeptides of the B800/850 complex. The arrangement of the different genes are B1A1, B2A2 and A3 where only B1 and B2 are preceded by typical Shine-Dalgarno sequences. In addition, typical nucleotide sequences for a rho-independent termination of transcription are located downstream of the genes A1 and A2. The deduced amino acid sequences revealed that the alpha-genes encoded for identical polypeptides, whereas the deduced beta-polypeptides differed in their amino acid sequence at four positions. Transcriptional operon analysis revealed that the genes A1B1 and A2B2 are both dicistronically transcribed, whereas the gene A3 is not.

Predicting the structure of the light-harvesting complex II of Rhodospirillum molischianum

We attempted to predict through computer modeling the structure of the light-harvesting complex II (LH-II) of Rhodospirillum molischianum, before the impending publication of the structure of a homologous protein solved by means of X-ray diffraction. The protein studied is an integral membrane protein of 16 independent polypeptides, 8 alpha-apoproteins and 8 beta-apoproteins, which aggregate and bind to 24 bacteriochlorophyll-a's and 12 lycopenes. Available diffraction data of a crystal of the protein, which could not be phased due to a lack of heavy metal derivatives, served to test the predicted structure, guiding the search. In order to determine the secondary structure, hydropathy analysis was performed to identify the putative transmembrane segments and multiple sequence alignment propensity analyses were used to pinpoint the exact sites of the 20-residue-long transmembrane segment and the 4-residue-long terminal sequence at both ends, which were independently verified and improved by homology modeling. A consensus assignment for the secondary structure was derived from a combination of all the prediction methods used. Three-dimensional structures for the alpha- and the beta-apoprotein were built by comparative modeling. The resulting tertiary structures are combined, using X-PLOR, into an alpha beta dimer pair with bacteriochlorophyll-a's attached under constraints provided by site-directed mutagenesis and spectral data. The alpha beta dimer pairs were then aggregated into a quaternary structure through further molecular dynamics simulations and energy minimization. The structure of LH-II so determined is an octamer of alpha beta heterodimers forming a ring with a diameter of 70 A.

Spectroscopic properties of the light-harvesting complexes from Rhodospirillum molischianum

Spectroscopic properties, including low-temperature absorbance, linear and circular dichroism and site-selection fluorescence of the antenna complexes from Rhodospirillum molischianum have been determined. The unique 'LH1-like' character of the amino acid sequence from LH2 of this bacterium is reflected in the circular dichroism of the B850 band of this complex. The wavelength dependence of the polarization of the LH2 complex shows an unusual shape that is attributed to the octameric state of this complex. The complete amino acid sequence for the LH1 alpha-polypeptide and most of the beta-polypeptides are presented. These conform to the general features of other LH1 polypeptides. This result, in combination with spectroscopic data for LH1 imply that the organisation of the core in this bacterium is not much different from that in other purple non-sulphur bacteria.

Protein structure modelling of the bacterial light-harvesting complex

Protein structure modelling offers a method of obtaining 3-dimensional information that can be tested and used to plan mutagenesis experiments when a crystallographically determined structure is not available. At its simplest a model may consist of little more than a secondary structure prediction coupled with a determination of the likely regions of transmembrane/membrane surface/globular configuration. These methods can yield an interesting topology map of the protein, which places the residues in their likely positions with respect to, for example, the membrane interface. If it is a member of a large family of related proteins then aligned protein sequences can be used to predict the residues that have an important function as these will be largely conserved in the alignments. Using all these methods a model can be constructed (using for example, the Nicholson Molecular Modelling Kit) to visualize the proposed structure in three dimensions following the premise of good design, that is, avoiding obvious steric clashes, packing of helices in a realistic manner, observing the correct H-bond lengths, etc. In this latter exercise the review of Chothia (Annu. Rev. Biochem. 53, 537-572, 1984) of the principles of protein structure is particularly helpful as it clearly sets out how proteins pack and their preferred configuration. There is a wealth of information about individual amino acid conformational preferences and observed frequencies of occurrence in known protein structures, which can help decide how the residues in the model can be oriented. In this article we have collated the various protein models of the bacterial light-harvesting complexes and present our own model, which is a synthesis of the available biophysical data and theoretical predictions, and show its performance in explaining recent results of site-directed mutants of the LH1 and LH2 light-harvesting complexes of Rhodobacter sphaeroides.