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PubMed1993

Specific binding of Thiobacillus ferrooxidans RbcR to the intergenic sequence between the rbc operon and the rbcR gene.

The presence of two sets (rbcL1-rbcS1 and rbcL2-rbcS2) of rbc operons has been demonstrated in Thiobacillus ferrooxidans Fe1 (T. Kusano, T. Takeshima, C. Inoue, and K. Sugawara, J. Bacteriol. 173:7313-7323, 1991). A possible regulatory gene, rbcR, 930 bp long and possibly translated into a 309-amino-acid protein, was found upstream from the rbcL1 gene as a single copy. The gene is located divergently to rbcL1 with a 144-bp intergenic sequence. As in the cases of the Chromatium vinosum RbcR and Alcaligenes eutrophus CfxR, T. ferrooxidans RbcR is thought to be a new member of the LysR family, and these proteins share 46.5 and 42.8% identity, respectively. Gel mobility shift assays showed that T. ferrooxidans RbcR, produced in Escherichia coli, binds specifically to the intergenic sequence between rbcL1 and rbcR. Footprinting and site-directed mutagenesis experiments further demonstrated that RbcR binds to overlapping promoter elements of the rbcR and rbcL1 genes. The above data strongly support the participation of RbcR in regulation of the rbcL1-rbcS1 operon and the rbcR gene in T. ferrooxidans.

Amino Acid Sequence↗
PubMed1994

The photoactive yellow protein from Ectothiorhodospira halophila as studied with a highly specific polyclonal antiserum: (intra)cellular localization, regulation of expression, and taxonomic distribution of cross-reacting proteins.

A rabbit antiserum was raised against the photoactive yellow protein (PYP) from Ectothiorhodospira halophila and purified by adsorption experiments to obtain a highly specific polyclonal antiserum. This antiserum was used to obtain the following results. (i) In E. halophila, PYP can be isolated from the fraction of soluble proteins. In the intact cell, however, PYP appeared to be associated with (intra)cytoplasmic membranes, as was concluded from analysis of immunogold-labelled thin sections of the organism. (ii) The regulation of expression of PYP was studied by using dot blot assays, Western blotting (immunoblotting), and rocket immunoelectrophoresis. Under all conditions investigated (light color, salt concentration, and growth phase), PYP was expressed constitutively in E. halophila. However, when Rhodospirillum salexigens was grown aerobically, the expression of PYP was suppressed. (iii) A large number of prokaryotic microorganisms contained a single protein, with an apparent size of approximately 15 kDa, that cross-reacted with the antiserum. Among the positively reacting organisms were both phototrophic and chemotrophic, as well as motile and nonmotile, organisms. After separation of cellular proteins into a membrane fraction and soluble proteins, it was established that organisms adapted to growth at higher salt concentrations tended to have the cross-reacting protein in the soluble fraction. In the cases of R. salexigens and Chromatium salexigens, we have shown that the cross-reacting protein involved is strongly homologous to PYP from E. halophila.

Amino Acid Sequence↗
PubMed1994

Phylogenetic analysis of sequences from diverse bacteria with homology to the Escherichia coli rho gene.

Genes from Pseudomonas fluorescens, Chromatium vinosum, Micrococcus luteus, Deinococcus radiodurans, and Thermotoga maritima with homology to the Escherichia coli rho gene were cloned and sequenced, and their sequences were compared with other available sequences. The species for all of the compared sequences are members of five bacterial phyla, including Thermotogales, the most deeply diverged phylum. This suggests that a rho-like gene is ubiquitous in the Bacteria and was present in their common ancestor. The comparative analysis revealed that the Rho homologs are highly conserved, exhibiting a minimum identity of 50% of their amino acid residues in pairwise comparisons. The ATP-binding domain had a particularly high degree of conservation, consisting of some blocks with sequences of residues that are very similar to segments of the alpha and beta subunits of F1-ATPase and of other blocks with sequences that are unique to Rho. The RNA-binding domain is more diverged than the ATP-binding domain. However, one of its most highly conserved segments includes a RNP1-like sequence, which is known to be involved in RNA binding. Overall, the degree of similarity is lowest in the first 50 residues (the first half of the RNA-binding domain), in the putative connector region between the RNA-binding and the ATP-binding domains, and in the last 50 residues of the polypeptide. Since functionally defective mutants for E. coli Rho exist in all three of these segments, they represent important parts of Rho that have undergone adaptive evolution.

