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At least 145 records · Page 8Linked to original sources
PubMed1985

The presence of a copper/zinc superoxide dismutase in the bacterium Photobacterium leiognathi: a likely case of gene transfer from eukaryotes to prokaryotes.

The free-living bacterium Photobacterium leiognathi is also known to be a symbiont of ponyfish. The presence of a copper/zinc superoxide dismutase in P. leiognathi has been considered to be a case of gene transfer from eukaryotes to prokaryotes because this form of superoxide dismutase is normally present only in higher eukaryotic species. However, the amino acid sequence of the enzyme from the bacterium exhibited low identities (25-30%) with the same enzyme from eukaryotes. When amino acid mutations are taken into consideration, the weighted sequence similarity increases significantly; furthermore, the bacterial enzyme has the same active site residues and similar predicted secondary structure as the eukaryotic enzymes. The possibility of convergence is ruled out and the case of divergence is considered unlikely because of the observed phylogenetic distribution of the enzyme. This indicates that the presence of the copper/zinc superoxide dismutase in P. leiognathi can indeed be considered a case of gene transfer from eukaryotic species to prokaryotic species.

Amino Acid Sequence↗
PubMed1988

Tandemly repeated tRNA pseudogenes in photobacterium.

A region distal to three tRNA genes in Photobacterium phosphoreum, a Gram-negative eubacterium, unexpectedly contains a high number of repeated DNA segments that are closely related to the adjacent tRNAPro gene. The 5' to 3' order of this cluster is tRNAPro-tRNAHis-tRNAPro followed by eight tRNAPro-like structures interspersed by rho-independent terminators. The two tRNAPro genes, which are identical, and the tRNAHis gene have 86% and 87% positional identity, respectively, to their counterparts in the argT operon of Escherichia coli. The facts that these tRNA-like structures are not transcribed, in contrast to the tRNA retropseudogenes of eukaryotes, and that these structures are clustered near their progenitor suggest they are an unusual class of tRNA pseudogenes that arose by tandem duplication.

Base Sequence↗
PubMed2004

Fatal infection of the hand due to Photobacterium damsela: a case report.

We report a case of fatal acute renal failure due to Photobacterium damsela infection of the hand. Although the patient received intensive medical care and surgical treatment, he died 8 h after arrival at the hospital. This is the first case of P. damsela sepsis proven by blood culture in Japan.

Acute Kidney Injury↗
PubMed1996

Purification and characterization of a marine bacterial beta-galactoside alpha 2,6-sialyltransferase from Photobacterium damsela JT0160.

A bacterial sialyltransferase, named sialyltransferase 0160, was purified from a marine bacterium that had been isolated from seawater from Sagami Bay, Kanagawa. This strain has been identified as Photobacterium damsela, and named P. damsela JT0160. Sialyltransferase 0160 was purified 688-fold to homogeneity from the crude extract of the cells with a yield of 19% using a combination of anion exchange chromatography, hydroxyapatite chromatography, gel filtration chromatography, and affinity chromatography. The purified enzyme migrated as a single band (61 kDa) on sodium dodecyl sulfate-polyacrylamide gel. This sialyltransferase was found to be a beta-galactoside alpha 2,6-sialyltransferase [EC 2.4.99.1] which catalyzes the incorporation of NeuAc from CMP-NeuAc into the galactose residue of the carbohydrate chain at position 6 on the basis of an analysis of the enzymatic reaction products with HPLC, 1H-, 13C-NMR spectroscopy, and fast atom bombardment mass spectroscopy.

Carbohydrate Sequence↗
PubMed1998

Cloning and expression of a marine bacterial beta-galactoside alpha2,6-sialyltransferase gene from Photobacterium damsela JT0160.

Sialyltransferase 0160, a bacterial sialyltransferase which catalyzes the incorporation of NeuAc from CMP-NeuAc into the galactose residue of the carbohydrate chain at position 6, is produced by Photobacterium damsela JT0160. The gene coding for sialyltransferase 0160 (bst) was cloned, sequenced, and expressed in Escherichia coli. The sialyltransferase 0160 gene contains an open reading frame of 2,028 base pairs encoding a protein of 675 amino acid residues. The deduced amino acid sequence of sialyltransferase 0160 did not contain the sialylmotif and had no significant similarity to mammalian sialyltransferases. Crude extracts of cultured E. coli MV1184 cells carrying an expression plasmid for the sialyltransferase 0160 gene showed sialyltransferase activity, which was identified as beta-galactoside alpha2,6-sialyltransferase activity by enzymatic reaction product analysis. In addition, when mutant genes, lacking 3'-coding regions for COOH-terminal portions of the protein, which are thought to form alpha-helix structures, were expressed in E. coli MV1184, soluble-form enzymes were obtained. This implies that the COOH-terminal portion of sialyltransferase 0160 is required for membrane binding.

