Cytochromes of the non-thiosulfate-utilizing green sulfur bacterium Chlorobium limicola

Flavocytochrome c-553 of the non-thiosulfateutilizing green sulfur bacterium Chlorobium limicola strain 6330 was partially purified by ion exchange column chromatography and ammonium sulfate fractionation (highest purity index obtained: A ₂₈₀/A _{417 red}=0.96). It is autoxidizable and located in the soluble fraction. This hemoprotein contains a flavin component and one heme per molecule. The dithionite reduced spectrum reveals the typical maxima of a c-type cytochrome: =553,5 nm; =523 nm; =417 nm, while the oxidized form shows a -band at 410 nm and two shoulders at 440 nm and 480 nm indicating the flavin component. The flavocytochrome is a basic protein with an isoelectric point at pH 9.0 (± 0.5), a redox potential of 65 mV, a molecular weight of 56,000. It participates in sulfide oxidation and shows neither adenylylsulfate reductase nor sulfite reductase activity. C. limicola further contains a soluble cytochrome c-555 (highest purity index obtained: A ₂₈₀/A _{412 ox}=0.13; isoelectric point between pH 9.5 and 10) and the non-heme iron-containing proteins rubredoxin and ferredoxin, but lacks cytochrome c-551. Besides these soluble electron transfer proteins a membrane-bound c-type cytochrome (=554,5 nm) can be detected spectrophotometrically.Non-common abbreviations HIPIP high-potential iron sulfur protein - APS adenylylsulfate     

Structure of a bacteriochlorophyll-protein from the green photosynthetic bacterium Chlorobium limicola: crystallographic evidence for a trimer

Crystals of the bacteriochlorophyll-protein from the green photosynthetic bacterium Chlorobium limicola, previously described by J. M. Olson et al. (1969), have been re-examined by X-ray diffraction. The space group is P6₃, as reported in the earlier work, but revised cell dimensions, $\text{a = b = 112.4 ± 0.4}\text{A}\text{?}\text{, c = 98.4 ± 0.4}\text{A}\text{?}$, were obtained, leading to a unit cell volume one third of that reported previously. Correction of this error leads to the conclusion that the bacteriochlorophyll-protein complex must be a trimer consisting of three identical subunits arranged about a crystallographic symmetry axis. Also a new trigonal crystal form of the bacteriochlorophyll-protein has been obtained, and is consistent only with a molecule composed of three identical or near-identical subunits. Models of the molecular packing for both crystal forms are presented.The molecular weight of the bacteriochlorophyll-protein complex, determined from crystal density measurements, is (1.53 ± 0.23) × 10⁵, and the overall molecular dimensions are about 55 Å along the trimer axis, and 83 Å at right angles to this. There are probably seven bacteriochlorophyll molecules in each subunit.     

ATP-citrate lyase from the green sulfur bacterium Chlorobium limicola is a heteromeric enzyme composed of two distinct gene products.

The reductive tricarboxylic acid cycle functions as a carbon dioxide fixation pathway in the green sulfur bacterium, Chlorobium limicola. ATP-citrate lyase, one of the key enzymes of this cycle, was partially purified from C. limicola strain M1 and the N-terminal sequence of a 65-kDa protein was found to show similarity toward eukaryotic ATP-citrate lyase. A DNA fragment was amplified with primers designed from this sequence and an internal sequence highly conserved among eukaryotic enzymes. Using this fragment as a probe, we isolated a DNA fragment containing two adjacent open reading frames, aclB (1197 bp) and aclA (1827 bp), whose products showed significant similarity to the N- and C-terminal regions of the human enzyme, respectively. Heterologous expression of these genes in Escherichia coli showed that both gene products were essential for ATP-citrate lyase activity. The recombinant enzyme was purified from the cell-free extract of E. coli harboring aclBA for further characterization. The molecular mass of the recombinant enzyme was determined to be approximately 532--557 kDa by gel-filtration. The enzyme catalyzed the cleavage of citrate in an ATP(-), CoA- and Mg(2+)-dependent manner, where ATP and Mg(2+) could be replaced by dATP and Mn(2+), respectively. ADP and oxaloacetate inhibited the reaction. These properties suggested that ATP-citrate lyase from C. limicola controlled the cycle flux depending on intracellular energy conditions. This paper provides the first direct evidence that a bacterial ATP-citrate lyase is a heteromeric enzyme, distinct from mammalian enzymes.     

