Chlorobi: A phylum of anoxygenic, phototrophic bacteria including the family Chlorobiaceae. They occur in aquatic sediments, sulfur springs, and hot springs and utilize reduced sulfur compounds instead of oxygen.Bacteroidetes: A phylum of bacteria comprised of three classes: Bacteroides, Flavobacteria, and Sphingobacteria.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Genome, Bacterial: The genetic complement of a BACTERIA as represented in its DNA.Encyclopedias as Topic: Works containing information articles on subjects in every field of knowledge, usually arranged in alphabetical order, or a similar work limited to a special field or subject. (From The ALA Glossary of Library and Information Science, 1983)Terminology as Topic: The terms, expressions, designations, or symbols used in a particular science, discipline, or specialized subject area.Bacteria: One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.Bacteriology: The study of the structure, growth, function, genetics, and reproduction of bacteria, and BACTERIAL INFECTIONS.RNA, Ribosomal, 16S: Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Capnocytophaga: A gram-negative gliding bacterium isolated from the oral cavity. It is a pathogen often causing PERIODONTITIS.Prevotella: A genus of gram-negative, anaerobic, nonsporeforming, nonmotile rods. Organisms of this genus had originally been classified as members of the BACTEROIDES genus but overwhelming biochemical and chemical findings in 1990 indicated the need to separate them from other Bacteroides species, and hence, this new genus was established.Sphingobacterium: A genus of gram-negative, chemoorganotrophic bacteria in the family Sphingobacteriaceae. They lack FLAGELLA but some species exhibit sliding motility.Irritable Bowel Syndrome: A disorder with chronic or recurrent colonic symptoms without a clearcut etiology. This condition is characterized by chronic or recurrent ABDOMINAL PAIN, bloating, MUCUS in FECES, and an erratic disturbance of DEFECATION.Metagenome: A collective genome representative of the many organisms, primarily microorganisms, existing in a community.Eubacterium: A genus of gram-positive, rod-shaped bacteria found in cavities of man and animals, animal and plant products, infections of soft tissue, and soil. Some species may be pathogenic. No endospores are produced. The genus Eubacterium should not be confused with EUBACTERIA, one of the three domains of life.Archaea: One of the three domains of life (the others being BACTERIA and Eukarya), formerly called Archaebacteria under the taxon Bacteria, but now considered separate and distinct. They are characterized by: (1) the presence of characteristic tRNAs and ribosomal RNAs; (2) the absence of peptidoglycan cell walls; (3) the presence of ether-linked lipids built from branched-chain subunits; and (4) their occurrence in unusual habitats. While archaea resemble bacteria in morphology and genomic organization, they resemble eukarya in their method of genomic replication. The domain contains at least four kingdoms: CRENARCHAEOTA; EURYARCHAEOTA; NANOARCHAEOTA; and KORARCHAEOTA.Gram-Negative Bacteria: Bacteria which lose crystal violet stain but are stained pink when treated by Gram's method.Gram-Positive Bacteria: Bacteria which retain the crystal violet stain when treated by Gram's method.Bacteria, AnaerobicChlorobium: A genus of phototrophic, obligately anaerobic bacteria in the family Chlorobiaceae. They are found in hydrogen sulfide-containing mud and water environments.Metatarsophalangeal Joint: The articulation between a metatarsal bone (METATARSAL BONES) and a phalanx.Cuba: An island in the Greater Antilles in the West Indies, south of Florida. With the adjacent islands it forms the Republic of Cuba. Its capital is Havana. It was discovered by Columbus on his first voyage in 1492 and conquered by Spain in 1511. It has a varied history under Spain, Great Britain, and the United States but has been independent since 1902. The name Cuba is said to be an Indian name of unknown origin but the language that gave the name is extinct, so the etymology is a conjecture. (From Webster's New Geographical Dictionary, 1988, p302 & Room, Brewer's Dictionary of Names, 1992, p132)Databases, Protein: Databases containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.Proteome: The protein complement of an organism coded for by its genome.Internet: A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.Ethnobotany: The study of plant lore and agricultural customs of a people. In the fields of ETHNOMEDICINE and ETHNOPHARMACOLOGY, the emphasis is on traditional medicine and the existence and medicinal uses of PLANTS and PLANT EXTRACTS and their constituents, both historically and in modern times.Medicine, Traditional: Systems of medicine based on cultural beliefs and practices handed down from generation to generation. The concept includes mystical and magical rituals (SPIRITUAL THERAPIES); PHYTOTHERAPY; and other treatments which may not be explained by modern medicine.Interior Design and Furnishings: The planning of the furnishings and decorations of an architectural interior.Classification: The systematic arrangement of entities in any field into categories classes based on common characteristics such