We investigated the fluorescence kinetics of LH2 complexes from Marichromatium purpuratum, the cryo-EM structure of which has been recently elucidated with 2.4 Å resolution. The experiments have been carried out as a function of the excitation density by varying both the excitation fluence and the repetition rate of the laser excitation. Instead of the usual multiexponential fitting procedure, we applied the less common phasor formalism for evaluating the transients because this allows for a model-free analysis of the data without a priori knowledge about the number of processes that contribute to a particular decay. For the various excitation conditions, this analysis reproduces consistently three lifetime components with decay times below 100 ps, 500 ps, and 730 ps, which were associated with the quenched state, singlet-triplet annihilation, and fluorescence decay, respectively. Moreover, it reveals that the number of decay components that contribute to the transients depends on whether the excitation wavelength is in resonance with the B800 BChl a molecules or with the carotenoids. Based on the mutual arrangement of the chromophores in their binding pockets, this leads us to conclude that the energy transfer pathways within the LH2 complex of this species differ significantly from each other for exciting either the B800 BChl molecules or the carotenoids. Finally, we speculate whether the illumination with strong laser light converts the LH2 complexes studied here into a quenched conformation that might be related to the development of the non-photochemical quenching mechanism that occurs in higher plants.
Euglenids represent a group of protists with diverse modes of feeding. To date, only a partial genomic sequence of Euglena gracilis and transcriptomes of several phototrophic and secondarily osmotrophic species are available, while primarily heterotrophic euglenids are seriously undersampled. In this work, we begin to fill this gap by presenting genomic and transcriptomic drafts of a primary osmotroph, Rhabdomonas costata. The current genomic assembly length of 100 Mbp is 14× smaller than that of E. gracilis. Despite being too fragmented for comprehensive gene prediction it provided fragments of the mitochondrial genome and comparison of the transcriptomic and genomic data revealed features of its introns, including several candidates for nonconventional types. A set of 39,456 putative R. costata proteins was predicted from the transcriptome. Annotation of the mitochondrial core metabolism provides the first data on the facultatively anaerobic mitochondrion of R. costata, which in most respects resembles the mitochondrion of E. gracilis with a certain level of streamlining. R. costata can synthetise thiamine by enzymes of heterogenous provenances and haem by a mitochondrial-cytoplasmic C4 pathway with enzymes orthologous to those found in E. gracilis. The low percentage of green algae-affiliated genes supports the ancestrally osmotrophic status of this species.
- MeSH
- biologická evoluce MeSH
- Chromatium genetika metabolismus MeSH
- Euglenida genetika metabolismus MeSH
- exony genetika MeSH
- fylogeneze MeSH
- genom MeSH
- heterotrofní procesy MeSH
- introny genetika MeSH
- mitochondrie genetika MeSH
- sekvenční analýza DNA metody MeSH
- transkriptom genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
There are two main types of bacterial photosynthesis: oxygenic (cyanobacteria) and anoxygenic (sulfur and non-sulfur phototrophs). Molecular mechanisms of photosynthesis in the phototrophic microorganisms can differ and depend on their location and pigments in the cells. This paper describes bacteria capable of molecular oxidizing hydrogen sulfide, specifically the families Chromatiaceae and Chlorobiaceae, also known as purple and green sulfur bacteria in the process of anoxygenic photosynthesis. Further, it analyzes certain important physiological processes, especially those which are characteristic for these bacterial families. Primarily, the molecular metabolism of sulfur, which oxidizes hydrogen sulfide to elementary molecular sulfur, as well as photosynthetic processes taking place inside of cells are presented. Particular attention is paid to the description of the molecular structure of the photosynthetic apparatus in these two families of phototrophs. Moreover, some of their molecular biotechnological perspectives are discussed.
- Klíčová slova
- anaerobes, anoxygenic bacteria, detoxification, hydrogen sulfide, molecular mechanisms of photosynthesis, water environment,
- MeSH
- anaerobióza MeSH
- Chlorobi klasifikace genetika fyziologie MeSH
- Chromatiaceae klasifikace genetika fyziologie MeSH
- fototrofní procesy genetika MeSH
- fylogeneze MeSH
- síra metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
- Názvy látek
- síra MeSH
The excitation energy transfer (EET) from the bacteriochlorophyll (BChl) Soret band to the second excited state(s) (S2) of carotenoids in pigment-protein complexes of purple bacteria was investigated. The efficiency of EET was determined, based on fluorescence excitation and absorption spectra of chromatophores, peripheral light-harvesting complexes (LH2), core complexes (LH1-RC), and pigments in solution. Carotenoid-containing and carotenoid-less samples were compared: LH1-RC and LH2 from Allochromatium minutissimum, Ectothiorhodospira haloalkaliphila, and chromatophores from Rhodobacter sphaeroides and Rhodospirillum rubrum wild type and carotenoid-free strains R-26 and G9. BChl-to-carotenoid EET was absent, or its efficiency was less than the accuracy of the measurements of ∼5%. Quantum chemical calculations support the experimental results: The transition dipole moments of spatially close carotenoid/BChl pairs were found to be nearly orthogonal. The structural arrangements suggest that Soret EET may be lacking for the studied systems, however, EET from carotenoids to Qx appears to be possible.
