Rhodospirillum Photometricum Research Articles

Microbiome - based agents can optimize composting of agricultural wastes by modifying microbial communities

Microorganisms that facilitate the decomposition of agricultural wastes are of importance during composting processes. Here, we assessed if microbial agents, comprising Clonostachys rosea, Bacillus amylolyticus and Rhodospirillum photometricum can facilitate the decomposition of a compost mix of vegetable waste, chicken manure, sawdust, and biochar. The results showed that inoculating the compost mix with the microbial agents elevated the compost temperature, increased the thermophilic period, and enhanced cellulose degradation. Microbial agent inoculation also changed the diversity and richness of decomposing microbial communities. Among the microbial agents, the mixture of C. rosea and B. amylolyticus performed better than other mixtures. Taken together, the results confirmed that the microbial agents comprising C. rosea can enhance the composting process by ameliorating the physiochemical conditions of agricultural wastes and promoting the diversity and proliferation of beneficial bacteria involved in the decomposition of cellulose.

Light Harvesting by Lamellar Chromatophores in Rhodospirillum photometricum

Purple photosynthetic bacteria harvest light using pigment-protein complexes which are often arranged in pseudo-organelles called chromatophores. A model of a chromatophore from Rhodospirillum photometricum was constructed based on atomic force microscopy data. Molecular-dynamics simulations and quantum-dynamics calculations were performed to characterize the intercomplex excitation transfer network and explore the interplay between close-packing and light-harvesting efficiency.

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 (φ) 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 φ(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.

Light-Harvesting Mechanism of Bacteria Exploits a Critical Interplay between the Dynamics of Transport and Trapping

Light-harvesting bacteria Rhodospirillum photometricum were recently found to adopt strikingly different architectures depending on illumination conditions. We present analytic and numerical calculations which explain this observation by quantifying a dynamical interplay between excitation transfer kinetics and reaction center cycling. High light-intensity membranes exploit dissipation as a photoprotective mechanism, thereby safeguarding a steady supply of chemical energy, while low light-intensity membranes efficiently process unused illumination intensity by channeling it to open reaction centers. More generally, our analysis elucidates and quantifies the trade-offs in natural network design for solar energy conversion.

Energy Transfer in Light-Adapted Photosynthetic Membranes: From Active to Saturated Photosynthesis

In bacterial photosynthesis light-harvesting complexes, LH2 and LH1 absorb sunlight energy and deliver it to reaction centers (RCs) with extraordinarily high efficiency. Submolecular resolution images have revealed that both the LH2:LH1 ratio, and the architecture of the photosynthetic membrane itself, adapt to light intensity. We investigate the functional implications of structural adaptations in the energy transfer performance in natural in vivo low- and high-light-adapted membrane architectures of Rhodospirillum photometricum. A model is presented to describe excitation migration across the full range of light intensities that cover states from active photosynthesis, where all RCs are available for charge separation, to saturated photosynthesis where all RCs are unavailable. Our study outlines three key findings. First, there is a critical light-energy density, below which the low-light adapted membrane is more efficient at absorbing photons and generating a charge separation at RCs, than the high-light-adapted membrane. Second, connectivity of core complexes is similar in both membranes, suggesting that, despite different growth conditions, a preferred transfer pathway is through core-core contacts. Third, there may be minimal subareas on the membrane which, containing the same LH2:LH1 ratio, behave as minimal functional units as far as excitation transfer efficiency is concerned.

Quinone Pathways in Entire Photosynthetic Chromatophores of Rhodospirillum photometricum

In photosynthetic organisms, membrane pigment–protein complexes [light-harvesting complex 1 (LH1) and light-harvesting complex 2 (LH2)] harvest solar energy and convert sunlight into an electrical and redox potential gradient (reaction center) with high efficiency. Recent atomic force microscopy studies have described their organization in native membranes. However, the cytochrome (cyt) bc1 complex remains unseen, and the important question of how reduction energy can efficiently pass from core complexes (reaction center and LH1) to distant cyt bc1 via membrane-soluble quinones needs to be addressed. Here, we report atomic force microscopy images of entire chromatophores of Rhodospirillum photometricum. We found that core complexes influence their molecular environment within a critical radius of ∼250 Å. Due to the size mismatch with LH2, lipid membrane spaces favorable for quinone diffusion are found within this critical radius around cores. We show that core complexes form a network throughout entire chromatophores, providing potential quinone diffusion pathways that will considerably speed the redox energy transfer to distant cyt bc1. These long-range quinone pathway networks result from cooperative short-range interactions of cores with their immediate environment.

