Variable LH2 stoichiometry and core clustering in native membranes of Rhodospirillum photometricum

Theory of photosynthetic membrane influence on B800-B850 energy transfer in the LH2 complex

Photosynthetic organisms rely on a network of light-harvesting protein-pigment complexes to efficiently absorb sunlight and transfer excitation energy to reaction center proteins where charge separation occurs. In photosynthetic purple bacteria, these complexes are embedded within the cell membrane, with lipid composition affecting complex clustering, thereby impacting inter-complex energy transfer. However, the impact of the lipid bilayer on intra-complex excitation dynamics is less understood. Recent experiments have addressed this question by comparing photo-excitation dynamics in detergent-isolated light-harvesting complex 2 (LH2) to LH2 complexes embedded in membrane discs mimicking the biological environment, revealing differences in spectra and energy-transfer rates. In this paper, we use available quantum chemical and spectroscopy data to develop a complementary theoretical study on the excitonic structure and intra-complex energy-transfer kinetics of the LH2 of photosynthetic purple bacteria Rhodoblastus (Rbl.) acidophilus (formerly Rhodopseudomonas acidophila) in two different conditions: the LH2 in a membrane environment and detergent-isolated LH2. We find that dark excitonic states, crucial for B800-B850 energy transfer within LH2, are more delocalized in the membrane model. Using nonperturbative and generalized Förster calculations, we show that such increased quantum delocalization results in a 30% faster B800 to B850 transfer rate in the membrane model, in agreement with experimental results. We identify the dominant energy-transfer pathways in each environment and demonstrate how differences in the B800 to B850 transfer rate arise from changes in LH2's electronic properties when embedded in the membrane. Furthermore, by accounting for the quasi-static variations of electronic excitation energies in the LH2, we show that the broadening of the distribution of the B800-B850 transfer rates is affected by the lipid composition. We argue that such variation in broadening could be a signature of a speed-accuracy trade-off, commonly seen in biological process.

A distinct double-ring LH1-LH2 photocomplex from an extremophilic phototroph

Halorhodospira (Hlr.) halophila strain BN9622 is an extremely halophilic and alkaliphilic phototrophic purple sulfur bacterium isolated from a hypersaline lake in the Libyan Desert whose total salinity exceeded 35% at pH 10.7. Here we present a cryo-EM structure of the native LH1-LH2 co-complex from strain BN9622 at 2.22 Å resolution. Surprisingly, the LH1-LH2 co-complex consists of a double-ring cylindrical structure with the larger LH1 ring encircling a smaller LH2 ring. The Hlr. halophila LH1 contains 18 αβ-subunits and additional bacteriochlorophyll a (BChl a) molecules that absorb maximally at 797 nm. The LH2 ring is composed of 9 αβ-subunits, and the BChl a molecules in the co-complex form extensive intra- and inter-complex networks to allow near 100% efficiency of energy transfer to its surrounding LH1. The additional LH1-B797 BChls a are located in such a manner that they facilitate exciton transfer from monomeric BChls in LH2 to the dimeric BChls in LH1. The structural features of the strain BN9622 LH1-LH2 co-complex may have evolved to allow a minimal LH2 complex to maximize excitation transfer to the core complex and effectively harvest light in the physiologically demanding ecological niche of this purple bacterium.

Insights into the divergence of the photosynthetic LH1 complex obtained from structural analysis of the unusual photocomplexes of Roseospirillum parvum

Purple phototrophic bacteria produce two kinds of light-harvesting complexes that function to capture and transmit solar energy: the core antenna (LH1) and the peripheral antenna (LH2). The apoproteins of these antennas, encoded respectively by the genes pufBA and pucBA within and outside the photosynthetic gene cluster, respectively, exhibit conserved amino acid sequences and structural topologies suggesting they were derived from a shared ancestor. Here we present the structures of two photosynthetic complexes from Roseospirillum (Rss.) parvum 930I: an LH1-RC complex and a variant of the LH1 complex also encoded by pufBA that we designate as LH1'. The LH1-RC complex forms a closed elliptical structure consisting of 16 pairs of αβ-polypeptides that surrounds the RC. By contrast, the LH1' complex is a closed ring structure composed of 14 pairs of αβ-polypeptides, and it shows significant similarities to LH2 complexes both spectrally and structurally. Although LH2-like, the LH1' complex is larger than any known LH2 complexes, and genomic analyses of Rss. parvum revealed the absence of pucBA, genes that encode classical LH2 complexes. Characterization of the unique Rss. parvum photocomplexes not only underscores the diversity of such structures but also sheds new light on the evolution of light-harvesting complexes from phototrophic bacteria.