ATP-linked citrate lyase activity in the green sulfur bacterium Chlorobium limicola forma thiosulfatophilum

Cell-free extracts of the green sulfur bacterium Chlorobium limicola forma thiosulfatophilum strains 1C and L have been shown to cleave citrate with the formation of oxaloacetate and acetyl-CoA. This capacity was found in autotrophically grown cells as well as in the cells grown on media with acetate or L-glutamate. Citrate lyase activity in cell-free extracts is only measurable in the presence of citrate, adenosine-5-triphosphate, coenzyme A and Mg²⁺ or Mn²⁺. It is concluded on the basis of the obtained data that C. limicola f. thiosulfatophilum contains adenosine-5-triphosphate-linked citrate lyase (E.C.4.1.3.8). In contrast to green bacteria in the purple bacteria Ectothiorhodospira shaposhnikovii, Rhodospirillum rubrum and Thiocapsa roseopersicina citrate lyase activity was not found.     

Optical and structural properties of chlorosomes of the photosynthetic green sulfur bacterium Chlorobium limicola

Isolated chlorosomes of the photosynthetic green sulfur bacterium Chorobium limicola upon cooling to 4 K showed, in addition to the near-infrared absorption band at 753 nm due to bacteriochlorophyll c, a weak band near 800 nm that could be attributed to bacteriochlorophyll a. The emission spectrum showed bands of bacteriochlorophyll c and a at 788 and 828 nm, respectively. The fluorescence excitation spectrum indicated a high efficiency of energy transfer from bacteriochlorophyll c to bacteriochlorophyll a. When all bacteriochlorophyll c absorption had been lost upon storage, no appreciable change in the optical properties of the bacteriochlorophyll a contained in these ‘depleted chlorosomes’ was observed. The fluorescence and absorption spectra of the chlorosomal bacteriochlorophyll a were clearly different from those of the soluble bacteriochlorophyll a protein present in these bacteria. The results provide strong evidence that bacteriochlorophyll a, although present in a small amount, is an integral constituent of the chlorosome. It presumably functions in the transfer of energy from the chlorosome to the photosynthetic membrane; its spectral properties and the orientation of its near-infrared optical transitions as determined by linear dichroism are such as to favor this energy transfer.     

Physical map of the genome of the green phototrophic bacterium Chlorobium tepidum.

A physical restriction map of the chromosome of the green sulfur bacterium Chlorobium tepidum was generated by determining the order of the fragments obtained after digestion with the restriction endonucleases XbaI and PacI and subsequent separation of the fragments by pulsed-field gel electrophoresis. The size of the chromosome is estimated to be 2.1 Mb. Fifteen genes and operons, mainly encoding proteins involved in photosynthesis, have been placed on this map by hybridization to fragments obtained after single- and double-restriction digestions.     

The complete amino acid sequence of rubredoxin from the green phototrophic bacterium Chlorobium thiosulphatophilum strain PM

A complete amino acid sequence for the rubredoxin from the photosynthetic bacterium Chlorobium thiosulphatophilum is proposed. The sequence, a single polypeptide chain of 53 amino acids, was deduced from the sequences of peptides obtained by chymotryptic, tryptic, thermolytic or mild acid digestion. The rubredoxin shows a high degree of sequence homology with rubredoxins from non-photosynthetic bacteria, and the evolutionary implications of this are considered.     

