Isolation and characterization of carotenosomes from a bacteriochlorophyll c-less mutant of Chlorobium tepidum

Predicting the future of excitation energy transfer in light-harvesting complex with artificial intelligence-based quantum dynamics

Exploring excitation energy transfer (EET) in light-harvesting complexes (LHCs) is essential for understanding the natural processes and design of highly-efficient photovoltaic devices. LHCs are open systems, where quantum effects may play a crucial role for almost perfect utilization of solar energy. Simulation of energy transfer with inclusion of quantum effects can be done within the framework of dissipative quantum dynamics (QD), which are computationally expensive. Thus, artificial intelligence (AI) offers itself as a tool for reducing the computational cost. Here we suggest AI-QD approach using AI to directly predict QD as a function of time and other parameters such as temperature, reorganization energy, etc., completely circumventing the need of recursive step-wise dynamics propagation in contrast to the traditional QD and alternative, recursive AI-based QD approaches. Our trajectory-learning AI-QD approach is able to predict the correct asymptotic behavior of QD at infinite time. We demonstrate AI-QD on seven-sites Fenna-Matthews-Olson (FMO) complex.

Cryo-Electron Tomography Reveals the Complex Ultrastructural Organization of Multicellular Filamentous Chloroflexota (Chloroflexi) Bacteria

The cell biology of Chloroflexota is poorly studied. We applied cryo-focused ion beam milling and cryo-electron tomography to study the ultrastructural organization of thermophilic Roseiflexus castenholzii and Chloroflexus aggregans, and mesophilic “Ca. Viridilinea mediisalina.” These species represent the three main lineages within a group of multicellular filamentous anoxygenic phototrophic Chloroflexota bacteria belonging to the Chloroflexales order. We found surprising structural complexity in the Chloroflexales. As with filamentous cyanobacteria, cells of C. aggregans and “Ca. Viridilinea mediisalina” share the outer membrane-like layers of their intricate multilayer cell envelope. Additionally, cells of R. castenholzii and “Ca. Viridilinea mediisalina” are connected by septal channels that resemble cyanobacterial septal junctions. All three strains possess long pili anchored close to cell-to-cell junctions, a morphological feature comparable to that observed in cyanobacteria. The cytoplasm of the Chloroflexales bacteria is crowded with intracellular organelles such as different types of storage granules, membrane vesicles, chlorosomes, gas vesicles, chemoreceptor-like arrays, and cytoplasmic filaments. We observed a higher level of complexity in the mesophilic strain compared to the thermophilic strains with regards to the composition of intracellular bodies and the organization of the cell envelope. The ultrastructural details that we describe in these Chloroflexales bacteria will motivate further cell biological studies, given that the function and evolution of the many discovered morphological traits remain enigmatic in this diverse and widespread bacterial group.

In situ high-resolution structure of the baseplate antenna complex in Chlorobaculum tepidum

Photosynthetic antenna systems enable organisms harvesting light and transfer the energy to the photosynthetic reaction centre, where the conversion to chemical energy takes place. One of the most complex antenna systems, the chlorosome, found in the photosynthetic green sulfur bacterium Chlorobaculum (Cba.) tepidum contains a baseplate, which is a scaffolding super-structure, formed by the protein CsmA and bacteriochlorophyll a. Here we present the first high-resolution structure of the CsmA baseplate using intact fully functional, light-harvesting organelles from Cba. tepidum, following a hybrid approach combining five complementary methods: solid-state NMR spectroscopy, cryo-electron microscopy, isotropic and anisotropic circular dichroism and linear dichroism. The structure calculation was facilitated through development of new software, GASyCS for efficient geometry optimization of highly symmetric oligomeric structures. We show that the baseplate is composed of rods of repeated dimers of the strongly amphipathic CsmA with pigments sandwiched within the dimer at the hydrophobic side of the helix.