Elucidating interprotein energy transfer dynamics within the antenna network from purple bacteria

In photosynthesis, absorbed light energy transfers through a network of antenna proteins with near-unity quantum efficiency to reach the reaction center, which initiates the downstream biochemical reactions. While the energy transfer dynamics within individual antenna proteins have been extensively studied over the past decades, the dynamics between the proteins are poorly understood due to the heterogeneous organization of the network. Previously reported timescales averaged over such heterogeneity, obscuring individual interprotein energy transfer steps. Here, we isolated and interrogated interprotein energy transfer by embedding two variants of the primary antenna protein from purple bacteria, light-harvesting complex 2 (LH2), together into a near-native membrane disc, known as a nanodisc. We integrated ultrafast transient absorption spectroscopy, quantum dynamics simulations, and cryogenic electron microscopy to determine interprotein energy transfer timescales. By varying the diameter of the nanodiscs, we replicated a range of distances between the proteins. The closest distance possible between neighboring LH2, which is the most common in native membranes, is 25 Å and resulted in a timescale of 5.7 ps. Larger distances of 28 to 31 Å resulted in timescales of 10 to 14 ps. Corresponding simulations showed that the fast energy transfer steps between closely spaced LH2 increase transport distances by ∼15%. Overall, our results introduce a framework for well-controlled studies of interprotein energy transfer dynamics and suggest that protein pairs serve as the primary pathway for the efficient transport of solar energy.

Atomic force microscopic analysis of the light-harvesting complex 2 from purple photosynthetic bacterium Thermochromatium tepidum

Structural information on the circular arrangements of repeating pigment-polypeptide subunits in antenna proteins of purple photosynthetic bacteria is a clue to a better understanding of molecular mechanisms for the ring-structure formation and efficient light harvesting of such antennas. Here, we have analyzed the ring structure of light-harvesting complex 2 (LH2) from the thermophilic purple bacterium Thermochromatium tepidum (tepidum-LH2) by atomic force microscopy. The circular arrangement of the tepidum-LH2 subunits was successfully visualized in a lipid bilayer. The average top-to-top distance of the ring structure, which is correlated with the ring size, was 4.8 ± 0.3 nm. This value was close to the top-to-top distance of the octameric LH2 from Phaeospirillum molischianum (molischianum-LH2) by the previous analysis. Gaussian distribution of the angles of the segments consisting of neighboring subunits in the ring structures of tepidum-LH2 yielded a median of 44°, which corresponds to the angle for the octameric circular arrangement (45°). These results indicate that tepidum-LH2 has a ring structure consisting of eight repeating subunits. The coincidence of an octameric ring structure of tepidum-LH2 with that of molischianum-LH2 is consistent with the homology of amino acid sequences of the polypeptides between tepidum-LH2 and molischianum-LH2.

Spatial Patterns of Light-Harvesting Antenna Complex Arrangements Tune the Transfer-to-Trap Efficiency of Excitons in Purple Bacteria

In photosynthesis, the efficiency with which a photogenerated exciton reaches the reaction center is dictated by chromophore energies and the arrangement of chromophores in the supercomplex. Here, we explore the interplay between the arrangement of light-harvesting antennae and the efficiency of exciton transport in purple bacterial photosynthesis. Using a Miller-Abrahams-based exciton hopping model, we compare different arrangements of light-harvesting proteins on the intracytoplasmic membrane. We find that arrangements with aggregated LH1s have a higher efficiency than arrangements with randomly distributed LH1s in a wide range of physiological light fluences. This effect is robust to the introduction of defects on the intracytoplasmic membrane. Our result explains the absence of species with aggregated LH1 arrangements in low-light niches and the large increase seen in the expression of LH1 dimer complexes in high fluences. We suggest that the effect seen in our study is an adaptive strategy toward solar light fluence across different purple bacterial species.

Do photosynthetic complexes use quantum coherence to increase their efficiency? Probably not

Answering the titular question has become a central motivation in the field of quantum biology, ever since the idea was raised following a series of experiments demonstrating wave-like behavior in photosynthetic complexes. Here, we report a direct evaluation of the effect of quantum coherence on the efficiency of three natural complexes. An open quantum systems approach allows us to simultaneously identify their level of "quantumness" and efficiency, under natural physiological conditions. We show that these systems reside in a mixed quantum-classical regime, characterized by dephasing-assisted transport. Yet, we find that the change in efficiency at this regime is minute at best, implying that the presence of quantum coherence does not play a substantial role in enhancing efficiency. However, in this regime, efficiency is independent of any structural parameters, suggesting that evolution may have driven natural complexes to their parameter regime to "design" their structure for other uses.

Membrane Dynamics in Phototrophic Bacteria

Photosynthetic membranes are typically densely packed with proteins, and this is crucial for their function in efficient trapping of light energy. Despite being crowded with protein, the membranes are fluid systems in which proteins and smaller molecules can diffuse. Fluidity is also crucial for photosynthetic function, as it is essential for biogenesis, electron transport, and protein redistribution for functional regulation. All photosynthetic membranes seem to maintain a delicate balance between crowding, order, and fluidity. How does this work in phototrophic bacteria? In this review, we focus on two types of intensively studied bacterial photosynthetic membranes: the chromatophore membranes of purple bacteria and the thylakoid membranes of cyanobacteria. Both systems are distinct from the plasma membrane, and both have a distinctive protein composition that reflects their specialized roles. Chromatophores are formed from plasma membrane invaginations, while thylakoid membranes appear to be an independent intracellular membrane system. We discuss the techniques that can be applied to study the organization and dynamics of these membrane systems, including electron microscopy techniques, atomic force microscopy, and many variants of fluorescence microscopy. We go on to discuss the insights that havebeen acquired from these techniques, and the role of membrane dynamics in the physiology of photosynthetic membranes. Membrane dynamics on multiple timescales are crucial for membrane function, from electron transport on timescales of microseconds to milliseconds to regulation and biogenesis on timescales of minutes to hours. We emphasize the open questions that remain in the field.