Atomic Force Microscopy Studies of Native Photosynthetic Membranes

In addition to providing the earliest surface images of a native photosynthetic membrane at submolecular resolution, examination of the intracytoplasmic membrane (ICM) of purple bacteria by atomic force microscopy (AFM) has revealed a wide diversity of species-dependent arrangements of closely packed light-harvesting (LH) antennae, capable of fulfilling the basic requirements for efficient collection, transmission, and trapping of radiant energy. A highly organized architecture was observed with fused preparations of the pseudocrystalline ICM of Blastochloris viridis, consiting of hexagonally packed monomeric reaction center light-harvesting 1 (RC-LH1) core complexes. Among strains which also form a peripheral LH2 antenna, images of ICM patches from Rhodobacter sphaeroides exhibited well-ordered, interconnected networks of dimeric RC-LH1 core complexes intercalated by rows of LH2, coexisting with LH2-only domains. Other peripheral antenna-containing species, notably Rhodospirillum photometricum and Rhodopseudomonas palustris, showed a less regular organization, with mixed regions of LH2 and RC-LH1 cores, intermingled with large, paracrystalline domains. The ATP synthase and cytochrome bc(1) complex were not observed in any of these topographs and are thought to be localized in the adjacent cytoplasmic membrane or in inaccessible ICM regions separated from the flat regions imaged by AFM. The AFM images have served as a basis for atomic-resolution modeling of the ICM vesicle surface, as well as forces driving segregation of photosynthetic complexes into distinct domains. Docking of atomic-resolution molecular structures into AFM topographs of Rsp. photometricum membranes generated precise in situ structural models of the core complex surrounded by LH2 rings and a region of tightly packed LH2 complexes. A similar approach has generated a model of the highly curved LH2-only membranes of Rba. sphaeroides which predicts that sufficient space exists between LH2 complexes for quinones to diffuse freely. Measurement of the intercomplex distances between adjacent LH2 rings of Phaeospirillum molischianum has permitted the first calculation of the separation of bacteriochlorophyll a molecules in the native ICM. A recent AFM analysis of the organization of green plant photosystem II (PSII) in grana thylakoids revealed the protruding oxygen-evolving complex, crowded together in parallel alignment at three distinct levels of stacked membranes over the lumenal surface. The results also confirmed that PSII-LHCII supercomplexes are displaced relative to one another in opposing grana membranes.

Rhodospirillum sulfurexigens sp. nov., a phototrophic alphaproteobacterium requiring a reduced sulfur source for growth

A Gram-negative, spiral-shaped, phototrophic, purple non-sulfur bacterial strain, JA143(T), was isolated from a freshwater habitat. Strain JA143(T) was motile by means of bipolar tufts of flagella. Intracellular photosynthetic membranes are of the lamellar stacked type. Bacteriochlorophyll a and carotenoids of the spirilloxanthin series with rhodovibrin are present as photosynthetic pigments. Thiamine and a reduced sulfur source are required for growth. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain JA143(T) clusters with species of the genus Rhodospirillum, belonging to the class Alphaproteobacteria. The highest sequence similarities of strain JA143(T) were found with the type strains of Rhodospirillum rubrum (95.6 %) and Rhodospirillum photometricum (95.7 %). Based on 16S rRNA gene sequence analysis and morphological and physiological characteristics, strain JA143(T) was significantly different from the other two recognized species of the genus Rhodospirillum and represents a novel species, for which the name Rhodospirillum sulfurexigens sp. nov. is proposed. The type strain is JA143(T) (=DSM 19785(T) =NBRC 104433(T)).

Dynamics and Diffusion in Photosynthetic Membranes from Rhodospirillum Photometricum

Photosynthetic organisms drive their metabolism by converting light energy into an electrochemical gradient with high efficiency. This conversion depends on the diffusion of quinones within the membrane. In purple photosynthetic bacteria, quinones reduced by the reaction center (RC) diffuse to the cytochrome bc 1 complex and then return once reoxidized to the RC. In Rhodospirillum photometricum the RC-containing core complexes are found in a disordered molecular environment, with fixed light-harvesting complex/core complex ratio but without a fixed architecture, whereas additional light-harvesting complexes synthesized under low-light conditions pack into large paracrystalline antenna domains. Here, we have analyzed, using time-lapse atomic force microscopy, the dynamics of the protein complexes in the different membrane domains and find that the disordered regions are dynamic whereas ordered antennae domains are static. Based on our observations we propose, and analyze using Monte Carlo simulations, a model for quinone diffusion in photosynthetic membranes. We show that the formation of large static antennae domains may represent a strategy for increasing electron transfer rates between distant complexes within the membrane and thus be important for photosynthetic efficiency.