The chlorosome of the photosynthetic bacterium C. tepidum harvests light and transfers the energy to the photosynthetic reaction centre. Here the authors determine the structure of the baseplate, a scaffolding super-structure, to show that the baseplate consists of rods of repeated CsmA dimers containing pigment molecules.

Glycolipid analyses of light-harvesting chlorosomes from envelope protein mutants of Chlorobaculum tepidum

Chlorosomes are large and efficient light-harvesting organelles in green photosynthetic bacteria, and they characteristically contain large numbers of bacteriochlorophyll c, d, or e molecules. Self-aggregated bacteriochlorophyll pigments are surrounded by a monolayer envelope membrane comprised of glycolipids and Csm proteins. Here, we analyzed glycolipid compositions of chlorosomes from the green sulfur bacterium Chlorobaculum tepidum mutants lacking one, two, or three Csm proteins by HPLC equipped with an evaporative light-scattering detector. The ratio of monogalactosyldiacylglyceride (MGDG) to rhamnosylgalactosyldiacylglyceride (RGDG) was smaller in chlorosomes from mutants lacking two or three proteins in CsmC/D/H motif family than in chlorosomes from the wild-type, whereas chlorosomes lacking CsmIJ showed relatively less RGDG than MGDG. The results suggest that the CsmC, CsmD, CsmH, and other chlorosome proteins are involved in organizing MGDG and RGDG and thereby affect the size and shape of the chlorosome.

Alternative Excitonic Structure in the Baseplate (BChl a-CsmA Complex) of the Chlorosome from Chlorobaculum tepidum

In the photosynthetic green sulfur bacterium Chlorobaculum tepidum, the baseplate mediates excitation energy transfer from the light-harvesting chlorosome to the Fenna-Matthews-Olson (FMO) complex and subsequently toward the reaction center (RC). Literature data suggest that the baseplate is a 2D lattice of BChl a-CsmA dimers. However, recently, it has been proposed, using 2D electronic spectroscopy (2DES) at 77 K, that at least four excitonically coupled BChl a are in close contact within the baseplate structure [ Dostál , J. ; et al., J. Phys. Chem. Lett. 2014 , 5 , 1743 ]. This finding is tested via hole burning (HB) spectroscopy (5 K). Our results indicate that the four excitonic states identified by 2DES likely correspond to contamination of the baseplate with the FMO antenna and possibly the RC. In contrast, HB reveals a different excitonic structure of the baseplate chromophores, where excitation is transferred to a localized trap state near 818 nm via exciton hopping, which leads to emission near 826 nm.

Automated robust and accurate assignment of protein resonances for solid state NMR

The process of resonance assignment represents a time-consuming and potentially error-prone bottleneck in structural studies of proteins by solid-state NMR (ssNMR). Software for the automation of this process is therefore of high interest. Procedures developed through the last decades for solution-state NMR are not directly applicable for ssNMR due to the inherently lower data quality caused by lower sensitivity and broader lines, leading to overlap between peaks. Recently, the first efforts towards procedures specifically aimed for ssNMR have been realized (Schmidt et al. in J Biomol NMR 56(3):243-254, 2013). Here we present a robust automatic method, which can accurately assign protein resonances using peak lists from a small set of simple 2D and 3D ssNMR experiments, applicable in cases with low sensitivity. The method is demonstrated on three uniformly (13)C, (15)N labeled biomolecules with different challenges on the assignments. In particular, for the immunoglobulin binding domain B1 of streptococcal protein G automatic assignment shows 100% accuracy for the backbone resonances and 91.8% when including all side chain carbons. It is demonstrated, by using a procedure for generating artificial spectra with increasing line widths, that our method, GAMES_ASSIGN can handle a significant amount of overlapping peaks in the assignment. The impact of including different ssNMR experiments is evaluated as well.

