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Photosynthetic antenna complexes capture and concentrate solar radiation by transferring the excitation to the reaction center that stores energy from the photon in chemical bonds. This process occurs with near-perfect quantum efficiency. Recent experiments at cryogenic temperatures have revealed that coherent energy transfer--a wave-like transfer mechanism--occurs in many photosynthetic pigment-protein complexes. Using the Fenna-Matthews-Olson antenna complex (FMO) as a model system, theoretical studies incorporating both incoherent and coherent transfer as well as thermal dephasing predict that environmentally assisted quantum transfer efficiency peaks near physiological temperature; these studies also show that this mechanism simultaneously improves the robustness of the energy transfer process. This theory requires long-lived quantum coherence at room temperature, which never has been observed in FMO. Here we present evidence that quantum coherence survives in FMO at physiological temperature for at least 300 fs, long enough to impact biological energy transport. These data prove that the wave-like energy transfer process discovered at 77 K is directly relevant to biological function. Microscopically, we attribute this long coherence lifetime to correlated motions within the protein matrix encapsulating the chromophores, and we find that the degree of protection afforded by the protein appears constant between 77 K and 277 K. The protein shapes the energy landscape and mediates an efficient energy transfer despite thermal fluctuations. biophysics | photosynthesis | quantum beating | ultrafast spectroscopy | quantum biology doi/ 10.1073/pnas.1005484107

The high excitation energy-transfer efficiency demanded in photosynthetic organisms relies on the optimal pigment-protein binding orientation in the individual protein complexes and also on the overall architecture of the photosystem. In green sulfur bacteria, the membrane-attached Fenna-Matthews-Olson (FMO) antenna protein functions as a 'wire' to connect the large peripheral chlorosome antenna complex with the reaction center (RC), which is embedded in the cytoplasmic membrane (CM). Energy collected by the chlorosome is funneled through the FMO to the RC. Although there has been considerable effort to understand the relationships between structure and function of the individual isolated complexes, the specific architecture for in vivo interactions of the FMO protein, the CM, and the chlorosome, ensuring highly efficient energy transfer, is still not established experimentally. Here, we describe a mass spectrometrybased method that probes solvent-exposed surfaces of the FMO by labeling solvent-exposed aspartic and glutamic acid residues. The locations and extents of labeling of FMO on the native membrane in comparison with it alone and on a chlorosome-depleted membrane reveal the orientation. The large differences in the modification of certain peptides show that the Bchl a #3 side of the FMO trimer interacts with the CM, which is consistent with recent theoretical predictions. Moreover, the results also provide direct experimental evidence to confirm the overall architecture of the photosystem from Chlorobaculum tepidum (C tepidum) and give information on the packing of the FMO protein in its native environment. chemical labeling | energy transfer | FMO protein | mass spectrometry | protein footprinting

Acaryochloris marina is a unique cyanobacterium that is able to produce chlorophyll d as its primary photosynthetic pigment and thus efficiently use far-red light for photosynthesis. Acaryochloris species have been isolated from marine environments in association with other oxygenic phototrophs, which may have driven the niche-filling introduction of chlorophyll d. To investigate these unique adaptations, we have sequenced the complete genome of A. marina. The DNA content of A. marina is composed of 8.3 million base pairs, which is among the largest bacterial genomes sequenced thus far. This large array of genomic data is distributed into nine single-copy plasmids that code for >25% of the putative ORFs. Heavy duplication of genes related to DNA repair and recombination (primarily recA) and transposable elements could account for genetic mobility and genome expansion. We discuss points of interest for the biosynthesis of the unusual pigments chlorophyll d and s-carotene and genes responsible for previously studied phycobilin aggregates. Our analysis also reveals that A. marina carries a unique complement of genes for these phycobiliproteins in relation to those coding for antenna proteins related to those in Prochlorococcus species. The global replacement of major photosynthetic pigments appears to have incurred only minimal specializations in reaction center proteins to accommodate these alternate pigments. These features clearly show that the genus Acaryochloris is a fitting candidate for understanding genome expansion, gene acquisition, ecological adaptation, and photosystem modification in the cyanobacteria. comparative microbial genomics | photosynthesis | oxygenic phototrophs | evolution