Architecture of the native photosynthetic apparatus of Phaeospirillum molischianum

The ubiquity and importance of photosynthetic organisms in nature has made the molecular mechanisms of photosynthesis a widely studied subject at both structural and functional levels. A current challenge is to understand the supramolecular assembly of the proteins involved in photosynthesis in native membranes. We have used atomic force microscopy to study the architecture of the photosynthetic apparatus and analyze the structure of single molecules in chromatophores of Phaeospirillum molischianum. Core complexes are formed by the reaction center enclosed by an elliptical light harvesting complex 1. LH2 are octameric rings, assembled either with cores or in hexagonally packed LH2 antenna domains. The symmetry mismatch caused by octameric LH2 packing in a hexagonal lattice, that could be avoided in a square lattice, suggests lipophobic effects rather than specific inter-molecular interactions drive protein organization. The core and LH2 complexes are organized to form a supramolecular assembly reminiscent to that found in Rhodospirillum photometricum, and very different from that observed in Rhodobacter sphaeroides, Rb. blasticus, and Blastochloris viridis.

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

The individual components of the photosynthetic unit (PSU), the light-harvesting complexes (LH2 and LH1) and the reaction center (RC), are structurally and functionally known in great detail. An important current challenge is the study of their assembly within native membranes. Here, we present AFM topographs at 12 A resolution of native membranes containing all constituents of the PSU from Rhodospirillum photometricum. Besides the major technical advance represented by the acquisition of such highly resolved data of a complex membrane, the images give new insights into the organization of this energy generating apparatus in Rsp. photometricum: (i) there is a variable stoichiometry of LH2, (ii) the RC is completely encircled by a closed LH1 assembly, (iii) the LH1 assembly around the RC forms an ellipse, (iv) the PSU proteins cluster together segregating out of protein free lipid bilayers, (v) core complexes cluster although enough LH2 are present to prevent core-core contacts, and (vi) there is no cytochrome bc1 complex visible in close proximity to the RCs. The functional significance of all these findings is discussed.

Protein folding in the periplasm in the absence of primary oxidant DsbA: modulation of redox potential in periplasmic space via OmpL porin

Corrigendum29 September 2004free access Protein folding in the periplasm in the absence of primary oxidant DsbA: modulation of redox potential in periplasmic space via OmpL porin Claire Dartigalongue Claire Dartigalongue Search for more papers by this author Hiroshi Nikaido Hiroshi Nikaido Search for more papers by this author Satish Raina Satish Raina Search for more papers by this author Claire Dartigalongue Claire Dartigalongue Search for more papers by this author Hiroshi Nikaido Hiroshi Nikaido Search for more papers by this author Satish Raina Satish Raina Search for more papers by this author Author Information Claire Dartigalongue, Hiroshi Nikaido and Satish Raina The EMBO Journal (2004)23:3907-3907https://doi.org/10.1038/sj.emboj.7600439 This article corrects the following: Protein folding in the periplasm in the absence of primary oxidant DsbA: modulation of redox potential in periplasmic space via OmpL porin15 November 2000 PDFDownload PDF of article text and main figures. ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InMendeleyWechatReddit Figures & Info Correction to: The EMBO Journal (2000) 19, 5980–5988. doi:10.1093/emboj/19.22.5980 During reconstruction of ompL/dsbA double mutants, we observed that null mutation in ompL suppressed the defects of dsbA mutant bacteria in oxidative folding of secreted proteins only partially (about 20–30%). During our initial series of experiments, we observed a complete suppression of dsbA phenotypes upon introduction of the ompL null allele. The discrepancy was repeatedly observed for Escherichia coli strain SR4444Δ (dsbA ompL). We conclude that this strain likely carries a second mutation, which contributes to the complete restoration of oxidative protein folding. Our conclusions for a role of OmpL in modulating the oxidative environment of E. coli periplasmic space gain further support as we have again cloned the ompL gene, which, when overexpressed from a plasmid, confers resistance to sublethal concentrations of oxidizing agents such as diamide. We would like to bring to the attention of readers that it was MC1000 that was used in our studies and is the parent of SR2262 and SR4444, and that in page 5987 temperature used for motility assay was 30°C and the agar concentration was 0.3%. Next ArticlePrevious Article Read MoreAbout the coverClose modalView large imageVolume 23,Issue 19,September 29, 2004Top view of a model membrane containing all the proteins of the photosynthetic unit in Rhodospirillum photometricum: LH2 light harvesting complexes and core complexes, consisting of LH1 light harvesting complexes surrounding reaction centers. The structures of the individual complexes were assembled following the arrangement observed in the native membrane by atomic force microscopy. The image was composed by Simon Scheuring from the Institut Curie, Paris, France, whose accompanying article will appear in one of the next printed issues of The EMBO Journal. Volume 23Issue 1929 September 2004In this issue RelatedDetailsLoading ...