as properties, morphology, subject matter, etc.Political Systems: The units based on political theory and chosen by countries under which their governmental power is organized and administered to their citizens.Phototrophic Processes: Processes by which phototrophic organisms use sunlight as their primary energy source. Contrasts with chemotrophic processes which do not depend on light and function in deriving energy from exogenous chemical sources. Photoautotrophy (or photolithotrophy) is the ability to use sunlight as energy to fix inorganic nutrients to be used for other organic requirements. Photoautotrophs include all GREEN PLANTS; GREEN ALGAE; CYANOBACTERIA; and green and PURPLE SULFUR BACTERIA. Photoheterotrophs or photoorganotrophs require a supply of organic nutrients for their organic requirements but use sunlight as their primary energy source; examples include certain PURPLE NONSULFUR BACTERIA. Depending on environmental conditions some organisms can switch between different nutritional modes (AUTOTROPHY; HETEROTROPHY; chemotrophy; or phototrophy) to utilize different sources to meet their nutrients and energy requirements.Technical ReportGlutathione: A tripeptide with many roles in cells. It conjugates to drugs to make them more soluble for excretion, is a cofactor for some enzymes, is involved in protein disulfide bond rearrangement and reduces peroxides.United States National Aeronautics and Space Administration: An independent Federal agency established in 1958. It conducts research for the solution of problems of flight within and outside the Earth's atmosphere and develops, constructs, tests, and operates aeronautical and space vehicles. (From U.S. Government Manual, 1993)Glutathione Reductase: Catalyzes the oxidation of GLUTATHIONE to GLUTATHIONE DISULFIDE in the presence of NADP+. Deficiency in the enzyme is associated with HEMOLYTIC ANEMIA. Formerly listed as EC Transferase: A transferase that catalyzes the addition of aliphatic, aromatic, or heterocyclic FREE RADICALS as well as EPOXIDES and arene oxides to GLUTATHIONE. Addition takes place at the SULFUR. It also catalyzes the reduction of polyol nitrate by glutathione to polyol and nitrite.Cataloging: Activities performed in the preparation of bibliographic records for CATALOGS. It is carried out according to a set of rules and contains information enabling the user to know what is available and where items can be found.Value of Life: The intrinsic moral worth ascribed to a living being. (Bioethics Thesaurus)Symbiosis: The relationship between two different species of organisms that are interdependent; each gains benefits from the other or a relationship between different species where both of the organisms in question benefit from the presence of the other.Plastids: Self-replicating cytoplasmic organelles of plant and algal cells that contain pigments and may synthesize and accumulate various substances. PLASTID GENOMES are used in phylogenetic studies.Eukaryota: One of the three domains of life (the others being BACTERIA and ARCHAEA), also called Eukarya. These are organisms whose cells are enclosed in membranes and possess a nucleus. They comprise almost all multicellular and many unicellular organisms, and are traditionally divided into groups (sometimes called kingdoms) including ANIMALS; PLANTS; FUNGI; and various algae and other taxa that were previously part of the old kingdom Protista.Rhodophyta: Plants of the division Rhodophyta, commonly known as red algae, in which the red pigment (PHYCOERYTHRIN) predominates. However, if this pigment is destroyed, the algae can appear purple, brown, green, or yellow. Two important substances found in the cell walls of red algae are AGAR and CARRAGEENAN. Some rhodophyta are notable SEAWEED (macroalgae).Sea Urchins: Somewhat flattened, globular echinoderms, having thin, brittle shells of calcareous plates. They are useful models for studying FERTILIZATION and EMBRYO DEVELOPMENT.Thiotrichaceae: A family of colorless sulfur bacteria in the order Thiotrichales, class GAMMAPROTEOBACTERIA.Mycoplasma: A genus of gram-negative, mostly facultatively anaerobic bacteria in the family MYCOPLASMATACEAE. The cells are bounded by a PLASMA MEMBRANE and lack a true CELL WALL. Its organisms are pathogens found on the MUCOUS MEMBRANES of humans, ANIMALS, and BIRDS.Radiation: Emission or propagation of acoustic waves (SOUND), ELECTROMAGNETIC ENERGY waves (such as LIGHT; RADIO WAVES; GAMMA RAYS; or X-RAYS), or a stream of subatomic particles (such as ELECTRONS; NEUTRONS; PROTONS; or ALPHA PARTICLES).NAD: A coenzyme composed of ribosylnicotinamide 5'-diphosphate coupled to adenosine 5'-phosphate by pyrophosphate linkage. It is found widely in nature and is involved in numerous enzymatic reactions in which it serves as an electron carrier by being alternately oxidized (NAD+) and reduced (NADH). (Dorland, 27th ed)Equilibrative Nucleoside Transport Proteins: A class of sodium-independent nucleoside transporters that mediate the facilitative transport of NUCLEOSIDES.Mycoplasma Infections: Infections with species of the genus MYCOPLASMA.Equilibrative Nucleoside Transporter 1: A subtype of equilibrative nucleoside transporter proteins that is sensitive to inhibition by 4-nitrobenzylthioinosine.