Amino Acid Sequence↗
PubMed1991

Crystallization and preliminary X-ray diffraction studies of a flavoprotein, FP390, from a luminescent bacterium, Photobacterium phosphoreum.

A flavoprotein, FP390, obtained from a luminescent bacterium, Photobacterium phosphoreum, in the purification of luciferase has been crystallized by the vapor-diffusion procedure. Crystals obtained from polyethylene glycol 4000 solutions, whose X-ray photographs show powder diffraction patterns, were unsuitable for further crystallographic work. However, tetragonal crystals grown from potassium phosphate solution well diffracted X-rays beyond 3 A resolution. The space group of this crystal is P4(1)22 or P4(3)22 with unit-cell dimensions of a = b = 76.8 and c = 241 A. Assuming two or three molecules in an asymmetric unit, the value for the crystal volume per unit molecular mass, Vm, is calculated as 3.3 or 2.2 A3/Da, respectively. A total of 13,555 independent reflections for the native crystal was collected up to 3 A resolution using a Weissenberg camera attached to the synchrotron radiation source, the merging R factor being 0.077 for 79,335 measurements.

Bacterial Proteins↗
PubMed1994

Preparation of P-flavin-bound and P-flavin-free luciferase and P-flavin-bound beta-subunit of luciferase from Photobacterium phosphoreum.

P-flavin-bound luciferase, P-flavin-free luciferase, and P-flavin-bound beta-subunit of luciferase were prepared from Photobacterium phosphoreum using hydrophobic interaction chromatography after conventional purification using DEAE-cellulose chromatography and gel-filtration. The P-flavin-bound luciferase preparation contained about 20% P-flavin-free luciferase not removable by the present procedure. Since the specific activity of the P-flavin-bound luciferase preparation was about 20% of that of the P-flavin-free luciferase, it was concluded that the P-flavin-bound luciferase is an enzyme-product complex and has no more luciferase activity. Unlike the absorption spectrum of FP390 or other flavoproteins, that of P-flavin-bound luciferase preparation has a high absorption peak around 370 nm and resembles the spectrum synthesized by superposing the P-flavin-free luciferase spectrum on the P-flavin-bound beta-subunit spectrum: the P-flavin-bound beta-subunit spectrum is similar to that of FP390, while that of P-flavin-free luciferase has an absorption peak around 370 nm but practically no peak around 450 nm. In addition, P-flavin-free luciferase exhibits a weak but distinct NADH-FMN oxidoreductase activity. These results suggest that a prosthetic group, which absorbs around 370 nm, binds to the luciferase and that this compound is required to yield P-flavin; and they support the hypothesis that the physiological function of bacterial luciferase is to produce P-flavin. Furthermore, the presence of P-flavin-bound beta-subunit of the luciferase in the cell extract supports the hypothesis that physiological function of the lux operon is the biosynthesis of FP390 including its prosthetic group.

Amino Acid Sequence↗
PubMed1995

Crystal structure determination of a flavoprotein FP390 from a luminescent bacterium, Photobacterium phosphoreum.

The three-dimensional structure of a flavoprotein, FP390, purified from a luminescent bacterium, Photobacterium phosphoreum, has been determined at 3 A resolution by X-ray crystallography. Crystallographic refinements of the structural model have led to an R-factor of 0.24 for the intensity data between 6 to 3 A resolution collected with synchrotron radiation. It was found that a homodimer of the FP390 molecules related by a non-crystallographic 2-fold axis is comprised in the asymmetric unit. Two homodimers are arranged around a crystallographic 2-fold axis to form a tetrameric assembly. The monomer molecule of FP390, to which two molecules of the flavin cofactor (Q-flavin) are bound, consists of a seven-stranded parallel beta-sheet which forms a half of the beta-barrel structure and seven alpha-helices which surround one side of the beta-barrel. We suggest that the reason why the Q-flavin sample prepared from FP390 is always a mixture of two components is connected with the fact that the monomer molecules has two flavin binding sites, at the dimer interface and at the molecular surface.

Bacterial Proteins↗
PubMed1976

Studies on luciferase from Photobacterium phosphoreum. VIII. FMN-H2O2 initiated bioluminescence and the thermodynamics of the elementary steps of the luciferase reaction.