Intermolecular electronic coupling dictates the optical properties of molecular aggregate systems. Of particular interest are photosynthetic pigment-protein complexes that absorb sunlight then efficiently direct energy toward the photosynthetic reaction center. Two-dimensional (2D) ultrafast spectroscopy has been used widely in the infrared (IR) and increasingly in the visible to probe excitonic couplings and observe dynamics, but the off-diagonal spectral signatures of coupling are often obscured by broad diagonal peaks, especially in the visible regime. Rotating the polarizations of the laser pulses exciting the sample can highlight certain spectral features, and the use of polarized pulse sequences to elucidate cross-peaks in 2D spectra has been demonstrated in the IR for vibrational transitions. Here we develop 2D electronic spectroscopy using cross-peak-specific pulse polarization conditions in an investigation of the Fenna-Matthews-Olson light harvesting complex from green photosynthetic bacteria. Our measurements successfully highlight off-diagonal features of the 2D spectra and, in combination with an analysis based on the signs of features arising from particular energy level pathways and theoretical simulation, we characterize the dominant response pathways responsible for the spectral features. Cross-peak-specific 2D electronic spectroscopy provides insight into the interchromophore couplings, as well as into the energetic pathways giving rise to the signal. With femtosecond resolution, we also observe dynamical processes that depend on these couplings and interactions with the protein environment. 2D spectroscopy | Fenna-Matthews-Olson | ultrafast spectroscopy

The abundance of life on Earth is almost entirely due to biological photosynthesis, which depends on light energy. The source of light in natural habitats has heretofore been thought to be the sun, thus restricting photosynthesis to solar photic environments on the surface of the Earth. If photosynthesis could take place in geothermally illuminated environments, it would increase the diversity of photosynthetic habitats both on Earth and on other worlds that have been proposed to possibly harbor life. Green sulfur bacteria are anaerobes that require light for growth by the oxidation of sulfur compounds to reduce C[O.sub.2] to organic carbon, and are capable of photosynthetic growth at extremely low light intensities. We describe the isolation and cultivation of a previously unknown green sulfur bacterial species from a deep-sea hydrothermal vent, where the only source of light is geothermal radiation that includes wavelengths absorbed by photosynthetic pigments of this organism. photosynthesis | anoxygenic | green sulfur bacterium | evolution | habitat

Chlorophyll d-producing cyanobacteria are a recently described group of phototrophic bacteria that is a major focus of photosynthesis research, previously known only from marine environments in symbiosis with eukaryotes. We have discovered a free-living member of this group from a eutrophic hypersaline lake. Phylo-genetic analyses indicated these strains are closely related to each other but not to prochlorophyte cyanobacteria that also use an alternative form of chlorophyll as the major light-harvesting pigment. We have also demonstrated that these bacteria acquired a fragment of the small-subunit rRNA gene encoding a conserved hairpin in the bacterial ribosome from a proteobacterial donor at least 10 million years before the present. Thus, our most widely used phylogenetic marker can be a mosaic of sequence fragments with widely divergent evolutionary histories. cyanobacteria | lateral gene transfer

Quantum coherences, observed as time-dependent beats in ultrafast spectroscopic experiments, arise when light-matter interactions prepare systems in superpositions of states with differing energy and fixed phase across the ensemble. Such coherences have been observed in photosynthetic systems following ultrafast laser excitation, but what these coherences imply about the underlying energy transfer dynamics remains subject to debate. Recent work showed that redox conditions tune vibronic coupling in the Fenna-Matthews-Olson (FMO) pigment-protein complex in green sulfur bacteria, raising the question of whether redox conditions may also affect the long-lived (>100 fs) quantum coherences observed in this complex. In this work, we perform ultrafast twodimensional electronic spectroscopy measurements on the FMO complex under both oxidizing and reducing conditions. We observe that many excited-state coherences are exclusively present in reducing conditions and are absent or attenuated in oxidizing conditions. Reducing conditions mimic the natural conditions of the complex more closely. Further, the presence of these coherences correlates with the vibronic coupling that produces faster, more efficient energy transfer through the complex under reducing conditions. The growth of coherences across the waiting time and the number of beating frequencies across hundreds of wavenumbers in the power spectra suggest that the beats are excitedstate coherences with a mostly vibrational character whose phase relationship is maintained through the energy transfer process. Our results suggest that excitonic energy transfer proceeds through a coherent mechanism in this complex and that the coherences may provide a tool to disentangle coherent relaxation from energy transfer driven by stochastic environmental fluctuations. [ABSTRACT FROM AUTHOR]