Temperature and carbon assimilation regulate the chlorosome biogenesis in green sulfur bacteria

Green photosynthetic bacteria adjust the structure and functionality of the chlorosome-the light-absorbing antenna complex-in response to environmental stress factors. The chlorosome is a natural self-assembled aggregate of bacteriochlorophyll (BChl) molecules. In this study, we report the regulation of the biogenesis of the Chlorobaculum tepidum chlorosome by carbon assimilation in conjunction with temperature changes. Our studies indicate that the carbon source and thermal stress culture of C. tepidum grows slower and incorporates fewer BChl c in the chlorosome. Compared with the chlorosome from other cultural conditions we investigated, the chlorosome from the carbon source and thermal stress culture displays (a) smaller cross-sectional radius and overall size, (b) simplified BChl c homologs with smaller side chains, (c) blue-shifted Qy absorption maxima, and (d) a sigmoid-shaped circular dichroism spectra. Using a theoretical model, we analyze how the observed spectral modifications can be associated with structural changes of BChl aggregates inside the chlorosome. Our report suggests a mechanism of metabolic regulation for chlorosome biogenesis.

Computational determination of the pigment binding motif in the chlorosome protein a of green sulfur bacteria

We present a molecular-scale model of Bacteriochlorophyll a (BChl a) binding to the chlorosome protein A (CsmA) of Chlorobaculum tepidum, and the aggregated pigment–protein dimer, as determined from protein–ligand docking and quantum chemistry calculations. Our calculations provide strong evidence that the BChl a molecule is coordinated to the His25 residue of CsmA, with the magnesium center of the bacteriochlorin ring situated\3 A° from the imidazole nitrogen atom of the histidine sidechain, and the phytyl tail aligned along the nonpolar residues of the a-helix of CsmA. We also confirm that the Qy band in the absorption spectra of BChl a experiences a large (?16 to ?43 nm) redshift when aggregated with another BChl a molecule in the CsmA dimer, compared to the BChl a in solvent; this redshift has been previously established by experimental researchers. We propose that our model of the BChl a–CsmA binding motif, where the dimer contains parallel aligned N-terminal regions, serves as the smallest repeating unit in a larger model of the para-crystalline chlorosome baseplate protein.

Chlorosome antenna complexes from green photosynthetic bacteria

Chlorosomes are the distinguishing light-harvesting antenna complexes that are found in green photosynthetic bacteria. They contain bacteriochlorophyll (BChl) c, d, e in natural organisms, and recently through mutation, BChl f, as their principal light-harvesting pigments. In chlorosomes, these pigments self-assemble into large supramolecular structures that are enclosed inside a lipid monolayer to form an ellipsoid. The pigment assembly is dictated mostly by pigment-pigment interactions as opposed to protein-pigment interactions. On the bottom face of the chlorosome, the CsmA protein aggregates into a paracrystalline baseplate with BChl a, and serves as the interface to the next energy acceptor in the system. The exceptional light-harvesting ability at very low light conditions of chlorosomes has made them an attractive subject of study for both basic and applied science. This review, incorporating recent advancements, considers several important aspects of chlorosomes: pigment biosynthesis, organization of pigments and proteins, spectroscopic properties, and applications to bio-hybrid and bio-inspired devices.

Comparison of the physical characteristics of chlorosomes from three different phyla of green phototrophic bacteria