LH1-RC light-harvesting photocycle under realistic light-matter conditions

Quantum master equations are used to simulate the photocycle of the light-harvesting complex 1 (LH1) and the associated reaction center (RC) in purple bacteria excited with natural incoherent light. The influence of the radiation and protein environments and the full photocycle of the complexes, including the charge separation and RC recovery processes, are taken into account. Particular emphasis is placed on the steady state excitation energy transfer rate between the LH1 and the RC and the steady state dependence on the light intensity. The transfer rate is shown to scale linearly with light intensity near the value in the natural habitat and at higher light intensities is found to be bounded by the rate-determining step of the photocycle, the RC recovery rate. Transient (e.g., pulsed laser induced) dynamics, however, shows rates higher than the steady state value and continues to scale linearly with the intensity. The results show a correlation between the transfer rate and the manner in which the donor state is prepared. In addition, the transition from the transient to the steady state results can be understood as a cascade of ever slower rate-determining steps and quasi-stationary states inherent in multi-scale sequential processes. This type of transition of rates is relevant in most light-induced biological machinery.

Comparison of the Energy-Transfer Rates in Structural and Spectral Variants of the B800-850 Complex from Purple Bacteria

Photosynthetic light harvesting can occur with a remarkable near-unity quantum efficiency. The B800-850 complex, also known as light-harvesting complex 2 (LH2), is the primary light-harvesting complex in purple bacteria and has been extensively studied as a model system. The bacteriochlorophylls of the B800-850 complex are organized into two concentric rings, known as the B800 and B850 rings. However, depending on the species and growth conditions, the number of constituent subunits, the pigment geometry, and the absorption energies vary. While the dynamics of some B800-850 variants have been exhaustively characterized, others have not been measured. Furthermore, a direct and simultaneous comparison of how both structural and spectral differences between variants affect these dynamics has not been performed. In this work, we utilize ultrafast transient absorption measurements to compare the B800 to B850 energy-transfer rates in the B800-850 complex as a function of the number of subunits, geometry, and absorption energies. The nonameric B800-850 complex from Rhodobacter (Rb.) sphaeroides is 40% faster than the octameric B800-850 complex from Rhodospirillum (Rs.) molischianum, consistent with structure-based predictions. In contrast, the blue-shifted B800-820 complex from Rs. molischianum is only 20% faster than the B800-850 complex from Rs. molischianum despite an increase in the spectral overlap between the rings that would be expected to produce a larger increase in the energy-transfer rate. These measurements support current models that contain dark, higher-lying excitonic states to bridge the energy gap between rings, thereby maintaining similar energy-transfer dynamics. Overall, these results demonstrate that energy-transfer dynamics in the B800-850 complex are robust to the spectral and structural variations between species used to optimize energy capture and flow in purple bacteria.

In vitro single-cell dissection revealing the interior structure of cable bacteria

Filamentous Desulfobulbaceae bacteria were recently discovered as long-range transporters of electrons from sulfide to oxygen in marine sediments. The long-range electron transfer through these cable bacteria has created considerable interests, but it has also raised many questions, such as what structural basis will be required to enable micrometer-sized cells to build into centimeter-long continuous filaments? Here we dissected cable bacteria cells in vitro by atomic force microscopy and further explored the interior, which is normally hidden behind the outer membrane. Using nanoscale topographical and mechanical maps, different types of bacterial cell-cell junctions and strings along the cable length were identified. More important, these strings were found to be continuous along the bacterial cells passing through the cell-cell junctions. This indicates that the strings serve an important function in maintaining integrity of individual cable bacteria cells as a united filament. Furthermore, ridges in the outer membrane are found to envelop the individual strings at cell-cell junctions, and they are proposed to strengthen the junctions. Finally, we propose a model for the division and growth of the cable bacteria, which illustrate the possible structural requirements for the formation of centimeter-length filaments in the recently discovered cable bacteria.

Light harvesting in phototrophic bacteria: structure and function

This review serves as an introduction to the variety of light-harvesting (LH) structures present in phototrophic prokaryotes. It provides an overview of the LH complexes of purple bacteria, green sulfur bacteria (GSB), acidobacteria, filamentous anoxygenic phototrophs (FAP), and cyanobacteria. Bacteria have adapted their LH systems for efficient operation under a multitude of different habitats and light qualities, performing both oxygenic (oxygen-evolving) and anoxygenic (non-oxygen-evolving) photosynthesis. For each LH system, emphasis is placed on the overall architecture of the pigment–protein complex, as well as any relevant information on energy transfer rates and pathways. This review addresses also some of the more recent findings in the field, such as the structure of the CsmA chlorosome baseplate and the whole-cell kinetics of energy transfer in GSB, while also pointing out some areas in need of further investigation.