Bacterial luciferase from Photobacterium phosohoreum was found to produce bioluminescence on reaction with FMN and H2O2 in the presence of aldehyde. This luminescence is presumably produced by the same X1 intermediate as that found in FMNH2-O2 initiated luminescence. From the ratio of the light intensities of the FMN-H2O2 initiated reactions, we calculated the association constant of the reaction, luciferase+FMN+H2O2in equilibriumX1, and estimated its temperature dependence. From these results we calculated the thermodynamic parameters of the reaction, luciferase+FMNH2+O2in equilibriumX1. We found that the free energy level of X1 is only 3.2 kcal below that of fr-e FMN and H2O2. We also estimated the thermodynamic parameters of other steps of the luminescent reaction. The values obtained showed that the formation of X1 from luciferase, FMNH2 and O2 involves a positive entropy change, but the intermediate is in a state stabilized against decomposition. Results also suggest a considerable degree of electronic rearrangement on formation of the excited-state molecule from the X1-aldehyde complex.

Aldehydes↗
PubMed1977

Luminescence and respiratory activities of Photobacterium phosphoreum. II. Control by monovalent cations.

Luminescent activity of spheroplasts of the cells of Photobacterium phosphoreum was stimulated by Rb+ and K+ and inhibited by Na+ in the medium. Opposite effects of these ions were observed on the rate of O2 consumption of the spheroplasts through the cytochrome and luciferase electron transfer systems. In vitro activities of NADH-FMN reductase and luciferase were only slightly stimulated by Rb+, K+, and Na+, while Na+ exhibited significant activation of the NADH-oxidizing activity of the cells. The redox level of cytochrome b in the spheroplasts during steady-state respiration in an Na+ medium was more reduced, while that of NAD(P) was more oxidized, than those in an Rb+ or K+ medium. Na+ activates the cytochrome electron transfer system at a point between NADH and cytochrome b, and thus has a stimulative effect on cellular O2 consumption. Rb+ and K+ do not show similar activation, but the cellular NAD(P) was brought to a more reduced level, so that in vivo luminescence is stimulated in an Rb+ or K+ medium.

Cations, Monovalent↗
PubMed1978

Properties and kinetics of salt activation of a membrane-bound NADH dehydrogenase from a marine bacterium Photobacterium phosphoreum.

A membrane-bound NADH dehydrogenase, solubilized and partially purified from a marine bacterium Photobacterium phosphoreum, contains FAD as the prosthetic group, and is specific for NADH. Ferricyanide, various other redox dyes and cytochrome c can act as electron acceptors. The enzymatic activity when assayed with electron acceptors other than cytochrome c, is activated by monovalent cations (Na+ and K+) and deactivated by high concentrations of monovalent anions (SCN-, NO3-, and Cl-) but not by phosphate ions. The enzymatic reaction follows a ping-pong mechanism and kinetic analysis of the enzyme showed that the activation by monovalent cations is due to increase of affinity of the enzyme for substrates; Vm was not affected. The increase of affinity was 62- and 46-fold for NADH and 57- and 31-fold for 2,6-dichlorophenol indophenol in the presence of Na+ and K+, respectively. On the other hand, NADH-cytochrome c reductase activity of the enzyme was strongly inhibited by these cations.

Anions↗
PubMed1978

Studies on luciferase from Photobacterium phosphoreum. XI. Interaction of 8-substituted FMNH2 with luciferase.

The interaction of bacterial luciferase from Photobacterium phosphoreum with reduced flavin was investigated using various 8-substituted FMNH2 analogs. Flavins tested were FMNH2 and FMNH2 substituted at the 8 position with HO-, CH3O-, C2H5O-, Cl-, Br-, I-, H2N-, (CH3)HN-, and (ch3)2n. 8-ch30-, c2h5o-, cl-, and Br-FMNH2 showed luminescent activity in the luciferase reaction with emission peaks at various wavelengths. 8-HO- and I-FMNH2 were competitive inhibitors toward FMNH2 in the luminescent reaction. 8-Amino analogs of FMNH2 showed no luminescent or inhibitor activity. The dissociation constant of the luciferase-FMNH2 analog complex was determined kinetically as a substrate or inhibitor constant. A contribution of the imino group at position 5 in the isoalloxazine ring to the FMNH2 binding to luciferase was suggested by a Hammett plot of the dissociation constants.

Flavin Mononucleotide↗
PubMed1980

Bioluminescence and cell growth of Photobacterium phosphoreum.

The bioluminescence activity of Photobacterium phosphoreum was compared at different times after cell division by the methods of density gradient centrifugation and synchronous culture. The bioluminescence intensity per cell mass increased linearly at a rate of 1.5 times per doubling time. The luciferase system in the cell is continuously activated during growth, independent of cell division.

Cell Division↗
PubMed1986

Regulation and properties of the glutamine synthetase purified from Photobacterium phosphoreum.