Chlorosomes, the major antenna complexes in green sulphur bacteria, filamentous anoxygenic phototrophs, and phototrophic acidobacteria, are attached to the cytoplasmic side of the inner cell membrane and contain thousands of bacteriochlorophyll (BChl) molecules that harvest light and channel the energy to membrane-bound reaction centres. Chlorosomes from phototrophs representing three different phyla, Chloroflexus (Cfx.) aurantiacus, Chlorobaculum (Cba.) tepidum and the newly discovered "Candidatus (Ca.) Chloracidobacterium (Cab.) thermophilum" were analysed using PeakForce Tapping atomic force microscopy (PFT-AFM). Gentle PFT-AFM imaging in buffered solutions that maintained the chlorosomes in a near-native state revealed ellipsoids of variable size, with surface bumps and undulations that differ between individual chlorosomes. Cba. tepidum chlorosomes were the largest (133×57×36nm; 141,000nm(3) volume), compared with chlorosomes from Cfx. aurantiacus (120×44×30nm; 84,000nm(3)) and Ca. Cab. thermophilum (99×40×31nm; 65,000nm(3)). Reflecting the contributions of thousands of pigment-pigment stacking interactions to the stability of these supramolecular assemblies, analysis by nanomechanical mapping shows that chlorosomes are highly stable and that their integrity is disrupted only by very strong forces of 1000-2000pN. AFM topographs of Ca. Cab. thermophilum chlorosomes that had retained their attachment to the cytoplasmic membrane showed that this membrane dynamically changes shape and is composed of protrusions of up to 30nm wide and 6nm above the mica support, possibly representing different protein domains. Spectral imaging revealed significant heterogeneity in the fluorescence emission of individual chlorosomes, likely reflecting the variations in BChl c homolog composition and internal arrangements of the stacked BChls within each chlorosome.

In situ solid-state NMR spectroscopy of protein in heterogeneous membranes: the baseplate antenna complex of Chlorobaculum tepidum

A clever combination: an in situ solid-state NMR analysis of CsmA proteins in the heterogeneous environment of the photoreceptor of Chlorobaculum tepidum is reported. Using different combinations of 2D and 3D solid-state NMR spectra, 90 % of the CsmA resonances are assigned and provide on the basis of chemical shift data information about the structure and conformation of CsmA in the CsmA-bacteriochlorophyll a complex.

CsmA Protein is Associated with BChl a in the Baseplate Subantenna of Chlorosomes of the Photosynthetic Green Filamentous Bacterium Oscillochloris trichoides belonging to the Family Oscillochloridaceae

The baseplate subantenna in chlorosomes of green anoxygenic photosynthetic bacteria, belonging to the families Chloroflexaceae and Chlorobiaceae, is known to represent a complex of bacteriochlorophyll (BChl) a with the ~6 kDa CsmA proteins. Earlier, we showed the existence of a similar BChl a subantenna in chlorosomes of the photosynthetic green bacterium Oscillochloris trichoides, member of Oscillochloridaceae, the third family of green photosynthetic bacteria. However, this BChl a subantenna was not visually identified in absorption spectra of isolated Osc. trichoides chlorosomes in contrast to those of Chloroflexaceae and Chlorobiaceae. In this work, using room and low-temperature absorbance and fluorescence spectroscopy and sodium dodecyl sulfate polyacrylamide gel electrophoresis analysis of alkaline-treated and untreated chlorosomes of Osc. trichoides, we showed that the baseplate BChl a subantenna does exist in Oscillochloridaceae chlorosomes as a complex of BChl a with the 5.7 kDa CsmA protein. The present results support the idea that the baseplate subantenna, representing a complex of BChl a with a ~6 kDa CsmA protein, is a universal interface between the BChl c subantenna of chlorosomes and the nearest light-harvesting BChl a subantenna in all three known families of green anoxygenic photosynthetic bacteria.

A model of the protein-pigment baseplate complex in chlorosomes of photosynthetic green bacteria

In contrast to photosynthetic reaction centers, which share the same structural architecture, more variety is found in the light-harvesting antenna systems of phototrophic organisms. The largest antenna system described, so far, is the chlorosome found in anoxygenic green bacteria, as well as in a recently discovered aerobic phototroph. Chlorosomes are the only antenna system, in which the major light-harvesting pigments are organized in self-assembled supramolecular aggregates rather than on protein scaffolds. This unique feature is believed to explain why some green bacteria are able to carry out photosynthesis at very low light intensities. Encasing the chlorosome pigments is a protein-lipid monolayer including an additional antenna complex: the baseplate, a two-dimensional paracrystalline structure containing the chlorosome protein CsmA and bacteriochlorophyll a (BChl a). In this article, we review current knowledge of the baseplate antenna complex, which physically and functionally connects the chlorosome pigments to the reaction centers via the Fenna-Matthews-Olson protein, with special emphasis on the well-studied green sulfur bacterium Chlorobaculum tepidum (previously Chlorobium tepidum). A possible role for the baseplate in the biogenesis of chlorosomes is discussed. In the final part, we present a structural model of the baseplate through combination of a recent NMR structure of CsmA and simulation of circular dichroism and optical spectra for the CsmA-BChl a complex.