Oriented Reconstitution of the Full-Length KcsA Potassium Channel in a Lipid Bilayer for AFM Imaging

Here, we have developed a method of oriented reconstitution of the KcsA potassium channel amenable to high-resolution AFM imaging. The solubilized full-length KcsA channels with histidine-tagged (His-tag) C-terminal ends were attached to a Ni²⁺-coated mica surface, and then detergent-destabilized liposomes were added to fill the interchannel space. AFM revealed that the membrane-embedded KcsA channels were oriented with their extracellular faces upward, seen as a tetrameric square shape. This orientation was corroborated by the visible binding of a peptide scorpion toxin, agitoxin-2. To observe the cytoplasmic side of the channel, a His-tag was inserted into the extracellular loop, and the oppositely oriented channels provided wholly different images. In either orientation, the channels were individually dispersed at acidic pH, whereas they were self-assembled at neutral pH, indicating that the oriented channels are allowed to diffuse in the membrane. This method is readily applicable to membrane proteins in general for AFM imaging.

Light Absorption and Energy Transfer in the Antenna Complexes of Photosynthetic Organisms

The process of photosynthesis is initiated by the capture of sunlight by a network of light-absorbing molecules (chromophores), which are also responsible for the subsequent funneling of the excitation energy to the reaction centers. Through evolution, genetic drift, and speciation, photosynthetic organisms have discovered many solutions for light harvesting. In this review, we describe the underlying photophysical principles by which this energy is absorbed, as well as the mechanisms of electronic excitation energy transfer (EET). First, optical properties of the individual pigment chromophores present in light-harvesting antenna complexes are introduced, and then we examine the collective behavior of pigment-pigment and pigment-protein interactions. The description of energy transfer, in particular multichromophoric antenna structures, is shown to vary depending on the spatial and energetic landscape, which dictates the relative coupling strength between constituent pigment molecules. In the latter half of the article, we focus on the light-harvesting complexes of purple bacteria as a model to illustrate the present understanding of the synergetic effects leading to EET optimization of light-harvesting antenna systems while exploring the structure and function of the integral chromophores. We end this review with a brief overview of the energy-transfer dynamics and pathways in the light-harvesting antennas of various photosynthetic organisms.

Aberrant assembly complexes of the reaction center light-harvesting 1 PufX (RC-LH1-PufX) core complex of Rhodobacter sphaeroides imaged by atomic force microscopy

In the purple phototrophic bacterium Rhodobacter sphaeroides, many protein complexes congregate within the membrane to form operational photosynthetic units consisting of arrays of light-harvesting LH2 complexes and monomeric and dimeric reaction center (RC)-light-harvesting 1 (LH1)-PufX “core” complexes. Each half of a dimer complex consists of a RC surrounded by 14 LH1 αβ subunits, with two bacteriochlorophylls (Bchls) sandwiched between each αβ pair of transmembrane helices. We used atomic force microscopy (AFM) to investigate the assembly of single molecules of the RC-LH1-PufX complex using membranes prepared from LH2-minus mutants. When the RC and PufX components were also absent, AFM revealed a series of LH1 variants where the repeating α₁β₁(Bchl)₂ units had formed rings of variable size, ellipses, and spirals and also arcs that could be assembly products. The spiral complexes occur when the LH1 ring has failed to close, and short arcs are suggestive of prematurely terminated LH1 complex assembly. In the absence of RCs, we occasionally observed captive proteins enclosed by the LH1 ring. When production of LH1 units was restricted by lowering the relative levels of the cognate pufBA transcript, we imaged a mixture of complete RC-LH1 core complexes, empty LH1 rings, and isolated RCs, leading us to conclude that once a RC associates with the first α₁β₁(Bchl)₂ subunit, cooperative associations between subsequent subunits and the RC tend to drive LH1 ring assembly to completion.

The architecture of Rhodobacter sphaeroides chromatophores

The chromatophores of Rhodobacter (Rb.) sphaeroides represent a minimal bio-energetic system, which efficiently converts light energy into usable chemical energy. Despite extensive studies, several issues pertaining to the morphology and molecular architecture of this elemental energy conversion system remain controversial or unknown. To tackle these issues, we combined electron microscope tomography, immuno-electron microscopy and atomic force microscopy. We found that the intracellular Rb. sphaeroides chromatophores form a continuous reticulum rather than existing as discrete vesicles. We also found that the cytochrome bc1 complex localizes to fragile chromatophore regions, which most likely constitute the tubular structures that interconnect the vesicles in the reticulum. In contrast, the peripheral light-harvesting complex 2 (LH2) is preferentially hexagonally packed within the convex vesicular regions of the membrane network. Based on these observations, we propose that the bc1 complexes are in the inter-vesicular regions and surrounded by reaction center (RC) core complexes, which in turn are bounded by arrays of peripheral antenna complexes. This arrangement affords rapid cycling of electrons between the core and bc1 complexes while maintaining efficient excitation energy transfer from LH2 domains to the RCs.