Glutamine synthetase from a marine enterobacterium, Photobacterium phosphoreum, was purified to homogeneity from cells grown in glycerol-yeast extract medium. The purified enzyme had a molecular weight of approximately 670,000 and a subunit size of 56,000, i.e. larger than that of the enzyme from E. coli. Regulation of the glutamine synthetase activity by adenylylation/deadenylylation was demonstrated on snake venom phosphodiesterase treatment. The state of adenylylation appeared to influence both the biosynthetic and gamma-glutamyltransferase activities of P. phosphoreum glutamine synthetase similar to in the case of the E. coli enzyme. The enzyme activity was controlled by adenylylation and possibly in combination with feedback inhibition by alanine, serine, and glycine, metabolites which are especially effective in inhibiting P. phosphoreum glutamine synthetase. When either Mn2+ or Mg2+ was added to the relaxed (divalent cation-free) enzyme, similar UV-difference spectra were obtained for the enzyme, indicating that the conformational states induced by these cations were also similar. The profile of these spectra varied from those published for E. coli, and three peaks were four 1 at 282.5, 288.5, and 298 nm.

Adenosine Monophosphate↗
PubMed1986

Purification and properties of a cytochrome b560-d complex, a terminal oxidase of the aerobic respiratory chain of Photobacterium phosphoreum.

A cytochrome b560-d complex, a terminal oxidase in the respiratory chain of Photobacterium phosphoreum grown under aerobic conditions, was purified to near homogeneity. The purified oxidase complex is composed of equimolar amounts of two polypeptides with molecular weights of 41,000 and 54,000, as determined by gel electrophoresis in the presence of sodium dodecyl sulfate. It contains 10.2 nmol of protoheme and 22.5 nmol of iron/mg of protein. The enzyme is a "cytochrome bd-type oxidase," showing absorption peaks at 560 and 625 nm in its reduced minus oxidized difference spectrum at 77K. This oxidase combined with CO, and its CO difference spectrum at room temperature in the Soret region showed a peak at 418 nm and a trough at 434 nm. In addition, a trough at 560 nm (cytochrome b), and a trough at 620 nm and a peak at 639 nm (cytochrome d) were observed in the CO-binding spectrum. This cytochrome b560-d complex catalyzed the oxidation of ubiquinol-1 and ascorbate in the presence of N,N,N',N'-tetramethyl-p-phenylenediamine dihydrochloride or phenazine methosulfate. The oxidase activity required phospholipids and was inhibited by the respiratory inhibitors, KCN and NaN3, and the divalent cation, ZnSO4. Formation of a membrane potential by the cytochrome b560-d complex reconstituted into liposomes was observed with the fluorescent dye, 3,3'-dipropylthiodicarbocyanine iodide, on the addition of ubiquinol-1, showing that the enzyme provided a coupling site for oxidative phosphorylation.

Amino Acids↗
PubMed1996

Interspecific luciferase beta subunit hybrids between Vibrio harveyi, Vibrio fischeri and Photobacterium leiognathi.

Bacterial luciferase (EC 1.14.14.3) is a heterodimer composed of alpha- and beta-chains encoded by luxA and luxB, respectively. Although some interspecific combinations of these subunits lead to active enzyme, others do not. The beta subunits of Vibrio fischeri and Photobacterium leiognathi form active enzyme with the alpha subunits of V.fischeri, P.leiognathi and Vibrio harveyi, while the beta subunit from V.harveyi only complements the alpha subunit of V.harveyi. Inactivity is caused by a lack of dimerization of the beta subunit of V.harveyi with the alpha subunits of V.fischeri and P.leiognathi. These observations served as the basis for a search to discover which segment of the beta polypeptide confers the ability to dimerize with the alpha subunits of V.fischeri and P.leiognathi. Intragenic beta subunit hybrids were made between V.harveyi, V.fischeri and P.leiognathi. Unique restriction sites were introduced into the respective luxB genes to divide them into four roughly equal segments. In all, 78 hybrids were constructed by in vitro techniques. The N-terminal segment of the peptide contains the signals that differentiate between the beta subunits of V.fischeri and P. leiognathi and the beta subunit of V. harveyi, and allow the former to dimerize with their alpha subunits. The second segment has no major effect on enzyme activity but does exhibit some context effects. Important interactions were found between the third and fourth segments of the polypeptide with respect to enzymatic activity.

Amino Acid Sequence↗
PubMed2005

Photobacterium damsela bacteremia in a child with sickle-cell disease.

Photobacterium damsela was identified in a blood culture taken from a child with sickle-cell disease. This is the first report of this organism in humans in the Caribbean. The microbiology of this organism and its identification are discussed. The clinical presentation in humans and the role of the immune status of the patient are reviewed.

Anemia, Sickle Cell↗