Adenosine Triphosphate↗
PubMed1997

Cloning and characterization of sulfite dehydrogenase, two c-type cytochromes, and a flavoprotein of Paracoccus denitrificans GB17: essential role of sulfite dehydrogenase in lithotrophic sulfur oxidation.

A 13-kb genomic region of Paracoccus dentrificans GB17 is involved in lithotrophic thiosulfate oxidation. Adjacent to the previously reported soxB gene (C. Wodara, S. Kostka, M. Egert, D. P. Kelly, and C. G. Friedrich, J. Bacteriol. 176:6188-6191, 1994), 3.7 kb were sequenced. Sequence analysis revealed four additional open reading frames, soxCDEF. soxC coded for a 430-amino-acid polypeptide with an Mr of 47,339 that included a putative signal peptide of 40 amino acids (Mr of 3,599) with a RR motif present in periplasmic proteins with complex redox centers. The mature soxC gene product exhibited high amino acid sequence similarity to the eukaryotic molybdoenzyme sulfite oxidase and to nitrate reductase. We constructed a mutant, GBsoxC delta, carrying an in-frame deletion in soxC which covered a region possibly coding for the molybdenum cofactor binding domain. GBsoxC delta was unable to grow lithoautotrophically with thiosulfate but grew well with nitrate as a nitrogen source or as an electron acceptor. Whole cells and cell extracts of mutant GBsoxC delta contained 10% of the thiosulfate-oxidizing activity of the wild type. Only a marginal rate of sulfite-dependent cytochrome c reduction was observed from cell extracts of mutant GBsoxC delta. These results demonstrated that sulfite dehydrogenase was essential for growth with thiosulfate of P. dentrificans GB17. soxD coded for a periplasmic diheme c-type cytochrome of 384 amino acids (Mr of 39,983) containing a putative signal peptide with an Mr of 2,363. soxE coded for a periplasmic monoheme c-type cytochrome of 236 amino acids (Mr of 25,926) containing a putative signal peptide with an Mr of 1,833. SoxD and SoxE were highly identical to c-type cytochromes of P. denitrificans and other organisms. soxF revealed an incomplete open reading frame coding for a peptide of 247 amino acids with a putative signal peptide (Mr of 2,629). The deduced amino acid sequence of soxF was 47% identical and 70% similar to the sequence of the flavoprotein of flavocytochrome c of Chromatium vinosum, suggesting the involvement of the flavoprotein in thiosulfate oxidation of P. denitrificans GB17.

Amino Acid Sequence↗
PubMed1977

Ribosomal ribonucleic acid cistron homologies among Hyphomicrobium and various other bacteria.

The extent of hybrid formation between the ribosomal ribonucleic acid (r-RNA) of Hyphomicrobium strain B-522 and deoxyribonucleic acid (DNA) from bacteria of 21 different genera was examined. Three generalized groupings were formed. Group I (72-100%) consisted entirely of other strains of Hyphomicrobium. Representatives of the genera Rhodopseudomonas, Chromatium, Caulobacter, Prosthecomicrobium, Rhodomicrobium, Hyphomonas, and Hyphomicrobium made up group II (49-69%). The remaining Gram-negative, Gram-positive, and cell wall--less bacteria fell into group III (12-40%). The taxonomic implications of these results are discussed.

Bacteria↗
PubMed2003

The crystal structure of a 26-nucleotide RNA containing a hook-turn.

A crystal structure has been obtained for a 26-nucleotide RNA that contains the loop E sequence from Chromatium minutissimum. Rather than having a loop E-like conformation, it consists of an A-form helix that splits into two separate strands following a sheared A-G base pair. The backbone of the strand containing the G of the A-G pair makes a turn of almost 180 degrees in the space of two nucleotides, and then interacts with the minor groove of the helix from which it originates. Similar structures, which we call hook-turns, occur in 16S and 23S rRNAs. They are found at places where the two strands of a helix separate at an A/G juxtaposition to interact with other sequences.

Base Sequence↗
PubMedDate not supplied

Cloning a gene encoding a light-harvesting I polypeptide from Ectothiorhodospira sp.