Combined topographic, spectroscopic, and model analyses of inhomogeneous energetic coupling of linear light harvesting complex II aggregates in native photosynthetic membranes

Light harvesting by LH1 and LH2 antenna proteins in the photosynthetic membranes of purple bacteria has been extensively studied in recent years for the fundamental understanding of the energy transfer dynamics and mechanism. Here we report the inhomogeneous structural organization of the LH2 complexes in photosynthetic membranes, giving evidence for the existence of energetically coupled linear LH2 aggregates in the native photosynthetic membranes of purple bacteria. Focusing on systematic model analyses, we combined AFM imaging and spectroscopic analysis with energetic coupling model analysis to characterize the inhomogeneous linear aggregation of LH2. Our AFM imaging results reveal that the LH2 complexes form linear aggregates with the monomer number varying from one to eight and each monomer tilted along the aggregated structure in photosynthetic membranes. The spectroscopic results support the attribution of aggregated LH2 complexes in the photosynthetic membranes, and the model calculation values for the absorption, emission and lifetime are consistent with the experimentally determined spectroscopic values, further proving a molecular-level understanding of the energetic coupling and energy transfer among the LH2 complexes in the photosynthetic membranes.

Investigation of photosynthetic membrane structure using atomic force microscopy

Photosynthetic processes, including light capture, electron transfer, and energy conversion, are not only ensured by the activities of individual photosynthetic complexes but also substantially determined and regulated by the composition and assembly of the overall photosynthetic apparatus at the supramolecular level. In recent years, atomic force microscopy (AFM) has matured as a unique and powerful tool for directly assessing the supramolecular assembly of integral membrane protein complexes in their native membrane environment at submolecular resolution. This review highlights the major contributions and advances of AFM studies to our understanding of the structure of the bacterial photosynthetic machinery and its regulatory arrangement during chromatic adaptation. AFM topographs of other biological membrane systems and potential future applications of AFM are also discussed.

Shotgun genome sequence of the large purple photosynthetic bacterium Rhodospirillum photometricum DSM122

Here, we present the shotgun genome sequence of the purple photosynthetic bacterium Rhodospirillum photometricum DSM122. The photosynthetic apparatus of this bacterium has been particularly well studied by microscopy. The knowledge of the genome of this oversize bacterium will allow us to compare it with the other purple bacterial organisms to follow the evolution of the photosynthetic apparatus.

Adaptation of intracytoplasmic membranes to altered light intensity in Rhodobacter sphaeroides

The model photosynthetic bacterium Rhodobacter sphaeroides uses a network of bacteriochlorophyll (BChl)-protein complexes embedded in spherical intracytoplasmic membranes (ICM) to collect and utilise solar energy. We studied the effects of high- and low-light growth conditions, where BChl levels increased approximately four-fold from 1.6×10(6) to 6.5×10(6) molecules per cell. Most of this extra pigment is accommodated in the proliferating ICM system, which increases from approximately 274 to 1468 vesicles per cell. Thus, 16×10(6)nm(2) of specialised membrane surface area is made available for harvesting and utilising solar energy compared to 3×10(6)nm(2) under high-light conditions. Membrane mapping using atomic force microscopy revealed closely packed dimeric and monomeric reaction centre-light harvesting 1-PufX (RC-LH1-PufX) complexes in high-light ICM with room only for small clusters of LH2, whereas extensive LH2-only domains form during adaptation to low light, with the LH2/RC ratio increasing three-fold. The number of upper pigmented band (UPB) sites where membrane invagination is initiated hardly varied; 704 (5.8×10(5) BChls/cell) and 829 (4.9×10(5) BChls/cell) UPB sites per cell were estimated under high- and low-light conditions, respectively. Thus, the lower ICM content in high-light cells is a consequence of fewer ICM invaginations reaching maturity. Taking into account the relatively poor LH2-to-LH1 energy transfer in UPB membranes it is likely that high-light cells are relatively inefficient at energy trapping, but can grow well enough without the need to fully develop their photosynthetic membranes from the relatively inefficient UPB to highly efficient mature ICM.

Topology and energy transport in networks of interacting photosynthetic complexes

We address the role of topology in the energy transport process that occurs in networks of photosynthetic complexes. We take inspiration from light-harvesting networks present in purple bacteria and simulate an incoherent dissipative energy transport process on more general and abstract networks, considering both regular structures (Cayley trees and hyperbranched fractals) and randomly generated ones. We focus on the the two primary light-harvesting complexes of purple bacteria, i.e., the LH1 and LH2, and we use network-theoretical centrality measures in order to select different LH1 arrangements. We show that different choices cause significant differences in the transport efficiencies, and that for regular networks, centrality measures allow us to identify arrangements that ensure transport efficiencies which are better than those obtained with a random disposition of the complexes. The optimal arrangements strongly depend on the dissipative nature of the dynamics and on the topological properties of the networks considered, and depending on the latter, they are achieved by using global versus local centrality measures. For randomly generated networks, a random arrangement of the complexes already provides efficient transport, and this suggests the process is strong with respect to limited amount of control in the structure design and to the disorder inherent in the construction of randomly assembled structures. Finally, we compare the networks considered with the real biological networks and find that the latter have in general better performances, due to their higher connectivity, but the former with optimal arrangements can mimic the real networks' behavior for a specific range of transport parameters. These results show that the use of network-theoretical concepts can be crucial for the characterization and design of efficient artificial energy transport networks.