The gene for a reaction center core polypeptide from the anoxygenic photosynthetic bacterium Heliobacillus mobilis was cloned and sequenced, and was found to have 609 residues of a molecular mass of 68 kDa. The primary sequence of the reaction center protein (P800) has a high percentage of sequence identity to photosystem I in a cysteine-comprising loop, which is the putative binding site of the iron-sulfur center Fx and in the earlier hydrophobic zone. A homodimeric organization of the reaction center was noticed. This varies from photosystem I and most other photosynthetic reaction centers, where the reaction center core consists of two parallel yet nonidentical subunits.

Photosynthetic species evolved to protect their light-harvesting apparatus from photoxidative damage driven by intracellular redox conditions or environmental conditions. The Fenna-Matthews-Olson (FMO) pigment-protein complex from green sulfur bacteria exhibits redox-dependent quenching behavior partially due to two internal cysteine residues. Here, we show evidence that a photosynthetic complex exploits the quantum mechanics of vibronic mixing to activate an oxidative photoprotective mechanism. We use two-dimensional electronic spectroscopy (2DES) to capture energy transfer dynamics in wild-type and cysteine-deficient FMO mutant proteins under both reducing and oxidizing conditions. Under reducing conditions, we find equal energy transfer through the exciton 4-1 and 4-2-1 pathways because the exciton 4-1 energy gap is vibronically coupled with a bacteriochlorophyll-a vibrational mode. Under oxidizing conditions, however, the resonance of the exciton 4-1 energy gap is detuned from the vibrational mode, causing excitons to preferentially steer through the indirect 4-2-1 pathway to increase the likelihood of exciton quenching. We use a Redfield model to show that the complex achieves this effect by tuning the site III energy via the redox state of its internal cysteine residues. This result shows how pigment-protein complexes exploit the quantum mechanics of vibronic coupling to steer energy transfer. [ABSTRACT FROM AUTHOR]

In oxygenic photosynthetic organisms, photosystem II (PSII) is a unique membrane protein complex that catalyzes light-driven oxidation of water. PSII undergoes frequent damage due to its demanding photochemistry. It must undergo a repair and reassembly process following photodamage, many facets of which remain unknown. We have discovered a PSII subcomplex that lacks 5 key PSII core reaction center polypeptides: D1, D2, PsbE, PsbF, and PsbI. This pigment–protein complex does contain the PSII core antenna proteins CP47 and CP43, as well as most of their associated low molecular mass subunits, and the assembly factor Psb27. Immunoblotting, mass spectrometry, and ultrafast spectroscopic results support the absence of a functional reaction center in this complex, which we call the “no reaction center” complex (NRC). Analytical ultracentrifugation and clear native PAGE analysis show that NRC is a stable pigment–protein complex and not a mixture of free CP47 and CP43 proteins. NRC appears in higher abundance in cells exposed to high light and impaired protein synthesis, and genetic deletion of PsbO on the PSII luminal side results in an increased NRC population, indicative that NRC forms in response to photodamage as part of the PSII repair process. Our finding challenges the current model of the PSII repair cycle and implies an alternative PSII repair strategy. Formation of this complex may maximize PSII repair economy by preserving intact PSII core antennas in a single complex available for PSII reassembly, minimizing the risk of randomly diluting multiple recycling components in the thylakoid membrane following a photodamage event. [ABSTRACT FROM AUTHOR]