Light-driven reduction of oxygen as a method for studying electron transport in the green photosynthetic bacterium Chlorobium limicola

The use of O₂ uptake as a valid assay for non-cyclic photosynthetic electron flow in membranes from Chlorobium limicola is discussed. It is recommended that methyl viologen, catalase and superoxide dismutase should be added to the experimental medium. The addition of methyl viologen more than doubled the rate of O₂ uptake observed on illumination with 1 mM sulphide as donor. Superoxide dismutation was shown to be efficient under the experimental conditions by means of standard additions of potassium superoxide dissolved in dimethylsulphoxide. The highest rates of light stimulated O₂ uptake were obtained with sulphide as electron donor, and approached 50 mol O₂ · h^-1 · mg bacteriochlorophyll c ^-1 with 0.2 mM sulphide. The presence of 5 mM 2-mercaptoethanol or 3 mM sulphite as electron donor led to lower light stimulated rates of O₂ uptake, while 5 mM thiosulphate had little effect. The rates were insensitive to uncoupler. The light stimulated O₂ uptake with 0.2 mM sulphide as donor was 20–30% inhibited by 10 M antimycin A and 50 M cyanide.Abbreviations APS Adenosine 5-phosphosulphate - FCCP carbonylcyanide-p-trifluoromethoxyphenylhydrazone - HEPES 4-(2-hydroxyethyl)-1-piperazineethanesulphonic acid - MeV methyl viologen - P-840 the photoreactive bacteriochlorophyll     

Transformation of Chlorobium limicola by a plasmid that confers the ability to utilize thiosulfate.

A modified transformation method for Chlorobium limicola confirms the role of an endogenous plasmid in thiosulfate metabolism. The plasmid was present in two forma specialis thiosulfatophilum (Tio+) strains and absent in one non-thiosulfate-utilizing (Tio-) strain. The plasmid (size, 14 kb) was transferred by transformation from Tio- to Tio+. The chromosomal restriction patterns, analyzed by pulsed-field gel electrophoresis, were used to distinguish between the different strains.     

Fast energy transfer between BChl d and BChl c in chlorosomes of the green sulfur bacterium Chlorobium limicola

We have studied energy transfer in chlorosomes of Chlorobium limicola UdG6040 containing a mixture of about 50% bacteriochlorophyll (BChl) c and BChl d each. BChl d-depleted chlorosomes were obtained by acid treatment. The energy transfer between the different pigment pools was studied using both steady-state and time-resolved fluorescence spectroscopy at room temperature and low temperature. The steady-state emission of the intact chlorosome originated mainly from BChl c, as judged by comparison of fluorescence emission spectra of intact and BChl d-depleted chlorosomes. This indicated that efficient energy transfer from BChl d to BChl c takes place. At room temperature BChl c/d to BChl a excitation energy transfer (EET) was characterized by two components of 27 and 74 ps. At low temperature we could also observe EET from BChl d to BChl c with a time constant of approximately 4 ps. Kinetic modeling of the low temperature data indicated heterogeneous fluorescence kinetics and suggested the presence of an additional BChl c pool, E790, which is more or less decoupled from the baseplate BChl a. This E790 pool is either a low-lying exciton state of BChl c which acts as a trap at low temperature or alternatively represents the red edge of a broad inhomogeneous absorption band of BChl c. We present a refined model for the organization of the spatially separated pigment pools in chlorosomes of Cb. limicola UdG6040 in which BChl d is situated distal and BChl c proximal with respect to the baseplate.     

Characterization of isocitrate dehydrogenase from the green sulfur bacterium Chlorobium limicola. A carbon dioxide-fixing enzyme in the reductive tricarboxylic acid cycle.