Combination of fluorescent in situ hybridization and microautoradiography-a new tool for structure-function analyses in microbial ecology. (1/146)

A new microscopic method for simultaneously determining in situ the identities, activities, and specific substrate uptake profiles of individual bacterial cells within complex microbial communities was developed by combining fluorescent in situ hybridization (FISH) performed with rRNA-targeted oligonucleotide probes and microautoradiography. This method was evaluated by using defined artificial mixtures of Escherichia coli and Herpetosiphon aurantiacus under aerobic incubation conditions with added [3H]glucose. Subsequently, we were able to demonstrate the potential of this method by visualizing the uptake of organic and inorganic radiolabeled substrates ([14C]acetate, [14C]butyrate, [14C]bicarbonate, and 33Pi) in probe-defined populations from complex activated sludge microbial communities by using aerobic incubation conditions and anaerobic incubation conditions (with and without nitrate). For both defined cell mixtures and activated sludge, the method proved to be useful for simultaneous identification and analysis of the uptake of labeled substrates under the different experimental conditions used. Optimal results were obtained when fluorescently labeled oligonucleotides were applied prior to the microautoradiographic developing procedure. For single-cell resolution of FISH and microautoradiographic signals within activated sludge flocs, cryosectioned sample material was examined with a confocal laser scanning microscope. The combination of in situ rRNA hybridization techniques, cryosectioning, microautoradiography, and confocal laser scanning microscopy provides a unique opportunity for obtaining cultivation-independent insights into the structure and function of bacterial communities.  (+info)

Sepiapterin reductase producing L-threo-dihydrobiopterin from Chlorobium tepidum. (2/146)

A novel type of NADPH-dependent sepiapterin reductase, which catalysed uniquely the reduction of sepiapterin to l-threo-dihydrobiopterin, was purified 533-fold from the cytosolic fraction of Chlorobium tepidum, with an overall yield of 3%. The native enzyme had a molecular mass of 55 kDa and SDS/PAGE revealed that the enzyme consists of two subunits with a molecular mass of 26 kDa. The enzyme was optimally active at pH8.8 and 50 degrees C. Apparent Km values for sepiapterin and NADPH were 21 and 6.2 microM, respectively, and the kcat value was 5.0 s-1. Diacetyl could also serve as a substrate, with a Km of 4.0 mM. The inhibitory effects of N-acetylserotonin, N-acetyldopamine and melatonin were very weak. The Ki value of N-acetyldopamine was measured as 400 microM. The N-terminal amino acid sequence was revealed as Met-Lys-His-Ile-Leu-Leu-Ile-Thr-Gly-Ala-Xaa-Lys - Lys - Ile - Xaa - Arg - Ala - Ile - Ala - Leu - Glu - Xaa - Ala - Arg - Xaa-Xaa-Xaa-His-His-His-, which shared relatively high sequence similarity with other sepiapterin reductases.  (+info)

Auracyanin A from the thermophilic green gliding photosynthetic bacterium Chloroflexus aurantiacus represents an unusual class of small blue copper proteins. (3/146)