Trying to detect the genes coding for light harvesting II polypeptides of the purple bacteria Ectothiorhodospira sp. a gene corresponding to a light harvesting I polypeptide was cloned. This paper discusses the probable reasons of this result. The sequence of this polypeptide underlines the strong similarity with light harvesting complexes from bacteria such as Rhodospirillum molischianum and Chromatium vinosum.

Amino Acid Sequence↗
PubMed1976

Primary structure of a high potential iron-sulfur protein from the purple non-sulfur photosynthetic bacterium Rhodopseudomonas gelatinosa.

The third amino acid sequence of a high potential iron-sulfur protein, that of the non-sulfur purple photosynthetic bacterium Rhodopseudomonas gelatinosa, has been determined. It consists of a single polypeptide chain of 74 amino acid residues, which is slightly smaller than the high potential iron-sulfur proteins from the sulfur purple bacteria Chromatium vinosum (85 residues) and Thiocapsa pfennigii (81 residues). The sequence of the gelatinosa protein is similar to the C. vinosum and T. pfennigii proteins with 38% and 37% identically matching residues, although six gaps are proposed for the comparison (the C. vinosum and T. pfennigii proteins have 44% identically matching residues out of 73 positions compared with only one 4-residue gap). Only 17 redisues, including the 4 cystein residues essential for binding the four-iron-sulfur chromophore, are invariant in the three known sequences. A discussion of the role of conserved residues in maintenance of the three-dimensional structure and in electron transport is presented.

Amino Acid Sequence↗
PubMed2003

Effect of duckweed cover on greenhouse gas emissions and odour release from waste stabilisation ponds.

Treatment of wastewater in stabilisation pond systems prevents the negative environmental impact of uncontrolled disposal of sewage. However, even a natural treatment system may generate secondary negative environmental impacts in terms of energy consumption, emission of greenhouse gases and emission of odorous compounds. Whereas natural systems have an advantage over electro-mechanical systems in that they use less hardware and less energy, it is not yet known whether secondary environmental effects in the form of greenhouse gas emissions are lower for these systems. This research intends to be a first step in the direction of answering this question by assessing gas emissions from two types of natural systems, namely algae-based and duckweed-based stabilisation ponds. The H2S volatilisation from laboratory scale pond-reactors has been determined by drawing the air above the water surface continuously through a solution of 1 M NaOH for absorption of sulphide. The amount of H2S that volatilised from the algae pond-reactor, and was trapped in the NaOH trap, was found to be 2.5-86 mg/m2/day. The H2S volatilisation from the duckweed pond-reactor was found to be negligible, even though the sulphide concentration was 9.7 mg/l S(2-). The duckweed cover was a physical barrier for volatilisation, since bubbles were trapped in the cover. In addition the duckweed layer was found to be afavourable environment for both aerobic sulphide oxidisers (Beggiatoa gigantae) as well as for photosynthetic purple sulphur bacteria belonging to the genus Chromatium. These may also have contributed to the prevention of H2S volatilisation. Results on methane emissions were not conclusive so far, but the same mechanisms that prevent H2S volatilisation may also prevent methane volatilisation. Therefore it was concluded that duckweed covers on stabilisation ponds may reduce the emission of both odorous and greenhouse gases.

Adsorption↗
PubMedDate not supplied

[Ecophysiological properties of photosynthesizing bacteria from the Black Sea chemocline zone].