Isocitrate dehydrogenase (IDH) catalyzes the reversible conversion between isocitrate and 2-oxoglutarate accompanied by decarboxylation/carboxylation and oxidoreduction of NAD(P)+ cofactor. While this enzyme has been well studied as a catabolic enzyme in the tricarboxylic acid (TCA) cycle, here we have characterized NADP-dependent IDH from Chlorobium limicola, a green sulfur bacterium that fixes CO2 through the reductive tricarboxylic acid (RTCA) cycle, focusing on the CO2-fixation ability of the enzyme. The gene encoding Cl-IDH consisted of 2226 bp, corresponding to a polypeptide of 742 amino acid residues. The primary structure and the size of the recombinant protein indicated that Cl-IDH was a monomeric enzyme of 80 kDa distinct from the dimeric NADP-dependent IDHs predominantly found in bacteria or eukaryotic mitochondria. Apparent Michaelis constants for isocitrate (45 +/- 13 microm) and NADP+ (27 +/- 10 microm) were much smaller than those for 2-oxoglutarate (1.1 +/- 0.5 mm) and CO2 (1.3 +/- 0.3 mm). No significant differences in kinetic properties were observed between Cl-IDH and the dimeric, NADP-dependent IDH from Saccharomyces cerevisiae (Sc-IDH) at the optimum pH of each enzyme. However, in contrast to the 20% activity of Sc-IDH toward carboxylation as compared with that toward decarboxylation at pH 7.0, the activities of Cl-IDH for both directions were almost equivalent at this pH, suggesting a more favorable property of Cl-IDH than Sc-IDH as a CO2-fixation enzyme under physiological pH. Furthermore, we found that among various intermediates, oxaloacetate was a competitive inhibitor (K(i) = 0.35 +/- 0.04 mm) for 2-oxoglutarate in the carboxylation reaction by Cl-IDH, a feature not found in Sc-IDH.     

Crystal structure of a RuBisCO-like protein from the green sulfur bacterium Chlorobium tepidum

Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) catalyzes the incorporation of atmospheric CO(2) into ribulose 1,5-bisphosphate (RuBP). RuBisCOs are classified into four forms based on sequence similarity: forms I, II and III are bona fide RuBisCOs; form IV, also called the RuBisCO-like protein (RLP), lacks several of the substrate binding and catalytic residues and does not catalyze RuBP-dependent CO(2) fixation in vitro. To contribute to understanding the function of RLPs, we determined the crystal structure of the RLP from Chlorobium tepidum. The overall structure of the RLP is similar to the structures of the three other forms of RuBisCO; however, the active site is distinct from those of bona fide RuBisCOs and suggests that the RLP is possibly capable of catalyzing enolization but not carboxylation. Bioinformatic analysis of the protein functional linkages suggests that this RLP coevolved with enzymes of the bacteriochlorophyll biosynthesis pathway and may be involved in processes related to photosynthesis.     

Sulfide utilization by the photosynthetic bacterium Chlorobium phaeobacteroides

Sulfide and sulfur are used by the photosynthetic bacterium Chlorobium phaeobacteroides as electron donors. Sulfide and sulfur consumption was found to be affected by sulfide concentration in the medium. Raising the sulfide concentration from 0.28 mM to 5.05 mM caused an increase in the amount of S⁼ utilized per growth unit from 0.58 mM to 2.32 mM. This increase in sulfide utilization was not reflected in a higher photosynthetic activity. Sulfide and sulfur consumption was also influenced by light intensity, with higher light intensity sulfide consumption was increased. In Lake Kinneret, Chlorobium phaeobacteroides did not bloom in the thermocline layer until sulfide concentrations reached 0.03–0.06 mM.     

Evidence for spatially separate bacteriochlorophyll c and bacteriochlorophyll d pools within the chlorosomal aggregate of the green sulfur bacterium Chlorobium limicola