Gene sequencing and characterization of the light-harvesting complex 2 from thermophilic purple sulfur bacterium Thermochromatium tepidum

In this study, gene sequences coding for the light-harvesting (LH) 2 polypeptides from a thermophilic purple sulfur bacterium Thermochromatium tepidum are reported and characterization of the LH2 complex is described. Three sets of pucBA genes have been identified, and the gene products have been analyzed by electrophoresis and reversed-phase chromatography. The result shows that all of the genes are expressed but the distribution of the expression is not uniform. The gene products undergo post-translational modification, where two of the β-polypeptides appear to be N-terminally methylated. Absorption spectrum of the purified LH2 complex exhibits Q (y) transitions at 800 and 854 nm in dodecyl β-maltopyranoside solution, and the circular dichroism spectrum shows a "molischianum"-like characteristic. No spectral change was observed for the LH2 when the bacterium was cultured under different conditions of light intensity. In lauryl dimethylamine N-oxide (LDAO) solution, significant changes in the absorption spectrum were observed. The B850 peak decreased and blue-shifted with increasing the LDAO concentration, whereas the B800 intensity increased without change in the peak position. The spectral changes can be partially or almost completely reversed by addition of metal ions, and the divalent cations seem to be more effective. The results indicate that ionic interactions may exist between LH2, detergent molecules and metal ions. Possible mechanisms involved in the detergent- and cation-induced spectral changes are discussed.

Through space singlet energy transfers in light-harvesting systems and cofacial bisporphyrin dyads

Recent discoveries from our research groups on the photophysics of a few cofacial bisporphyrin dyads for through space singlet and triplet energy transfers raised several important investigations about the mechanism of energy transfers and energy migration in light-harvesting devices, notably LH II, in the heavily investigated purple photosynthetic bacteria. The key feature is that for face-to-face and slipped dyads with controlled structure using rigid spacers or spacers with limited flexibilities, our fastest rates for singlet energy transfer are in the 10 × 109 s -1 (i.e. 100 ps time scale) for donor-acceptor distances of ~3.5–3.6 Å. The time scale for energy transfers between different bacteriochlorophylls, notably B800*→B850, is in the ps despite the long Mg ⋯ Mg separation (~18 Å). This short rate drastically contrasts with the well-accepted Förster theory. This review focuses on the photophysical processes and dynamics in LH II and compares these parameters with our investigated model dyads build upon octa-etio-porphyrin chromophores and rigid and semi-rigid spacers. The recently discovered role of the rhodopin glucoside (carotenoid) will be analyzed as possible relay for energy transfers, including the possibility of uphill processes at room temperature. In this context the concept of energy migration may be complemented by parallel relays and uphill processes. It is also becoming more obvious that the irreversible electron transfer at the reaction center (electron transfer from the special pair to the phaeophytin) renders the rates for energy transfer and migration faster precluding all possibility of back transfers.

Quantum chemical description of absorption properties and excited-state processes in photosynthetic systems

The theoretical description of the initial steps in photosynthesis has gained increasing importance over the past few years. This is caused by more and more structural data becoming available for light-harvesting complexes and reaction centers which form the basis for atomistic calculations and by the progress made in the development of first-principles methods for excited electronic states of large molecules. In this Review, we discuss the advantages and pitfalls of theoretical methods applicable to photosynthetic pigments. Besides methodological aspects of excited-state electronic-structure methods, studies on chlorophyll-type and carotenoid-like molecules are discussed. We also address the concepts of exciton coupling and excitation-energy transfer (EET) and compare the different theoretical methods for the calculation of EET coupling constants. Applications to photosynthetic light-harvesting complexes and reaction centers based on such models are also analyzed.

Molecular origins and consequences of High-800 LH2 in Roseobacter denitrificans

Roseobacter denitrificans is a marine bacterium capable of using a wide variety of different metabolic schemes and in particular is an anoxygenic aerobic photosynthetic bacterium. In the work reported here we use a deletion mutant that we have constructed to investigate the structural origin of the unusual High-800 light-harvesting complex absorption in this bacterium. We suggest that the structure is essentially unaltered when compared to the usual nonameric complexes but that a change in the environment of the C(13:1) carbonyl group is responsible for the change in spectrum. We tentatively relate this change to the presence of a serine residue in the α-polypeptide. Surprisingly, the low spectral overlap between the peripheral and core light-harvesting systems appears not to compromise energy collection efficiency too severely. We suggest that this may be at the expense of maintaining a low antenna size.