Cytochrome c (cyt c), required for electron transport in mitochondria, possesses a covalently attached heme cofactor. Attachment is catalyzed by holocytochrome c synthase (HCCS), leading to two thioether bonds between heme and a conserved CXXCH motif of cyt c. In cyt c, histidine (His19) of CXXCH acts as an axial ligand to heme iron and upon release of holocytochrome c from HCCS, folding leads to formation of a second axial interaction with methionine (Met81). We previously discovered mutations in human HCCS that facilitate increased biosynthesis of cyt c in recombinant Escherichia coli. Focusing on HCCS E159A, novel cyt c variants in quantities that are sufficient for biophysical analysis are biosynthesized. Cyt c H19M, the first bis-Met liganded cyt c, is compared with other axial ligand variants (M81A, M81H) and single thioether cyt c variants. For variants with axial ligand substitutions, electronic absorption, near-UV circular dichroism, and electron paramagnetic resonance spectroscopy provide evidence that axial ligands are changed and the heme environment is altered. Circular dichroism spectra in far UV and thermal denaturation analyses demonstrate that axial ligand changes do not affect secondary structures and stability. Redox potentials span a 400-mV range (+349 mV vs. standard hydrogen electrode, H19M; +252 mV, WT; −19 mV, M81A; −69 mV, M81H). We discuss the results in the context of a four-step mechanism for HCCS, whereby HCCS mutants such as E159A are enhanced in release (step 4) of cyt c from the HCCS active site; thus, we term these “release mutants.” [ABSTRACT FROM AUTHOR]

Light-harvesting antenna complexes not only aid in the capture of solar energy for photosynthesis, but regulate the quantity of transferred energy as well. Light-harvesting regulation is important for protecting reaction center complexes from overexcitation, generation of reactive oxygen species, and metabolic overload. Usually, this regulation is controlled by the association of lightharvesting antennas with accessory quenchers such as carotenoids. One antenna complex, the Fenna-Matthews-Olson (FMO) antenna protein from green sulfur bacteria, completely lacks carotenoids and other known accessory quenchers. Nonetheless, the FMO protein is able to quench energy transfer in aerobic conditions effectively, indicating a previously unidentified type of regulatory mechanism. Through de novo sequencing MS, chemical modification, and mutagenesis, we have pinpointed the source of the quenching action to cysteine residues (Cys49 and Cys353) situated near two lowenergy bacteriochlorophylls in the FMO protein from Chlorobaculum tepidum. Removal of these cysteines (particularly removal of the completely conserved Cys353) through N-ethylmaleimide modification or mutagenesis to alanine abolishes the aerobic quenching effect. Electrochemical analysis and electron paramagnetic resonance spectra suggest that in aerobic conditions the cysteine thiols are converted to thiyl radicals which then are capable of quenching bacteriochlorophyll excited states through electron transfer photochemistry. This simple mechanism has implications for the design of bio-inspired light-harvesting antennas and the redesign of natural photosynthetic systems. [ABSTRACT FROM AUTHOR]

The world's crop productivity is stagnating whereas population growth, rising affluence, and mandates for biofuels put increasing demands on agriculture. Meanwhile, demand for increasing cropland competes with equally crucial global sustainability and environmental protection needs. Addressing this looming agricultural crisis will be one of our greatest scientific challenges in the coming decades, and success will require substantial improvements at many levels. We assert that increasing the efficiency and productivity of photosynthesis in crop plants will be essential if this grand challenge is to be met. Here, we explore an array of prospective redesigns of plant systems at various scales, all aimed at increasing crop yields through improved photosynthetic efficiency and performance. Prospects range from straightforward alterations, already supported by preliminary evidence of feasibility, to substantial redesigns that are currently only conceptual, but that may be enabled by new developments in synthetic biology. Although some proposed redesigns are certain to face obstacles that will require alternate routes, the efforts should lead to new discoveries and technical advances with important impacts on the global problem of crop productivity and bioenergy production. [ABSTRACT FROM AUTHOR]