We have studied the organization of the bacteriochlorophylls (BChl) in isolated chlorosomes of the green sulfur bacterium Chlorobium limicola UdG6040 containing about 50% BChl d and BChl c each. When the chlorosomes are treated in acidic buffer (pH 3.0) two phases in the conversion from BChl to bacteriopheophytin (BPhe) are observed as evidenced by the changes in the absorption spectrum. In the early phase the pheophytinization of BChl d occurs much faster than that of BChl c. In the later phase BChl c and BChl d are converted at similar rates. The delayed BChl c conversion observed in intact chlorosomes is interpreted in terms of spatial separation within the same chlorosome that makes BChl d more accessible to reaction with acid than BChl c. This was supported by acid treatment of in vitro pigment-lipid aggregates which showed that the pheophytinization of aggregates consisting of only BChl c or BChl d takes place with the same rate. Moreover in mixed in vitro aggrega tes where BChl d and BChl c are supposed to be scrambled the two pigments are converted to BPhe simultaneously. Acid treatment of hexanol exposed chlorosomes indicates that the spatial separation of BChl d and BChl c within the chlorosomes is maintained even if the excitonic interaction between BChls has been disturbed by hexanol. Based on these findings it is suggested that BChl d and BChl c in the chlorosome are located distal and proximal, respectively, relative to the chlorosome baseplate.     

Investigations by picosecond polarized fluorescence spectrochronography of structural aspects of energy transfer in living cells of the green bacterium Chlorobium limicola

The orientation of the long-wavelength (Q_y) transition moments of the antenna bacterioviridin (BVr) was examined in living cells of Chlorobium limicola. Previous linear dichroism studies [(1986) FEBS Lett. 199, 234–236] indicated that in each individual chromatophore of C. limicola the Q_y, transition moment vectors of the whole chlorosome BVr are essentially parallel to each other and are practically ideally oriented along the long axis of the chlorosome. We measured the picosecond polarized fluorescence decay kinetics for antenna bacteriochlorophyll (BChl) emissions upon selective excitation with polarized light of the Q_y, transition of BVr. The polarization (p) of the BVr fluorescence is measured to be constant during the BVr excited-state lifetime and to be equal to the limiting value of p achieved in monomeric BChl: P = + 0.42 ± 0.02. The results indicate convincingly that the excitation energy transfer within chlorosomes of C. limicola cells takes place between chromophores (or their coupled associates) with parallel transition moment vectors.     

The amino acid sequence of a major protein component in the light harvesting complex of the green photosynthetic bacterium Chlorobium limicola f. thiosulfatophilum

A 7.5-kDa protein has been isolated from chlorosomes of Chlorobium limicola f. thiosulfatophilum and the complete primary structure determined by a combination of automatic Edman degradation and plasma desorption mass spectrometry. The 74-residue protein shows great homology to a similar protein of unknown function which has been isolated from Pelodictyon luteolum but otherwise no significant homology to other proteins can be found. The possible role of the protein in the structure and function of the chlorosome is discussed.     

Chromosomal gene inactivation in the green sulfur bacterium Chlorobium tepidum by natural transformation

Conditions for inactivating chromosomal genes of Chlorobium tepidum by natural transformation and homologous recombination were established. As a model, mutants unable to perform nitrogen fixation were constructed by interrupting nifD with various antibiotic resistance markers. Growth of wild-type C. tepidum at 40 degrees C on agar plates could be completely inhibited by 100 microg of gentamicin ml(-1), 2 microg of erythromycin ml(-1), 30 microg of chloramphenicol ml(-1), or 1 microg of tetracycline ml(-1) or a combination of 300 microg of streptomycin ml(-1) and 150 microg of spectinomycin ml(-1). Transformation was performed by spotting cells and DNA on an agar plate for 10 to 20 h. Transformation frequencies on the order of 10(-7) were observed with gentamicin and erythromycin markers, and transformation frequencies on the order of 10(-3) were observed with a streptomycin-spectinomycin marker. The frequency of spontaneous mutants resistant to gentamicin, erythromycin, or spectinomycin-streptomycin was undetectable or significantly lower than the transformation frequency. Transformation with the gentamicin marker was observed when the transforming DNA contained 1 or 3 kb of total homologous flanking sequence but not when the transforming DNA contained only 0.3 kb of homologous sequence. Linearized plasmids transformed at least an order of magnitude better than circular plasmids. This work forms a foundation for the systematic targeted inactivation of genes in C. tepidum, whose 2.15-Mb genome has recently been completely sequenced.