The amino acid sequence of the small copper protein auracyanin A isolated from the thermophilic photosynthetic green bacterium Chloroflexus aurantiacus has been determined to be a polypeptide of 139 residues. His58, Cys123, His128, and Met132 are spaced in a way to be expected if they are the evolutionary conserved metal ligands as in the known small copper proteins plastocyanin and azurin. Secondary structure prediction also indicates that auracyanin has a general beta-barrel structure similar to that of azurin from Pseudomonas aeruginosa and plastocyanin from poplar leaves. However, auracyanin appears to have sequence characteristics of both small copper protein sequence classes. The overall similarity with a consensus sequence of azurin is roughly the same as that with a consensus sequence of plastocyanin, namely 30.5%. We suggest that auracyanin A, together with the B forms, is the first example of a new class of small copper proteins that may be descendants of an ancestral sequence to both the azurin proteins occurring in prokaryotic nonphotosynthetic bacteria and the plastocyanin proteins occurring in both prokaryotic cyanobacteria and eukaryotic algae and plants. The N-terminal sequence region 1-18 of auracyanin is remarkably rich in glycine and hydroxy amino acids, and required mass spectrometric analysis to be determined. The nature of the blocking group X is not yet known, although its mass has been determined to be 220 Da. The auracyanins are the first small blue copper proteins found and studied in anoxygenic photosynthetic bacteria and are likely to mediate electron transfer between the cytochrome bc1 complex and the photosynthetic reaction center.  (+info)

Exciton delocalization in the B808-866 antenna of the green bacterium Chloroflexus aurantiacus as revealed by ultrafast pump-probe spectroscopy. (4/146)

A model of pigment organization in the B808-866 bacteriochlorophyll a antenna of the green photosynthetic bacterium Chloroflexus aurantiacus based on femtosecond pump-probe studies is proposed. The building block of the antenna was assumed to be structurally similar to that of the B800-850 light-harvesting 2 (LH2) antenna of purple bacteria and to have the form of two concentric rings of N strongly coupled BChl866 pigments and of N/2 weakly coupled BChl808 monomers, where N = 24 or 32. We have shown that the Qy transition dipoles of BChl808 and BChl866 molecules form the angles 43 degrees +/- 3 degrees and 8 degrees +/- 4 degrees, respectively, with the plane of the corresponding rings. Using the exciton model, we have obtained a quantitative fit of the pump-probe spectra of the B866 and B808 bands. The anomalously high bleaching value of the B866 band with respect to the B808 monomeric band provided the direct evidence for a high degree of exciton delocalization in the BChl866 ring antenna. The coherence length of the steady-state exciton wave packet corresponds to five or six BChl866 molecules at room temperature.  (+info)

In situ analysis of sulfur in the sulfur globules of phototrophic sulfur bacteria by X-ray absorption near edge spectroscopy. (5/146)

During the oxidation of sulfide and thiosulfate purple and green sulfur bacteria accumulate globules of 'elemental' sulfur. Although essential for a thorough understanding of sulfur metabolism in these organisms, the exact chemical nature of the stored sulfur is still unclear. We applied sulfur K-edge X-ray absorption near edge spectroscopy (XANES) to probe the forms of sulfur in intact cells. Comparing XANES spectra of Allochromatium vinosum, Thiocapsa roseopersicina, Marichromatium purpuratum, Halorhodospira halophila and Chlorobium vibrioforme grown photolithoautotrophically on sulfide with reference probes (fingerprint method), we found sulfur chains with the structure R-S(n)-R. Evidence for the presence of sulfur rings, polythionates and anionic polysulfides in the sulfur globules of these bacteria was not obtained.  (+info)

Exciton levels structure of antenna bacteriochlorophyll c aggregates in the green bacterium Chloroflexus aurantiacus as probed by 1.8-293 K fluorescence spectroscopy. (6/146)

We have demonstrated temperature-dependence of the steady-state fluorescence lineshape of the bacteriochlorophyll (BChl) c band measured for intact cells of the green bacterium Chloroflexus aurantiacus over the 1.8-293 K range. The measured temperature-dependence has been shown to be in good agreement with the theoretical one, calculated for our original model of pigment organization in the chlorosomal oligomeric antenna of green photosynthetic bacteria based on spectral hole-burning studies (Fetisova, Z.G. et al. (1996) Biophys. J. 71, 995-1010). This model implies that the BChl c antenna unit is a tubular aggregate of six exciton-coupled linear pigment chains having the exciton level structure with strongly allowed higher levels.  (+info)

Rubredoxin from the green sulfur bacterium Chlorobium tepidum functions as an electron acceptor for pyruvate ferredoxin oxidoreductase. (7/146)