- MeSH
- bakteriochlorofyly MeSH
- Chromatiaceae MeSH
- Ectothiorhodospira MeSH
- fluorescenční spektrometrie MeSH
- fotosyntetické reakční centrum - proteinové komplexy * metabolismus MeSH
- karotenoidy MeSH
- přenos energie MeSH
- Proteobacteria metabolismus MeSH
- Rhodobacter sphaeroides * metabolismus MeSH
- světlosběrné proteinové komplexy metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- bakteriochlorofyly MeSH
- fotosyntetické reakční centrum - proteinové komplexy * MeSH
- karotenoidy MeSH
- světlosběrné proteinové komplexy MeSH
All purple photosynthetic bacteria contain RC-LH1 'Core' complexes. The structure of this complex from Rhodobacter sphaeroides, Rhodopseudomonas palustris and Thermochromatium tepidum has been solved using X-ray crystallography. Recently, the application of single particle cryo-EM has revolutionised structural biology and the structure of the RC-LH1 'Core' complex from Blastochloris viridis has been solved using this technique, as well as the complex from the non-purple Chloroflexi species, Roseiflexus castenholzii. It is apparent that these structures are variations on a theme, although with a greater degree of structural diversity within them than previously thought. Furthermore, it has recently been discovered that the only phototrophic representative from the phylum Gemmatimonadetes, Gemmatimonas phototrophica, also contains a RC-LH1 'Core' complex. At present only a low-resolution EM-projection map exists but this shows that the Gemmatimonas phototrophica complex contains a double LH1 ring. This short review compares these different structures and looks at the functional significance of these variations from two main standpoints: energy transfer and quinone exchange.
- Klíčová slova
- Anoxygenic phototrophs, Light harvesting, Purple photosynthetic bacteria, RC–LH1, Reaction centres, Structures,
- MeSH
- bakteriální proteiny chemie genetika metabolismus MeSH
- benzochinony metabolismus MeSH
- Chromatiaceae genetika metabolismus MeSH
- fotosyntetické reakční centrum - proteinové komplexy chemie genetika metabolismus MeSH
- fotosyntéza * MeSH
- genetická variace MeSH
- konformace proteinů MeSH
- molekulární modely MeSH
- přenos energie MeSH
- Rhodobacter sphaeroides genetika metabolismus MeSH
- Rhodopseudomonas genetika metabolismus MeSH
- světlosběrné proteinové komplexy chemie genetika metabolismus MeSH
- vztahy mezi strukturou a aktivitou MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
- srovnávací studie MeSH
- Názvy látek
- bakteriální proteiny MeSH
- benzochinony MeSH
- fotosyntetické reakční centrum - proteinové komplexy MeSH
- quinone MeSH Prohlížeč
- světlosběrné proteinové komplexy MeSH
Sulphide-driven anoxygenic photosynthesis is an ancient microbial metabolism that contributes significantly to inorganic carbon fixation in stratified, sulphidic water bodies. Methods commonly applied to quantify inorganic carbon fixation by anoxygenic phototrophs, however, cannot resolve the contributions of distinct microbial populations to the overall process. We implemented a straightforward workflow, consisting of radioisotope labelling and flow cytometric cell sorting based on the distinct autofluorescence of bacterial photopigments, to discriminate and quantify contributions of co-occurring anoxygenic phototrophic populations to in situ inorganic carbon fixation in environmental samples. This allowed us to assign 89.3% ± 7.6% of daytime inorganic carbon fixation by anoxygenic phototrophs in Lake Rogoznica (Croatia) to an abundant chemocline-dwelling population of green sulphur bacteria (dominated by Chlorobium phaeobacteroides), whereas the co-occurring purple sulphur bacteria (Halochromatium sp.) contributed only 1.8% ± 1.4%. Furthermore, we obtained two metagenome assembled genomes of green sulphur bacteria and one of a purple sulphur bacterium which provides the first genomic insights into the genus Halochromatium, confirming its high metabolic flexibility and physiological potential for mixo- and heterotrophic growth.