Theoretical examination of quantum coherence in a photosynthetic system at physiological temperature

The observation of long-lived electronic coherence in a photosynthetic pigment-protein complex, the Fenna-Matthews-Olson (FMO) complex, is suggestive that quantum coherence might play a significant role in achieving the remarkable efficiency of photosynthetic electronic energy transfer (EET), although the data were acquired at cryogenic temperature [Engel GS, et al. (2007) Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems. Nature 446:782-786]. In this paper, the spatial and temporal dynamics of EET through the FMO complex at physiological temperature are investigated theoretically. The numerical results reveal that quantum wave-like motion persists for several hundred femtoseconds even at physiological temperature, and suggest that the FMO complex may work as a rectifier for unidirectional energy flow from the peripheral light-harvesting antenna to the reaction center complex by taking advantage of quantum coherence and the energy landscape of pigments tuned by the protein scaffold. A potential role of quantum coherence is to overcome local energetic traps and aid efficient trapping of electronic energy by the pigments facing the reaction center complex.

Envelope proteins of the CsmB/CsmF and CsmC/CsmD motif families influence the size, shape, and composition of chlorosomes in Chlorobaculum tepidum

The chlorosome envelope of Chlorobaculum tepidum contains 10 proteins that belong to four structural motif families. A previous mutational study (N.-U. Frigaard, H. Li, K. J. Milks, and D. A. Bryant, J. Bacteriol. 186:646-653, 2004) suggested that some of these proteins might have redundant functions. Six multilocus mutants were constructed to test the effects of eliminating the proteins of the CsmC/CsmD and CsmB/CsmF motif families, and the resulting strains were characterized physiologically and biochemically. Mutants lacking all proteins of either motif family still assembled functional chlorosomes, and as measured by growth rates of the mutant strains, light harvesting was affected only at the lowest light intensities tested (9 and 32 micromol photons m(-2) s(-1)). The size, composition, and biogenesis of the mutant chlorosomes differed from those of wild-type chlorosomes. Mutants lacking proteins of the CsmC/CsmD motif family produced smaller chlorosomes than did the wild type, and the Q(y) absorbance maximum for the bacteriochlorophyll c aggregates in these chlorosomes was strongly blueshifted. Conversely, the chlorosomes of mutants lacking proteins of the CsmB/CsmF motif family were larger than wild-type chlorosomes, and the Q(y) absorption for their bacteriochlorophyll c aggregates was redshifted. When CsmH was eliminated in addition to other proteins of either motif family, chlorosomes had smaller diameters. These data show that the chlorosome envelope proteins of the CsmB/CsmF and CsmC/CsmD families play important roles in determining chlorosome size as well as the assembly and supramolecular organization of the bacteriochlorophyll c aggregates within the chlorosome.

Mutational analysis of three bchH paralogs in (bacterio-)chlorophyll biosynthesis in Chlorobaculum tepidum

The first committed step in the biosynthesis of (bacterio-)chlorophyll is the insertion of Mg2+ into protoporphyrin IX by Mg-chelatase. In all known (B)Chl-synthesizing organisms, Mg-chelatase is encoded by three genes that are homologous to bchH, bchD, and bchI of Rhodobacter spp. The genomes of all sequenced strains of green sulfur bacteria (Chlorobi) encode multiple bchH paralogs, and in the genome of Chlorobaculum tepidum, there are three bchH paralogs, denoted CT1295 (bchT), CT1955 (bchS), and CT1957 (bchH). Cba. tepidum mutants lacking one or two of these paralogs were constructed and characterized. All of the mutants lacking only one of these BchH homologs, as well as bchS bchT and bchH bchT double mutants, which can only produce BchH or BchS, respectively, were viable. However, attempts to construct a bchH bchS double mutant, in which only BchT was functional, were consistently unsuccessful. This result suggested that BchT alone is unable to support the minimal (B)Chl synthesis requirements of cells required for viability. The pigment compositions of the various mutant strains varied significantly. The BChl c content of the bchS mutant was only approximately 10% of that of the wild type, and this mutant excreted large amounts of protoporphyrin IX into the growth medium. The observed differences in BChl c production of the mutant strains were consistent with the hypothesis that the three BchH homologs function in end product regulation and/or substrate channeling of intermediates in the BChl c biosynthetic pathway.