The high excitation energy-transfer efficiency demanded in photo-synthetic organisms relies on the optimal pigment-protein binding orientation in the individual protein complexes and also on the overall architecture of the photosystem. In green sulfur bacteria, the membrane-attached Fenna-Matthews-Olson (FMO) antenna protein functions as a "wire" to connect the large peripheral chlorosome antenna complex with the reaction center (RC), which is embedded in the cytoplasmic membrane (CM). Energy collected by the chlorosome is funneled through the FMO to the RC. Although there has been considerable effort to understand the relationships between structure and function of the individual isolated complexes, the specific architecture for in vivo interactions of the FMO protein, the CM, and the chlorosome, ensuring highly efficient energy transfer, is still not established experimentally. Here, we describe a mass spectrometrybased method that probes solvent-exposed surfaces of the FMO by labeling solvent-exposed aspartic and glutamic acid residues. The locations and extents of labeling of FMO on the native membrane in comparison with it alone and on a chlorosome-depleted membrane reveal the orientation. The large differences in the modification of certain peptides show that the Bchl a #3 side of the FMO trimer interacts with the CM, which is consistent with recent theoretical predictions. Moreover, the results also provide direct experimental evidence to confirm the overall architecture of the photosystem from Chiorobaculum tepidum (C tepidum) and give information on the packing of the FMO protein in its native environment. [ABSTRACT FROM AUTHOR]

Intermolecular electronic coupling dictates the optical properties of molecular aggregate systems. Of particular interest are photosynthetic pigment-protein complexes that absorb sunlight then efficiently direct energy toward the photosynthetic reaction center. Two-dimensional (2D) ultrafast spectroscopy has been used widely in the infrared (IR) and increasingly in the visible to probe excitonic couplings and observe dynamics, but the off-diagonal spectral signatures of coupling are often obscured by broad diagonal peaks, especially in the visible regime. Rotating the polarizations of the laser pulses exciting the sample can highlight certain spectral features, and the use of polarized pulse sequences to elucidate cross-peaks in 2D spectra has been demonstrated in the IR for vibrational transitions. Here we develop 2D electronic spectroscopy using cross-peak-specific pulse polarization conditions in an investigation of the Fenna-Matthews-Olson light harvesting complex from green photosynthetic bacteria. Our measurements successfully highlight off-diagonal features of the 2D spectra and, in combination with an analysis based on the signs of features arising from particular energy level pathways and theoretical simulation, we characterize the dominant response pathways responsible for the spectral features. Cross-peak-specific 2D electronic spectroscopy provides insight into the interchromophore couplings, as well as into the energetic pathways giving rise to the signal. With femtosecond resolution, we also observe dynamical processes that depend on these couplings and interactions with the protein environment. [ABSTRACT FROM AUTHOR]

Chlorophyll d-producing cyanobacteria are a recently described group of phototrophic bacteria that is a major focus of photosynthesis research, previously known only from marine environments in symbiosis with eukaryotes. We have discovered a free-living member of this group from a eutrophic hypersaline lake. Phylogenetic analyses indicated these strains are closely related to each other but not to prochlorophyte cyanobacteria that also use an alternative form of chlorophyll as the major light-harvesting pigment We have also demonstrated that these bacteria acquired a fragment of the small-subunit rRNA gene encoding a conserved hairpin in the bacterial ribosome from a proteobacterial donor at least 10 million years before the present. Thus, our most widely used phylogenetic marker can be a mosaic of sequence fragments with widely divergent evolutionary histories. [ABSTRACT FROM AUTHOR]

The article focuses on photosynthetic organisms' antenna systems, which were designed for absorption of photons and transfer of energy in the form of excited states or excitons to the photosynthetic reaction center. Topics discussed include features and functions of the phycobilisomes, the structure of the trimeric building block that makes up the phycobilisome and the two pigments discovered by Wang and Moerner's analysis of a photosynthetic antenna complex.

Examines the impact of horizontal gene transfer on eukaryote genomes of the algae Bigelowiella natans. Primary endosymbiotic event; Gene transfer from the relict nucleus into the host genome; Photosynthesis.