In May 1998, during the fifty-first voyage on board the research vessel Professor Vodyanitskii, a comparative study was conducted of the species diversity of green and purple sulfur bacteria in the water column of the chemocline zone at deep-sea stations and on the bottom surface of the Black Sea shallow regions. At three deep-sea stations, the accumulation of photosynthesizing bacteria in the chemocline zone at a depth of 85-115 m was revealed on the basis of the distribution of potential values of carbon dioxide light fixation. The location of the site of potential carbon dioxide light fixation suggests that the photosynthesis may be determined by the activity of the brown Chlorobium sp., revealed earlier at these depths. Enrichment cultures of brown sulfur bacteria were obtained from samples taken at the deep-sea stations. By morphology, these bacteria, assigned to Chlorobium sp., appear as nonmotile straight or slightly curved rods 0.3-0.5 x 0.7-1.2 microm in size; sometimes, they form short chains. Ultrathin sections show photosynthesizing antenna-like structures, chlorosomes, typical of Chlorobiaceae. The cultures depended on the presence of NaCl (20 g/l) for growth, which corresponds to the mineralization of Black Sea water. The bacteria could grow photoautotrophically, utilizing sulfide, but the Black Sea strains grew much more slowly than the known species of brown sulfur bacteria isolated from saline or freshwater meromictic lakes. The best growth of the strains studied in this work occurred in media containing ethanol (0.5 g) or sodium acetate (1 g/l) and low amounts of sulfide (0.4 mM), which is consistent with the conditions of syntrophic growth with sulfidogens. The data obtained allow us to conclude that the cultures of brown sulfur bacteria are especially adapted to developing at large depths under conditions of electron donor deficiency owing to syntrophic development with sulfate reducers. The species composition of the photosynthetic bacteria developing in the bottom sediments of shallow stations differed substantially from that observed at deep-sea stations. Pure cultures of the green Chlorobium sp. BS 1C and BS 2C (chlorobactin as the carotenoid), purple sulfur bacteria Chromatium sp. BS 1Ch (containing spirilloxanthine series pigments), and Thiocapsa marina BS 2Tc (containing the carotenoid okenone) were obtained from samples of sediments at shallow-water stations. Brown sulfur bacteria were absent in the sediment samples obtained from the Black Sea shallow-water stations 1 and 2.

Carbon Dioxide↗
PubMedDate not supplied

[Effect of pesticides on bacterial membranes].

The effect of pure preparation of ordram, fosalon, DDT, methoxychlorine, hydrel, dihydrel, 2,4-D, 2M-4C and of technical preparations of saturn, linuron, ronstar and keltan on the membrane functions (respiration and motility) of Azospirillum brasilense and Chromatium minutissimum cells and on malate and NADH oxidation by the isolated membranes of Micrococcus lysodeikticus was investigated. The effect varied from irreversible impairment to undetectable impairment of the measured activities depending on the type of bacteria and on the chemical used. The ordram induced permeability of the A. brasilense membranes without inhibition of the respiratory chain activity and selective inhibition of malate oxidase accompanied by stimulation of NADH oxidation in the M. lysodeikticus membranes indicates a possibility of ordram application as a regulator of bacterial metabolism.

Bacteria↗
PubMedDate not supplied

[Results of the storage of freeze dried microbial cultures for 25 years].

Saprophytic microorganisms belonging to different physiological groups (Azotobacter, acetic, ammonifying, lactic and nodule bacteria, a phototrophous purple bacterium of the Chromatium genus, bacteria of the Micrococcus and Pseudomonas genera, and a yeast of the Candida genus) were stored at 3-6 degrees C for 25 years in the freeze-dried state. All of the strains were found to be viable after the storage. The number of viable cells decreased for some bacteria, but to a far less degree than when the cultures were kept immediately after the freeze-drying for a year at 30 degrees C.

Bacterial Physiological Phenomena↗
PubMedDate not supplied

[Kinetics of the generation of a photo-induced electric potential in chromatophores of photosynthetizing bacteria].

Flash-induced formation of an electric potential difference (delta psi) was monitored by a direct method in chromatophores associated with the collodion phospholipid membrane. In Rhodospirillum rubrum and Rhodopseudomonas sphaeriodes chromatophores, the kinetics of delta psi generation exhibit fast (tau less than or equal to 0.3 microseconds) and slow (tau congruent to 200 microseconds) phases, the latter observed in the presence of exogenous quinones. Comparison of the kinetic and potentiometric characteristics of the process with those of electron transport reactions suggests that the fast phase of delta psi rise is due to charge separation between the primary electron donor, P870, and primary electron acceptor QIFe; the slow phase, which is inhibited by o-phenanthroline, is due to electron donation from QIFe to the secondary acceptor, quinone QII. The kinetics of delta psi decay include components arising form the recombination of primary separated charges (tau congruent to 30 ms) and from the passive discharge of the membrane (tau congruent to 400 ms; tau congruent to 1400 ms). From a redox titration of the photo-induced electric signal and the photo-induced absorption changes of P870 at different pH meanings, the value of pK for the primary acceptor FeQI was found to be 7.4 in Rps. sphaeroides chromatophores. In Chromatium minutissimum, a phase ( tau congruent to 20 microseconds) was observed in addition to those seen in Rps. sphaeroids and R. rubrum which was explained by the reduction of P890+ from the high potential cytochrome c555. Possible distribution of the electron transport components in the chromatophore membrane are discussed.