- MeSH
- Chlorobium izolace a purifikace metabolismus MeSH
- Chromatiaceae izolace a purifikace metabolismus MeSH
- fotosyntéza MeSH
- jezera mikrobiologie MeSH
- koloběh uhlíku MeSH
- mořská voda mikrobiologie MeSH
- síra metabolismus MeSH
- sulfidy metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Chorvatsko MeSH
- Názvy látek
- síra MeSH
- sulfidy MeSH
Ultra-intense femtosecond X-ray pulses from X-ray lasers permit structural studies on single particles and biomolecules without crystals. We present a large data set on inherently heterogeneous, polyhedral carboxysome particles. Carboxysomes are cell organelles that vary in size and facilitate up to 40% of Earth's carbon fixation by cyanobacteria and certain proteobacteria. Variation in size hinders crystallization. Carboxysomes appear icosahedral in the electron microscope. A protein shell encapsulates a large number of Rubisco molecules in paracrystalline arrays inside the organelle. We used carboxysomes with a mean diameter of 115±26 nm from Halothiobacillus neapolitanus. A new aerosol sample-injector allowed us to record 70,000 low-noise diffraction patterns in 12 min. Every diffraction pattern is a unique structure measurement and high-throughput imaging allows sampling the space of structural variability. The different structures can be separated and phased directly from the diffraction data and open a way for accurate, high-throughput studies on structures and structural heterogeneity in biology and elsewhere.
The initial energy transfer steps in photosynthesis occur on ultrafast timescales. We analyze the carotenoid to bacteriochlorophyll energy transfer in LH2 Marichromatium purpuratum as well as in an artificial light-harvesting dyad system by using transient grating and two-dimensional electronic spectroscopy with 10 fs time resolution. We find that Förster-type models reproduce the experimentally observed 60 fs transfer times, but overestimate coupling constants, which lead to a disagreement with both linear absorption and electronic 2D-spectra. We show that a vibronic model, which treats carotenoid vibrations on both electronic ground and excited states as part of the system's Hamiltonian, reproduces all measured quantities. Importantly, the vibronic model presented here can explain the fast energy transfer rates with only moderate coupling constants, which are in agreement with structure based calculations. Counterintuitively, the vibrational levels on the carotenoid electronic ground state play the central role in the excited state population transfer to bacteriochlorophyll; resonance between the donor-acceptor energy gap and the vibrational ground state energies is the physical basis of the ultrafast energy transfer rates in these systems.
- MeSH
- bakteriochlorofyly chemie metabolismus MeSH
- Chromatium chemie metabolismus MeSH
- karotenoidy chemie metabolismus MeSH
- přenos energie * MeSH
- spektrální analýza MeSH
- světlosběrné proteinové komplexy chemie metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- bakteriochlorofyly MeSH
- karotenoidy MeSH
- světlosběrné proteinové komplexy MeSH
We explored the use of Raman spectroscopy to simultaneously monitor the presence of different biomarkers (carotenoids, elemental sulfur) within single cells of the purple sulfur photosynthetic bacteria Allochromatium vinosum and A. warmingii. Raman microspectrometry using excitation at 532 nm allowed the detection of different carotenoids. Raman signals of elemental sulfur appeared soon after feeding starved cells with sulfide. Raman spectroscopy is thus a convenient and sensitive technique to qualitatively and semiquantitatively assess the presence of different compounds of interest within single bacterial cells.
- Klíčová slova
- Allochromatium vinosum, Allochromatium warmingii, Raman spectroscopy, carotenoids, purple sulfur bacteria, sulfur,
- MeSH
- analýza jednotlivých buněk * metody MeSH
- Chromatiaceae chemie ultrastruktura MeSH
- karotenoidy analýza MeSH
- Ramanova spektroskopie metody MeSH
- síra analýza MeSH
- sulfidy metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- karotenoidy MeSH
- síra MeSH
- sulfidy MeSH
The newly discovered di-haem cytochrome c4 from the purple sulfur photosynthetic bacterium Thiocapsa roseopersicina is the first cytochrome c4 to be crystallized from an anaerobic organism. It was crystallized using the addition of metal-ion salts to the standard vapour-diffusion method. Coloured well shaped three-dimensional crystals with dimensions of approximately 0.6 x 0.05 x 0.02 mm grew within 3-4 d at pH 5 and diffracted to 1.72 angstroms without radiation damage. Cytochrome c4 crystallized in space group P4(1)2(1)2 as a primitive tetragonal system with unit-cell parameters a = b = 75.29, c = 37.12 angstroms, alpha = beta = gamma = 90 degrees.
- MeSH
- bakteriální proteiny chemie izolace a purifikace MeSH
- cytochromy skupiny c chemie izolace a purifikace MeSH
- difrakce rentgenového záření MeSH
- krystalizace MeSH
- Thiocapsa enzymologie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- bakteriální proteiny MeSH
- cytochrome C4 MeSH Prohlížeč
- cytochromy skupiny c MeSH