Rubredoxin (Rd) from the moderately thermophilic green sulfur bacterium Chlorobium tepidum was found to function as an electron acceptor for pyruvate ferredoxin oxidoreductase (PFOR). This enzyme, which catalyzes the conversion of pyruvate to acetyl-CoA and CO(2), exhibited an absolute dependence upon the presence of Rd. However, Rd was incapable of participating in the pyruvate synthase or CO(2) fixation reaction of C. tepidum PFOR, for which two different reduced ferredoxins are employed as electron donors. These results suggest a specific functional role for Rd in pyruvate oxidation and provide the initial indication that the two important physiological reactions catalyzed by PFOR/pyruvate synthase are dependent on different electron carriers in the cell. The UV-visible spectrum of oxidized Rd, with a monomer molecular weight of 6500, gave a molar absorption coefficient at 492 nm of 6.89 mM(-1) cm(-1) with an A(492)/A(280) ratio of 0.343 and contained one iron atom/molecule. Further spectroscopic studies indicated that the CD spectrum of oxidized C. tepidum Rd exhibited a unique absorption maximum at 385 nm and a shoulder at 420 nm. The EPR spectrum of oxidized Rd also exhibited unusual anisotropic resonances at g = 9.675 and g = 4.322, which is composed of a narrow central feature with broader shoulders to high and low field. The midpoint reduction potential of C. tepidum Rd was determined to be -87 mV, which is the most electronegative value reported for Rd from any source.  (+info)

Exogenous quinones inhibit photosynthetic electron transfer in Chloroflexus aurantiacus by specific quenching of the excited bacteriochlorophyll c antenna. (8/146)

In the photosynthetic green filamentous bacterium Chloroflexus aurantiacus, excitation energy is transferred from a large bacteriochlorophyll (BChl) c antenna via smaller BChl a antennas to the reaction center. The effects of substituted 1,4-naphthoquinones on BChl c and BChl a fluorescence and on flash-induced cytochrome c oxidation were studied in whole cells under aerobic conditions. BChl c fluorescence in a cell suspension with 5.4 microM BChl c was quenched to 50% by addition of 0.6 microM shikonin ((R)-2-(1-hydroxy-4-methyl-3-pentenyl)-5,8-dihydroxy-1, 4-naphthoquinone), 0.9 microM 5-hydroxy-1,4-naphthoquinone, or 4 microM 2-acetyl-3-methyl-1,4-naphthoquinone. Between 25 and 100 times higher quinone concentrations were needed to quench BChl a fluorescence to a similar extent. These quinones also efficiently inhibited flash-induced cytochrome c oxidation when BChl c was excited, but not when BChl a was excited. The quenching of BChl c fluorescence induced by these quinones correlated with the inhibition of flash-induced cytochrome c oxidation. We concluded that the quinones inhibited electron transfer in the reaction center by specifically quenching the excitation energy in the BChl c antenna. Our results provide a model system for studying the redox-dependent antenna quenching in green sulfur bacteria because the antennas in these bacteria inherently exhibit a sensitivity to O(2) similar to the quinone-supplemented cells of Cfx. aurantiacus.  (+info)

  • The genome of a member of the phylum Chlorobi was assembled from a shotgun metagenomic sequence of a hot spring in Mammoth Lakes, CA. This organism appears to be a novel, aerobic, photosynthetic Chlorobi member, expanding the knowledge of this underrepresented phylum. (
  • Relatively few members of the phylum Chlorobi have been cultivated and characterized. (
  • Chromosomal synteny of genes is not preserved in the phylum Chlorobi. (
  • In addition, other genes associated with the production of bacteriochlorophyll and chlorosomes common to the Chlorobi were also present. (
  • These can be discrete disks like the chlorosomes of Chlorobi, or concentric layers of thylakoid membrane around the periphery of the cell. (
  • This draft genome, therefore, represents a potentially novel genus within the Chlorobi . (
  • The genome sequenced represents a potentially deep branching member of the Chlorobi and provides crucial data to this underrepresented group of microorganisms. (
  • Phototrophic species are green or orange en masse, the color depending of which photopigments are produced. (
  • Aerobic members of the Chlorobi have recently been described, but only through metagenomic approaches ( 2 ). (
  • Since many RNA-binding proteins regulate their own expression in a feedback mechanism by binding or acting up their 5' UTR, it was proposed that the Chlorobi-RRM is a component in an analogous feedback mechanism. (
  • Eleven completely sequenced Chlorobi genomes were compared in oligonucleotide usage, gene contents, and synteny. (
  • Gba561951 cite pmid 15239383 lpsn classifphyla classification chlorobi chlorobea in cavalier smith megaclassification bacteroidetes which differs from cavalier smith megaclassification as it is composed of the classes lucky 31 avis bacteroidia equivalent to cavalier smith s bacteroidetes cytophagia and flavobacteria and sphingobacteria fibrobacteres an analogous situation is see with the pvc group planctobacteria. (