Bacterial Chromatophores↗
PubMed1978

[Change in the concentration of RNA in the cytoplasm of cells of the inferior colliculus in cats during monaural and binaural stimulation].

The method of cytospectrophotometry of the gallocyanin-chromatium stained sections was used to show that the 2-hour monaural and 1.5-hour binaural stimulation with rhythmical noise signals result in a pronounced increase in cytoplasmatic RNA content per cell in the principal and large multipolar neurons. The increase in cytoplasmatic RNA amount in the principal cells both from ipsi- and contralateral central nuclei of the inferior colliculus with monaural and binaural stimulations allows to suggest a uniform distribution of the binaurally converging connection from the lower auditory nuclei to the principal cells. The increase in cytoplasmatic RNA in the large multipolar cells of the contralateral central nucleus following monaural stimulation shows predominant contralateral projections to these cells. A conclusion is made on patterns of binaurally converging connections on the principal and large multipolar cells of the central nucleus of the inferior colliculus.

Animals↗
PubMedDate not supplied

[Preservation of lyophilized cultures of saprophytic microorganisms].

All of the tested saprophytic microbial cultures remained viable upon 11--16 years of storage in the lyophilized state at 3--6 degrees. The cultures belonged to the following taxonomic groups: Acetobacter, Achromobacter, Azotobacter, Bacillus, Chromatium, Escherichia, Flavobacterium, Lactobacillus, Micrococcus, Proteus, Propionibacterium, Pseudomonas, Rhizobium, Sarcina, Serratia, Streptococcus, Torula, Mycobacterium, Actinomyces. The number of viable cells in the tubes decredased only slightly within this time and remained at the same level as immediately after lyophilization.

Bacterial Physiological Phenomena↗
PubMed1997

Structure and composition of freshwater microbial mats from a sulfur spring ("Font Pudosa", NE Spain).

Different types of microbial mats developing on the wall on a non-thermal sulfur freshwater spring have been studied. Both, light and electron microscopy as well as HPLC analysis of photosynthetic pigments revealed their structure and composition. Prokaryotic chlorophylls and carotenoids helped in the taxonomical assignment of the main photosynthetic groups. "Inverted position" mats (Mat-I) were dominated by Chromatiaceae; they were located closed to the water outlets (0.3 mM sulfide). "Normal position", that is, cyanobacterial-covered mats (Mat-II and Mat-IV), developed elsewhere on the stone walls at lower sulfide concentrations. A third type of mat (Mat-III), covered by chemolithotrophic bacteria, was distinguishable at the water-air interface, strongly attached to the walls of the spring. Up to six physiological types of microorganisms have been recognized: cyanobacteria, Chromatiaceae, purple nonsulfur bacteria. Chlorobiaceae, Chloroflexaceae, and chemolithotrophic bacteria. Cyanobacteria Lyngbya-like, Oscillatoria-like and Pseudanabaena sp. were found. The diversity of Chromatiaceae (six morpho-/pigment types of the genus Chromatium, plus two non identified Chromatiaceae, named PB1 and PB2 were observed) was noticeable. Chemolithotrophic bacteria were represented by the genera Beggiatoa and Thiothrix. Finally, small numbers of Chloroflexus-like bacteria and Chlorobium limicola were found in all the studied mats.

Carotenoids↗
PubMedDate not supplied

[On the ecology of marine chromatiaceae and chlorobiaceae (author's transl)].

Number and genera (types) of phototrophic red and green sulfur bacteria have been determined in the upper layer of eleven marine sediment samples from the euphotic zone in the Mediterranean Sea. Origin and nature of the sediment samples are given as well as their pH, total nitrogen and sulfide content. The results show that the sediments studied did not provide good growth conditions for Chromatiaceae (Chromatium, Thiocystis, Thiocapsa) and Chlorobiaceae (Prosthecochloris). The total number of these bacteria varied in agreement with the total nitrogen content (organic matter) of the samples; the organic matter content is, therefore, of primary importance for the occurrence of the red and green sulfur bacteria in the samples.

Chromatiaceae↗