Membrane orientation of the FMO antenna protein from Chlorobaculum tepidum as determined by mass spectrometry-based footprinting

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 spectrometry-based 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.

X-ray scattering and electron cryomicroscopy study on the effect of carotenoid biosynthesis to the structure of Chlorobium tepidum chlorosomes

Chlorosomes, the main antenna complexes of green photosynthetic bacteria, were isolated from null mutants of Chlorobium tepidum, each of which lacked one enzyme involved in the biosynthesis of carotenoids. The effects of the altered carotenoid composition on the structure of the chlorosomes were studied by means of x-ray scattering and electron cryomicroscopy. The chlorosomes from each mutant strain exhibited a lamellar arrangement of the bacteriochlorophyll c aggregates, which are the major constituents of the chlorosome interior. However, the carotenoid content and composition had a pronounced effect on chlorosome biogenesis and structure. The results indicate that carotenoids with a sufficiently long conjugated system are important for the biogenesis of the chlorosome baseplate. Defects in the baseplate structure affected the shape of the chlorosomes and were correlated with differences in the arrangement of lamellae and spacing between the lamellar planes of bacteriochlorophyll aggregates. In addition, comparisons among the various mutants enabled refinement of the assignments of the x-ray scattering peaks. While the main scattering peaks come from the lamellar structure of bacteriochlorophyll c aggregates, some minor peaks may originate from the paracrystalline arrangement of CsmA in the baseplate.

Hypothesis on chlorosome biogenesis in green photosynthetic bacteria

Chlorosomes are specialized compartments that constitute the main light harvesting system of green sulfur bacteria (GSB) and some filamentous anoxygenic phototrophs (FAP). Chlorosome biogenesis promises to be a complex process requiring the generation of a unilayer membrane and the targeting of bacteriochlorophyll, carotenoids, quinones, and proteins to the chlorosome. The biogenesis of chlorosomes as well as their presence in two distinct bacterial groups, GSB and FAP, remains enigmatic. The photosynthetic machinery and overall metabolic characteristics of these two bacterial groups are very different, and horizontal gene transfer has been proposed to explain chlorosome distribution. Chlorosomes have been considered to be unique structures that require a specific assembly machinery. We propose that no special machinery is required for chlorosome assembly. Instead, it is suggested that chlorosomes are a special form of lipid body. We present a model for chlorosome biogenesis that combines aspects of lipid body biogenesis with established chlorosome characteristics and may help explain the presence of chlorosomes in two metabolically diverse organism groups.

The light-harvesting antenna of Chlorobium tepidum: interactions between the FMO protein and the major chlorosome protein CsmA studied by surface plasmon resonance

Green sulfur bacteria possess two external light-harvesting antenna systems, the chlorosome and the FMO protein, which participate in a sequential energy transfer to the reaction centers embedded in the cytoplasmic membrane. However, little is known about the physical interaction between these two antenna systems. We have studied the interaction between the major chlorosome protein, CsmA, and the FMO protein in Chlorobium tepidum using surface plasmon resonance (SPR). Our results show an interaction between the FMO protein and an immobilized synthetic peptide corresponding to 17 amino acids at the C terminal of CsmA. This interaction is dependent on the presence of a motif comprising six amino acids that are highly conserved in all the currently available CsmA protein sequences.