In silico predictions of LH2 ring sizes from the crystal structure of a single subunit using molecular dynamics simulations

Most of the currently known light-harvesting complexes 2 (LH2) rings are formed by 8 or 9 subunits. As of now, questions like "what factors govern the LH2 ring size?" and "are there other ring sizes possible?" remain largely unanswered. Here, we investigate by means of molecular dynamics (MD) simulations and stochastic modeling the possibility of predicting the size of an LH2 ring from the sole knowledge of the high resolution crystal structure of a single subunit. Starting with single subunits of two LH2 rings with known size, that is, an 8-ring from Rs. moliscianum (MOLI) and a 9-ring from Rps. acidophila (ACI), and one with unknown size (referred to as X), we build atomic models of subunit dimers corresponding to assumed 8-, 9-, and 10-ring geometries. After inserting each of the dimers into a lipid-water environment, we determine the preferred angle between the corresponding subunits by three methods: (1) energy minimization, (2) free MD simulations, and (3) potential of mean force calculations. We find that the results from all three methods are consistent with each other, and when taken together, it allows one to predict with reasonable level of confidence the sizes of the corresponding ring structures. One finds that X and ACI very likely form a 9-ring, while MOLI is more likely to form an 8-ring than a 9-ring. Finally, we discuss both the merits and limitations of all three prediction methods.

Forces guiding assembly of light-harvesting complex 2 in native membranes

Interaction forces of membrane protein subunits are of importance in their structure, assembly, membrane insertion, and function. In biological membranes, and in the photosynthetic apparatus as a paradigm, membrane proteins fulfill their function by ensemble actions integrating a tight assembly of several proteins. In the bacterial photosynthetic apparatus light-harvesting complexes 2 (LH2) transfer light energy to neighboring tightly associated core complexes, constituted of light-harvesting complexes 1 (LH1) and reaction centers (RC). While the architecture of the photosynthetic unit has been described, the forces and energies assuring the structural and functional integrity of LH2, the assembly of LH2 complexes, and how LH2 interact with the other proteins in the supramolecular architecture are still unknown. Here we investigate the molecular forces of the bacterial LH2 within the native photosynthetic membrane using atomic force microscopy single-molecule imaging and force measurement in combination. The binding between LH2 subunits is fairly weak, of the order of k(B)T, indicating the importance of LH2 ring architecture. In contrast LH2 subunits are solid with a free energy difference of 90 k(B)T between folded and unfolded states. Subunit α-helices unfold either in one-step, α- and β-polypeptides unfold together, or sequentially. The unfolding force of transmembrane helices is approximately 150 pN. In the two-step unfolding process, the β-polypeptide is stabilized by the molecular environment in the membrane. Hence, intermolecular forces influence the structural and functional integrity of LH2.

Prokaryotic gene clusters: a rich toolbox for synthetic biology

Bacteria construct elaborate nanostructures, obtain nutrients and energy from diverse sources, synthesize complex molecules, and implement signal processing to react to their environment. These complex phenotypes require the coordinated action of multiple genes, which are often encoded in a contiguous region of the genome, referred to as a gene cluster. Gene clusters sometimes contain all of the genes necessary and sufficient for a particular function. As an evolutionary mechanism, gene clusters facilitate the horizontal transfer of the complete function between species. Here, we review recent work on a number of clusters whose functions are relevant to biotechnology. Engineering these clusters has been hindered by their regulatory complexity, the need to balance the expression of many genes, and a lack of tools to design and manipulate DNA at this scale. Advances in synthetic biology will enable the large-scale bottom-up engineering of the clusters to optimize their functions, wake up cryptic clusters, or to transfer them between organisms. Understanding and manipulating gene clusters will move towards an era of genome engineering, where multiple functions can be "mixed-and-matched" to create a designer organism.

Examination of the putative Ca2+-binding site in the light-harvesting complex 1 of thermophilic purple sulfur bacterium Thermochromatium tepidum

The core light-harvesting complex (LH1) of purple sulfur photosynthetic bacterium Thermochromatium tepidum exhibits an unusual absorption maximum at 915 nm for the Q (y) transition, and is highly stable when copurified with reaction center (RC) in a LH1-RC complex form. In previous studies, we demonstrated that the calcium ions are involved in both the large red shift and the enhanced thermal stability, and possible Ca(2+)-binding sites were proposed. In this study, we further examine the putative binding sites in the LH1 polypeptides using purified chromatophores. Incubation of the chromatophores in the presence of EDTA revealed no substantial change in the absorption maximum of LH1 Q (y) transition, whereas further addition of detergents to the chromatophores-EDTA solution resulted in a blue-shift for the LH1 Q (y) peak with the final position at 892 nm. The change of the LH1 Q (y) peak to shorter wavelengths was relatively slow compared to that of the purified LH1-RC complex. The blue-shifted LH1 Q (y) transition in chromatophores can be restored to its original position by addition of Ca(2+) ions. The results suggest that the Ca(2+)-binding site is exposed on the inner surface of chromatophores, corresponding to the C-terminal region of LH1. An Asp-rich fragment in the LH1 α-polypeptide is considered to form a crucial part of the binding network. The slow response of LH1 Q (y) transition upon exposure to EDTA is discussed in terms of the membrane environment in the chromatophores.