Watching the photosynthetic apparatus in native membranes.

Over the last 9 years, the structures of the various components of the bacterial photosynthetic apparatus or their homologues have been determined by x-ray crystallography to at least 4.8-A resolution. Despite this wealth of structural information on the individual proteins, there remains an urgent need to examine the architecture of the photosynthetic apparatus in intact photosynthetic membranes. Information on the arrangement of the different complexes in a native system will help us to understand the processes that ensure the remarkably high quantum efficiency of the system. In this work we report images obtained with an atomic force microscope of native photosynthetic membranes from the bacterium Rhodospirillum photometricum. Several proteins can be seen and identified at molecular resolution, allowing the analysis and modeling of the lateral organization of multiple components of the photosynthetic apparatus within a native membrane. Analysis of the distribution of the complexes shows that their arrangement is far from random, with significant clustering both of antenna complexes and core complexes. The functional significance of the observed distribution is discussed.

Reclassification of species of the spiral-shaped phototrophic purple non-sulfur bacteria of the alpha-Proteobacteria: description of the new genera Phaeospirillum gen. nov., Rhodovibrio gen. nov., Rhodothalassium gen. nov. and Roseospira gen. nov. as well as transfer of Rhodospirillum fulvum to Phaeospirillum fulvum comb. nov., of Rhodospirillum molischianum to Phaeospirillum molischianum comb. nov., of Rhodospirillum salinarum to Rhodovibrio salexigens.

The 165 rDNA sequence of Rhodospirillum mediosalinum was determined and compared with corresponding sequences from other spiral-shaped purple non-sulfur bacteria classified as or related to the genus Rhodospirillum in the alpha subclass of the Proteobacteria. Sequence similarities separate the currently recognized Rhodospirillum species into five different groups with no more than 91% sequence similarity, clearly indicating the necessity to recognize these groups as different genera. Major diagnostic properties of these bacteria are compared and new genera Phaeospirillum gen. nov., Roseospira gen. nov., Rhodothalassium gen. nov. and Rhodovibrio gen. nov. are described with the species Phaeospirillum fulvum comb. nov., Phaeospirillum molischianum comb. nov., Rhodovibrio salinarum comb. nov., Rhodovibrio sodomensis comb. nov., Rhodothalassium salexigens comb. nov. and Roseospira mediosalina comb. nov. The genus Rhodospirillum is represented by Rhodospirillum rubrum and Rhodospirillum photometricum and an emended description of this genus is also given.

Reductive dehalogenation of halocarboxylic acids by the phototrophic genera Rhodospirillum and Rhodopseudomonas.

Type strains of the purple nonsulfur species Rhodospirillum rubrum, Rhodospirillum photometricum, and Rhodopseudomonas palustris grew phototrophically on a number of two- and three-carbon halocarboxylic acids in the presence of CO2, by reductive dehalogenation and assimilation of the resulting acid. Strains of each of these species were able to grow on chloroacetic, 2-bromopropionic, 2-chloropropionic, and 3-chloropropionic acids at a concentration of 2 mM. Only R. palustris DSM 123 was able to grow on bromoacetic acid and then only at a reduced concentration of 1 mM. R. palustris ATCC 33872 (formerly R. rutila) was unable to grow on any of the substrates tested. The ability of these organisms to utilize halocarboxylic acids indicates that they may have a significant role to play in the removal of these environmental pollutants from illuminated anaerobic habitats such as lakes, waste lagoons, sediments of ditches and ponds, mud, and moist soil.

Quinones of phototrophic purple bacteria

The quinone composition of the recognized species of the phototrophic purple nonsulfur bacteria, the Ectothiorhodospiraceae, and some Chromatiaceae species has been determined. Altogether more than 50 strains of 33 species have been investigated. Some of the purple nonsulfur bacteria have Q-10 as sole quinone component, while others have Q-10, Q-9, or Q-8, respectively, together with menaquinones of the same isoprenoid chain length as the major components. Rhodoquinone is present in Rhodospirillum rubrum and Rhodospirillum photometricum. The Ectothiorhodospira species have either Q-8 and MK-8, like the Chromatiaceae species, or Q-7 and MK-7 as the major components.

Nicotinic acid as an essential growth factor of Rhodospirillum photometricum and a new Rhodospirillum isolate

Nicotinic acid as an essential growth factor of Rhodospirillum photometricum and a new Rhodospirillum isolate