Experimental evidence that the membrane-spanning helix of PufX adopts a bent conformation that facilitates dimerisation of the Rhodobacter sphaeroides RC-LH1 complex through N-terminal interactions

The PufX polypeptide is an integral component of some photosynthetic bacterial reaction center-light harvesting 1 (RC-LH1) core complexes. Many aspects of the structure of PufX are unresolved, including the conformation of its long membrane-spanning helix and whether C-terminal processing occurs. In the present report, NMR data recorded on the Rhodobacter sphaeroides PufX in a detergent micelle confirmed previous conclusions derived from equivalent data obtained in organic solvent, that the α-helix of PufX adopts a bent conformation that would allow the entire helix to reside in the membrane interior or at its surface. In support of this, it was found through the use of site-directed mutagenesis that increasing the size of a conserved glycine on the inside of the bend in the helix was not tolerated. Possible consequences of this bent helical structure were explored using a series of N-terminal deletions. The N-terminal sequence ADKTIFNDHLN on the cytoplasmic face of the membrane was found to be critical for the formation of dimers of the RC-LH1 complex. It was further shown that the C-terminus of PufX is processed at an early stage in the development of the photosynthetic membrane. A model in which two bent PufX polypeptides stabilise a dimeric RC-LH1 complex is presented, and it is proposed that the N-terminus of PufX from one half of the dimer engages in electrostatic interactions with charged residues on the cytoplasmic surface of the LH1α and β polypeptides on the other half of the dimer.

Native architecture of the photosynthetic membrane from Rhodobacter veldkampii

The photosynthetic membrane in purple bacteria contains several pigment-protein complexes that assure light capture and establishment of the chemiosmotic gradient. The bioenergetic tasks of the photosynthetic membrane require the strong interaction between these various complexes. In the present work, we acquired the first images of the native outer membrane architecture and the supramolecular organization of the photosynthetic apparatus in vesicular chromatophores of Rhodobacter (Rb.) veldkampii. Mixed with LH2 (light-harvesting complex 2) rings, the PufX-containing LH1-RC (light-harvesting complex 1--reaction center) core complexes appear as C-shaped monomers, with random orientations in the photosynthetic membrane. Within the LH1 fence surrounding the RC, a remarkable gap that is probably occupied (or partially occupied) by PufX is visualized. Sequence alignment revealed that one specific region in PufX may be essential for PufX-induced core dimerization. In this region of ten amino acids in length all Rhodobacter species had five conserved amino acids, with the exception of Rb. veldkampii. Our findings provide direct evidence that the presence of PufX in Rb. veldkampii does not directly govern the dimerization of LH1-RC core complexes in the native membrane. It is indicated, furthermore, that the high membrane curvature of Rb. veldkampii chromatophores (Rb. veldkampii features equally small vesicular chromatophores alike Rb. sphaeroides) is not due to membrane bending induced by dimeric RC-LH1-PufX cores, as it has been proposed in Rb. sphaeroides.

Excitation transfer connectivity in different purple bacteria: a theoretical and experimental study

Photosynthetic membranes accommodate densely packed light-harvesting complexes which absorb light and convey excitation to the reaction center (RC). The relationship between the fluorescence yield (phi) and the fraction (x) of closed RCs is informative about the probability for an excitation reaching a closed RC to be redirected to another RC. In this work, we have examined in this respect membranes from various bacteria and searched for a correlation with the arrangement of the light-harvesting complexes as known from atomic force or electron microscopies. A first part of the paper is devoted to a theoretical study analyzing the phi(x) relationship in various models: monomeric or dimeric RC-LH1 core complexes, with or without the peripheral LH2 complexes. We show that the simple "homogeneous" kinetic treatment used here agrees well with more detailed master equation calculations. We also discuss the agreement between information derived from the present technique and from singlet annihilation experiments. The experimental results show that the enhancement of the cross section of open RCs due to excitation transfer from closed units varies from 1.5 to 3 depending on species. The ratio of the core to core transfer rate (including the indirect pathway via LH2) to the rate of trapping in open units is in the range of 0.5 to 4. It is about 1 in Rhodobacter sphaeroides and does not increase significantly in mutants lacking LH2-despite the more numerous contacts between the dimeric core complexes expected in this case. The connectivity in this bacterium is due in good part to the fast transfer between the two partners of the dimeric (RC-LH1-PufX)(2) complex. The connectivity is however increased in the carotenoidless and LH2-less strain R26, which we ascribe to an anomalous LH1. A relatively high connectivity was found in Rhodospirillum photometricum, although not as high as predicted in the calculations of Fassioli et al. (2010). This illustrates a more general discrepancy between the measured efficiency of core to core excitation transfer and theoretical estimates. We argue that the limited core to core connectivity found in purple bacteria may reflect a trade-off between light-harvesting efficiency and the hindrance to quinone diffusion that would result from too tightly packed LH complexes.